› 4uql

X-ray diffraction
1.22Å resolution

High-resolution structure of a Ni-A Ni-Sox mixture of the D. fructosovorans NiFe-hydrogenase L122A mutant

Released:
DOI: 10.2210/pdb4uql/pdb
PDB entry 4uql coloured by chain, front view.
PDB entry 4uql coloured by chain, side view.
PDB entry 4uql coloured by chain, top view.
Source organism: Solidesulfovibrio fructosivorans
Primary publication:
Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states.
Volbeda A, Martin L, Barbier E, Gutiérrez-Sanz O, De Lacey AL, Liebgott PP, Dementin S, Rousset M, Fontecilla-Camps JC
J Biol Inorg Chem 20 11-22 (2015)
PMID: 25315838

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
Molecule details ›
Chains: A, B
Length: 265 amino acids
Theoretical weight: 28.42 KDa
Source organism: Solidesulfovibrio fructosivorans
Expression system: Solidesulfovibrio fructosivorans
UniProt:
  • Canonical: P18187 (Residues: 50-314; Coverage: 100%)
Gene name: hydA
Sequence domains:
Structure domains:
Periplasmic [NiFe] hydrogenase large subunit Chains: Q, R
Molecule details ›
Chains: Q, R
Length: 563 amino acids
Theoretical weight: 61.19 KDa
Source organism: Solidesulfovibrio fructosivorans
Expression system: Solidesulfovibrio fructosivorans
UniProt:
  • Canonical: P18188 (Residues: 2-549; Coverage: 97%)
Gene name: hydB
Sequence domains: Nickel-dependent hydrogenase
Structure domains: Cytochrome-c3 Hydrogenase, chain B

Ligands and Environments

10 bound ligands:
Ligand SF4 4 x SF4
Ligand F3S 2 x F3S
Ligand GOL 11 x GOL
Ligand GLY 3 x GLY
Ligand SOT 1 x SOT
Ligand H2S 1 x H2S
Ligand FCO 2 x FCO
Ligand NI 2 x NI
Ligand MG 2 x MG
Ligand CL 1 x CL
2 modified residues:
Ligand CSX 2 x CSX
Ligand CSS 2 x CSS

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 64.69Å b: 100.85Å c: 116.7Å
α: 90° β: 105.96° γ: 90°
R-values:
R R work R free
0.122 0.12 0.152
Expression system: Solidesulfovibrio fructosivorans

Quick links

Citations

6 review citations

Structure and function of [NiFe] hydrogenases.
Ogata et al. (2016)
5 more