8DI7 | pdb_00008di7

CMY-2

• PDB DOI: https://doi.org/10.2210/pdb8DI7/pdb

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


• Deposited: 2022-06-28 Released: 2023-06-14 
• Deposition Author(s): Ahmadvand, P., Call, D.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.239 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of CMY-2 and its interactions with ampicillin and the cephalosporins - ceftiofur, DFC, DFC-dimer, DFC-cysteine, and nitrocefin

Ahmadvand, P., Call, D.R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 159.69 kDa 
• Atom Count: 12,800 
• Modeled Residue Count: 1,436 
• Deposited Residue Count: 1,436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth D], B [auth A], C [auth B], D [auth C]	359	Escherichia coli	Mutation(s): 0  Gene Names: blaCMY-61 EC: 3.5.2.6
UniProt
Find proteins for G3F7G9 (Escherichia coli) Explore G3F7G9  Go to UniProtKB:  G3F7G9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	E [auth D], F [auth D], G [auth A], H [auth A], I [auth B], J [auth C], K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.239 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.939	α = 81.19
b = 75.374	β = 87.84
c = 97.552	γ = 69.51

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Ahmadvand, P., Call, D.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NA

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description