› 1yqw

X-ray diffraction
1.83Å resolution

Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

Released:
DOI: 10.2210/pdb1yqw/pdb
PDB entry 1yqw coloured by chain, front view.
PDB entry 1yqw coloured by chain, side view.
PDB entry 1yqw coloured by chain, top view.
Source organism: Solidesulfovibrio fructosivorans
Primary publication:
Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
Volbeda A, Martin L, Cavazza C, Matho M, Faber BW, Roseboom W, Albracht SP, Garcin E, Rousset M, Fontecilla-Camps JC
J Biol Inorg Chem 10 239-49 (2005)
PMID: 15803334

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 analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148312 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Periplasmic [NiFe] hydrogenase small subunit Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 264 amino acids
Theoretical weight: 28.35 KDa
Source organism: Solidesulfovibrio fructosivorans
UniProt:
  • Canonical: P18187 (Residues: 51-314; Coverage: 100%)
Gene name: hydA
Sequence domains:
Structure domains:
Periplasmic [NiFe] hydrogenase large subunit Chains: Q, R, S
Molecule details ›
Chains: Q, R, S
Length: 549 amino acids
Theoretical weight: 59.71 KDa
Source organism: Solidesulfovibrio fructosivorans
UniProt:
  • Canonical: P18188 (Residues: 1-549; Coverage: 97%)
Gene name: hydB
Sequence domains: Nickel-dependent hydrogenase
Structure domains: Cytochrome-c3 Hydrogenase, chain B

Ligands and Environments

9 bound ligands:
Ligand SF4 6 x SF4
Ligand F3S 3 x F3S
Ligand GOL 17 x GOL
Ligand NI 3 x NI
Ligand FE2 3 x FE2
Ligand BCT 1 x BCT
Ligand MG 3 x MG
Ligand FCO 3 x FCO
Ligand PER 3 x PER
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21
Unit cell:
a: 64.41Å b: 99.7Å c: 182.83Å
α: 90° β: 91.42° γ: 90°
R-values:
R R work R free
0.148 0.146 0.185

Quick links

Citations

23 review citations

Maturation of [NiFe]-hydrogenases in Escherichia coli.
Forzi et al. (2007)
22 more

5 mentions without citation

Chemical approaches to detect and analyze protein sulfenic acids.
Furdui et al. (2014)
4 more