3OCC

Crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis

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

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase deoD-type
A, B, C, D, E, F
239Yersinia pseudotuberculosis serotype O:3 (strain YPIII)Mutation(s): 0 
Gene Names: deoD
EC: 2.4.2.1
Find proteins for B1JL34 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII))
Go to UniProtKB:  B1JL34
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DIH
Query on DIH

Download SDF File 
Download CCD File 
A, B, C, D, E, F
7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one
C12 H17 N4 O3
AFNHHLILYQEHKK-BDAKNGLRSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 91.647α = 90.00
b = 109.829β = 90.00
c = 154.747γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2018-12-12
    Type: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary