2OXF | pdb_00002oxf

X-ray structure of the unliganded uridine phosphorylase from Salmonella typhimurium in homodimeric form at 1.76A resolution

• PDB DOI: https://doi.org/10.2210/pdb2OXF/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-02-20 Released: 2008-02-26 
• Deposition Author(s): Timofeev, V.I., Pavlyk, B.P., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.207 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.161 (DCC) 

Literature

X-ray structure of the unliganded uridine phosphorylase from Salmonella typhimurium in homodimeric form at 1.76A resolution

Timofeev, V.I., Pavlyk, B.P., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 53.74 kDa 
• Atom Count: 3,807 
• Modeled Residue Count: 475 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B [auth F]	250	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: UDP EC: 2.4.2.3
UniProt
Find proteins for P0A1F6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A1F6  Go to UniProtKB:  P0A1F6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.207 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.161 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.86	α = 90
b = 150.86	β = 90
c = 47.84	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Timofeev, V.I., Pavlyk, B.P., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations