› 3vkp

X-ray diffraction
1.4Å resolution

Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with low X-ray dose

Released:
DOI: 10.2210/pdb3vkp/pdb
PDB entry 3vkp coloured by chain, front view.
PDB entry 3vkp coloured by chain, side view.
PDB entry 3vkp coloured by chain, top view.
Source organism: Nicotiana tabacum
Primary publication:
The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-visible microspectroscopy.
Nakano S, Takahashi M, Sakamoto A, Morikawa H, Katayanagi K
Proteins 80 2035-45 (2012)
PMID: 22499059

Function and Biology Details

Reaction catalysed: 
NH(3) + 2 H(2)O + 6 oxidized ferredoxin = nitrite + 6 reduced ferredoxin + 7 H(+)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181164 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ferredoxin--nitrite reductase, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 591 amino acids
Theoretical weight: 66.46 KDa
Source organism: Nicotiana tabacum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q76KB0 (Residues: 19-587; Coverage: 97%)
Gene name: nii3
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand SRM 1 x SRM
4 bound ligands:
Ligand SF4 1 x SF4
Ligand K 1 x K
Ligand CL 2 x CL
Ligand NO2 1 x NO2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P4212
Unit cell:
a: 133.107Å b: 133.107Å c: 77.796Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.175 0.189
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Recent structural insights into the function of copper nitrite reductases.
Horrell et al. (2017)
3 other articles