› 3use

X-ray diffraction
1.67Å resolution

Crystal Structure of E. coli hydrogenase-1 in its as-isolated form

Released:
DOI: 10.2210/pdb3use/pdb
PDB entry 3use coloured by chain, front view.
PDB entry 3use coloured by chain, side view.
PDB entry 3use coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.
Volbeda A, Amara P, Darnault C, Mouesca JM, Parkin A, Roessler MM, Armstrong FA, Fontecilla-Camps JC
Proc Natl Acad Sci U S A 109 5305-10 (2012)
PMID: 22431599

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 dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-142262 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Hydrogenase-1 small chain Chains: S, T
Molecule details ›
Chains: S, T
Length: 335 amino acids
Theoretical weight: 36.81 KDa
Source organism: Escherichia coli
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: L, M
Molecule details ›
Chains: L, M
Length: 582 amino acids
Theoretical weight: 64.75 KDa
Source organism: Escherichia coli
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

Ligands and Environments

12 bound ligands:
Ligand SF4 2 x SF4
Ligand F3S 2 x F3S
Ligand F4S 2 x F4S
Ligand SF3 2 x SF3
Ligand LMT 2 x LMT
Ligand SO4 6 x SO4
Ligand CL 3 x CL
Ligand FCO 2 x FCO
Ligand 3NI 2 x 3NI
Ligand MG 2 x MG
Ligand LI 2 x LI
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 93.93Å b: 97.79Å c: 183.29Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.122 0.12 0.168
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Mitochondrial complex I.
Hirst J. (2013)
13 more

5 mentions without citation

Protein cage assembly across multiple length scales.
Aumiller et al. (2018)
4 more