› 1ubj

X-ray diffraction
1.35Å resolution

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Released:
DOI: 10.2210/pdb1ubj/pdb
PDB entry 1ubj coloured by chain, front view.
PDB entry 1ubj coloured by chain, side view.
PDB entry 1ubj coloured by chain, top view.
Source organism: Nitratidesulfovibrio vulgaris str. 'Miyazaki F'
Primary publication:
Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen.
Ogata H, Mizoguchi Y, Mizuno N, Miki K, Adachi S, Yasuoka N, Yagi T, Yamauchi O, Hirota S, Higuchi Y
J Am Chem Soc 124 11628-35 (2002)
PMID: 12296727

Function and Biology Details

Reaction catalysed: 
H(2) + 2 ferricytochrome c3 = 2 H(+) + 2 ferrocytochrome c3
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149443 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Periplasmic [NiFe] hydrogenase small subunit Chain: S
Molecule details ›
Chain: S
Length: 267 amino acids
Theoretical weight: 28.79 KDa
Source organism: Nitratidesulfovibrio vulgaris str. 'Miyazaki F'
UniProt:
  • Canonical: P21853 (Residues: 51-317; Coverage: 100%)
Gene names: DvMF_0271, hydA
Sequence domains:
Structure domains:
Periplasmic [NiFe] hydrogenase large subunit Chain: L
Molecule details ›
Chain: L
Length: 534 amino acids
Theoretical weight: 59.21 KDa
Source organism: Nitratidesulfovibrio vulgaris str. 'Miyazaki F'
UniProt:
  • Canonical: P21852 (Residues: 19-552; Coverage: 94%)
Gene names: DvMF_0270, hydB
Sequence domains: Nickel-dependent hydrogenase
Structure domains: Cytochrome-c3 Hydrogenase, chain B

Ligands and Environments

5 bound ligands:
Ligand SF4 2 x SF4
Ligand F3S 1 x F3S
Ligand MG 1 x MG
Ligand FNE 1 x FNE
Ligand CMO 1 x CMO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 97.74Å b: 125.86Å c: 66.57Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.136 0.121 0.183

Quick links

Citations

12 review citations

Metal and redox modulation of cysteine protein function.
Giles et al. (2003)
11 more

1 mention without citation

Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120.
Devine et al. (2009)