7XCD | pdb_00007xcd

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

PDB DOI: https://doi.org/10.2210/pdb7XCD/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., Chen, P.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.196 (Depositor), 0.198 (DCC)
R-Value Work:
0.180 (Depositor), 0.185 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 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: 1,592
Modeled Residue Count: 178
Deposited Residue Count: 178
Unique protein chains: 1

Macromolecules

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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 Q00844 (Rice stripe virus (isolate T)) Explore Q00844 Go to UniProtKB: Q00844
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00844
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: 1.71 Å
R-Value Free: 0.196 (Depositor), 0.198 (DCC)
R-Value Work: 0.180 (Depositor), 0.185 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.327	α = 90
b = 81.311	β = 90
c = 122.037	γ = 90

Software Package:

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

Structure Validation

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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: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

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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.