› 5d51

X-ray diffraction
1.47Å resolution

Krypton derivatization of an O2-tolerant membrane-bound [NiFe] hydrogenase reveals a hydrophobic gas tunnel network

Released:
DOI: 10.2210/pdb5d51/pdb
PDB entry 5d51 coloured by chain, front view.
PDB entry 5d51 coloured by chain, side view.
PDB entry 5d51 coloured by chain, top view.
Source organism: Cupriavidus necator
Primary publication:
Krypton Derivatization of an O2 -Tolerant Membrane-Bound [NiFe] Hydrogenase Reveals a Hydrophobic Tunnel Network for Gas Transport.
Kalms J, Schmidt A, Frielingsdorf S, van der Linden P, von Stetten D, Lenz O, Carpentier P, Scheerer P
Angew Chem Int Ed Engl 55 5586-90 (2016)
PMID: 26913499

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
Expression system: Cupriavidus necator
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
Expression system: Cupriavidus necator
UniProt:
  • Canonical: P31892 (Residues: 44-360; Coverage: 100%)
Gene names: PHG001, hoxK
Sequence domains:
Structure domains:

Ligands and Environments

7 bound ligands:
Ligand NFV 1 x NFV
Ligand MG 1 x MG
Ligand KR 19 x KR
Ligand CL 2 x CL
Ligand SF4 1 x SF4
Ligand F3S 1 x F3S
Ligand F4S 1 x F4S
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 73.387Å b: 95.574Å c: 119.752Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.134 0.133 0.15
Expression system: Cupriavidus necator

Quick links

Citations

4 review citations

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

1 mention without citation

Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential.
Abdullatypov AV. (2020)