Download MendeleyCrystal 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.
5X70
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
- Funding Organization(s): JSPS
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 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
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 Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P14583 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
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 |  | |
Sequence AnnotationsExpand | |||||
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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 = 80.754 | α = 104.74 |
| b = 80.657 | β = 104 |
| c = 145.734 | γ = 95.29 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-02-28 Deposition Author(s): Nakamichi, Y., Higashiura, A., Nakagawa, A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| JSPS | Japan | JP25251009 |
Revision History (Full details and data files)
- Version 1.0: 2018-02-28
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
