8IXX

Crystal structure of Class A beta-lactamase BlaA WT - complex with Ertapenem

• PDB DOI: https://doi.org/10.2210/pdb8IXX/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Yersinia enterocolitica
• Expression System: Escherichia
• Mutation(s): No 


• Deposited: 2023-04-03 Released: 2024-04-03 
• Deposition Author(s): Bhattacharya, S., Hazra, S.
• Funding Organization(s): Indian Council of Medical Research, Science and Engineering Research Board (SERB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.218 
• R-Value Work: 0.185 

Starting Model: experimental

Literature

Crystal structure of Class A beta-lactamase BlaA WT - complex with Ertapenem

Bhattacharya, S., Hazra, S.

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.73 kDa 
• Atom Count: 2,268 
• Modelled Residue Count: 262 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	294	Yersinia enterocolitica	Mutation(s): 0  Gene Names: blaA EC: 3.5.2.6
UniProt
Find proteins for Q01166 (Yersinia enterocolitica) Explore Q01166  Go to UniProtKB:  Q01166

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1RG (Subject of Investigation/LOI)	B [auth A]	(4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid C22 H27 N3 O7 S PGRRQYXTRXQDDJ-SKHPLXCOSA-N
PO4 (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.218 
• R-Value Work: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.743	α = 90
b = 72.818	β = 95.776
c = 43.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
Coot	model building
CrysalisPro	data collection
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Bhattacharya, S., Hazra, S.

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Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	5/3/8/17/GIA-ITR
Indian Council of Medical Research	India	BIC/12(15)/2014,
Science and Engineering Research Board (SERB)	India	YSS/2014/000492

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary