8PGM | pdb_00008pgm

Crystal structure of the metallo-beta-lactamase VIM1 with 3062

• PDB DOI: https://doi.org/10.2210/pdb8PGM/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: 1.27 Å
• R-Value Free: 
  0.156 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the metallo-beta-lactamase VIM1 with 3062

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: 28.65 kDa 
• Atom Count: 2,261 
• Modeled 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 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
YU0 (Subject of Investigation/LOI)	D [auth A]	3-[4-[(azanyl-methyl-oxidanyl-$l^{4}-sulfanyl)methyl]-3-fluoranyl-phenyl]-7-propan-2-yl-1~{H}-indole-2-carboxylic acid C20 H23 F N2 O3 S MQEDGVPPDOWGOB-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.156 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.42	α = 90
b = 67.83	β = 93.28
c = 40.08	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