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Yorodumi- PDB-5y6j: Structure of Tomato spotted wilt virus nucleocapsid protein with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y6j | ||||||
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Title | Structure of Tomato spotted wilt virus nucleocapsid protein with alternative oligomerization state | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / TSWV / nucleocapsid protein / NP / oligomerization | ||||||
Function / homology | Tospovirus nucleocapsid protein / Tospovirus nucleocapsid protein / viral nucleocapsid / RNA binding / Nucleoprotein Function and homology information | ||||||
Biological species | Tomato spotted wilt virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.811 Å | ||||||
Authors | Guo, Y. / Dong, S. / Lou, Z. | ||||||
Citation | Journal: J. Virol. / Year: 2017 Title: Distinct Mechanism for the Formation of the Ribonucleoprotein Complex of Tomato Spotted Wilt Virus. Authors: Guo, Y. / Liu, B. / Ding, Z. / Li, G. / Liu, M. / Zhu, D. / Sun, Y. / Dong, S. / Lou, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y6j.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y6j.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 5y6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y6j_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 5y6j_full_validation.pdf.gz | 461.1 KB | Display | |
Data in XML | 5y6j_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5y6j_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/5y6j ftp://data.pdbj.org/pub/pdb/validation_reports/y6/5y6j | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28841.566 Da / Num. of mol.: 3 / Mutation: R94A, R95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tomato spotted wilt virus / Production host: Escherichia coli (E. coli) / References: UniProt: H6UMW9 #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: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.05 M BIS-TRIS pH 7.0; 22% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH); 20% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 20050 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 4.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.811→49.492 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.65 / 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: 2.811→49.492 Å
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Refine LS restraints |
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LS refinement shell |
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