› 2dy2

X-ray diffraction
2.26Å resolution

Nitrite reductase pH 6.0

Released:
DOI: 10.2210/pdb2dy2/pdb
PDB entry 2dy2 coloured by chain, front view.
PDB entry 2dy2 coloured by chain, side view.
PDB entry 2dy2 coloured by chain, top view.
Source organism: Cereibacter sphaeroides
Primary publication:
pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase.
Jacobson F, Pistorius A, Farkas D, De Grip W, Hansson O, Sjölin L, Neutze R
J Biol Chem 282 6347-55 (2007)
PMID: 17148448

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-176049 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Copper-containing nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 329 amino acids
Theoretical weight: 35.91 KDa
Source organism: Cereibacter sphaeroides
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q53239 (Residues: 44-372; Coverage: 96%)
Gene names: Rsph17025_1595, nirK
Sequence domains:
Structure domains: Cupredoxins - blue copper proteins

Ligands and Environments

1 bound ligand:
Ligand CU 2 x CU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: R3
Unit cell:
a: 74.996Å b: 74.996Å c: 153.611Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.192 0.241
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

Copper active sites in biology.
Solomon et al. (2014)
6 more

9 mentions without citation

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