2PGA | pdb_00002pga

X-ray Structure of the Uridine Phosphorylase From SALMONELLA TYPHIMURIUM in Complex with Inhibitor and Phosphate and Potassium Ion at 1.74 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb2PGA/pdb

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


• Deposited: 2007-04-09 Released: 2008-04-15 
• Deposition Author(s): Timofeev, V.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.210 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.176 (DCC) 

Literature

X-ray Structure of the Uridine Phosphorylase From SALMONELLA TYPHIMURIUM in Complex with Inhibitor and Phosphate and Potassium Ion at 1.74 A Resolution

Timofeev, V.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., 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: 164.1 kDa 
• Atom Count: 11,631 
• Modeled Residue Count: 1,456 
• Deposited Residue Count: 1,518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E, F	253	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANU	J [auth B], L [auth D], O [auth F]	2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil C9 H10 N2 O5 UUGITDASWNOAGG-CCXZUQQUSA-N
PO4	H [auth B], K [auth D], N [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	G [auth A], I [auth B], M [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.210 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.176 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.79	α = 90
b = 124.07	β = 90
c = 134.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Timofeev, V.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations