1Y1Q

Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Uridine-5p-monophosphate and Sulfate Ion at 2.35A Resolution

• PDB DOI: https://doi.org/10.2210/pdb1Y1Q/pdb

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


• Deposited: 2004-11-19 Released: 2005-11-22 
• Deposition Author(s): Gabdoulkhakov, A.G., Dontsova, M.V., Kachalova, G.S., Betzel, C., Ealick, S.E., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.234 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Crystal Structures of Salmonella Typhimurium Uridine Phosphorylase in Native and Three Complexes Forms - with Uridine, Uracil and Sulfate.

Gabdoulkhakov, A.G., Dontsova, M.V., Kachalova, G.S., Betzel, C., Ealick, S.E., 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 (software)

Macromolecule Content

• Total Structure Weight: 163.72 kDa 
• Atom Count: 11,160 
• Modelled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	I [auth C]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
SO4	G [auth A], H [auth A], J [auth E], K [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.234 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.37	α = 90
b = 123.73	β = 90
c = 134.14	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-22 
Deposition Author(s): Gabdoulkhakov, A.G., Dontsova, M.V., Kachalova, G.S., Betzel, C., Ealick, S.E., Mikhailov, A.M.

Revision History  

• Version 1.0: 2005-11-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: 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
• Version 2.0: 2024-10-16
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary