5EFT | pdb_00005eft

Structural Basis for Specific Recognition of ssDNA by SRBSDV P9-1 Octamers

• PDB DOI: https://doi.org/10.2210/pdb5EFT/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Rice black-streaked dwarf virus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-26 Released: 2016-10-26 
• Deposition Author(s): Li, X.Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Literature

Structural Basis for Specific Recognition of ssDNA by SRBSDV P9-1 Octamers

Li, X.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B1C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 155.2 kDa 
• Atom Count: 8,792 
• Modeled Residue Count: 1,084 
• Deposited Residue Count: 1,348 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
p9-1	A, C, E, G	16	Rice black-streaked dwarf virus 2	Mutation(s): 0
UniProt
Find proteins for B6SCH3 (Rice black-streaked dwarf virus 2) Explore B6SCH3  Go to UniProtKB:  B6SCH3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p9-1	B, D, F, H	321	Rice black-streaked dwarf virus 2	Mutation(s): 0
UniProt
Find proteins for B6SCH3 (Rice black-streaked dwarf virus 2) Explore B6SCH3  Go to UniProtKB:  B6SCH3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.52	α = 90
b = 155.72	β = 90
c = 157.63	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Li, X.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31460460
National Natural Science Foundation of China	China	21132003

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description