3DDO | pdb_00003ddo

X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with by Phosphate Ion at 1.5A Resolution

• PDB DOI: https://doi.org/10.2210/pdb3DDO/pdb

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


• Deposited: 2008-06-06 Released: 2009-06-09 
• Deposition Author(s): Lashkov, A.A., Mikhailov, A.M., Gabdoulkhakov, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with by Phosphate Ion at 1.5A Resolution

Lashkov, A.A., Mikhailov, A.M., Gabdoulkhakov, A.G.

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: 163.49 kDa 
• Atom Count: 12,812 
• Modeled Residue Count: 1,469 
• 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	Mutation(s): 0  Gene Names: udp, STM3968, STMD1.21 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth B], I [auth C], J [auth D], K [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.6	α = 90
b = 124.92	β = 90
c = 134.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
EMBL	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-09 
Deposition Author(s): Lashkov, A.A., Mikhailov, A.M., Gabdoulkhakov, A.G.

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description