+Open data
-Basic information
Entry | Database: PDB / ID: 7y5m | ||||||||||||||||||||||||
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Title | The OTU domain of Tacheng Tick Virus 1 | ||||||||||||||||||||||||
Components | RNA-directed RNA polymerase | ||||||||||||||||||||||||
Keywords | VIRAL PROTEIN | ||||||||||||||||||||||||
Function / homology | Function and homology information RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Tacheng Tick Virus 1 | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||||||||||||||||||||
Authors | Li, Z. / Wang, W.J. / Xiao, Y.S. / Sun, L.T. | ||||||||||||||||||||||||
Funding support | 7items
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Citation | Journal: To Be Published Title: The OTU domain of Tacheng Tick Virus 1 Authors: Li, Z. / Wang, W.J. / Xiao, Y.S. / Sun, L.T. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y5m.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y5m.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 7y5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y5m_validation.pdf.gz | 411.5 KB | Display | wwPDB validaton report |
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Full document | 7y5m_full_validation.pdf.gz | 411.6 KB | Display | |
Data in XML | 7y5m_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 7y5m_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/7y5m ftp://data.pdbj.org/pub/pdb/validation_reports/y5/7y5m | HTTPS FTP |
-Related structure data
Related structure data | 3phuS 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
#1: Protein | Mass: 19229.670 Da / Num. of mol.: 1 / Fragment: OTU domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tacheng Tick Virus 1 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0B5KXW6, RNA-directed RNA polymerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 4000,Lithium sulfate monohydrate,MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 27019 / % possible obs: 99.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.54 Å2 / CC1/2: 0.976 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Num. unique obs: 2598 / CC1/2: 0.813 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PHU Resolution: 1.5→18.75 Å / SU ML: 0.1667 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9014 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→18.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.24717073409 Å / Origin y: 12.8360933563 Å / Origin z: -15.7325286471 Å
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Refinement TLS group | Selection details: all |