4ZEJ

Crystal Structure of DIM-1 Metallo-beta-Lactamase exposed to Ceftazidime

• PDB DOI: https://doi.org/10.2210/pdb4ZEJ/pdb

• Classification: HYDROLASE
• Organism(s): Stutzerimonas stutzeri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-20 Released: 2015-05-27 
• Deposition Author(s): Booth, M.P.S., Kosmopoulou, M., Spencer, J.
• Funding Organization(s): British Society for Antimicrobial Chemotherapy

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.189 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

Crystal Stricture of DIM-1 Metallo-beta-Lactamase

Booth, M.P.S., Kosmopoulou, M., Poirel, L., Nordmann, P., Spencer, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.87 kDa 
• Atom Count: 3,640 
• Modelled Residue Count: 438 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase	A, B	232	Stutzerimonas stutzeri	Mutation(s): 0  Gene Names: blaDIM-1
UniProt
Find proteins for D5JGF6 (Stutzerimonas stutzeri) Explore D5JGF6  Go to UniProtKB:  D5JGF6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], L [auth B], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.189 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.397	α = 90
b = 46.977	β = 90
c = 183.758	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-27 
Deposition Author(s): Booth, M.P.S., Kosmopoulou, M., Spencer, J.

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Funding Organization	Location	Grant Number
British Society for Antimicrobial Chemotherapy	United Kingdom	GA820

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description