5X70

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mRNA capping enzyme P5A, D [auth B], B [auth C], C [auth D]804Rice 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
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3')E, F [auth G]6Rice dwarf virus
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.30 Å
    • R-Value Free: 0.269 
    • R-Value Work: 0.220 
    • R-Value Observed: 0.223 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 80.754α = 104.74
    b = 80.657β = 104
    c = 145.734γ = 95.29
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    MOLREPphasing

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    JSPSJapanJP25251009

    Revision History  (Full details and data files)

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