4EAD | pdb_00004ead

Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine

• PDB DOI: https://doi.org/10.2210/pdb4EAD/pdb

• Classification: Transferase/Transferase inhibitor
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-22 Released: 2013-03-27 
• Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine

Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.46 kDa 
• Atom Count: 3,984 
• Modeled Residue Count: 440 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine phosphorylase	A	440	Escherichia coli K-12	Mutation(s): 0  Gene Names: b4382, deoA, JW4345, tpp, ttg EC: 2.4.2.4
UniProt
Find proteins for P07650 (Escherichia coli (strain K12)) Explore P07650  Go to UniProtKB:  P07650

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0NP	B [auth A]	2',3'-dideoxy-2'-fluoro-3'-triaza-1,2-dien-2-ium-1-yluridine C9 H11 F N5 O4 YRIDFNZYEULFDH-XVFCMESISA-O
SO4	C [auth A], D [auth A], E [auth A], G [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.862	α = 90
b = 129.862	β = 90
c = 67.656	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description