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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.237 (Depositor), 0.238 (DCC)
R-Value Work:
0.188 (Depositor), 0.189 (DCC)
R-Value Observed:
0.191 (Depositor)

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This is version 1.1 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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14583
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth C] SDF format, chain E [auth C] MOL2 format, chain J [auth D] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] mmCIF format, chain J [auth D] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth C]	E [auth C] F [auth C] G [auth A] H [auth A] I [auth A] 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		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.237 (Depositor), 0.238 (DCC)
R-Value Work: 0.188 (Depositor), 0.189 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

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: 2024-03-27
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.