5EY3 | pdb_00005ey3

X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate

• PDB DOI: https://doi.org/10.2210/pdb5EY3/pdb

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


• Deposited: 2015-11-24 Released: 2016-12-07 
• Deposition Author(s): Balaev, V.V., Lashkov, A.A., Gabdulkhakov, A.G., Betzel, C., Mikhailov, A.M.
• Funding Organization(s): Russian Foundation for Basic Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate

Balaev, V.V., Lashkov, A.A., Gabdulkhakov, A.G., Betzel, C., Mikhailov, A.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.74 kDa 
• Atom Count: 6,913 
• Modeled Residue Count: 882 
• Deposited Residue Count: 884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine phosphorylase	A, B	442	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: deoA, STM4568 EC: 2.4.2.4
UniProt
Find proteins for Q7CP66 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q7CP66  Go to UniProtKB:  Q7CP66

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTN	O [auth B]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C9 H13 N3 O5 UHDGCWIWMRVCDJ-XVFCMESISA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.398	α = 90
b = 193.398	β = 90
c = 58.208	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Balaev, V.V., Lashkov, A.A., Gabdulkhakov, A.G., Betzel, C., Mikhailov, A.M.

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Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	14-04-00952

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Advisory, Author supporting evidence
• Version 1.2: 2024-01-10
  Changes: Advisory, Data collection, Database references, Refinement description