› 1xem

X-ray diffraction
1.76Å resolution

High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate

Released:
DOI: 10.2210/pdb1xem/pdb
PDB entry 1xem coloured by chain, front view.
PDB entry 1xem coloured by chain, side view.
PDB entry 1xem coloured by chain, top view.
Source organism: Escherichia coli BL21(DE3)
Primary publication:
Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal.
Jain R, Hao B, Liu RP, Chan MK
J Am Chem Soc 127 4558-9 (2005)
PMID: 15796505

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 domain:

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: 168 amino acids
Theoretical weight: 19.23 KDa
Source organism: Escherichia coli BL21(DE3)
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

2 bound ligands:
Ligand ZN 1 x ZN
Ligand FMT 10 x FMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P6122
Unit cell:
a: 54.64Å b: 54.64Å c: 224Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.163 0.163 0.204

Quick links

Citations

2 review citations

Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation.
Merchant et al. (2012)
1 more

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)