› 4upe

X-ray diffraction
1.8Å resolution

Structure of the unready Ni-A state of the S499C mutant of D. fructosovorans NiFe-hydrogenase

Released:
DOI: 10.2210/pdb4upe/pdb
PDB entry 4upe coloured by chain, front view.
PDB entry 4upe coloured by chain, side view.
PDB entry 4upe 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, C
Molecule details ›
Chains: A, B, C
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, S
Molecule details ›
Chains: Q, R, S
Length: 548 amino acids
Theoretical weight: 59.67 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

8 bound ligands:
Ligand SF4 6 x SF4
Ligand F3S 3 x F3S
Ligand FCO 3 x FCO
Ligand NI 3 x NI
Ligand CA 4 x CA
Ligand GOL 5 x GOL
Ligand PO4 2 x PO4
Ligand MES 1 x MES
1 modified residue:
Ligand CSX 3 x CSX

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21
Unit cell:
a: 65.43Å b: 98.96Å c: 184.95Å
α: 90° β: 91.19° γ: 90°
R-values:
R R work R free
0.153 0.151 0.19
Expression system: Solidesulfovibrio fructosivorans

Quick links

Citations

6 review citations

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