3ODG

crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis

Kim, J.Ramagopal, U.A.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xanthosine phosphorylaseA287Yersinia pseudotuberculosisMutation(s): 0 
Gene Names: pndAxapAYPTB1201
EC: 2.4.2 (PDB Primary Data), 2.4.2.1 (UniProt)
Find proteins for Q66D48 (Yersinia pseudotuberculosis serotype I (strain IP32953))
Explore Q66D48 
Go to UniProtKB:  Q66D48
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XAN
Query on XAN

Download Ideal Coordinates CCD File 
B [auth A]XANTHINE
C5 H4 N4 O2
LRFVTYWOQMYALW-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.47α = 90
b = 96.47β = 90
c = 48.906γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-02-10
    Changes: Derived calculations, Structure summary