5X6X

Crystal structure of the capping enzyme P5 from Rice Dwarf Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of the capping enzyme P5 from Rice Dwarf Virus

Nakamichi, Y.Higashiura, A.Narita, H.Hagiwara, K.Uehara-Ichiki, T.Omura, T.Nakagawa, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA capping enzyme P5
C, A, B, D
804Rice dwarf virus (isolate Akita)Mutation(s): 0 
Find proteins for P14583 (Rice dwarf virus (isolate Akita))
Go to UniProtKB:  P14583
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.188 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 77.230α = 103.41
b = 83.854β = 102.47
c = 143.250γ = 95.37
Software Package:
Software NamePurpose
HKL-2000data reduction
AutoSolphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapanJP25251009

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release