3OCC

Crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase deoD-type
A, B, C, D, E
A, B, C, D, E, F
239Yersinia pseudotuberculosis YPIIIMutation(s): 0 
Gene Names: deoDYPK_3624
EC: 2.4.2.1
UniProt
Find proteins for B1JL34 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII))
Explore B1JL34 
Go to UniProtKB:  B1JL34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1JL34
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DIH
Query on DIH

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth 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
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.647α = 90
b = 109.829β = 90
c = 154.747γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-12-12
    Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description