1TGY | pdb_00001tgy

Structure of E. coli Uridine Phosphorylase complexed with uracil and ribose 1-phosphate

• PDB DOI: https://doi.org/10.2210/pdb1TGY/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2004-05-31 Released: 2005-06-14 
• Deposition Author(s): Bu, W., Settembre, E.C., Sanders, J.M., Begley, T.P., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.211 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Structures of E. coli Uridine Phosphorylase

Bu, W., Settembre, E.C., Sanders, J.M., Begley, T.P., Ealick, S.E.

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: 55.67 kDa 
• Atom Count: 4,100 
• Modeled Residue Count: 500 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uridine phosphorylase	A, B	256	Escherichia coli	Mutation(s): 0  Gene Names: UDP, B3831 EC: 2.4.2.3
UniProt
Find proteins for P12758 (Escherichia coli (strain K12)) Explore P12758  Go to UniProtKB:  P12758

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R1P	C [auth A], F [auth B]	1-O-phosphono-alpha-D-ribofuranose C5 H11 O8 P YXJDFQJKERBOBM-TXICZTDVSA-N
URA	E [auth A], G [auth B]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.211 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.972	α = 90
b = 149.972	β = 90
c = 49.566	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-14 
Deposition Author(s): Bu, W., Settembre, E.C., Sanders, J.M., Begley, T.P., Ealick, S.E.

Revision History  

• Version 1.0: 2005-06-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-02-14
  Changes: Data collection, Database references, Structure summary