4TYF | pdb_00004tyf

Structure of a Metallo-beta-lactamase

• PDB DOI: https://doi.org/10.2210/pdb4TYF/pdb

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


• Deposited: 2014-07-08 Released: 2015-07-15 
• Deposition Author(s): Ferguson, J.A., Makena, A., Brem, J., McDonough, M.A., Schofield, C.J.
• Funding Organization(s): Medical Research Council (United Kingdom)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Structure of a 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.46 kDa 
• Atom Count: 1,982 
• Modeled Residue Count: 230 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NDM-4	A	231	Escherichia coli	Mutation(s): 0  Gene Names: blaNDM-4
UniProt
Find proteins for H6WZS9 (Escherichia coli) Explore H6WZS9  Go to UniProtKB:  H6WZS9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.7	α = 90
b = 59.08	β = 97.61
c = 42	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-15 
Deposition Author(s): Ferguson, J.A., Makena, A., Brem, J., McDonough, M.A., Schofield, C.J.

---

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

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 2.0: 2017-09-13
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations
• Version 2.1: 2018-01-31
  Changes: Database references
• Version 2.2: 2023-12-20
  Changes: Data collection, Database references, Refinement description