7AFY | pdb_00007afy

Crystal structure of the metallo-beta-lactamase VIM1 with 1306

• PDB DOI: https://doi.org/10.2210/pdb7AFY/pdb

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


• Deposited: 2020-09-21 Released: 2021-10-06 
• Deposition Author(s): Brem, J., Schofield, C.J.
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.145 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the metallo-beta-lactamase VIM2 with 139

Brem, J., Schofield, C.J.

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

Macromolecule Content 

• Total Structure Weight: 26.02 kDa 
• Atom Count: 2,247 
• Modeled Residue Count: 233 
• Deposited Residue Count: 241 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase VIM-1	A	241	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245, F7O93_29240, F7O93_29270 EC: 3.5.2.6
UniProt
Find proteins for Q9XAY4 (Pseudomonas aeruginosa) Explore Q9XAY4  Go to UniProtKB:  Q9XAY4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RBW (Subject of Investigation/LOI)	B [auth A]	3-[3-chloranyl-4-(methylsulfonylmethyl)phenyl]-7-propan-2-yl-1~{H}-indole-2-carboxylic acid C20 H20 Cl N O4 S GFIQTTYHVBGLFD-UHFFFAOYSA-N
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.145 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.648	α = 90
b = 68.015	β = 92.94
c = 40.236	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Brem, J., Schofield, C.J.

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	United Kingdom	Enable

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description