+Open data
-Basic information
Entry | Database: PDB / ID: 7e6m | ||||||
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Title | Crystal structure of Human coronavirus NL63 3C-like protease | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / HCoV-NL63 3C-like protease | ||||||
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 / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm ...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 / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human coronavirus NL63 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83445027837 Å | ||||||
Authors | Gao, H.X. / Zhang, Y.T. / Zhong, F.L. / Zhou, X.L. / Li, J. / Zhang, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Crystal structures of human coronavirus NL63 main protease at different pH values Authors: Gao, H. / Zhang, Y. / Jiang, H. / Hu, X. / Zhang, Y. / Zhou, X. / Zhong, F. / Lin, C. / Li, J. / Luo, 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 | 7e6m.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e6m.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 7e6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e6m_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 7e6m_full_validation.pdf.gz | 439.7 KB | Display | |
Data in XML | 7e6m_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 7e6m_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/7e6m ftp://data.pdbj.org/pub/pdb/validation_reports/e6/7e6m | HTTPS FTP |
-Related structure data
Related structure data | 7e6lC 7e6nC 7e6rC 3tloS S: Starting model for refinement C: citing same article (ref.) |
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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: 32763.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus NL63 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P0C6U6, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Water | ChemComp-HOH / | |
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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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2M Potassion formate, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→60.1162394835 Å / Num. obs: 52288 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 26.9907173262 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.83→1.88 Å / Rmerge(I) obs: 0.285 / Num. unique obs: 3849 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TLO Resolution: 1.83445027837→60.1162394835 Å / SU ML: 0.177540220788 / Cross valid method: NONE / σ(F): 1.37734988252 / Phase error: 23.990064591 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: 34.9371938357 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83445027837→60.1162394835 Å
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Refine LS restraints |
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LS refinement shell |
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