› 3vpe

X-ray diffraction
1.6Å resolution

Crystal Structure of Metallo-beta-Lactamase SMB-1

Released:
DOI: 10.2210/pdb3vpe/pdb
PDB entry 3vpe coloured by chain, front view.
PDB entry 3vpe coloured by chain, side view.
PDB entry 3vpe coloured by chain, top view.
Source organism: Serratia marcescens
Primary publication:
Structural insights into the subclass B3 metallo-β-lactamase SMB-1 and the mode of inhibition by the common metallo-β-lactamase inhibitor mercaptoacetate.
Wachino J, Yamaguchi Y, Mori S, Kurosaki H, Arakawa Y, Shibayama K
Antimicrob Agents Chemother 57 101-9 (2013)
PMID: 23070156

Function and Biology Details

Reaction catalysed: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124534 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 262 amino acids
Theoretical weight: 27.75 KDa
Source organism: Serratia marcescens
Expression system: Escherichia coli
UniProt:
  • Canonical: G5ELM3 (Residues: 19-280; Coverage: 100%)
Gene name: SMB-1
Sequence domains: Metallo-beta-lactamase superfamily
Structure domains: Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand SO4 3 x SO4
Ligand ACT 3 x ACT
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P31
Unit cell:
a: 67.829Å b: 67.829Å c: 48.67Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.166 0.165 0.2
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Metallo-β-lactamase: inhibitors and reporter substrates.
Fast et al. (2013)
3 more

8 mentions without citation

Structural insights into the subclass B3 metallo-β-lactamase SMB-1 and the mode of inhibition by the common metallo-β-lactamase inhibitor mercaptoacetate.
Wachino et al. (2013)
7 more