4OGK

X-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4OGK/pdb

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


• Deposited: 2014-01-16 Released: 2015-03-04 
• Deposition Author(s): Sotnichenko, S.E., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.236 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Literature

X-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution

Sotnichenko, S.E., Lashkov, A.A., Gabdoulkhakov, A.G., 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: 164.87 kDa 
• Atom Count: 11,404 
• Modelled Residue Count: 1,495 
• 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: STM3968, STMD1.21, 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THM	G [auth A], J [auth B], L [auth D], N [auth E], Q [auth F]	THYMIDINE C10 H14 N2 O5 IQFYYKKMVGJFEH-XLPZGREQSA-N
PG4	O [auth E]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	M [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	I [auth A], K [auth C], P [auth E], S [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	H [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
K	R [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.236 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.97	α = 90
b = 89.97	β = 90
c = 256.56	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Sotnichenko, S.E., Lashkov, A.A., Gabdoulkhakov, A.G., Mikhailov, A.M.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description