2dfb - Revision history

OCA at 07:35, 9 October 2024

2024-10-09T07:35:56Z

← Older revision		Revision as of 07:35, 9 October 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2dfb_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2dfb_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 08:26, 25 October 2023

2023-10-25T08:26:25Z

← Older revision		Revision as of 08:26, 25 October 2023
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	<StructureSection load='2dfb' size='340' side='right'caption='[[2dfb]], [[Resolution\|resolution]] 1.11Å' scene=''>		<StructureSection load='2dfb' size='340' side='right'caption='[[2dfb]], [[Resolution\|resolution]] 1.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Hypocrea_jecorina Hypocrea jecorina~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DFB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DFB FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.11Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~PCA~~:~~PYROGLUTAMIC~~+~~ACID~~'>~~PCA~~</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[2dfc\|2dfc]]~~</~~div~~><~~/td></tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8]~~ </~~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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [https://pdbe.org/2dfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [https://www.ebi.ac.uk/pdbsum/2dfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfb 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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [https://pdbe.org/2dfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [https://www.ebi.ac.uk/pdbsum/2dfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfb ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/XYN2_HYPJR XYN2_HYPJR] Glycoside hydrolase involved in the hydrolysis of xylan, a major plant cell wall hemicellulose made up of 1,4-beta-linked D-xylopyranose residues. Catalyzes the endohydrolysis of the main-chain 1,4-beta-glycosidic bonds connecting the xylose subunits yielding various xylooligosaccharides and xylose (PubMed:1369024, Ref.5). The catalysis proceeds by a double-displacement reaction mechanism with a putative covalent glycosyl-enzyme intermediate, with retention of the anomeric configuration (PubMed:7988708). Produces xylobiose and xylose as the main degradation products (PubMed:19556747).<ref>PMID:1369024</ref> <ref>PMID:19556747</ref> <ref>PMID:7988708</ref> <ref>PMID:1369024</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Endo-1,4-beta-xylanase]]~~
	~~[[Category: Hypocrea jecorina]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Akiba, T~~]]		[[Category: Trichoderma reesei]]
	[[Category: ~~Harata, K~~]]		[[Category: Akiba T]]
	[[Category: ~~Bent beta sheet]]~~		[[Category: Harata K]]
	~~[[Category: Hydrolase~~]]

OCA at 20:37, 20 October 2021

2021-10-20T20:37:41Z

← Older revision		Revision as of 20:37, 20 October 2021
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	<StructureSection load='2dfb' size='340' side='right'caption='[[2dfb]], [[Resolution\|resolution]] 1.11Å' scene=''>		<StructureSection load='2dfb' size='340' side='right'caption='[[2dfb]], [[Resolution\|resolution]] 1.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DFB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DFB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dfc\|2dfc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dfc\|2dfc]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [~~http~~://pdbe.org/2dfb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dfb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfb 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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [https://pdbe.org/2dfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [https://www.ebi.ac.uk/pdbsum/2dfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 09:40, 25 December 2019

2019-12-25T09:40:07Z

← Older revision		Revision as of 09:40, 25 December 2019
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	==Xylanase II from Tricoderma reesei at 100K==		==Xylanase II from Tricoderma reesei at 100K==
	<StructureSection load='2dfb' size='340' side='right' caption='[[2dfb]], [[Resolution\|resolution]] 1.11Å' scene=''>		<StructureSection load='2dfb' size='340' side='right'caption='[[2dfb]], [[Resolution\|resolution]] 1.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFB FirstGlance]. <br>
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	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Hypocrea jecorina]]		[[Category: Hypocrea jecorina]]
			[[Category: Large Structures]]
	[[Category: Akiba, T]]		[[Category: Akiba, T]]
	[[Category: Harata, K]]		[[Category: Harata, K]]
	[[Category: Bent beta sheet]]		[[Category: Bent beta sheet]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 06:09, 30 May 2018

2018-05-30T06:09:36Z

← Older revision		Revision as of 06:09, 30 May 2018
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	==Xylanase II from Tricoderma reesei at 100K==		==Xylanase II from Tricoderma reesei at 100K==
	<StructureSection load='2dfb' size='340' side='right' caption='[[2dfb]], [[Resolution\|resolution]] 1.11Å' scene=''>		<StructureSection load='2dfb' size='340' side='right' caption='[[2dfb]], [[Resolution\|resolution]] 1.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Trichoderma_reesei Trichoderma reesei~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dfc\|2dfc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dfc\|2dfc]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [http://pdbe.org/2dfb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [http://www.ebi.ac.uk/pdbsum/2dfb 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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [http://pdbe.org/2dfb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [http://www.ebi.ac.uk/pdbsum/2dfb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dfb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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/df/2dfb_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2dfb_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>
	</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=2dfb 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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	</StructureSection>		</StructureSection>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: ~~Trichoderma reesei~~]]		[[Category: Hypocrea jecorina]]
	[[Category: Akiba, T]]		[[Category: Akiba, T]]
	[[Category: Harata, K]]		[[Category: Harata, K]]
	[[Category: Bent beta sheet]]		[[Category: Bent beta sheet]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:12, 11 September 2015

2015-09-11T08:12:23Z

← Older revision		Revision as of 08:12, 11 September 2015
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dfc\|2dfc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dfc\|2dfc]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [http://www.ebi.ac.uk/pdbsum/2dfb 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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [http://pdbe.org/2dfb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [http://www.ebi.ac.uk/pdbsum/2dfb 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 2dfb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:25, 15 January 2015

2015-01-15T17:25:57Z

← Older revision		Revision as of 17:25, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFB FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dfc\|2dfc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dfc\|2dfc]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [http://www.ebi.ac.uk/pdbsum/2dfb 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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [http://www.ebi.ac.uk/pdbsum/2dfb PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Trichoderma reesei]]		[[Category: Trichoderma reesei]]
	[[Category: Akiba, T.]]		[[Category: Akiba, T]]
	[[Category: Harata, K.]]		[[Category: Harata, K]]
	[[Category: Bent beta sheet]]		[[Category: Bent beta sheet]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 00:41, 30 September 2014

2014-09-30T00:41:06Z

← Older revision		Revision as of 00:41, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2dfb~~.~~png~~\|~~left~~\|~~200px~~]]		==Xylanase II from Tricoderma reesei at 100K==
			<StructureSection load='2dfb' size='340' side='right' caption='[[2dfb]], [[Resolution\|resolution]] 1.11Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dfb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DFB FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dfc\|2dfc]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=2dfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dfb RCSB], [http://www.ebi.ac.uk/pdbsum/2dfb 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/df/2dfb_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 ==
			An orthorhombic crystal of xylanase II from Trichoderma reesei was grown in the presence of sodium iodide. Crystal structures at atomic resolution were determined at 100 and 293 K. Protein molecules were aligned along a crystallographic twofold screw axis, forming a helically extended polymer-like chain mediated by an iodide ion. The iodide ion connected main-chain peptide groups between two adjacent molecules by an N-H...I-...H-N hydrogen-bond bridge, thus contributing to regulation of the molecular arrangement and suppression of the rigid-body motion in the crystal with high diffraction quality. The structure at 293 K showed considerable thermal motion in the loop regions connecting the beta-strands that form the active-site cleft. TLS model analysis of the thermal motion and a comparison between this structure and that at 100 K suggest that the fluctuation of these loop regions is attributable to the hinge-like movement of the beta-strands.

	~~{{STRUCTURE_2dfb\| PDB=2dfb \| SCENE= }}~~		Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement.,Watanabe N, Akiba T, Kanai R, Harata K Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):784-92. Epub 2006, Jun 20. PMID:16790934<ref>PMID:16790934</ref>

	~~===Xylanase II from Tricoderma reesei at 100K===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16790934}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2dfb]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Trichoderma_reesei Trichoderma reesei]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016790934<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Trichoderma reesei]]		[[Category: Trichoderma reesei]]

OCA: Protected "2dfb" [edit=sysop:move=sysop]

2013-01-06T10:02:42Z

Protected "2dfb" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:02, 6 January 2013
(No difference)

OCA at 10:02, 6 January 2013

2013-01-06T10:02:39Z

← Older revision		Revision as of 10:02, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2dfb.png\|left\|200px]]		[[Image:2dfb.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dfb", 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_2dfb\| PDB=2dfb \| SCENE= }}		{{STRUCTURE_2dfb\| PDB=2dfb \| SCENE= }}

	===Xylanase II from Tricoderma reesei at 100K===		===Xylanase II from Tricoderma reesei at 100K===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16790934}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16790934 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16790934}}		{{ABSTRACT_PUBMED_16790934}}

	==About this Structure==		==About this Structure==
	~~2DFB~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Hypocrea_jecorina Hypocrea jecorina~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA].		[[2dfb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFB OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16790934~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016790934</ref><references group="xtra"/>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: ~~Hypocrea jecorina~~]]		[[Category: Trichoderma reesei]]
	[[Category: Akiba, T.]]		[[Category: Akiba, T.]]
	[[Category: Harata, K.]]		[[Category: Harata, K.]]
	[[Category: Bent beta sheet]]		[[Category: Bent beta sheet]]
			[[Category: Hydrolase]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 17:42:32 2009''~~