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Yorodumi- PDB-7xjw: Crystal structure of canine coronavirus main protease in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xjw | ||||||
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Title | Crystal structure of canine coronavirus main protease in complex with GC376 | ||||||
Components | ORF1a polyprotein | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / 3C-like proteinase / VIRAL PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy ...host cell membrane / viral genome replication / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / proteolysis / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Canine coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Wang, Y.C. / Yang, C.S. / Hou, M.H. / Tsai, C.L. / Chiu, Y.F. / Chen, Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: A Structural Comparison of SARS-CoV-2 Main Protease and Animal Coronaviral Main Protease Reveals Species-Specific Ligand Binding and Dimerization Mechanism. Authors: Ho, C.Y. / Yu, J.X. / Wang, Y.C. / Lin, Y.C. / Chiu, Y.F. / Gao, J.Y. / Lai, S.J. / Chen, M.J. / Huang, W.C. / Tien, N. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xjw.cif.gz | 457.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xjw.ent.gz | 376.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xjw_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 7xjw_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 7xjw_validation.xml.gz | 90.8 KB | Display | |
Data in CIF | 7xjw_validation.cif.gz | 117.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/7xjw ftp://data.pdbj.org/pub/pdb/validation_reports/xj/7xjw | HTTPS FTP |
-Related structure data
Related structure data | 4f49S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33073.426 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canine coronavirus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2WXL6 #2: Chemical | ChemComp-K36 / ( #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.97 Å3/Da / Density % sol: 58.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium citrate, 0.1 M Bis Tris propane 7.0, 25 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. obs: 79392 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.036 / Net I/σ(I): 20.39 |
Reflection shell | Resolution: 2.75→2.85 Å / Rmerge(I) obs: 0.386 / Num. unique obs: 7891 / CC1/2: 0.914 / Rpim(I) all: 0.234 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F49 Resolution: 2.75→27.82 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.376 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→27.82 Å
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