4xia - Revision history

OCA at 13:00, 1 March 2024

2024-03-01T13:00:57Z

← Older revision		Revision as of 13:00, 1 March 2024
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	<StructureSection load='4xia' size='340' side='right'caption='[[4xia]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4xia' size='340' side='right'caption='[[4xia]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xia]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arts7 Arts7~~]. The February 2006 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xia]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_sp._NRRL_B3728 Arthrobacter sp. NRRL B3728]. The February 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XIA FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MG:MAGNESIUM+ION'>MG</scene~~>, ~~<scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</td></tr>
	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase]~~, ~~with EC number [http~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5]~~ </~~span~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xia OCA], [~~http~~://pdbe.org/4xia PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xia RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xia PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xia ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xia OCA], [https://pdbe.org/4xia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xia RCSB], [https://www.ebi.ac.uk/pdbsum/4xia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xia ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/XYLA_ARTS7 XYLA_ARTS7]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4xia ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4xia ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The structures of D-xylose isomerase from Arthrobacter strain B3728 containing the polyol inhibitors xylitol and D-sorbitol have been solved at 2.5 A and 2.3 A, respectively. The structures have been refined using restrained least-squares refinement methods. The final crystallographic R-factors for the D-sorbitol (xylitol) bound molecules, for 43,615 (32,989) reflections are 15.6 (14.7). The molecule is a tetramer and the asymmetric unit of the crystal contains a dimer, the final model of which, incorporates a total of 6086 unique protein, inhibitor and magnesium atoms together with 535 bound solvent molecules. Each subunit of the enzyme contains two domains: the main domain is a parallel-stranded alpha-beta barrel, which has been reported in 14 other enzymes. The C-terminal domain is a loop structure consisting of five helical segments and is involved in intermolecular contacts between subunits that make up the tetramer. The structures have been analysed with respect to molecular symmetry, intersubunit contacts, inhibitor binding and active site geometry. The refined model shows the two independent subunits to be similar apart from local deviations due to solvent contacts in the solvent-exposed helices. The enzyme is dependent on a divalent cation for catalytic activity. Two metal ions are required per monomer, and the high-affinity magnesium(II) site has been identified from the structural results presented here. The metal ion is complexed, at the high-affinity site, by four carboxylate side-chains of the conserved residues, Glu180, Glu216, Asp244 and Asp292. The inhibitor polyols are bound in the active site in an extended open chain conformation and complete an octahedral co-ordination shell for the magnesium cation via their oxygen atoms O-2 and O-4. The active site lies in a deep pocket near the C-terminal ends of the beta-strands of the barrel domain and includes residues from a second subunit. The tetrameric molecule can be considered to be a dimer of "active" dimers, the active sites being composed of residues from both subunits. The analysis has revealed the presence of several internal salt-bridges stabilizing the tertiary and quaternary structure. One of these, between Asp23 and Arg139, appears to play a key role in stabilizing the active dimer and is conserved in the known sequences of this enzyme.(ABSTRACT TRUNCATED AT 400 WORDS)

	Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively.,Henrick K, Collyer CA, Blow DM J Mol Biol. 1989 Jul 5;208(1):129-57. PMID:2769749<ref>PMID:2769749</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4xia" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[D-xylose isomerase\|D-xylose isomerase]]		*[[D-xylose isomerase 3D structures\|D-xylose isomerase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: ~~Arts7~~]]		[[Category: Arthrobacter sp. NRRL B3728]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	~~[[Category: Xylose isomerase]]~~		[[Category: Blow DM]]
	[[Category: Blow~~, D M~~]]		[[Category: Collyer CA]]
	[[Category: Collyer~~, C A~~]]		[[Category: Henrick K]]
	[[Category: Henrick, K]]

OCA at 07:51, 4 March 2020

2020-03-04T07:51:16Z

← Older revision		Revision as of 07:51, 4 March 2020
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	==STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2.5 ANGSTROMS AND 2.3 ANGSTROMS RESOLUTION, RESPECTIVELY==		==STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2.5 ANGSTROMS AND 2.3 ANGSTROMS RESOLUTION, RESPECTIVELY==
	<StructureSection load='4xia' size='340' side='right' caption='[[4xia]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4xia' size='340' side='right'caption='[[4xia]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xia]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arts7 Arts7]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xia]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arts7 Arts7]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XIA FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xi/4xia_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xi/4xia_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 4xia" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xia" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[D-xylose isomerase\|D-xylose isomerase]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Arts7]]		[[Category: Arts7]]
			[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

OCA at 07:21, 29 November 2017

2017-11-29T07:21:20Z

← Older revision		Revision as of 07:21, 29 November 2017
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	==STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2.5 ANGSTROMS AND 2.3 ANGSTROMS RESOLUTION, RESPECTIVELY==		==STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2.5 ANGSTROMS AND 2.3 ANGSTROMS RESOLUTION, RESPECTIVELY==
	<StructureSection load='4xia' size='340' side='right' caption='[[4xia]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4xia' size='340' side='right' caption='[[4xia]], [[Resolution\|resolution]] 2.30Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xia OCA], [http://pdbe.org/4xia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xia RCSB], [http://www.ebi.ac.uk/pdbsum/4xia PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xia OCA], [http://pdbe.org/4xia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xia RCSB], [http://www.ebi.ac.uk/pdbsum/4xia PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xia ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 4xia" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xia" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[D-xylose isomerase\|D-xylose isomerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:44, 9 February 2016

2016-02-09T13:44:35Z

← Older revision		Revision as of 13:44, 9 February 2016
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	<StructureSection load='4xia' size='340' side='right' caption='[[4xia]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4xia' size='340' side='right' caption='[[4xia]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xia]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Arthrobacter_sp. Arthrobacter sp.~~]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xia]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arts7 Arts7]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XIA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xia RCSB], [http://www.ebi.ac.uk/pdbsum/4xia PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xia OCA], [http://pdbe.org/4xia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xia RCSB], [http://www.ebi.ac.uk/pdbsum/4xia PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4xia ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 4xia" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: ~~Arthrobacter sp~~]]		[[Category: Arts7]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

OCA at 08:59, 5 January 2015

2015-01-05T08:59:00Z

← Older revision		Revision as of 08:59, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xia]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xia]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XIA FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xia RCSB], [http://www.ebi.ac.uk/pdbsum/4xia PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xia RCSB], [http://www.ebi.ac.uk/pdbsum/4xia PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Arthrobacter sp.]]		[[Category: Arthrobacter sp]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Blow, D M.]]		[[Category: Blow, D M]]
	[[Category: Collyer, C A.]]		[[Category: Collyer, C A]]
	[[Category: Henrick, K.]]		[[Category: Henrick, K]]

OCA: Protected "4xia" [edit=sysop:move=sysop]

2014-06-05T08:10:57Z

Protected "4xia" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:10, 5 June 2014
(No difference)

OCA at 08:10, 5 June 2014

2014-06-05T08:10:54Z

← Older revision		Revision as of 08:10, 5 June 2014
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	~~{{Seed}}~~		==STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2.5 ANGSTROMS AND 2.3 ANGSTROMS RESOLUTION, RESPECTIVELY==
	[[Image:~~4xia~~.~~png~~\|~~left~~\|~~200px~~]]		<StructureSection load='4xia' size='340' side='right' caption='[[4xia]], [[Resolution\|resolution]] 2.30Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4xia]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XIA FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene><br>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xia RCSB], [http://www.ebi.ac.uk/pdbsum/4xia PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xi/4xia_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The structures of D-xylose isomerase from Arthrobacter strain B3728 containing the polyol inhibitors xylitol and D-sorbitol have been solved at 2.5 A and 2.3 A, respectively. The structures have been refined using restrained least-squares refinement methods. The final crystallographic R-factors for the D-sorbitol (xylitol) bound molecules, for 43,615 (32,989) reflections are 15.6 (14.7). The molecule is a tetramer and the asymmetric unit of the crystal contains a dimer, the final model of which, incorporates a total of 6086 unique protein, inhibitor and magnesium atoms together with 535 bound solvent molecules. Each subunit of the enzyme contains two domains: the main domain is a parallel-stranded alpha-beta barrel, which has been reported in 14 other enzymes. The C-terminal domain is a loop structure consisting of five helical segments and is involved in intermolecular contacts between subunits that make up the tetramer. The structures have been analysed with respect to molecular symmetry, intersubunit contacts, inhibitor binding and active site geometry. The refined model shows the two independent subunits to be similar apart from local deviations due to solvent contacts in the solvent-exposed helices. The enzyme is dependent on a divalent cation for catalytic activity. Two metal ions are required per monomer, and the high-affinity magnesium(II) site has been identified from the structural results presented here. The metal ion is complexed, at the high-affinity site, by four carboxylate side-chains of the conserved residues, Glu180, Glu216, Asp244 and Asp292. The inhibitor polyols are bound in the active site in an extended open chain conformation and complete an octahedral co-ordination shell for the magnesium cation via their oxygen atoms O-2 and O-4. The active site lies in a deep pocket near the C-terminal ends of the beta-strands of the barrel domain and includes residues from a second subunit. The tetrameric molecule can be considered to be a dimer of "active" dimers, the active sites being composed of residues from both subunits. The analysis has revealed the presence of several internal salt-bridges stabilizing the tertiary and quaternary structure. One of these, between Asp23 and Arg139, appears to play a key role in stabilizing the active dimer and is conserved in the known sequences of this enzyme.(ABSTRACT TRUNCATED AT 400 WORDS)

	<!--		Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively.,Henrick K, Collyer CA, Blow DM J Mol Biol. 1989 Jul 5;208(1):129-57. PMID:2769749<ref>PMID:2769749</ref>
	~~The line below this paragraph~~, ~~containing "STRUCTURE_4xia"~~, ~~creates the "Structure Box" on the page~~.
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter~~ (~~which sets the initial scene displayed when the page is loaded~~),
	~~or leave the SCENE parameter empty for the default display~~.
	-->
	~~{{STRUCTURE_4xia\| PDB=4xia \| SCENE= }}~~

	~~===STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2~~.~~5 ANGSTROMS AND 2~~.~~3 ANGSTROMS RESOLUTION, RESPECTIVELY===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

			==See Also==
	~~<!--~~		*[[D-xylose isomerase\|D-xylose isomerase]]
	~~The line below this paragraph, {{ABSTRACT_PUBMED_2769749}}, adds the Publication Abstract to the page~~		== References ==
	~~(as it appears on PubMed at http://www.pubmed.gov), where 2769749 is the PubMed ID number.~~		<references/>
	~~-->~~		__TOC__
	~~{{ABSTRACT_PUBMED_2769749}}~~		</StructureSection>

	==~~About this Structure~~==
	~~4XIA is a 2 chains structure with sequences from~~ [~~http://en.wikipedia.org/wiki/Arthrobacter_sp._nrrl_b3728 Arthrobacter sp. nrrl b3728]. The February 2006 RCSB PDB~~ [~~http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha~~-~~amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA~~].

	==~~Reference~~==
	<~~ref group="xtra">PMID:2769749<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Arthrobacter sp. ~~nrrl b3728~~]]		[[Category: Arthrobacter sp.]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
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	[[Category: Collyer, C A.]]		[[Category: Collyer, C A.]]
	[[Category: Henrick, K.]]		[[Category: Henrick, K.]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 21 09:41:50 2010''~~

OCA at 07:41, 21 January 2010

2010-01-21T07:41:55Z

← Older revision		Revision as of 07:41, 21 January 2010
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	==About this Structure==		==About this Structure==
	4XIA is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA].		4XIA is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Arthrobacter_sp._nrrl_b3728 Arthrobacter sp. nrrl b3728]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:2769749</ref><references group="xtra"/>		<ref group="xtra">PMID:2769749</ref><references group="xtra"/>
	[[Category: Alpha-amylase]]		[[Category: Alpha-amylase]]
	[[Category: Arthrobacter sp.]]		[[Category: Arthrobacter sp. nrrl b3728]]
			[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Blow, D M.]]		[[Category: Blow, D M.]]
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	[[Category: Henrick, K.]]		[[Category: Henrick, K.]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 10~~:13:~~35 2009~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 21 09:41:50 2010''

OCA at 08:13, 17 February 2009

2009-02-17T08:13:36Z

← Older revision		Revision as of 08:13, 17 February 2009
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	==About this Structure==		==About this Structure==
	4XIA is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. ~~Additional information on 4XIA is available in a page on~~ [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/~~pdb74_1~~.html Alpha ~~Amylase] at the RCSB PDB~~ [http://~~pdb~~.~~rcsb~~.org/~~pdb~~/~~static~~.~~do?p=education_discussion~~/~~molecule_of_the_month~~/~~index.html Molecule of the Month~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA].		4XIA is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA].

	==Reference==		==Reference==
	Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively., Henrick K, Collyer CA, Blow DM, J Mol Biol. 1989 Jul 5;208(1):129-57. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~2769749 2769749]~~		<ref group="xtra">PMID:2769749</ref><references group="xtra"/>
	[[Category: Alpha ~~Amylase~~]]		[[Category: Alpha-amylase]]
	[[Category: Arthrobacter sp.]]		[[Category: Arthrobacter sp.]]
	~~[[Category: Single protein]]~~
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Blow, D M.]]		[[Category: Blow, D M.]]
Line 32:		Line 31:
	[[Category: Henrick, K.]]		[[Category: Henrick, K.]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 23~~ 10:55:~~51 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:13:35 2009''

OCA at 07:55, 23 July 2008

2008-07-23T07:55:52Z

← Older revision		Revision as of 07:55, 23 July 2008
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	==About this Structure==		==About this Structure==
	4XIA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. ~~The following page contains interesting~~ information on ~~the relation of~~ 4XIA ~~with [~~[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb74_1.html Alpha~~-amylase~~]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA].		4XIA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. Additional information on 4XIA is available in a page on [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb74_1.html Alpha Amylase] at the RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIA OCA].

	==Reference==		==Reference==
	Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively., Henrick K, Collyer CA, Blow DM, J Mol Biol. 1989 Jul 5;208(1):129-57. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2769749 2769749]		Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively., Henrick K, Collyer CA, Blow DM, J Mol Biol. 1989 Jul 5;208(1):129-57. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2769749 2769749]
	[[Category: Alpha~~-amylase~~]]		[[Category: Alpha Amylase]]
	[[Category: Arthrobacter sp.]]		[[Category: Arthrobacter sp.]]
	[[Category: Single protein]]		[[Category: Single protein]]
Line 32:		Line 32:
	[[Category: Henrick, K.]]		[[Category: Henrick, K.]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Jul ~~3 13~~:54:43 2008''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 10:55:51 2008''