› 4gd3

X-ray diffraction
3.3Å resolution

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

Released:
DOI: 10.2210/pdb4gd3/pdb
PDB entry 4gd3 coloured by chain, front view.
PDB entry 4gd3 coloured by chain, side view.
PDB entry 4gd3 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structure of the O(2)-tolerant membrane-bound hydrogenase 1 from Escherichia coli in complex with its cognate cytochrome b.
Volbeda A, Darnault C, Parkin A, Sargent F, Armstrong FA, Fontecilla-Camps JC
Structure 21 184-190 (2013)
PMID: 23260654

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero pentamer
hetero dimer
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-141993 (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: 36.82 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 8 x SF4
Ligand F4S 4 x F4S
Ligand CL 10 x CL
Ligand FCO 4 x FCO
Ligand NI 4 x NI
Ligand MG 4 x MG
Ligand LMT 4 x LMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 126Å b: 165.3Å c: 212.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.2 0.236
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides.
Schilter et al. (2016)
4 more

9 mentions without citation

Electrochemical insights into the mechanism of NiFe membrane-bound hydrogenases.
Flanagan et al. (2016)
8 more