› 5mdj

X-ray diffraction
1.48Å resolution

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in a its as-isolated high-pressurized form

Released:
DOI: 10.2210/pdb5mdj/pdb
PDB entry 5mdj coloured by chain, front view.
PDB entry 5mdj coloured by chain, side view.
PDB entry 5mdj coloured by chain, top view.
Source organism: Cupriavidus necator H16
Primary publication:
Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.
Kalms J, Schmidt A, Frielingsdorf S, Utesch T, Gotthard G, von Stetten D, van der Linden P, Royant A, Mroginski MA, Carpentier P, Lenz O, Scheerer P
OpenAccess logo Proc Natl Acad Sci U S A 115 E2229-E2237 (2018)
PMID: 29463722

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152104 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Uptake hydrogenase large subunit Chain: L
Molecule details ›
Chain: L
Length: 603 amino acids
Theoretical weight: 67.25 KDa
Source organism: Cupriavidus necator H16
Expression system: Cupriavidus necator H16
UniProt:
  • Canonical: P31891 (Residues: 1-603; Coverage: 98%)
Gene names: PHG002, hoxG
Sequence domains: Nickel-dependent hydrogenase
Structure domains: Cytochrome-c3 Hydrogenase, chain B
Uptake hydrogenase small subunit Chain: S
Molecule details ›
Chain: S
Length: 328 amino acids
Theoretical weight: 36.03 KDa
Source organism: Cupriavidus necator H16
Expression system: Cupriavidus necator H16
UniProt:
  • Canonical: P31892 (Residues: 44-360; Coverage: 100%)
Gene names: PHG001, hoxK
Sequence domains:
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand NFV 1 x NFV
Ligand MG 1 x MG
Ligand SF4 1 x SF4
Ligand F3S 1 x F3S
Ligand F4S 1 x F4S
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 73.395Å b: 95.696Å c: 121.565Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.144 0.142 0.172
Expression system: Cupriavidus necator H16

Quick links

Citations

5 review citations

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

1 mention without citation

Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.
Kalms et al. (2018)