› 3k1a

X-ray diffraction
2.23Å resolution

Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70Ile MoFe protein variant

Released:
DOI: 10.2210/pdb3k1a/pdb
PDB entry 3k1a coloured by chain, front view.
PDB entry 3k1a coloured by chain, side view.
PDB entry 3k1a coloured by chain, top view.
Source organism: Azotobacter vinelandii
Primary publication:
Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70(Ile) MoFe protein variant.
Sarma R, Barney BM, Keable S, Dean DR, Seefeldt LC, Peters JW
J Inorg Biochem 104 385-9 (2010)
PMID: 20022118

Function and Biology Details

Reaction catalysed: 
8 reduced ferredoxin + 8 H(+) + N(2) + 16 ATP + 16 H(2)O = 8 oxidized ferredoxin + H(2) + 2 NH(3) + 16 ADP + 16 phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139505 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Nitrogenase molybdenum-iron protein alpha chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 491 amino acids
Theoretical weight: 55.25 KDa
Source organism: Azotobacter vinelandii
Expression system: Escherichia coli
UniProt:
  • Canonical: P07328 (Residues: 2-492; Coverage: 100%)
Gene name: nifD
Sequence domains: Nitrogenase component 1 type Oxidoreductase
Structure domains: Nitrogenase molybdenum iron protein domain
Nitrogenase molybdenum-iron protein beta chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 522 amino acids
Theoretical weight: 59.4 KDa
Source organism: Azotobacter vinelandii
Expression system: Escherichia coli
UniProt:
  • Canonical: P07329 (Residues: 2-523; Coverage: 100%)
Gene name: nifK
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand HCA 2 x HCA
Ligand CFN 2 x CFN
Ligand CLF 2 x CLF
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P21
Unit cell:
a: 77.019Å b: 129.458Å c: 107.088Å
α: 90° β: 109.01° γ: 90°
R-values:
R R work R free
0.207 0.204 0.254
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Mechanism of nitrogen fixation by nitrogenase: the next stage.
Hoffman et al. (2014)
3 more

9 mentions without citation

Biosynthesis of Nitrogenase Cofactors.
Burén et al. (2020)
8 more