1oad - Revision history

OCA at 08:58, 9 May 2024

2024-05-09T08:58:29Z

← Older revision		Revision as of 08:58, 9 May 2024
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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=1oad 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=1oad ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Glucose isomerase from Streptomyces rubiginosus was crystallized in two forms: I222, with one molecule of 44 kDa in the asymmetric unit, and P2(1)2(1)2, with two unique molecules. The I222 structure is known, but the P2(1)2(1)2 form has not been solved before. X-ray diffraction data for the P2(1)2(1)2 form were collected at a wavelength of 1.54 A and data for the I222 form were collected at three different wavelengths: 1.34, 1.07 and 0.98 A. The amount of anomalous signal from one Mn and eight S atoms in these data sets varies from 1.24% to as low as 0.56%. The dual-space direct-methods program SHELXD, run against the Bijvoet differences, gave a clear solution of all anomalous scatterers for all data sets. The Mn positions only were used for SAD phasing of all four data sets. The electron-density map after density modification, resulting from the phasing of a single-wavelength data set and based purely on the anomalous deltaf" contribution, was clearly interpretable; an almost complete model of the protein was built by wARP without human intervention in all four cases. As far as is known, this is the first time that an anomalous signal as low as 0.6% has successfully been used to determine the structure of a macromolecule.

			SAD manganese in two crystal forms of glucose isomerase.,Ramagopal UA, Dauter M, Dauter Z Acta Crystallogr D Biol Crystallogr. 2003 May;59(Pt 5):868-75. Epub 2003, Apr 25. PMID:12777803<ref>PMID:12777803</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 1oad" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[D-xylose isomerase 3D structures\|D-xylose isomerase 3D structures]]		*[[D-xylose isomerase 3D structures\|D-xylose isomerase 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:56, 10 April 2024

2024-04-10T08:56:20Z

← Older revision		Revision as of 08:56, 10 April 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OAD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OAD FirstGlance]. <br>
	</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MQD:2-METHYLPENTANE-1,2,4-TRIOL'>MQD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.5Å</td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</div></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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MQD:2-METHYLPENTANE-1,2,4-TRIOL'>MQD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [https://pdbe.org/1oad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [https://www.ebi.ac.uk/pdbsum/1oad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oad 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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [https://pdbe.org/1oad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [https://www.ebi.ac.uk/pdbsum/1oad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oad ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism.
	== 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=1oad 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=1oad ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Glucose isomerase from Streptomyces rubiginosus was crystallized in two forms: I222, with one molecule of 44 kDa in the asymmetric unit, and P2(1)2(1)2, with two unique molecules. The I222 structure is known, but the P2(1)2(1)2 form has not been solved before. X-ray diffraction data for the P2(1)2(1)2 form were collected at a wavelength of 1.54 A and data for the I222 form were collected at three different wavelengths: 1.34, 1.07 and 0.98 A. The amount of anomalous signal from one Mn and eight S atoms in these data sets varies from 1.24% to as low as 0.56%. The dual-space direct-methods program SHELXD, run against the Bijvoet differences, gave a clear solution of all anomalous scatterers for all data sets. The Mn positions only were used for SAD phasing of all four data sets. The electron-density map after density modification, resulting from the phasing of a single-wavelength data set and based purely on the anomalous deltaf" contribution, was clearly interpretable; an almost complete model of the protein was built by wARP without human intervention in all four cases. As far as is known, this is the first time that an anomalous signal as low as 0.6% has successfully been used to determine the structure of a macromolecule.

	SAD manganese in two crystal forms of glucose isomerase.,Ramagopal UA, Dauter M, Dauter Z Acta Crystallogr D Biol Crystallogr. 2003 May;59(Pt 5):868-75. Epub 2003, Apr 25. PMID:12777803<ref>PMID:12777803</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 1oad" 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: Large Structures]]		[[Category: Large Structures]]
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	~~[[Category: Xylose isomerase]]~~		[[Category: Dauter M]]
	[[Category: Dauter, M]]		[[Category: Dauter Z]]
	[[Category: Dauter, Z]]		[[Category: Ramagopal UA]]
	[[Category: Ramagopal~~, U A]]~~
	~~[[Category: Glucose isomerase]]~~
	~~[[Category: Isomerase~~]]

OCA at 09:56, 12 May 2021

2021-05-12T09:56:35Z

← Older revision		Revision as of 09:56, 12 May 2021
Line 3:		Line 3:
	<StructureSection load='1oad' size='340' side='right'caption='[[1oad]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1oad' size='340' side='right'caption='[[1oad]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1OAD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OAD 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MQD:2-METHYLPENTANE-1,2,4-TRIOL'>MQD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MQD:2-METHYLPENTANE-1,2,4-TRIOL'>MQD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</div></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'>[https://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [https://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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [~~http~~://pdbe.org/1oad PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1oad PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1oad 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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [https://pdbe.org/1oad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [https://www.ebi.ac.uk/pdbsum/1oad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oad ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 06:58, 7 August 2019

2019-08-07T06:58:35Z

← Older revision		Revision as of 06:58, 7 August 2019
Line 1:		Line 1:

	==Glucose isomerase from Streptomyces rubiginosus in P21212 crystal form==		==Glucose isomerase from Streptomyces rubiginosus in P21212 crystal form==
	<StructureSection load='1oad' size='340' side='right' caption='[[1oad]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1oad' size='340' side='right'caption='[[1oad]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OAD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OAD FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oa/1oad_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oa/1oad_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>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1oad" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1oad" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[D-xylose isomerase\|D-xylose isomerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

OCA at 09:42, 1 November 2017

2017-11-01T09:42:51Z

← Older revision		Revision as of 09:42, 1 November 2017
Line 1:		Line 1:
	==~~GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN~~ P21212 ~~CRYSTAL FORM~~==
			==Glucose isomerase from Streptomyces rubiginosus in P21212 crystal form==
	<StructureSection load='1oad' size='340' side='right' caption='[[1oad]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1oad' size='340' side='right' caption='[[1oad]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [http://pdbe.org/1oad PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [http://www.ebi.ac.uk/pdbsum/1oad 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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [http://pdbe.org/1oad PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [http://www.ebi.ac.uk/pdbsum/1oad PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1oad ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=1oad ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1oad" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1oad" style="background-color:#fffaf0;"></div>

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

OCA at 15:20, 11 September 2015

2015-09-11T15:20:41Z

← Older revision		Revision as of 15:20, 11 September 2015
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [http://www.ebi.ac.uk/pdbsum/1oad 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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [http://pdbe.org/1oad PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [http://www.ebi.ac.uk/pdbsum/1oad PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 1oad" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 15:47, 5 January 2015

2015-01-05T15:47:42Z

← Older revision		Revision as of 15:47, 5 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OAD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OAD 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MQD:2-METHYLPENTANE-1,2,4-TRIOL'>MQD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MQD:2-METHYLPENTANE-1,2,4-TRIOL'>MQD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [http://www.ebi.ac.uk/pdbsum/1oad 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=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [http://www.ebi.ac.uk/pdbsum/1oad 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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	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Dauter, M.]]		[[Category: Dauter, M]]
	[[Category: Dauter, Z.]]		[[Category: Dauter, Z]]
	[[Category: Ramagopal, U A.]]		[[Category: Ramagopal, U A]]
	[[Category: Glucose isomerase]]		[[Category: Glucose isomerase]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	~~[[Category: Xylose isomerase]]~~

OCA at 16:58, 28 September 2014

2014-09-28T16:58:03Z

← Older revision		Revision as of 16:58, 28 September 2014
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	[[Image:~~1oad~~.~~png~~\|~~left~~\|~~200px~~]]		==GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN P21212 CRYSTAL FORM==
			<StructureSection load='1oad' size='340' side='right' caption='[[1oad]], [[Resolution\|resolution]] 1.50Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1oad]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OAD 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MQD:2-METHYLPENTANE-1,2,4-TRIOL'>MQD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gw9\|1gw9]], [[1mnz\|1mnz]], [[1o1h\|1o1h]], [[1xib\|1xib]], [[1xic\|1xic]], [[1xid\|1xid]], [[1xie\|1xie]], [[1xif\|1xif]], [[1xig\|1xig]], [[1xih\|1xih]], [[1xii\|1xii]], [[1xij\|1xij]], [[1xis\|1xis]], [[2xis\|2xis]], [[3xis\|3xis]], [[4xis\|4xis]], [[8xia\|8xia]], [[9xia\|9xia]]</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oad OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oad RCSB], [http://www.ebi.ac.uk/pdbsum/1oad 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/oa/1oad_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 ==
			Glucose isomerase from Streptomyces rubiginosus was crystallized in two forms: I222, with one molecule of 44 kDa in the asymmetric unit, and P2(1)2(1)2, with two unique molecules. The I222 structure is known, but the P2(1)2(1)2 form has not been solved before. X-ray diffraction data for the P2(1)2(1)2 form were collected at a wavelength of 1.54 A and data for the I222 form were collected at three different wavelengths: 1.34, 1.07 and 0.98 A. The amount of anomalous signal from one Mn and eight S atoms in these data sets varies from 1.24% to as low as 0.56%. The dual-space direct-methods program SHELXD, run against the Bijvoet differences, gave a clear solution of all anomalous scatterers for all data sets. The Mn positions only were used for SAD phasing of all four data sets. The electron-density map after density modification, resulting from the phasing of a single-wavelength data set and based purely on the anomalous deltaf" contribution, was clearly interpretable; an almost complete model of the protein was built by wARP without human intervention in all four cases. As far as is known, this is the first time that an anomalous signal as low as 0.6% has successfully been used to determine the structure of a macromolecule.

	~~{{STRUCTURE_1oad\| PDB=1oad \| SCENE= }}~~		SAD manganese in two crystal forms of glucose isomerase.,Ramagopal UA, Dauter M, Dauter Z Acta Crystallogr D Biol Crystallogr. 2003 May;59(Pt 5):868-75. Epub 2003, Apr 25. PMID:12777803<ref>PMID:12777803</ref>

	~~===GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN P21212 CRYSTAL FORM===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	~~{{ABSTRACT_PUBMED_12777803}}~~		==See Also==
			*[[D-xylose isomerase\|D-xylose isomerase]]
	==~~About this Structure~~==		== References ==
	[[~~1oad~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA].		<references/>
			__TOC__
	==~~Reference~~==		</StructureSection>
	<~~ref group="xtra">PMID:012777803<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

OCA: Protected "1oad" [edit=sysop:move=sysop]

2012-12-12T21:38:18Z

Protected "1oad" [edit=sysop:move=sysop]

← Older revision	Revision as of 21:38, 12 December 2012
(No difference)

OCA at 21:38, 12 December 2012

2012-12-12T21:38:13Z

← Older revision		Revision as of 21:38, 12 December 2012
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	~~{{Seed}}~~
	[[Image:1oad.png\|left\|200px]]		[[Image:1oad.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_1oad", 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_1oad\| PDB=1oad \| SCENE= }}		{{STRUCTURE_1oad\| PDB=1oad \| SCENE= }}

	===GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN P21212 CRYSTAL FORM===		===GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN P21212 CRYSTAL FORM===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_12777803}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 12777803 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_12777803}}		{{ABSTRACT_PUBMED_12777803}}

	==About this Structure==		==About this Structure==
	~~1OAD~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA].		[[1oad]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OAD OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~12777803~~</ref><references group="xtra"/>		<ref group="xtra">PMID:012777803</ref><references group="xtra"/>
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
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	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:57:07 2009''~~