5ZR8 | pdb_00005zr8

Crystal Structure Of NDM-1 Metallo-beta-lactamase

• PDB DOI: https://doi.org/10.2210/pdb5ZR8/pdb

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


• Deposited: 2018-04-23 Released: 2019-04-24 
• Deposition Author(s): Wachino, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Of NDM-1 Metallo-beta-lactamase

Wachino, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 52.77 kDa 
• Atom Count: 4,000 
• Modeled Residue Count: 460 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B [auth E]	246	Escherichia coli	Mutation(s): 0  Gene Names:  blaNDM-1, bla NDM-1, AM434_27040, APU18_05360, AZ95_0035, BET08_16280, BVL39_26630, CA268_28970, ECS01_0033, MS6198_A142, NDM1Dok01_N0175, pNDM102337_147, pNDM10505_149 EC: 3.5.2.6
UniProt
Find proteins for E5KIY2 (Escherichia coli) Explore E5KIY2  Go to UniProtKB:  E5KIY2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], E [auth A], I [auth A], J [auth E], K [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.08	α = 90
b = 73.9	β = 90
c = 77.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Wachino, J.

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description