› 2w3t

X-ray diffraction
1.69Å resolution

Chloro complex of the Ni-Form of E.coli deformylase

Released:
DOI: 10.2210/pdb2w3t/pdb
PDB entry 2w3t coloured by chain, front view.
PDB entry 2w3t coloured by chain, side view.
PDB entry 2w3t coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres.
Yen NT, Bogdanović X, Palm GJ, Kühl O, Hinrichs W
J Biol Inorg Chem 15 195-201 (2010)
PMID: 20112455

Function and Biology Details

Reaction catalysed: 
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141367 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chain: A
Molecule details ›
Chain: A
Length: 188 amino acids
Theoretical weight: 21.44 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0A6K3 (Residues: 2-169; Coverage: 99%)
Gene names: JW3248, b3287, def, fms
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

3 bound ligands:
Ligand NI 1 x NI
Ligand CL 1 x CL
Ligand EOH 1 x EOH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: C2
Unit cell:
a: 82.08Å b: 35.98Å c: 67.59Å
α: 90° β: 113.43° γ: 90°
R-values:
R R work R free
0.216 0.213 0.243
Expression system: Escherichia coli BL21

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Citations

2 citation in other articles

Structural basis for the inhibition of M1 family aminopeptidases by the natural product actinonin: Crystal structure in complex with E. coli aminopeptidase N.
Ganji et al. (2015)
1 more