5X6X | pdb_00005x6x

Crystal structure of the capping enzyme P5 from Rice Dwarf Virus

• PDB DOI: https://doi.org/10.2210/pdb5X6X/pdb

• Classification: TRANSFERASE
• Organism(s): Rice dwarf virus (isolate O)
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-02-23 Released: 2018-02-28 
• Deposition Author(s): Nakamichi, Y., Higashiura, A., Nakagawa, A.
• Funding Organization(s): JSPS

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 363.58 kDa 
• Atom Count: 26,049 
• Modeled Residue Count: 3,111 
• Deposited Residue Count: 3,216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA capping enzyme P5	A [auth C], B [auth A], C [auth B], D	804	Rice dwarf virus (isolate O)	Mutation(s): 0  EC: 2.7.7.50
UniProt
Find proteins for P14583 (Rice dwarf virus (isolate Akita)) Explore P14583  Go to UniProtKB:  P14583

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth C], F [auth C], G [auth A], H [auth A], I [auth A], J [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.23	α = 103.41
b = 83.854	β = 102.47
c = 143.25	γ = 95.37

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Nakamichi, Y., Higashiura, A., Nakagawa, A.

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Funding Organization	Location	Grant Number
JSPS	Japan	JP25251009

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references