› 1xdb

X-ray diffraction
2.8Å resolution

Crystal Structure of the Nitrogenase Fe protein Asp129Glu

Released:
DOI: 10.2210/pdb1xdb/pdb
PDB entry 1xdb coloured by chain, front view.
PDB entry 1xdb coloured by chain, side view.
PDB entry 1xdb 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: 31.43 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

1 bound ligand:
Ligand SF4 1 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 57.574Å b: 92.138Å c: 63.934Å
α: 90° β: 100.799° γ: 90°
R-values:
R R work R free
0.305 0.227 0.299
Expression system: Escherichia coli

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Citations

3 review citations

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