1Y1R | pdb_00001y1r

Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Inhibitor and Phosphate Ion at 2.11A Resolution

• PDB DOI: https://doi.org/10.2210/pdb1Y1R/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): Dontsova, M.V., Gabdoulkhakov, A.G., Kachalova, G.S., Betzel, C., Ealick, S.E., Mikhailov, A.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Salmonella Typhimurium Uridine Phosphorylase in Complex with Inhibitor and Phosphate.

Dontsova, M.V., Gabdoulkhakov, A.G., 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: 163.75 kDa 
• Atom Count: 11,625 
• Modeled Residue Count: 1,458 
• Deposited Residue Count: 1,518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B [auth C], C [auth D], D [auth F], E, F [auth B]	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
BJE	H [auth D], K [auth B]	2,2'-Anhydro-(1-beta-D-ribofuranosyl)uracil C9 H10 N2 O5 UUGITDASWNOAGG-XVFCMESISA-N
PO4	G [auth D], I [auth F], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.88	α = 90
b = 124.07	β = 90
c = 134.4	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): Dontsova, M.V., Gabdoulkhakov, A.G., 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 2.0: 2017-10-18
  Changes: Atomic model, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description