› 7mec

X-ray diffraction
1.73Å resolution

CDD-1 beta-lactamase in imidazole/MPD 4 minute avibactam complex

Released:
DOI: 10.2210/pdb7mec/pdb
PDB entry 7mec coloured by chain, front view.
PDB entry 7mec coloured by chain, side view.
PDB entry 7mec coloured by chain, top view.
Source organism: Clostridioides difficile
Primary publication:
In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D β-lactamases.
Stewart NK, Toth M, Stasyuk A, Vakulenko SB, Smith CA
ACS Infect Dis 7 1765-1776 (2021)
PMID: 33908775

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-168492 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-lactamase Chain: A
Molecule details ›
Chain: A
Length: 250 amino acids
Theoretical weight: 28.62 KDa
Source organism: Clostridioides difficile
Expression system: Escherichia coli

Ligands and Environments

4 bound ligands:
Ligand NXL 1 x NXL
Ligand CO2 1 x CO2
Ligand SO4 3 x SO4
Ligand MPD 1 x MPD
1 modified residue:
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P4332
Unit cell:
a: 123.352Å b: 123.352Å c: 123.352Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.187 0.217
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.
Jones et al. (2022)
3 other articles

1 mention without citation

In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D β-lactamases.
Stewart et al. (2021)