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Yorodumi- PDB-7dra: Crystal structure of MERS-CoV 3CL protease (C148A) in spacegroup ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dra | ||||||
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Title | Crystal structure of MERS-CoV 3CL protease (C148A) in spacegroup P212121,pH 9.0 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / MERS-CoV / 3CL protease | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / methyltransferase activity / 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 / cysteine-type deubiquitinase activity ...host cell membrane / viral genome replication / methyltransferase activity / 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 / cysteine-type deubiquitinase activity / 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 / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Middle East respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78409685655 Å | ||||||
Authors | Zhang, Y.T. / Zhou, X.L. / Li, J. / Zhang, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of MERS-CoV 3CL protease (C148A) in spacegroup P212121,pH 9.0 Authors: Zhang, Y.T. / Zhou, X.L. / 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 | 7dra.cif.gz | 139.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dra.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 7dra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dra_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 7dra_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 7dra_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 7dra_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/7dra ftp://data.pdbj.org/pub/pdb/validation_reports/dr/7dra | HTTPS FTP |
-Related structure data
Related structure data | 7dr8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33322.109 Da / Num. of mol.: 2 / Mutation: C148A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: T2B9I2, SARS coronavirus main proteinase |
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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: 2.76 Å3/Da / Density % sol: 55.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 4% 2-propanol, 0.1M BIS-TRIS Propane pH9.0 20% PEG5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97913 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97913 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→51.76 Å / Num. obs: 18515 / % possible obs: 96.7 % / Redundancy: 13.2 % / Biso Wilson estimate: 58.3822186756 Å2 / Rpim(I) all: 0.048 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.78→2.93 Å / Num. unique obs: 2739 / Rpim(I) all: 0.321 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DR8 Resolution: 2.78409685655→47.2425 Å / SU ML: 0.350511238448 / Cross valid method: NONE / σ(F): 1.34235233213 / Phase error: 27.0389175882 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: 50.9556542432 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.78409685655→47.2425 Å
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Refine LS restraints |
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LS refinement shell |
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