2VRI | pdb_00002vri

Structure of the NSP3 X-domain of human coronavirus NL63

• PDB DOI: https://doi.org/10.2210/pdb2VRI/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human coronavirus NL63
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-08 Released: 2009-06-09 
• Deposition Author(s): Piotrowski, Y., Mesters, J.R., Moll, R., Hilgenfeld, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structure of the Nsp3 X-Domain of Human Coronavirus Nl63

Piotrowski, Y., Mesters, J.R., Van Der Hoek, L., Moll, R., Hilgenfeld, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 19 kDa 
• Atom Count: 1,443 
• Modeled Residue Count: 173 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NON-STRUCTURAL PROTEIN 3	A	174	Human coronavirus NL63	Mutation(s): 0
UniProt
Find proteins for P0C6U6 (Human coronavirus NL63) Explore P0C6U6  Go to UniProtKB:  P0C6U6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.97	α = 90
b = 54.77	β = 90
c = 57.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-09 
Deposition Author(s): Piotrowski, Y., Mesters, J.R., Moll, R., Hilgenfeld, R.

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description