5S73

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain

• PDB DOI: https://doi.org/10.2210/pdb5S73/pdb
• Deposition Group: G_1002177 (ground state) ExploreG_1002177

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-23 Released: 2021-01-13 
• Deposition Author(s): Fearon, D., Schuller, M., Rangel, V.L., Douangamath, A., Rack, J.G.M., Zhu, K., Aimon, A., Brandao-Neto, J., Dias, A., Dunnet, L., Gorrie-Stone, T.J., Powell, A.J., Krojer, T., Skyner, R., Thompson, W., Ahel, I., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.223 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain

Fearon, D., Schuller, M., Rangel, V.L., Douangamath, A., Aimon, A., Powell, A.J., Dias, A., Dunnet, L., Brandao-Neto, J., Skyner, R., Gorrie-Stone, T.J., Thompson, W., Krojer, T., Rack, J.G.M., Zhu, K., Ahel, I., von Delft, F.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.36 kDa 
• Atom Count: 2,943 
• Modelled Residue Count: 334 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	169	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.223 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.93	α = 90
b = 87.93	β = 90
c = 38.464	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Fearon, D., Schuller, M., Rangel, V.L., Douangamath, A., Rack, J.G.M., Zhu, K., Aimon, A., Brandao-Neto, J., Dias, A., Dunnet, L., Gorrie-Stone, T.J., Powell, A.J., Krojer, T., Skyner, R., Thompson, W., Ahel, I., von Delft, F.

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Structure summary
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references