4EAF

Thymidine phosphorylase from E.coli

PDB DOI: https://doi.org/10.2210/pdb4EAF/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.207
R-Value Work: 0.158
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Thymidine phosphorylase from E.coli

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

To be published.

Macromolecule Content

Total Structure Weight: 48.1 kDa
Atom Count: 3,928
Modelled Residue Count: 440
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine phosphorylase	A	440	Escherichia coli K-12	Mutation(s): 0 Gene Names: deoA, tpp, ttg, b4382, JW4345 EC: 2.4.2.4
UniProt
Find proteins for P07650 (Escherichia coli (strain K12)) Explore P07650 Go to UniProtKB: P07650
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07650
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.207
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.951	α = 90
b = 129.951	β = 90
c = 67.809	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

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Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Revision History (Full details and data files)

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

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Deposit Data

Help and Resources

4EAF

Thymidine phosphorylase from E.coli

Thymidine phosphorylase from E.coli

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)