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3c8y

From Proteopedia

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[[Image:3c8y.png|left|200px]]
 
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{{STRUCTURE_3c8y| PDB=3c8y | SCENE= }}
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==1.39 Angstrom crystal structure of Fe-only hydrogenase==
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<StructureSection load='3c8y' size='340' side='right'caption='[[3c8y]], [[Resolution|resolution]] 1.39&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.39&#8491;</td></tr>
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<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>
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PHF1_CLOPA PHF1_CLOPA]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/3c8y_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3c8y ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===1.39 Angstrom crystal structure of Fe-only hydrogenase===
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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>
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{{ABSTRACT_PUBMED_18324814}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 3c8y" style="background-color:#fffaf0;"></div>
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[[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].
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== References ==
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<references/>
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==Reference==
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__TOC__
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<ref group="xtra">PMID:018324814</ref><ref group="xtra">PMID:020418861</ref><references group="xtra"/>
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</StructureSection>
[[Category: Clostridium pasteurianum]]
[[Category: Clostridium pasteurianum]]
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[[Category: Ferredoxin hydrogenase]]
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[[Category: Large Structures]]
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[[Category: Lemon, B J.]]
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[[Category: Lemon BJ]]
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[[Category: Pandey, A S.]]
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[[Category: Pandey AS]]
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[[Category: Peters, J W.]]
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[[Category: Peters JW]]
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[[Category: Dithiomethylether]]
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[[Category: H-cluster]]
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[[Category: Hydrogenase]]
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[[Category: Iron]]
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[[Category: Iron-sulfur]]
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[[Category: Metal-binding]]
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[[Category: Oxidoreductase]]
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Current revision

1.39 Angstrom crystal structure of Fe-only hydrogenase

PDB ID 3c8y

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