5YD7 | pdb_00005yd7

Crystal Structure OF VIM-2 Metallo-beta-lactamase

• PDB DOI: https://doi.org/10.2210/pdb5YD7/pdb

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


• Deposited: 2017-09-11 Released: 2018-09-19 
• Deposition Author(s): Wachino, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.213 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Of VIM-2 Metallo-beta-lactamase

Wachino, J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.91 kDa 
• Atom Count: 3,910 
• Modeled Residue Count: 462 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase class B VIM-2	A, B	246	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, PAERUG_P32_London_17_VIM_2_10_11_06255 EC: 3.5.2.6
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0  Go to UniProtKB:  Q9K2N0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	F [auth A], G [auth A], K [auth B], L [auth B], M [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.213 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.8	α = 90
b = 79.27	β = 130.15
c = 67.39	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: 2018-09-19 
Deposition Author(s): Wachino, J.

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description