› 3vm1

X-ray diffraction
1.5Å resolution

assimilatory nitrite reductase (Nii3) - N226K mutant - HCO3 complex from tobacco leaf

Released:
DOI: 10.2210/pdb3vm1/pdb
PDB entry 3vm1 coloured by chain, front view.
PDB entry 3vm1 coloured by chain, side view.
PDB entry 3vm1 coloured by chain, top view.
Source organism: Nicotiana tabacum
Primary publication:
X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity.
Nakano S, Takahashi M, Sakamoto A, Morikawa H, Katayanagi K
Chem Biodivers 9 1989-99 (2012)
PMID: 22976986

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:
  • not assigned
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:
Nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 584 amino acids
Theoretical weight: 65.59 KDa
Source organism: Nicotiana tabacum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q76KB0 (Residues: 19-580; Coverage: 96%)
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 BCT 1 x BCT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P4212
Unit cell:
a: 133.616Å b: 133.616Å c: 77.742Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.163 0.179
Expression system: Escherichia coli

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Citations

1 review citation

Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling.
Reed et al. (2021)
1 other article