This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3c8y

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 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 PD...)
Current revision (12:24, 30 August 2023) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3c8y.jpg|left|200px]]
 
-
<!--
+
==1.39 Angstrom crystal structure of Fe-only hydrogenase==
-
The line below this paragraph, containing "STRUCTURE_3c8y", creates the "Structure Box" on the page.
+
<StructureSection load='3c8y' size='340' side='right'caption='[[3c8y]], [[Resolution|resolution]] 1.39&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<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>
-
or leave the SCENE parameter empty for the default display.
+
</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>
-
-->
+
<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>
-
{{STRUCTURE_3c8y| PDB=3c8y | SCENE= }}
+
<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>
-
'''1.39 Angstrom crystal structure of Fe-only hydrogenase'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/PHF1_CLOPA PHF1_CLOPA]
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[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/main_output.php?pdb_ID=3c8y 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.
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.
-
==About this Structure==
+
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>
-
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].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
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]
+
</div>
 +
<div class="pdbe-citations 3c8y" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Clostridium pasteurianum]]
[[Category: Clostridium pasteurianum]]
-
[[Category: Ferredoxin hydrogenase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Lemon BJ]]
-
[[Category: Lemon, B J.]]
+
[[Category: Pandey AS]]
-
[[Category: Pandey, A S.]]
+
[[Category: Peters JW]]
-
[[Category: Peters, J W.]]
+
-
[[Category: 4fe-4]]
+
-
[[Category: Dithiomethylether]]
+
-
[[Category: H-cluster]]
+
-
[[Category: Hydrogenase]]
+
-
[[Category: Iron]]
+
-
[[Category: Iron-sulfur]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Oxidoreductase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:53:22 2008''
+

Current revision

1.39 Angstrom crystal structure of Fe-only hydrogenase

PDB ID 3c8y

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3c8y"
Personal tools