› 1xd9

X-ray diffraction
2.8Å resolution

Crystal Structure of the Nitrogenase Fe protein Asp39Asn with MgADP bound

Released:
DOI: 10.2210/pdb1xd9/pdb
PDB entry 1xd9 coloured by chain, front view.
PDB entry 1xd9 coloured by chain, side view.
PDB entry 1xd9 coloured by chain, top view.
Source organism: Azotobacter vinelandii
Primary publication:
Structural and biochemical implications of single amino acid substitutions in the nucleotide-dependent switch regions of the nitrogenase Fe protein from Azotobacter vinelandii.
Jang SB, Jeong MS, Seefeldt LC, Peters JW
J Biol Inorg Chem 9 1028-33 (2004)
PMID: 15549494

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132539 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nitrogenase iron protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 289 amino acids
Theoretical weight: 31.42 KDa
Source organism: Azotobacter vinelandii
Expression system: Escherichia coli
UniProt:
  • Canonical: P00459 (Residues: 2-290; Coverage: 100%)
Gene name: nifH1
Sequence domains: 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand SF4 1 x SF4
Ligand ADP 2 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 57.052Å b: 92.214Å c: 61.375Å
α: 90° β: 101.23° γ: 90°
R-values:
R R work R free
0.314 0.229 0.299
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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