3ZR9 | pdb_00003zr9

Structure of New Delhi Metallo-Beta-lactamase 1 (NDM-1)

• PDB DOI: https://doi.org/10.2210/pdb3ZR9/pdb

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


• Deposited: 2011-06-15 Released: 2011-06-29 
• Deposition Author(s): Green, V.L., Verma, A., Owens, R.J., Phillips, S.E.V., Carr, S.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.210 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1).

Green, V.L., Verma, A., Owens, R.J., Phillips, S.E., Carr, S.B.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1160

• PubMed: 22102018 
• DOI: https://doi.org/10.1107/S1744309111029654
• Primary Citation Related Structures: 
  3ZR9


• PubMed Abstract: 
  

  Antibiotic resistance in bacterial pathogens poses a serious threat to human health and the metallo-β-lactamase (MBL) enzymes are responsible for much of this resistance. The recently identified New Delhi MBL 1 (NDM-1) is a novel member of this family that is capable of hydrolysing a wide variety of clinically important antibiotics. Here, the crystal structure of NDM-1 from Klebsiella pneumoniae is reported and its structure and active site are discussed in the context of other recently deposited coordinates of NDM-1.

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Organizational Affiliation: 
• Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon OX11 0FA, England.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.81 kDa 
• Atom Count: 1,829 
• Modeled Residue Count: 231 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE NDM-1	A	231	Klebsiella pneumoniae	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422  Go to UniProtKB:  C7C422

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: 1.91 Å
• R-Value Free:  0.210 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.3	α = 90
b = 120.3	β = 90
c = 88.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Green, V.L., Verma, A., Owens, R.J., Phillips, S.E.V., Carr, S.B.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-08-03
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2011-11-30
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description