› 1vev

X-ray diffraction
2.51Å resolution

Crystal structure of peptide deformylase from Leptospira Interrogans (LiPDF) at pH6.5

Released:
DOI: 10.2210/pdb1vev/pdb
PDB entry 1vev coloured by chain, front view.
PDB entry 1vev coloured by chain, side view.
PDB entry 1vev coloured by chain, top view.
Source organism: Leptospira interrogans
Primary publication:
Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift.
Zhou Z, Song X, Gong W
J Biol Chem 280 42391-6 (2005)
PMID: 16239225

Function and Biology Details

Reaction catalysed: 
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
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-188095 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 177 amino acids
Theoretical weight: 20.27 KDa
Source organism: Leptospira interrogans
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q93LE9 (Residues: 2-178; Coverage: 99%)
Gene names: LA_2438, def, pdf
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand MES 3 x MES
Ligand FMT 2 x FMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BSRF BEAMLINE 3W1A
Spacegroup: P41212
Unit cell:
a: 82.192Å b: 82.192Å c: 201.04Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.258 0.258 0.29
Expression system: Escherichia coli BL21

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Citations

1 review citation

Vital significance of addition of "shape similarity" between solutes to shape complementarity for more precise molecular recognition in aqueous binary solvents.
Endo T. (2011)
6 other articles

1 mention without citation

How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.
Cui et al. (2014)