7XI2 | pdb_00007xi2

Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with phosphate

• PDB DOI: https://doi.org/10.2210/pdb7XI2/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-04-11 Released: 2023-04-12 
• Deposition Author(s): Yadav, P., Kushwaha, G.S., Bhavesh, N.S.
• Funding Organization(s): Indian Council of Mefical Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with phosphate

Yadav, P., Kushwaha, G.S., Bhavesh, N.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: 40.08 kDa 
• Atom Count: 3,251 
• Modeled Residue Count: 363 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine phosphoribosyltransferase	A, B	183	Escherichia coli K-12	Mutation(s): 0  Gene Names: apt, b0469, JW0458 EC: 2.4.2.7
UniProt
Find proteins for P69503 (Escherichia coli (strain K12)) Explore P69503  Go to UniProtKB:  P69503

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	D [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	E [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.014	α = 106.72
b = 47.752	β = 103.09
c = 54.074	γ = 111.02

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Yadav, P., Kushwaha, G.S., Bhavesh, N.S.

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Funding Organization	Location	Grant Number
Indian Council of Mefical Research	India	BMI/11(45)/2020

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description