7PXZ

Reduced form of SARS-CoV-2 Main Protease determined by XFEL radiation

• PDB DOI: https://doi.org/10.2210/pdb7PXZ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-10-08 Released: 2023-01-18 
• Deposition Author(s): Schubert, R., Reinke, P., Galchenkova, M., Oberthuer, D., Murillo, G.E.P., Kim, C., Bean, R., Turk, D., Hinrichs, W., Middendorf, P., Round, A., Schmidt, C., Mills, G., Kirkwood, H., Han, H., Koliyadu, J., Bielecki, J., Gelisio, L., Sikorski, M., Kloos, M., Vakilii, M., Yefanov, O.N., Vagovic, P., de-Wijn, R., Letrun, R., Guenther, S., White, T.A., Sato, T., Srinivasan, V., Kim, Y., Chretien, A., Han, S., Brognaro, H., Maracke, J., Knoska, J., Seychell, B.C., Brings, L., Norton-Baker, B., Geng, T., Dore, A.S., Uetrecht, C., Redecke, L., Beck, T., Lorenzen, K., Betzel, C., Mancuso, A.P., Bajt, S., Chapman, H.N., Meents, A., Lane, T.J.
• Funding Organization(s): Helmholtz Association, German Research Foundation (DFG), European Commission, German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.212 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Reduced form of SARS-CoV-2 Main Protease determined by XFEL radiation

Schubert, R., Reinke, P., Galchenkova, M., Oberthuer, D., Murillo, G., Kim, C., Bean, R., Turk, D., Hinrichs, W., Middendorf, P., Round, A., Schmidt, C., Mills, G., Kirkwood, H., Han, H., Koliyadu, J., Bielecki, J., Gelisio, L., Sikorski, M., Kloos, M., Vakilii, M., Yefanov, O., Vagovic, P., de-Wijn, R., Letrun, R., Guenther, S., White, T., Sato, T., Srinivasan, V., Kim, Y., Chretien, A., Han, S., Brognaro, H., Maracke, J., Knoska, J., Seychell, B., Brings, L., Norton-Baker, B., Geng, T., Dore, A., Uetrecht, C., Redecke, L., Beck, T., Lorenzen, K., Betzel, C., Mancuso, A., Bajt, S., Chapman, H., Meents, A., Lane, T.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.86 kDa 
• Atom Count: 2,724 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.212 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115	α = 90
b = 54	β = 102
c = 45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Schubert, R., Reinke, P., Galchenkova, M., Oberthuer, D., Murillo, G.E.P., Kim, C., Bean, R., Turk, D., Hinrichs, W., Middendorf, P., Round, A., Schmidt, C., Mills, G., Kirkwood, H., Han, H., Koliyadu, J., Bielecki, J., Gelisio, L., Sikorski, M., Kloos, M., Vakilii, M., Yefanov, O.N., Vagovic, P., de-Wijn, R., Letrun, R., Guenther, S., White, T.A., Sato, T., Srinivasan, V., Kim, Y., Chretien, A., Han, S., Brognaro, H., Maracke, J., Knoska, J., Seychell, B.C., Brings, L., Norton-Baker, B., Geng, T., Dore, A.S., Uetrecht, C., Redecke, L., Beck, T., Lorenzen, K., Betzel, C., Mancuso, A.P., Bajt, S., Chapman, H.N., Meents, A., Lane, T.J.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--
German Research Foundation (DFG)	Germany	--
European Commission	European Union	--
German Federal Ministry for Education and Research	Germany	--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection
• Version 2.0: 2024-02-14
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Other, Refinement description, Structure summary