› 6z9g

X-ray diffraction
1.76Å resolution

Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491A-O2

Released:
DOI: 10.2210/pdb6z9g/pdb
PDB entry 6z9g coloured by chain, front view.
PDB entry 6z9g coloured by chain, side view.
PDB entry 6z9g coloured by chain, top view.
Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Primary publication:
Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.
Zacarias S, Temporão A, Carpentier P, van der Linden P, Pereira IAC, Matias PM
J Biol Inorg Chem 25 863-874 (2020)
PMID: 32865640

Function and Biology Details

Reactions catalysed: 
H(2) + 2 ferricytochrome c3 = 2 H(+) + 2 ferrocytochrome c3
H(2) + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H(+)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180786 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
cytochrome-c3 hydrogenase Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 283 amino acids
Theoretical weight: 30.26 KDa
Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Expression system: Desulfovibrio vulgaris str. Hildenborough
UniProt:
  • Canonical: Q72AS4 (Residues: 35-317; Coverage: 89%)
Gene names: DVU_1917, hysB
Sequence domains:
Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 484 amino acids
Theoretical weight: 53.37 KDa
Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Expression system: Desulfovibrio vulgaris str. Hildenborough
UniProt:
  • Canonical: Q72AS3 (Residues: 12-495; Coverage: 95%)
Gene names: DVU_1918, hysA
Sequence domains: Nickel-dependent hydrogenase

Ligands and Environments

7 bound ligands:
Ligand SF4 12 x SF4
Ligand 6ML 4 x 6ML
Ligand FCO 4 x FCO
Ligand NI 4 x NI
Ligand FE2 4 x FE2
Ligand H2S 4 x H2S
Ligand CL 4 x CL
2 modified residues:
Ligand CSD 3 x CSD
Ligand OCS 1 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P21
Unit cell:
a: 120.306Å b: 93.815Å c: 126.951Å
α: 90° β: 105.201° γ: 90°
R-values:
R R work R free
0.194 0.192 0.24
Expression system: Desulfovibrio vulgaris str. Hildenborough

Quick links

Citations

1 citations in other articles

Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms.
Taborda et al. (2023)

1 mention without citation

Molecular regulation of conditioning film formation and quorum quenching in sulfate reducing bacteria.
Raya et al. (2022)