2OEC | pdb_00002oec

Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with 2,2'-anhydrouridine and potassium ion at 2.194A resolution

• PDB DOI: https://doi.org/10.2210/pdb2OEC/pdb

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


• Deposited: 2006-12-29 Released: 2008-01-01 
• Deposition Author(s): Timofeev, V.I., Lashkov, A.A., Pavlyuk, B.P., Mikhailov, A.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.240 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.189 (DCC) 

Literature

Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with 2,2'-anhydrouridine and potassium ion at 2.194A resolution

Timofeev, V.I., Lashkov, A.A., Pavlyuk, B.P., Gabdoulkhakov, A.G., Kachalova, G.S., 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: 163.6 kDa 
• Atom Count: 11,603 
• Modeled Residue Count: 1,486 
• Deposited Residue Count: 1,512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E, F	252	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	I [auth B], J [auth B], L [auth D]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
ANU	H [auth B], N [auth F]	2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil C9 H10 N2 O5 UUGITDASWNOAGG-CCXZUQQUSA-N
GOL	O [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	G [auth A], K [auth C], M [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.240 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.189 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.52	α = 90
b = 123.98	β = 90
c = 133.52	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-01 
Deposition Author(s): Timofeev, V.I., Lashkov, A.A., Pavlyuk, B.P., Mikhailov, A.M.

Revision History  

• Version 1.0: 2008-01-01
  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: 2023-12-27
  Changes: Data collection, Database references, Derived calculations