5XVD image
Deposition Date 2017-06-27
Release Date 2018-06-27
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5XVD
Keywords:
OXIDOREDUCTASE
Title:
[NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an air-oxidized condition
Biological Source:
Source Organism:
Citrobacter sp. S-77 (Taxon ID: 1080067)
Citrobacter sp. MGH106 (Taxon ID: 1686381)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.57 Å
R-Value Free:
0.16
R-Value Work:
0.12
R-Value Observed:
0.12
Space Group:
P 1 21 1
5XVD validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:[NiFe]-hydrogenase 2 large subunit
Chain IDs:A (auth: L), C (auth: M)
Chain Length:552
Number of Molecules:2
Biological Source:Citrobacter sp. S-77
UniProt ID:A0A3B6UEQ1 Pfam ID:PF00374
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hydrogenase-2 small chain
Gene (Uniprot):SK36_00260
Chain IDs:B (auth: S), D (auth: T)
Chain Length:335
Number of Molecules:2
Biological Source:Citrobacter sp. MGH106
UniProt ID:A0A0J1PJ79 Pfam ID:PF01058, PF14720
Ligand Molecules
8JU
F3S
GOL
MG
NA
NFV
SF4
Primary Citation
Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.
Chem.Commun.(Camb.) 54 12385 12388 (2018)
PMID: 30328414 DOI: 10.1039/c8cc06261g

Abstact

Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.

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Protein

Chemical

Disease

Primary Citation of related structures
5XVD