4ko3: Difference between revisions

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==Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air==
==Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air==
<StructureSection load='4ko3' size='340' side='right' caption='[[4ko3]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='4ko3' size='340' side='right'caption='[[4ko3]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4ko3]] 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=4KO3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KO3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4ko3]] 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=4KO3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KO3 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]] 1.7&#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=SF4:IRON/SULFUR+CLUSTER'>SF4</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]], [[4ko4|4ko4]]</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=4ko3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ko3 OCA], [https://pdbe.org/4ko3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ko3 RCSB], [https://www.ebi.ac.uk/pdbsum/4ko3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ko3 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=4ko3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ko3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ko3 RCSB], [http://www.ebi.ac.uk/pdbsum/4ko3 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 ==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 4ko3" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</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 19:02, 20 September 2023

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

Structural highlights

4ko3 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 1.7Å
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

4ko3, resolution 1.70Å

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