3ONY

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with Fucose

• PDB DOI: https://doi.org/10.2210/pdb3ONY/pdb

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


• Deposited: 2010-08-30 Released: 2011-05-11 
• Deposition Author(s): Hansman, G.S., Biertumpfel, C., Chen, L., Georgiev, I., McLellan, J.S., Katayama, K., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.189 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 105.27 kDa 
• Atom Count: 7,949 
• Modelled Residue Count: 928 
• Deposited Residue Count: 954 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C	318	Norwalk virus	Mutation(s): 0
UniProt
Find proteins for Q5F4T5 (Norwalk virus) Explore Q5F4T5  Go to UniProtKB:  Q5F4T5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC	G [auth A], L [auth B], P [auth C]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
EDO	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.189 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.529	α = 90
b = 115.905	β = 90
c = 267.801	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Hansman, G.S., Biertumpfel, C., Chen, L., Georgiev, I., McLellan, J.S., Katayama, K., Kwong, P.D.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary