4NQ4 | pdb_00004nq4

Bacillus cereus Zn-dependent metallo-beta-lactamase at pH 7

• PDB DOI: https://doi.org/10.2210/pdb4NQ4/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus cereus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-23 Released: 2014-11-26 
• Deposition Author(s): Gonzalez, J.M., Gonzalez, M.M., Vila, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.300 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Literature

Inhibition of metallo-lactamases with bicyclic compounds

Gonzalez, M.M., Gonzalez, J.M., Vila, A.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.59 kDa 
• Atom Count: 1,853 
• Modeled Residue Count: 221 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase 2	A	222	Bacillus cereus	Mutation(s): 0  Gene Names: blm EC: 3.5.2.6
UniProt
Find proteins for P04190 (Bacillus cereus) Explore P04190  Go to UniProtKB:  P04190

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.300 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.115	α = 90
b = 60.81	β = 93
c = 69.251	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Gonzalez, J.M., Gonzalez, M.M., Vila, A.J.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations