3c8y - Revision history

OCA at 12:24, 30 August 2023

OCA — Wed, 30 Aug 2023 12:24:41 GMT

←Older revision		Revision as of 12:24, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3c8y' size='340' side='right'caption='[[3c8y]], [[Resolution\|resolution]] 1.39Å' scene=''>		<StructureSection load='3c8y' size='340' side='right'caption='[[3c8y]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3c8y]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3C8Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3c8y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C8Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.39Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [~~http~~://pdbe.org/3c8y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3c8y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8y 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=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [https://pdbe.org/3c8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [https://www.ebi.ac.uk/pdbsum/3c8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8y ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PHF1_CLOPA PHF1_CLOPA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Clostridium pasteurianum]]		[[Category: Clostridium pasteurianum]]
-	[[Category: Ferredoxin hydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lemon~~, B J~~]]	+	[[Category: Lemon BJ]]
-	[[Category: Pandey~~, A S~~]]	+	[[Category: Pandey AS]]
-	[[Category: Peters~~, J W]]~~	+	[[Category: Peters JW]]
-	~~[[Category: Dithiomethylether]]~~	+
-	~~[[Category: H-cluster]]~~	+
-	~~[[Category: Hydrogenase]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Iron-sulfur]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:24, 12 August 2020

OCA — Wed, 12 Aug 2020 10:24:45 GMT

←Older revision		Revision as of 10:24, 12 August 2020
Line 1:		Line 1:

	==1.39 Angstrom crystal structure of Fe-only hydrogenase==		==1.39 Angstrom crystal structure of Fe-only hydrogenase==
-	<StructureSection load='3c8y' size='340' side='right' caption='[[3c8y]], [[Resolution\|resolution]] 1.39Å' scene=''>	+	<StructureSection load='3c8y' size='340' side='right'caption='[[3c8y]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3c8y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3C8Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3c8y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3C8Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </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=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [http://pdbe.org/3c8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [http://www.ebi.ac.uk/pdbsum/3c8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8y ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [http://pdbe.org/3c8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [http://www.ebi.ac.uk/pdbsum/3c8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8y ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	[[Category: Clostridium pasteurianum]]		[[Category: Clostridium pasteurianum]]
	[[Category: Ferredoxin hydrogenase]]		[[Category: Ferredoxin hydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Lemon, B J]]		[[Category: Lemon, B J]]
	[[Category: Pandey, A S]]		[[Category: Pandey, A S]]

OCA at 14:05, 7 November 2018

OCA — Wed, 07 Nov 2018 14:05:24 GMT

←Older revision		Revision as of 14:05, 7 November 2018
Line 1:		Line 1:
		+
	==1.39 Angstrom crystal structure of Fe-only hydrogenase==		==1.39 Angstrom crystal structure of Fe-only hydrogenase==
	<StructureSection load='3c8y' size='340' side='right' caption='[[3c8y]], [[Resolution\|resolution]] 1.39Å' scene=''>		<StructureSection load='3c8y' size='340' side='right' caption='[[3c8y]], [[Resolution\|resolution]] 1.39Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </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=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [http://pdbe.org/3c8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [http://www.ebi.ac.uk/pdbsum/3c8y 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=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [http://pdbe.org/3c8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [http://www.ebi.ac.uk/pdbsum/3c8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3c8y ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/3c8y_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/3c8y_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>

OCA at 23:52, 7 February 2016

OCA — Sun, 07 Feb 2016 23:52:02 GMT

←Older revision		Revision as of 23:52, 7 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </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=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [http://www.ebi.ac.uk/pdbsum/3c8y 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=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [http://pdbe.org/3c8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [http://www.ebi.ac.uk/pdbsum/3c8y PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 15:
	<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=3c8y ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	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 3c8y" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:56, 20 January 2015

OCA — Tue, 20 Jan 2015 10:56:39 GMT

←Older revision		Revision as of 10:56, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3c8y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C8Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[3c8y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C8Y FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </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=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [http://www.ebi.ac.uk/pdbsum/3c8y 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=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [http://www.ebi.ac.uk/pdbsum/3c8y 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 31:		Line 31:
	[[Category: Clostridium pasteurianum]]		[[Category: Clostridium pasteurianum]]
	[[Category: Ferredoxin hydrogenase]]		[[Category: Ferredoxin hydrogenase]]
-	[[Category: Lemon, B J.]]	+	[[Category: Lemon, B J]]
-	[[Category: Pandey, A S.]]	+	[[Category: Pandey, A S]]
-	[[Category: Peters, J W.]]	+	[[Category: Peters, J W]]
	[[Category: Dithiomethylether]]		[[Category: Dithiomethylether]]
	[[Category: H-cluster]]		[[Category: H-cluster]]

OCA at 21:38, 2 October 2014

OCA — Thu, 02 Oct 2014 21:38:02 GMT

←Older revision		Revision as of 21:38, 2 October 2014
Line 1:		Line 1:
-	[[~~Image~~:3c8y.~~png\|left~~\|200px]]	+	==1.39 Angstrom crystal structure of Fe-only hydrogenase==
		+	<StructureSection load='3c8y' size='340' side='right' caption='[[3c8y]], [[Resolution\|resolution]] 1.39Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3c8y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C8Y FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HCN:2+IRON/2+SULFUR/3+CARBONYL/2+CYANIDE/WATER/METHYLETHER+CLUSTER'>HCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] </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=3c8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c8y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c8y RCSB], [http://www.ebi.ac.uk/pdbsum/3c8y 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/c8/3c8y_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 X-ray crystallographic refinement of the H-cluster of [FeFe]-hydrogenase from Clostridium pasteurianum has been carried out to close-to atomic resolution and is the highest resolution [FeFe]-hydrogenase presented to date. The 1.39 A, anisotropically refined [FeFe]-hydrogenase structure provides a basis for examining the outstanding issue of the composition of the unique nonprotein dithiolate ligand of the H-cluster. In addition to influencing the electronic structure of the H-cluster, the composition of the ligand has mechanistic implications due to the potential of the bridge-head gamma-group participating in proton transfer during catalysis. In this work, sequential density functional theory optimizations of the dithiolate ligand embedded in a 3.5-3.9 A protein environment provide an unbiased approach to examining the most likely composition of the ligand. Structural, conformational, and energetic considerations indicate a preference for dithiomethylether as an H-cluster ligand and strongly disfavor the dithiomethylammonium as a catalytic base for hydrogen production.

-	~~{{STRUCTURE_3c8y\| PDB=3c8y \| SCENE= }}~~	+	Dithiomethylether as a ligand in the hydrogenase h-cluster.,Pandey AS, Harris TV, Giles LJ, Peters JW, Szilagyi RK J Am Chem Soc. 2008 Apr 2;130(13):4533-40. Epub 2008 Mar 7. PMID:18324814<ref>PMID:18324814</ref>

-	~~===1.39 Angstrom crystal structure~~ of ~~Fe-only hydrogenase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18324814}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3c8y]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018324814<~~/~~ref~~><~~ref group="xtra">PMID:020418861</ref><references group="xtra"~~/>	+
	[[Category: Clostridium pasteurianum]]		[[Category: Clostridium pasteurianum]]
	[[Category: Ferredoxin hydrogenase]]		[[Category: Ferredoxin hydrogenase]]

OCA: Protected "3c8y" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 19:48:52 GMT

Protected "3c8y" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:48, 7 January 2013

OCA at 19:48, 7 January 2013

OCA — Mon, 07 Jan 2013 19:48:47 GMT

←Older revision		Revision as of 19:48, 7 January 2013
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-	{{Seed}}
	[[Image:3c8y.png\|left\|200px]]		[[Image:3c8y.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3c8y", 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_3c8y\| PDB=3c8y \| SCENE= }}		{{STRUCTURE_3c8y\| PDB=3c8y \| SCENE= }}

	===1.39 Angstrom crystal structure of Fe-only hydrogenase===		===1.39 Angstrom crystal structure of Fe-only hydrogenase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18324814}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18324814 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18324814}}		{{ABSTRACT_PUBMED_18324814}}

	==About this Structure==		==About this Structure==
-	~~3C8Y~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA].	+	[[3c8y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18324814~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018324814</ref><ref group="xtra">PMID:020418861</ref><references group="xtra"/>
	[[Category: Clostridium pasteurianum]]		[[Category: Clostridium pasteurianum]]
	[[Category: Ferredoxin hydrogenase]]		[[Category: Ferredoxin hydrogenase]]
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	[[Category: Pandey, A S.]]		[[Category: Pandey, A S.]]
	[[Category: Peters, J W.]]		[[Category: Peters, J W.]]
-	[[Category: 4fe-4]]
	[[Category: Dithiomethylether]]		[[Category: Dithiomethylether]]
	[[Category: H-cluster]]		[[Category: H-cluster]]
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	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:19:03 2009''

OCA at 15:19, 16 February 2009

OCA — Mon, 16 Feb 2009 15:19:04 GMT

←Older revision		Revision as of 15:19, 16 February 2009
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	==About this Structure==		==About this Structure==
-	3C8Y is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA].	+	3C8Y is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C8Y OCA].

	==Reference==		==Reference==
-	~~Dithiomethylether as a ligand in the hydrogenase h-cluster., Pandey AS, Harris TV, Giles LJ, Peters JW, Szilagyi RK, J Am Chem Soc. 2008 Apr 2;130(13):4533-40. Epub 2008 Mar 7.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18324814 18324814]~~	+	<ref group="xtra">PMID:18324814</ref><references group="xtra"/>
	[[Category: Clostridium pasteurianum]]		[[Category: Clostridium pasteurianum]]
	[[Category: Ferredoxin hydrogenase]]		[[Category: Ferredoxin hydrogenase]]
-	[[Category: Single protein]]
	[[Category: Lemon, B J.]]		[[Category: Lemon, B J.]]
	[[Category: Pandey, A S.]]		[[Category: Pandey, A S.]]
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	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 20~~:41:~~09 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:19:03 2009''

OCA at 17:41, 27 July 2008

OCA — Sun, 27 Jul 2008 17:41:11 GMT

←Older revision		Revision as of 17:41, 27 July 2008
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-	[[Image:3c8y.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3c8y.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3c8y\| PDB=3c8y \| SCENE= }}		{{STRUCTURE_3c8y\| PDB=3c8y \| SCENE= }}

-	~~'''~~1.39 Angstrom crystal structure of Fe-only hydrogenase~~'''~~	+	===1.39 Angstrom crystal structure of Fe-only hydrogenase===


-	~~==Overview==~~	+	<!--
-	~~An X~~-~~ray crystallographic refinement of the H~~-~~cluster of [FeFe]-hydrogenase from Clostridium pasteurianum has been carried out to close-to atomic resolution and is the highest resolution [FeFe]-hydrogenase presented to date.~~ The ~~1.39 A~~, anisotropically refined [FeFe]-hydrogenase structure provides a basis for examining the outstanding issue of the composition of the unique nonprotein dithiolate ligand of the H-cluster. In addition to influencing the electronic structure of the H-cluster, the ~~composition of the ligand has mechanistic implications due~~ to the ~~potential of the bridge-head gamma-group participating in proton transfer during catalysis~~. ~~In this work~~, ~~sequential density functional theory optimizations of~~ the ~~dithiolate ligand embedded in a 3~~.5-3.9 A protein environment provide an unbiased approach to examining the most likely composition of the ligand. Structural, conformational, and energetic considerations indicate a preference for dithiomethylether as an H-~~cluster ligand and strongly disfavor the dithiomethylammonium as a catalytic base for hydrogen production.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_18324814}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18324814 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18324814}}

	==About this Structure==		==About this Structure==
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	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Apr 24 09~~:53:22 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 20:41:09 2008''