+Open data
-Basic information
Entry | Database: PDB / ID: 6ntv | |||||||||
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Title | SFTSV L endonuclease domain | |||||||||
Components | RNA polymerase | |||||||||
Keywords | TRANSCRIPTION / SFTSV / RDRP / Cap-snatching | |||||||||
Function / homology | Function and homology information RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription Similarity search - Function | |||||||||
Biological species | Severe fever with thrombocytopenia virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | |||||||||
Authors | Wang, W. / Amarasinghe, G.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell Rep / Year: 2020 Title: The Cap-Snatching SFTSV Endonuclease Domain Is an Antiviral Target. Authors: Wang, W. / Shin, W.J. / Zhang, B. / Choi, Y. / Yoo, J.S. / Zimmerman, M.I. / Frederick, T.E. / Bowman, G.R. / Gross, M.L. / Leung, D.W. / Jung, J.U. / Amarasinghe, G.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ntv.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ntv.ent.gz | 115.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ntv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/6ntv ftp://data.pdbj.org/pub/pdb/validation_reports/nt/6ntv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 25167.273 Da / Num. of mol.: 3 / Fragment: Endonuclease domain, residues 1-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe fever with thrombocytopenia virus Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: A0A2U8JAJ4, UniProt: A0A125SZQ2*PLUS #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: 2.63 Å3/Da / Density % sol: 53.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 10% PEG 20K, 0.1 M Na Citrate pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.09 Å / Num. obs: 32031 / % possible obs: 98.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 36.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1225 / Rpim(I) all: 0.04736 / Rrim(I) all: 0.1316 / Net I/σ(I): 14.02 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 8 % / Rmerge(I) obs: 0.7682 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2936 / CC1/2: 0.798 / Rpim(I) all: 0.2938 / Rrim(I) all: 0.8235 / % possible all: 93.83 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→47.09 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.09 Å
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Refine LS restraints |
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LS refinement shell |
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