4JP5

X-ray structure of uridine phosphorylase from Yersinia pseudotuberculosis in unliganded state at 2.27 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4JP5/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-19 Released: 2014-04-09 
• Deposition Author(s): Balaev, V.V., Lashkov, A.A., Prokofev, I.I., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.202 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

X-ray structure of uridine phosphorylase from Yersinia pseudotuberculosis in unliganded state at 2.27 A resolution

Balaev, V.V., Lashkov, A.A., Prokofev, I.I., Gabdoulkhakov, A.G., Betzel, C., 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: 163.22 kDa 
• Atom Count: 11,305 
• Modelled Residue Count: 1,441 
• 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	Yersinia pestis	Mutation(s): 0  Gene Names: udp, y0444, YP_3263 EC: 2.4.2.3
UniProt
Find proteins for Q8D1I4 (Yersinia pestis) Explore Q8D1I4  Go to UniProtKB:  Q8D1I4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth E], J [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth A], K [auth F], L [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.202 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.75	α = 90
b = 93.75	β = 90
c = 146.58	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Balaev, V.V., Lashkov, A.A., Prokofev, I.I., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description