3C74 | pdb_00003c74

X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with 2,2'-anhydrouridine at 2.38a resolution

• PDB DOI: https://doi.org/10.2210/pdb3C74/pdb

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


• Deposited: 2008-02-06 Released: 2009-02-10 
• Deposition Author(s): Lashkov, A.A., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with 2,2'-anhydrouridine at 2.38a resolution

Lashkov, A.A., Mikhailov, A.M.

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: 164.36 kDa 
• Atom Count: 11,475 
• 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 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
ANU	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil C9 H10 N2 O5 UUGITDASWNOAGG-CCXZUQQUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.37	α = 90
b = 125.308	β = 90
c = 135.177	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Lashkov, A.A., Mikhailov, A.M.

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations