› 4gyq

X-ray diffraction
1.35Å resolution

Crystal Structure of New Delhi Metallo-beta-Lactamase-1 D223A mutant from Klebsiella pneumoniae

Released:
DOI: 10.2210/pdb4gyq/pdb
PDB entry 4gyq coloured by chain, front view.
PDB entry 4gyq coloured by chain, side view.
PDB entry 4gyq coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Entry authors: Kim Y, Tesar C, Jedrzejczak R, Babnigg J, Binkowski TA, Mire J, Sacchettini J, Joachimiak A, MCSG, Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

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

Assemblies composition:
monomeric
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111681 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase type 2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 243 amino acids
Theoretical weight: 25.67 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: C7C422 (Residues: 31-270; Coverage: 99%)
Gene name: blaNDM-1
Sequence domains: Metallo-beta-lactamase superfamily
Structure domains: Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Ligands and Environments

2 bound ligands:
Ligand EDO 3 x EDO
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 69.14Å b: 74.225Å c: 76.599Å
α: 90° β: 90.11° γ: 90°
R-values:
R R work R free
0.145 0.143 0.18
Expression system: Escherichia coli BL21

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