8PH1

Crystal structure of the metallo-beta-lactamase VIM1 with 3708

• PDB DOI: https://doi.org/10.2210/pdb8PH1/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-18 Released: 2024-07-10 
• Deposition Author(s): Calvopina, K., Brem, J., Farley, A.J.M., Allen, M.D., Schofield, C.J.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.153 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 

Starting Model: experimental

Literature

Crystal structure of the metallo-beta-lactamase VIM1 with 3708

Calvopina, K., Brem, J., Farley, A.J.M., Allen, M.D., 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: 28.59 kDa 
• Atom Count: 2,279 
• Modelled Residue Count: 232 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase VIM-1	A	266	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245
UniProt
Find proteins for Q9XAY4 (Pseudomonas aeruginosa) Explore Q9XAY4  Go to UniProtKB:  Q9XAY4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YMF (Subject of Investigation/LOI)	D [auth A]	7-[(1~{S})-1-[(5~{R})-5-[(2~{R})-3-azanyl-2-methyl-propyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid C21 H25 N5 O4 OJYBICGUZCKJGO-MBNYWOFBSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.153 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.47	α = 90
b = 67.82	β = 93.62
c = 40.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Calvopina, K., Brem, J., Farley, A.J.M., Allen, M.D., Schofield, C.J.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	099141/Z/12/Z

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release