5W82 | pdb_00005w82

Crystal structure of Orsay virus delta protein N-terminal fragment (aa 1-101)

• PDB DOI: https://doi.org/10.2210/pdb5W82/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Orsay virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-21 Released: 2018-12-26 
• Deposition Author(s): Guo, Y.R., Tao, Y.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

To be published

Guo, Y.R., Tao, Y.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.33 kDa 
• Atom Count: 4,539 
• Modeled Residue Count: 504 
• Deposited Residue Count: 515 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein delta	A [auth C], B, C [auth D], D [auth E], E [auth A]	103	Orsay virus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.746	α = 90
b = 58.22	β = 90
c = 163.235	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Guo, Y.R., Tao, Y.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI122356

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description