› 5i2b

X-ray diffraction
1.7Å resolution

Crystal structure of a peptide deformylase from Burkholderia ambifaria with actinonin

Released:
DOI: 10.2210/pdb5i2b/pdb
PDB entry 5i2b coloured by chain, front view.
PDB entry 5i2b coloured by chain, side view.
PDB entry 5i2b coloured by chain, top view.
Source organism: Burkholderia ambifaria IOP40-10
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-109293 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chain: A
Molecule details ›
Chain: A
Length: 185 amino acids
Theoretical weight: 20.9 KDa
Source organism: Burkholderia ambifaria IOP40-10
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B1FPK4 (Residues: 1-177; Coverage: 100%)
Gene names: BamIOP4010DRAFT_5965, def
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand BB2 1 x BB2
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: I222
Unit cell:
a: 38.59Å b: 70.25Å c: 140.73Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.174 0.204
Expression system: Escherichia coli BL21(DE3)

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