4TZ9 | pdb_00004tz9

Structure of Metallo-beta-lactamase

• PDB DOI: https://doi.org/10.2210/pdb4TZ9/pdb

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


• Deposited: 2014-07-09 Released: 2015-07-29 
• Deposition Author(s): Ferguson, J.A., Brem, J., Makena, A., McDonough, A.M., Schofield, C.J.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Structure of Metallo-beta-lactamase

Ferguson, J.A., Makena, A., Brem, J., McDonough, A.M., Schofield, C.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: 24.81 kDa 
• Atom Count: 1,832 
• Modeled Residue Count: 231 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class B metallo-beta-lactamase	A	231	Escherichia coli	Mutation(s): 0  Gene Names: NDM-3, blaNDM-3
UniProt
Find proteins for I3VKD5 (Escherichia coli) Explore I3VKD5  Go to UniProtKB:  I3VKD5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	E [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NI	D [auth A], F [auth A], G [auth A], H [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.908	α = 90
b = 120.908	β = 90
c = 90.19	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Ferguson, J.A., Brem, J., Makena, A., McDonough, A.M., 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: Atomic model, Author supporting evidence, Derived calculations
• Version 3.0: 2023-12-20
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description