4ko4: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:


==High X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air==
==High X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air==
<StructureSection load='4ko4' size='340' side='right' caption='[[4ko4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='4ko4' size='340' side='right'caption='[[4ko4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4ko4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfomicrobium_baculatum Desulfomicrobium baculatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KO4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KO4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4ko4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfomicrobium_baculatum Desulfomicrobium baculatum] and [https://en.wikipedia.org/wiki/Desulfomicrobium_baculatum_DSM_4028 Desulfomicrobium baculatum DSM 4028]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KO4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KO4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SE7:2-AMINO-3-SELENINO-PROPIONIC+ACID'>SE7</scene>, <scene name='pdbligand=UOX:3-(OXIDO-LAMBDA~4~-SELANYL)-L-ALANINE'>UOX</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SE7:2-AMINO-3-SELENINO-PROPIONIC+ACID'>SE7</scene>, <scene name='pdbligand=UOX:3-(OXIDO-LAMBDA~4~-SELANYL)-L-ALANINE'>UOX</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1cc1|1cc1]], [[4kl8|4kl8]], [[4kn9|4kn9]], [[4ko1|4ko1]], [[4ko2|4ko2]], [[4ko3|4ko3]]</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=4ko4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ko4 OCA], [https://pdbe.org/4ko4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ko4 RCSB], [https://www.ebi.ac.uk/pdbsum/4ko4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ko4 ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.99.6 1.12.99.6] </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=4ko4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ko4 OCA], [http://pdbe.org/4ko4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ko4 RCSB], [http://www.ebi.ac.uk/pdbsum/4ko4 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PHSS_DESBA PHSS_DESBA]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 24: Line 24:
</StructureSection>
</StructureSection>
[[Category: Desulfomicrobium baculatum]]
[[Category: Desulfomicrobium baculatum]]
[[Category: Cavazza, C]]
[[Category: Desulfomicrobium baculatum DSM 4028]]
[[Category: Fontecilla-Camps, J C]]
[[Category: Large Structures]]
[[Category: Volbeda, A]]
[[Category: Cavazza C]]
[[Category: H2 cleavage/production]]
[[Category: Fontecilla-Camps JC]]
[[Category: Nifese-site]]
[[Category: Volbeda A]]
[[Category: Oxidoreductase]]
[[Category: Seleninate]]

Latest revision as of 10:07, 27 November 2024

High X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under airHigh X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

Structural highlights

4ko4 is a 4 chain structure with sequence from Desulfomicrobium baculatum and Desulfomicrobium baculatum DSM 4028. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, , , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHSS_DESBA

Publication Abstract from PubMed

This study shows how the NiFeSe site of an anaerobically purified O2-resistant hydrogenase reacts with air to give a seleninate as the first product. Less oxidized states of the active site are readily reduced in the presence of X-rays. Reductive enzyme activation requires an efficient pathway for water escape.

Structural foundations for the O2 resistance of Desulfomicrobium baculatum [NiFeSe]-hydrogenase.,Volbeda A, Amara P, Iannello M, De Lacey AL, Cavazza C, Fontecilla-Camps JC Chem Commun (Camb). 2013 Jul 11;49(63):7061-3. doi: 10.1039/c3cc43619e. PMID:23811828[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Volbeda A, Amara P, Iannello M, De Lacey AL, Cavazza C, Fontecilla-Camps JC. Structural foundations for the O2 resistance of Desulfomicrobium baculatum [NiFeSe]-hydrogenase. Chem Commun (Camb). 2013 Jul 11;49(63):7061-3. doi: 10.1039/c3cc43619e. PMID:23811828 doi:10.1039/c3cc43619e

4ko4, resolution 2.00Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=4ko4&oldid=4216060"