+Open data
-Basic information
Entry | Database: PDB / ID: 8ddl | ||||||
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Title | SARS-CoV-2 Main Protease (Mpro) H163A Mutant Apo Structure | ||||||
Components | (ORF1a polyprotein) x 2 | ||||||
Keywords | HYDROLASE / cysteine protease / SARS-CoV-2 / 3CL-like / disulfide bond / VIRAL PROTEIN | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated suppression of host gene expression / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated suppression of host gene expression / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Tran, N. / McLeod, M.J. / Kalyaanamoorthy, S. / Ganesan, A. / Holyoak, T. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Authors: Tran, N. / Dasari, S. / Barwell, S.A.E. / McLeod, M.J. / Kalyaanamoorthy, S. / Holyoak, T. / Ganesan, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ddl.cif.gz | 262 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ddl.ent.gz | 209.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ddl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ddl_validation.pdf.gz | 466.3 KB | Display | wwPDB validaton report |
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Full document | 8ddl_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 8ddl_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 8ddl_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/8ddl ftp://data.pdbj.org/pub/pdb/validation_reports/dd/8ddl | HTTPS FTP |
-Related structure data
Related structure data | 8dd6C 8sg6C 7alhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 33758.477 Da / Num. of mol.: 1 / Mutation: H163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U3EDN3 |
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#2: Protein | Mass: 33774.477 Da / Num. of mol.: 1 / Mutation: H163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U3EDN3 |
-Non-polymers , 5 types, 382 molecules
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % / Description: Thin plates |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, pH 8.5 and 26% (v/v) PEG Smear Broad (BCS B11) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→102.95 Å / Num. obs: 52678 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.047 / Rrim(I) all: 0.176 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 14.04 % / Rmerge(I) obs: 1.082 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2569 / CC1/2: 0.759 / Rpim(I) all: 0.297 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ALH Resolution: 1.95→56.54 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / Phase error: 19.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→56.54 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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