› 3uqy

X-ray diffraction
1.47Å resolution

H2-reduced structure of E. coli hydrogenase-1

Released:
DOI: 10.2210/pdb3uqy/pdb
PDB entry 3uqy coloured by chain, front view.
PDB entry 3uqy coloured by chain, side view.
PDB entry 3uqy 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

10 bound ligands:
Ligand SF4 2 x SF4
Ligand F3S 2 x F3S
Ligand F4S 2 x F4S
Ligand LMT 2 x LMT
Ligand CL 5 x CL
Ligand SO4 5 x SO4
Ligand FCO 2 x FCO
Ligand NI 2 x NI
Ligand MG 2 x MG
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: 93.71Å b: 97.4Å c: 183.73Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.124 0.122 0.16
Expression system: Escherichia coli

Quick links

Citations

14 review citations

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

10 mentions without citation

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase.
Stripp et al. (2022)
9 more