› 7mde

X-ray diffraction
2.7Å resolution

Full-length S95A ClbP

Released:
DOI: 10.2210/pdb7mde/pdb
PDB entry 7mde coloured by chain, front view.
PDB entry 7mde coloured by chain, side view.
PDB entry 7mde coloured by chain, top view.
Source organism: Escherichia coli CFT073
Primary publication:
Structural basis of colibactin activation by the ClbP peptidase.
Velilla JA, Volpe MR, Kenney GE, Walsh RM, Balskus EP, Gaudet R
OpenAccess logo Nat Chem Biol (2022)
PMID: 36253550

Function and Biology Details

Reaction catalysed: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101545 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-lactamase Chain: A
Molecule details ›
Chain: A
Length: 480 amino acids
Theoretical weight: 53.51 KDa
Source organism: Escherichia coli CFT073
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0H2V8D3 (Residues: 31-504; Coverage: 100%)
Gene name: c2452
Sequence domains: Beta-lactamase

Ligands and Environments

6 bound ligands:
Ligand OLC 2 x OLC
Ligand 2PE 4 x 2PE
Ligand IMD 1 x IMD
Ligand DMS 1 x DMS
Ligand SO4 1 x SO4
Ligand CL 3 x CL
1 modified residue:
Ligand MSE 11 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P42212
Unit cell:
a: 97.475Å b: 97.475Å c: 183.973Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.195 0.235
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Intestinal bacteria and colorectal cancer: etiology and treatment.
Dougherty et al. (2023)
4 more