7XCC | pdb_00007xcc

Crystal Structure of the Disease-Specific Protein of Rice Stripe Virus

PDB DOI: https://doi.org/10.2210/pdb7XCC/pdb

Classification: VIRAL PROTEIN
Organism(s): Tenuivirus oryzaclavatae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-24 Released: 2023-04-26
Deposition Author(s): Wu, Y.K., Chen, L.F.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.208 (Depositor), 0.170 (DCC)
R-Value Work:
0.165 (Depositor), 0.170 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the Disease-Specific Protein of Rice Stripe Virus

Wu, Y.K., Chen, L.F.

To be published.

Macromolecule Content

Total Structure Weight: 20.85 kDa
Atom Count: 1,536
Modeled Residue Count: 164
Deposited Residue Count: 178
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disease specific protein	A	178	Tenuivirus oryzaclavatae	Mutation(s): 0 Gene Names: SP, sp
UniProt
Find proteins for Q705B3 (Tenuivirus oryzaclavatae) Explore Q705B3 Go to UniProtKB: Q705B3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q705B3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.208 (Depositor), 0.170 (DCC)
R-Value Work: 0.165 (Depositor), 0.170 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.408	α = 90
b = 74.193	β = 90
c = 78.684	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	National Natural Science Foundation of China (32002049)

Revision History (Full details and data files)

Version 1.0: 2023-04-26
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary

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.