› 4dr9

X-ray diffraction
1.9Å resolution

Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin

Released:
DOI: 10.2210/pdb4dr9/pdb
PDB entry 4dr9 coloured by chain, front view.
PDB entry 4dr9 coloured by chain, side view.
PDB entry 4dr9 coloured by chain, top view.
Source organism: Synechococcus elongatus PCC 6301
Primary publication:
Structure and function of a cyanophage-encoded peptide deformylase.
Frank JA, Lorimer D, Youle M, Witte P, Craig T, Abendroth J, Rohwer F, Edwards RA, Segall AM, Burgin AB
ISME J 7 1150-60 (2013)
PMID: 23407310

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102012 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 192 amino acids
Theoretical weight: 21.33 KDa
Source organism: Synechococcus elongatus PCC 6301
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0H3JZJ4 (Residues: 2-192; Coverage: 100%)
Gene names: def, syc0213_d
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand BR 5 x BR
Ligand BB2 4 x BB2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P1
Unit cell:
a: 43.25Å b: 65.78Å c: 68.29Å
α: 80.87° β: 76.82° γ: 82.75°
R-values:
R R work R free
0.185 0.182 0.235
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Phage puppet masters of the marine microbial realm.
Breitbart et al. (2018)
4 more

1 mention without citation

Structure and function of a cyanophage-encoded peptide deformylase.
Frank et al. (2013)