4TZE

Structure of metallo-beta-lactamase

• PDB DOI: https://doi.org/10.2210/pdb4TZE/pdb

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


• Deposited: 2014-07-10 Released: 2015-07-29 
• Deposition Author(s): Ferguson, J.A., Makena, A., Brem, J., McDonough, M.A., Schofield, C.J.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

stucuture of metallo-beta-lactamase

Ferguson, J.A., Makena, A., Brem, J., McDonough, M.A., Schofield, C.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: 48.94 kDa 
• Atom Count: 3,704 
• Modelled Residue Count: 459 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class B carbapenemase NDM-5	A, B	231	Escherichia coli	Mutation(s): 0  Gene Names: blaNDM-5
UniProt
Find proteins for G3K399 (Escherichia coli) Explore G3K399  Go to UniProtKB:  G3K399

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: 1.57 Å
• R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.773	α = 90
b = 59.216	β = 92.19
c = 62.968	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Ferguson, J.A., Makena, A., Brem, J., McDonough, M.A., Schofield, C.J.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	G1100135

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 2.0: 2017-09-13
  Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description