› 2pp9

X-ray diffraction
1.8Å resolution

Nitrate bound wild type oxidized AfNiR

Released:
DOI: 10.2210/pdb2pp9/pdb
PDB entry 2pp9 coloured by chain, front view.
PDB entry 2pp9 coloured by chain, side view.
PDB entry 2pp9 coloured by chain, top view.
Source organism: Alcaligenes faecalis
Primary publication:
Conserved active site residues limit inhibition of a copper-containing nitrite reductase by small molecules.
Tocheva EI, Eltis LD, Murphy ME
Biochemistry 47 4452-60 (2008)
PMID: 18358002

Function and Biology Details

Reaction catalysed: 
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153659 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Copper-containing nitrite reductase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 341 amino acids
Theoretical weight: 36.88 KDa
Source organism: Alcaligenes faecalis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P38501 (Residues: 40-376; Coverage: 98%)
Gene names: nir, nirK
Sequence domains:
Structure domains: Cupredoxins - blue copper proteins

Ligands and Environments

5 bound ligands:
Ligand CU1 3 x CU1
Ligand CU 3 x CU
Ligand NO3 3 x NO3
Ligand ACT 8 x ACT
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 60.91Å b: 102.084Å c: 145.83Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.169 0.195
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Protein design: toward functional metalloenzymes.
Yu et al. (2014)
3 more