5X70 | pdb_00005x70

Crystal structure of Rice Dwarf Virus P5 in complex with a ssRNA oligomer

• PDB DOI: https://doi.org/10.2210/pdb5X70/pdb
• NAKB: 5X70

• Classification: TRANSFERASE/RNA
• Organism(s): Rice dwarf virus (isolate O), Rice dwarf virus
• 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: 3.30 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of capping enzyme 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 367.09 kDa 
• Atom Count: 24,258 
• Modeled Residue Count: 3,047 
• Deposited Residue Count: 3,228 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA capping enzyme P5	A, B [auth C], C [auth D], D [auth B]	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3')	E, F [auth G]	6	Rice dwarf virus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.754	α = 104.74
b = 80.657	β = 104
c = 145.734	γ = 95.29

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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: 2023-11-22
  Changes: Data collection, Database references, Refinement description