› 6g94

X-ray diffraction
2.5Å resolution

Structure of E. coli hydrogenase-1 C19G variant in complex with cytochrome b

Released:
DOI: 10.2210/pdb6g94/pdb
PDB entry 6g94 coloured by chain, front view.
PDB entry 6g94 coloured by chain, side view.
PDB entry 6g94 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
X-ray structural, functional and computational studies of the O2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster.
Volbeda A, Mouesca JM, Darnault C, Roessler MM, Parkin A, Armstrong FA, Fontecilla-Camps JC
Chem Commun (Camb) 54 7175-7178 (2018)
PMID: 29888350

Function and Biology Details

Reaction catalysed: 
H(2) + A = AH(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-199625 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Hydrogenase-1 small chain Chains: Q, R, S, T
Molecule details ›
Chains: Q, R, S, T
Length: 335 amino acids
Theoretical weight: 36.77 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P69739 (Residues: 46-372; Coverage: 100%)
Gene names: JW0954, b0972, hyaA
Sequence domains:
Structure domains:
Hydrogenase-1 large chain Chains: J, K, L, M
Molecule details ›
Chains: J, K, L, M
Length: 582 amino acids
Theoretical weight: 64.75 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ACD8 (Residues: 1-582; Coverage: 98%)
Gene names: JW0955, b0973, hyaB
Sequence domains: Nickel-dependent hydrogenase
Structure domains: Cytochrome-c3 Hydrogenase, chain B
Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit Chains: A, B
Molecule details ›
Chains: A, B
Length: 235 amino acids
Theoretical weight: 27.63 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AAM1 (Residues: 1-235; Coverage: 100%)
Gene names: JW0956, b0974, hyaC
Sequence domains: Prokaryotic cytochrome b561
Structure domains: Transmembrane di-heme cytochromes, Chain C

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
7 bound ligands:
Ligand SF4 4 x SF4
Ligand F3S 4 x F3S
Ligand ER2 4 x ER2
Ligand FCO 4 x FCO
Ligand NI 4 x NI
Ligand MG 4 x MG
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 124.41Å b: 165.03Å c: 206.22Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.222 0.253
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Stepwise conversion of the Cys6[4Fe-3S] to a Cys4[4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase.
Schmidt et al. (2023)

2 mentions without citation

Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14).
Schaeffer et al. (2021)
1 more