3cix - Revision history

OCA at 14:58, 1 November 2023

2023-11-01T14:58:32Z

←Older revision		Revision as of 14:58, 1 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cix]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CIX FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cix]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CIX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SAT:SULFOACETIC+ACID'>SAT</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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]] 1.7Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SAT:SULFOACETIC+ACID'>SAT</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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;'>[[3ciw\|3ciw]]</div></td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])~~</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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [https://pdbe.org/3cix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [https://www.ebi.ac.uk/pdbsum/3cix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cix 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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [https://pdbe.org/3cix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [https://www.ebi.ac.uk/pdbsum/3cix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cix ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/HYDE_THEMA HYDE_THEMA] Required for the maturation of the [FeFe]-hydrogenase HydA (By similarity). Catalyzes the reductive cleavage of S-adenosyl-L-methionine (in vitro), suggesting it may contribute to the biosynthesis of an essential sulfur-containing ligand that binds to the hydrogenase active site [2Fe-2S] cluster (PubMed:16137685).[UniProtKB:Q97IK9]<ref>PMID:16137685</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
-	[[Category: Amara, P]]	+	[[Category: Amara P]]
-	[[Category: Atta, M]]	+	[[Category: Atta M]]
-	[[Category: Fontecave, M]]	+	[[Category: Fontecave M]]
-	[[Category: Fontecilla-Camps~~, J C~~]]	+	[[Category: Fontecilla-Camps JC]]
-	[[Category: Mathevon, C]]	+	[[Category: Mathevon C]]
-	[[Category: Nicolet, Y]]	+	[[Category: Nicolet Y]]
-	[[Category: Posewitz~~, M C~~]]	+	[[Category: Posewitz MC]]
-	[[Category: Ruback~~, J K]]~~	+	[[Category: Ruback JK]]
-	~~[[Category: Adomet binding protein]]~~	+
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Fe2s2 cluster]]~~	+
-	~~[[Category: Fe4s4 cluster]]~~	+
-	~~[[Category: Fefe-hydrogenase maturation]]~~	+
-	~~[[Category: Radical adomet protein]]~~	+
-	~~[[Category: Thiocyanate~~]]	+

OCA at 07:57, 27 January 2022

2022-01-27T07:57:30Z

←Older revision		Revision as of 07:57, 27 January 2022
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	==X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate==		==X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate==
-	<StructureSection load='3cix' size='340' side='right' caption='[[3cix]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='3cix' size='340' side='right'caption='[[3cix]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3cix]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3CIX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3cix]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CIX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SAT:SULFOACETIC+ACID'>SAT</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SAT:SULFOACETIC+ACID'>SAT</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ciw\|3ciw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ciw\|3ciw]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [~~http~~://pdbe.org/3cix PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3cix PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3cix 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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [https://pdbe.org/3cix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [https://www.ebi.ac.uk/pdbsum/3cix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cix ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ci/3cix_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ci/3cix_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 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
	[[Category: Amara, P]]		[[Category: Amara, P]]

OCA at 08:28, 25 October 2017

2017-10-25T08:28:32Z

←Older revision		Revision as of 08:28, 25 October 2017
Line 1:		Line 1:
		+
	==X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate==		==X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate==
	<StructureSection load='3cix' size='340' side='right' caption='[[3cix]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='3cix' size='340' side='right' caption='[[3cix]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ciw\|3ciw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ciw\|3ciw]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [http://pdbe.org/3cix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [http://www.ebi.ac.uk/pdbsum/3cix 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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [http://pdbe.org/3cix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [http://www.ebi.ac.uk/pdbsum/3cix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cix ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 20:48, 7 February 2016

2016-02-07T20:48:57Z

←Older revision		Revision as of 20:48, 7 February 2016
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ciw\|3ciw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ciw\|3ciw]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [http://www.ebi.ac.uk/pdbsum/3cix 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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [http://pdbe.org/3cix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [http://www.ebi.ac.uk/pdbsum/3cix PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		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=3cix ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	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 3cix" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:19, 20 January 2015

2015-01-20T09:19:39Z

←Older revision		Revision as of 09:19, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cix]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CIX FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cix]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CIX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SAT:SULFOACETIC+ACID'>SAT</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SAT:SULFOACETIC+ACID'>SAT</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ciw\|3ciw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ciw\|3ciw]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [http://www.ebi.ac.uk/pdbsum/3cix 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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [http://www.ebi.ac.uk/pdbsum/3cix 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 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
-	[[Category: Amara, P.]]	+	[[Category: Amara, P]]
-	[[Category: Atta, M.]]	+	[[Category: Atta, M]]
-	[[Category: Fontecave, M.]]	+	[[Category: Fontecave, M]]
-	[[Category: Fontecilla-Camps, J C.]]	+	[[Category: Fontecilla-Camps, J C]]
-	[[Category: Mathevon, C.]]	+	[[Category: Mathevon, C]]
-	[[Category: Nicolet, Y.]]	+	[[Category: Nicolet, Y]]
-	[[Category: Posewitz, M C.]]	+	[[Category: Posewitz, M C]]
-	[[Category: Ruback, J K.]]	+	[[Category: Ruback, J K]]
	[[Category: Adomet binding protein]]		[[Category: Adomet binding protein]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]

OCA at 21:08, 2 October 2014

2014-10-02T21:08:55Z

←Older revision		Revision as of 21:08, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3cix.~~png~~\|~~left~~\|200px]]	+	==X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate==
		+	<StructureSection load='3cix' size='340' side='right' caption='[[3cix]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3cix]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CIX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SAT:SULFOACETIC+ACID'>SAT</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ciw\|3ciw]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HydE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</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=3cix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cix RCSB], [http://www.ebi.ac.uk/pdbsum/3cix 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/ci/3cix_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 ==
		+	Maturation of the [FeFe]-hydrogenase active site depends on at least the expression of three gene products called HydE, HydF, and HydG. We have solved the high resolution structure of recombinant, reconstituted S-adenosine-L-methionine-dependent HydE from Thermotoga maritima. Besides the conserved [Fe(4)S(4)] cluster involved in the radical-based reaction, this HydE was reported to have a second [Fe(4)S(4)] cluster coordinated by three Cys residues. However, in our crystals, depending on the reconstitution and soaking conditions, this second cluster is either a [Fe(2)S(2)] center, with water occupying the fourth ligand site or is absent. We have carried out site-directed mutagenesis studies on the related HydE from Clostridium acetobutylicum, along with in silico docking and crystal soaking experiments, to define the active site region and three anion-binding sites inside a large, positive cavity, one of which binds SCN(-) with high affinity. Although the overall triose-phosphate isomerase-barrel structure of HydE is very similar to that of biotin synthase, the residues that line the internal cavity are significantly different in the two enzymes.

-	~~{{STRUCTURE_3cix\| PDB=3cix \| SCENE= }}~~	+	X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima.,Nicolet Y, Rubach JK, Posewitz MC, Amara P, Mathevon C, Atta M, Fontecave M, Fontecilla-Camps JC J Biol Chem. 2008 Jul 4;283(27):18861-72. Epub 2008 Apr 8. PMID:18400755<ref>PMID:18400755</ref>

-	~~===X-RAY structure~~ of the ~~[FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18400755}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3cix]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermotoga_maritima Thermotoga maritima]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018400755<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
	[[Category: Amara, P.]]		[[Category: Amara, P.]]

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

2013-01-07T18:45:18Z

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

←Older revision

Revision as of 18:45, 7 January 2013

OCA at 18:45, 7 January 2013

2013-01-07T18:45:14Z

←Older revision		Revision as of 18:45, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3cix.png\|left\|200px]]		[[Image:3cix.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3cix", 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_3cix\| PDB=3cix \| SCENE= }}		{{STRUCTURE_3cix\| PDB=3cix \| SCENE= }}

	===X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate===		===X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18400755}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18400755 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18400755}}		{{ABSTRACT_PUBMED_18400755}}

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

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18400755~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018400755</ref><references group="xtra"/>
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
	[[Category: Amara, P.]]		[[Category: Amara, P.]]
Line 40:		Line 28:
	[[Category: Radical adomet protein]]		[[Category: Radical adomet protein]]
	[[Category: Thiocyanate]]		[[Category: Thiocyanate]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:24:47 2009''

OCA at 14:24, 16 February 2009

2009-02-16T14:24:47Z

←Older revision		Revision as of 14:24, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3CIX is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA].	+	3CIX is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA].

	==Reference==		==Reference==
-	X-ray Structure of the [FeFe]-Hydrogenase Maturase HydE from Thermotoga maritima., Nicolet Y, Rubach JK, Posewitz MC, Amara P, Mathevon C, Atta M, Fontecave M, Fontecilla-Camps JC, J Biol Chem. 2008 Jul 4;283(27):18861-18872. Epub 2008 Apr 8. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18400755 18400755]~~	+	<ref group="xtra">PMID:18400755</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
	[[Category: Amara, P.]]		[[Category: Amara, P.]]
Line 42:		Line 41:
	[[Category: Thiocyanate]]		[[Category: Thiocyanate]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul~~ 16 08:55:~~42 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:24:47 2009''

OCA at 05:55, 16 July 2008

2008-07-16T05:55:42Z

←Older revision		Revision as of 05:55, 16 July 2008
Line 1:		Line 1:
-	[[Image:3cix.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3cix.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_3cix\| PDB=3cix \| SCENE= }}		{{STRUCTURE_3cix\| PDB=3cix \| SCENE= }}

-	~~'''~~X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate~~'''~~	+	===X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18400755}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18400755 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18400755}}

	==About this Structure==		==About this Structure==
	3CIX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA].		3CIX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CIX OCA].
		+
		+	==Reference==
		+	X-ray Structure of the [FeFe]-Hydrogenase Maturase HydE from Thermotoga maritima., Nicolet Y, Rubach JK, Posewitz MC, Amara P, Mathevon C, Atta M, Fontecave M, Fontecilla-Camps JC, J Biol Chem. 2008 Jul 4;283(27):18861-18872. Epub 2008 Apr 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18400755 18400755]
	[[Category: Single protein]]		[[Category: Single protein]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
Line 31:		Line 41:
	[[Category: Radical adomet protein]]		[[Category: Radical adomet protein]]
	[[Category: Thiocyanate]]		[[Category: Thiocyanate]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr~~ 16 23:10:13 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 16 08:55:42 2008''