› 1wui

X-ray diffraction
1.04Å resolution

Ultra-High resolution Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Released:
DOI: 10.2210/pdb1wui/pdb
PDB entry 1wui coloured by chain, front view.
PDB entry 1wui coloured by chain, side view.
PDB entry 1wui coloured by chain, top view.
Source organism: Nitratidesulfovibrio vulgaris str. 'Miyazaki F'
Primary publication:
Activation process of [NiFe] hydrogenase elucidated by high-resolution X-ray analyses: conversion of the ready to the unready state.
Ogata H, Hirota S, Nakahara A, Komori H, Shibata N, Kato T, Kano K, Higuchi Y
Structure 13 1635-42 (2005)
PMID: 16271886

Function and Biology Details

Reaction catalysed: 
H(2) + 2 ferricytochrome c3 = 2 H(+) + 2 ferrocytochrome c3
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149443 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Periplasmic [NiFe] hydrogenase small subunit Chain: S
Molecule details ›
Chain: S
Length: 267 amino acids
Theoretical weight: 28.79 KDa
Source organism: Nitratidesulfovibrio vulgaris str. 'Miyazaki F'
UniProt:
  • Canonical: P21853 (Residues: 51-317; Coverage: 100%)
Gene names: DvMF_0271, hydA
Sequence domains:
Structure domains:
Periplasmic [NiFe] hydrogenase large subunit Chain: L
Molecule details ›
Chain: L
Length: 534 amino acids
Theoretical weight: 59.24 KDa
Source organism: Nitratidesulfovibrio vulgaris str. 'Miyazaki F'
UniProt:
  • Canonical: P21852 (Residues: 19-552; Coverage: 94%)
Gene names: DvMF_0270, hydB
Sequence domains: Nickel-dependent hydrogenase
Structure domains: Cytochrome-c3 Hydrogenase, chain B

Ligands and Environments

6 bound ligands:
Ligand SF4 2 x SF4
Ligand F3S 1 x F3S
Ligand MPD 3 x MPD
Ligand MG 1 x MG
Ligand NFC 1 x NFC
Ligand MRD 1 x MRD
1 modified residue:
Ligand CSO 2 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44B2
Spacegroup: P212121
Unit cell:
a: 98.069Å b: 125.966Å c: 66.38Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.11 0.096 0.134

Quick links

Citations

16 review citations

A third type of hydrogenase catalyzing H2 activation.
Shima et al. (2007)
15 more

7 mentions without citation

Chemical approaches to detect and analyze protein sulfenic acids.
Furdui et al. (2014)
6 more