› 6gal

X-ray diffraction
1.25Å resolution

Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collected at pH 10

Released:
DOI: 10.2210/pdb6gal/pdb
PDB entry 6gal coloured by chain, front view.
PDB entry 6gal coloured by chain, side view.
PDB entry 6gal coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase.
Evans RM, Ash PA, Beaton SE, Brooke EJ, Vincent KA, Carr SB, Armstrong FA
J Am Chem Soc 140 10208-10220 (2018)
PMID: 30070475

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142263 (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 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: L, M
Molecule details ›
Chains: L, M
Length: 582 amino acids
Theoretical weight: 64.75 KDa
Source organism: Escherichia coli K-12
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

9 bound ligands:
Ligand SF4 2 x SF4
Ligand F3S 2 x F3S
Ligand SF3 2 x SF3
Ligand CL 2 x CL
Ligand SO4 2 x SO4
Ligand EJ2 2 x EJ2
Ligand MG 2 x MG
Ligand CXS 1 x CXS
Ligand LI 2 x LI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P212121
Unit cell:
a: 94.906Å b: 95.224Å c: 183.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.121 0.12 0.147
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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

321 mentions without citation

Communication among oral bacteria.
Kolenbrander et al. (2002)
320 more