7VQJ | pdb_00007vqj

Crystal structure of NDM-1 in complex with hydrolyzed 1u.

• PDB DOI: https://doi.org/10.2210/pdb7VQJ/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Klebsiella pneumoniae
• Mutation(s): No 


• Deposited: 2021-10-20 Released: 2022-10-26 
• Deposition Author(s): Xie, H.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NDM-1 in complex with hydrolyzed 1u.

Xie, H.X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.02 kDa 
• Atom Count: 3,550 
• Modeled Residue Count: 457 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase NDM-1	A, B	242	Escherichia coli	Mutation(s): 0  Gene Names: blaNDM-1 EC: 3.5.2.6
UniProt
Find proteins for A0A0A7Y424 (Escherichia coli) Explore A0A0A7Y424  Go to UniProtKB:  A0A0A7Y424

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7T6 (Subject of Investigation/LOI)	E [auth A], H [auth B]	(2R)-2-[(1S)-1-methoxy-2-oxidanyl-2-oxidanylidene-ethyl]-5-methylidene-2H-1,3-thiazine-4-carboxylic acid C9 H11 N O5 S DOPBSRLSQLUMSV-RNFRBKRXSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.385	α = 90
b = 74.188	β = 90
c = 147.982	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-26 
Deposition Author(s): Xie, H.X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2022-10-26
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description