4RJ2 | pdb_00004rj2

Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4RJ2/pdb

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


• Deposited: 2014-10-08 Released: 2014-12-03 
• Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution

Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 154.88 kDa 
• Atom Count: 12,253 
• Modeled Residue Count: 1,422 
• Deposited Residue Count: 1,422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase DeoD-type	A, B, C, D, E, F	237	Escherichia coli	Mutation(s): 0  Gene Names: deoD EC: 2.4.2.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth C], I [auth D], J [auth D], K [auth D], L [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.12	α = 90
b = 110.22	β = 111.08
c = 88.21	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Experimental preparation