4WD6 | pdb_00004wd6

Crystal Structure of DIM-1 metallo-beta-lactamase

• PDB DOI: https://doi.org/10.2210/pdb4WD6/pdb

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


• Deposited: 2014-09-07 Released: 2014-09-17 
• Deposition Author(s): Booth, M.P.S., Kosmopoulou, M., Spencer, J.
• Funding Organization(s): British Society for Antimicrobial Chemotherapy

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure 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 and generated by (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 51.74 kDa 
• Atom Count: 3,522 
• Modeled Residue Count: 433 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase	A, B	233	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.719	α = 90
b = 47.856	β = 90
c = 185.216	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Booth, M.P.S., Kosmopoulou, M., Spencer, J.

---

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

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description