› 8dfc

Electron Microscopy
2.48Å resolution

CryoEM structure of the 1:1 ADP-tetrafluoroaluminate stabilized nitrogenase complex from Azotobacter vinelandii

Released:
DOI: 10.2210/pdb8dfc/pdb
PDB entry 8dfc coloured by chain, front view.
PDB entry 8dfc coloured by chain, side view.
PDB entry 8dfc coloured by chain, top view.
Source organism: Azotobacter vinelandii
Primary publication:
Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins.
Warmack RA, Wenke BB, Spatzal T, Rees DC
Nat Protoc (2024)
PMID: 38575747
Related structures: EMD-27404

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:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-132540 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Nitrogenase molybdenum-iron protein alpha chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 492 amino acids
Theoretical weight: 55.36 KDa
Source organism: Azotobacter vinelandii
UniProt:
  • Canonical: P07328 (Residues: 1-492; Coverage: 100%)
Gene name: nifD
Sequence domains: Nitrogenase component 1 type Oxidoreductase
Nitrogenase molybdenum-iron protein beta chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 523 amino acids
Theoretical weight: 59.54 KDa
Source organism: Azotobacter vinelandii
UniProt:
  • Canonical: P07329 (Residues: 1-523; Coverage: 100%)
Gene name: nifK
Sequence domains:
Nitrogenase iron protein 1 Chains: E, F

Ligands and Environments

8 bound ligands:
Ligand ICS 2 x ICS
Ligand HCA 2 x HCA
Ligand CLF 2 x CLF
Ligand FE 2 x FE
Ligand SF4 1 x SF4
Ligand ADP 2 x ADP
Ligand ALF 2 x ALF
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.48Å
Relevant EMDB volumes: EMD-27404

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