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Yorodumi- PDB-7xry: Crystal structure of MERS main protease in complex with inhibitor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xry | ||||||
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Title | Crystal structure of MERS main protease in complex with inhibitor YH-53 | ||||||
Components | ORF1a | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Chem-HUR Function and homology information | ||||||
Biological species | Middle East respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Lin, C. / Zhong, F.L. / Zhou, X.L. / Li, J. / Zhang, J. | ||||||
Funding support | 1items
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Citation | Journal: Viruses / Year: 2022 Title: Structural Basis for the Inhibition of Coronaviral Main Proteases by a Benzothiazole-Based Inhibitor. Authors: Hu, X. / Lin, C. / Xu, Q. / Zhou, X. / Zeng, P. / McCormick, P.J. / Jiang, H. / Li, J. / Zhang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xry.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xry.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xry_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7xry_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7xry_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 7xry_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/7xry ftp://data.pdbj.org/pub/pdb/validation_reports/xr/7xry | HTTPS FTP |
-Related structure data
Related structure data | 7xrsC 7ygqC 7vtcS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 32839.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Gene: orf1ab / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 #2: Chemical | #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: 2.92 Å3/Da / Density % sol: 57.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium formate, 0.1M BICINE pH8.5 20% PEG5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→44.86 Å / Num. obs: 53633 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 27.3489656876 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.99→2.09 Å / Rmerge(I) obs: 0.926 / Num. unique obs: 53633 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VTC Resolution: 1.99→44.86 Å / SU ML: 0.273274265818 / Cross valid method: FREE R-VALUE / σ(F): 1.34360112772 / Phase error: 24.1207739763 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9946313228 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→44.86 Å
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Refine LS restraints |
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LS refinement shell |
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