8BS2 | pdb_00008bs2

Room-temperature structure of SARS-CoV-2 Main protease at 104 MPa helium gas pressure in a sapphire capillary

PDB DOI: https://doi.org/10.2210/pdb8BS2/pdb

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

Deposited: 2022-11-24 Released: 2023-12-13
Deposition Author(s): Lieske, J., Saouane, S., Guenther, S., Reinke, P.Y.A., Rahmani Mashhour, A., Meents, A.
Funding Organization(s): German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.175 (Depositor), 0.176 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

High-pressure macromolecular crystallography to explore the conformational space of proteins

Lieske, J., Saouane, S., Guenther, S., Reinke, P.Y.A., Falke, S., Ewert, W., Meyer, J., Pakendorf, T., Reime, B., Burkhardt, A., Crosas, E., Hakanpaeae, J., Stachnik, K., Sieg, J., Rarey, M., Assmann, M., Zaun, H., Kuballa, J., Chapman, H.N., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 34 kDa
Atom Count: 2,411
Modeled Residue Count: 305
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.219 (Depositor), 0.220 (DCC)
R-Value Work: 0.175 (Depositor), 0.176 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.58	α = 90
b = 54.5	β = 101.246
c = 45.05	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Rahmani Mashhour, A.

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	031B0405A

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.