8J6Y | pdb_00008j6y

Crystal structure of class A beta-lactamase PSE-4 WT- Apo state

• PDB DOI: https://doi.org/10.2210/pdb8J6Y/pdb

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


• Deposited: 2023-04-26 Released: 2024-05-01 
• Deposition Author(s): Sarkar, M., 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: 2.40 Å
• R-Value Free: 
  0.272 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.191 (DCC) 

Starting Model: experimental

Literature

Crystal structure of class A beta-lactamase PSE-4 WT- Apo state

Sarkar, M., Bhattacharya, S., Hazra, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.2 kDa 
• Atom Count: 2,153 
• Modeled Residue Count: 266 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase PSE-4	A	288	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: pse4, carB1 EC: 3.5.2.6
UniProt
Find proteins for P16897 (Pseudomonas aeruginosa) Explore P16897  Go to UniProtKB:  P16897

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.272 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.191 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.951	α = 90
b = 95.951	β = 90
c = 61.509	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Sarkar, M., 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: 2024-05-01
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Structure summary