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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

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

Wu, Y.K., Chen, L.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

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

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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), 0.200 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Wu, Y.K., Chen, L.F., Chen, P.

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

Revision History  

• 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