5X71 | pdb_00005x71

Crystal structure of Rice Dwarf Virus P5 in space group P212121

PDB DOI: https://doi.org/10.2210/pdb5X71/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: 2.57 Å
R-Value Free:
0.235 (Depositor), 0.240 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 182.33 kDa
Atom Count: 12,735
Modeled Residue Count: 1,591
Deposited Residue Count: 1,608
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA capping enzyme P5	A, 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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP Query on 5GP Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.235 (Depositor), 0.240 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.814	α = 90
b = 122.631	β = 90
c = 192.262	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.