› 5vcp

X-ray diffraction
1.95Å resolution

Crystal structure of a peptide deformylase from Burkholderia xenovorans in complex with actinonin

Released:
DOI: 10.2210/pdb5vcp/pdb
PDB entry 5vcp coloured by chain, front view.
PDB entry 5vcp coloured by chain, side view.
PDB entry 5vcp coloured by chain, top view.
Source organism: Paraburkholderia xenovorans LB400
Entry author: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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-171893 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 185 amino acids
Theoretical weight: 20.94 KDa
Source organism: Paraburkholderia xenovorans LB400
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13XB1 (Residues: 1-177; Coverage: 100%)
Gene names: Bxe_A1677, def
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

3 bound ligands:
Ligand FE2 4 x FE2
Ligand BB2 4 x BB2
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P212121
Unit cell:
a: 63.11Å b: 90.33Å c: 140.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.162 0.192
Expression system: Escherichia coli BL21(DE3)

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