1RYZ

Uridine Phosphorylase from Salmonella typhimurium. Crystal Structure at 2.9 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb1RYZ/pdb

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


• Deposited: 2003-12-23 Released: 2004-12-28 
• Deposition Author(s): Dontsova, M.V., Gabdoulkhakov, A.G., Lyashenko, A.V., Nikonov, S.V., Ealick, S.E., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.284 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Structure-functions studies of uridine phosphorylase from Salmonella typhimurium

Dontsova, M.V., Gabdoulkhakov, A.G., Lyashenko, A.V., Nikonov, S.V., Ealick, S.E., Mikhailov, A.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 6-mer - A6 

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PQS (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 163.13 kDa 
• Atom Count: 11,270 
• Modelled Residue Count: 1,500 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	G [auth B], H [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.284 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.26	α = 90
b = 92.26	β = 90
c = 267.46	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-28 
Deposition Author(s): Dontsova, M.V., Gabdoulkhakov, A.G., Lyashenko, A.V., Nikonov, S.V., Ealick, S.E., Mikhailov, A.M.

Revision History  

• Version 1.0: 2004-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description