› 3o5a

X-ray diffraction
1.72Å resolution

Crystal Structure of partially reduced Periplasmic Nitrate Reductase from Cupriavidus necator using Ionic Liquids

Released:
DOI: 10.2210/pdb3o5a/pdb
PDB entry 3o5a coloured by chain, front view.
PDB entry 3o5a coloured by chain, side view.
PDB entry 3o5a coloured by chain, top view.
Source organism: Cupriavidus necator H16
Primary publication:
The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states.
Coelho C, González PJ, Moura JG, Moura I, Trincão J, João Romão M
J Mol Biol 408 932-48 (2011)
PMID: 21419779

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153852 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Periplasmic nitrate reductase Chain: A
Molecule details ›
Chain: A
Length: 802 amino acids
Theoretical weight: 90.56 KDa
Source organism: Cupriavidus necator H16
Expression system: Cupriavidus necator
UniProt:
  • Canonical: P39185 (Residues: 30-831; Coverage: 100%)
Gene names: PHG211, napA
Sequence domains:
Structure domains:
Periplasmic nitrate reductase, electron transfer subunit Chain: B
Molecule details ›
Chain: B
Length: 135 amino acids
Theoretical weight: 15.39 KDa
Source organism: Cupriavidus necator H16
Expression system: Cupriavidus necator
UniProt:
  • Canonical: P39186 (Residues: 35-169; Coverage: 100%)
Gene names: PHG212, napB
Sequence domains: Nitrate reductase cytochrome c-type subunit (NapB)

Ligands and Environments


Cofactor: Ligand MGD 2 x MGD

Cofactor: Ligand HEC 2 x HEC
4 bound ligands:
Ligand SF4 1 x SF4
Ligand MOS 1 x MOS
Ligand FMT 19 x FMT
Ligand CL 1 x CL
1 modified residue:
Ligand OCS 1 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: C2
Unit cell:
a: 119.4Å b: 71.41Å c: 128.41Å
α: 90° β: 121.04° γ: 90°
R-values:
R R work R free
0.144 0.143 0.182
Expression system: Cupriavidus necator

Quick links

Citations

14 review citations

Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers.
Liu et al. (2014)
13 more

3 mentions without citation

Structural and mechanistic insights on nitrate reductases.
Coelho et al. (2015)
2 more