› 6za1

X-ray diffraction
1.37Å resolution

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

Released:
DOI: 10.2210/pdb6za1/pdb
PDB entry 6za1 coloured by chain, front view.
PDB entry 6za1 coloured by chain, side view.
PDB entry 6za1 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 Chain: A
Molecule details ›
Chain: A
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 Chain: B
Molecule details ›
Chain: B
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

8 bound ligands:
Ligand SF4 3 x SF4
Ligand 6ML 1 x 6ML
Ligand GOL 1 x GOL
Ligand OXY 5 x OXY
Ligand FCO 1 x FCO
Ligand NI 1 x NI
Ligand FE2 1 x FE2
Ligand H2S 2 x H2S
1 modified residue:
Ligand CSD 1 x CSD

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: C2
Unit cell:
a: 106.156Å b: 63.415Å c: 110.044Å
α: 90° β: 104.785° γ: 90°
R-values:
R R work R free
0.144 0.143 0.163
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)