› 4iud

X-ray diffraction
1.45Å resolution

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form with ascorbate - partly reduced state

Released:
DOI: 10.2210/pdb4iud/pdb
PDB entry 4iud coloured by chain, front view.
PDB entry 4iud coloured by chain, side view.
PDB entry 4iud coloured by chain, top view.
Source organism: Cupriavidus necator H16
Primary publication:
Reversible [4Fe-3S] cluster morphing in an O(2)-tolerant [NiFe] hydrogenase.
Frielingsdorf S, Fritsch J, Schmidt A, Hammer M, Löwenstein J, Siebert E, Pelmenschikov V, Jaenicke T, Kalms J, Rippers Y, Lendzian F, Zebger I, Teutloff C, Kaupp M, Bittl R, Hildebrandt P, Friedrich B, Lenz O, Scheerer P
Nat Chem Biol 10 378-85 (2014)
PMID: 24705592

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: 67.26 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: 339 amino acids
Theoretical weight: 37.38 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 S3F 1 x S3F
Ligand CL 1 x CL
1 modified residue:
Ligand CSO 1 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P212121
Unit cell:
a: 73.775Å b: 95.795Å c: 120.679Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.136 0.135 0.165
Expression system: Cupriavidus necator H16

Quick links

Citations

6 review citations

Structure and function of [NiFe] hydrogenases.
Ogata et al. (2016)
5 more

3 mentions without citation

Structural Enzymology of Nitrogenase Enzymes.
Einsle et al. (2020)
2 more