› 5n5g

X-ray diffraction
1.29Å resolution

Crystal structure of di-zinc metallo-beta-lactamase VIM-1

Released:
DOI: 10.2210/pdb5n5g/pdb
PDB entry 5n5g coloured by chain, front view.
PDB entry 5n5g coloured by chain, side view.
PDB entry 5n5g coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-β-lactamases.
Salimraj R, Hinchliffe P, Kosmopoulou M, Tyrrell JM, Brem J, van Berkel SS, Verma A, Owens RJ, McDonough MA, Walsh TR, Schofield CJ, Spencer J
OpenAccess logo FEBS J 286 169-183 (2019)
PMID: 30430727

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-194976 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase type 2 Chain: A
Molecule details ›
Chain: A
Length: 253 amino acids
Theoretical weight: 26.9 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9XAY4 (Residues: 21-266; Coverage: 100%)
Gene names: CAZ10_38240, CAZ10_38245, blaVIM, blaVIM-1
Sequence domains: Metallo-beta-lactamase superfamily
Structure domains: Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand BCN 1 x BCN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 39.76Å b: 67.94Å c: 40.36Å
α: 90° β: 94.01° γ: 90°
R-values:
R R work R free
0.145 0.144 0.156
Expression system: Escherichia coli

Quick links

Citations

5 review citations

β-Lactamases and β-Lactamase Inhibitors in the 21st Century.
Tooke et al. (2019)
4 more

7 mentions without citation

Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design.
Bahr et al. (2021)
6 more