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Yorodumi- PDB-4jnx: Crystal structure of RNA silencing suppressor p19 complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jnx | ||||||
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Title | Crystal structure of RNA silencing suppressor p19 complexed with double-helical RNA 20mer pG(CUG)6C | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA silencing suppression / trinucleotide repeats / protein-RNA complex / dimer / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information virion component / virus-mediated perturbation of host defense response / RNA binding Similarity search - Function | ||||||
Biological species | Tomato bushy stunt virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Katorcha, E. / Popov, A.N. / Malinina, L. | ||||||
Citation | Journal: To be Published Title: Procrustean bed of RNA silencing suppression Authors: Katorcha, E. / Tamjar, J. / Popov, A.N. / Malinina, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jnx.cif.gz | 189.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jnx.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 4jnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jnx_validation.pdf.gz | 481.2 KB | Display | wwPDB validaton report |
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Full document | 4jnx_full_validation.pdf.gz | 495.6 KB | Display | |
Data in XML | 4jnx_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 4jnx_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/4jnx ftp://data.pdbj.org/pub/pdb/validation_reports/jn/4jnx | HTTPS FTP |
-Related structure data
Related structure data | 4j39C 4jgnC 4jk0C 1r9fS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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Details | THE BIOLOGICAL UNIT IS A P19 HOMODIMER BOUND TO DOUBLE-STRANDED RNA. |
-Components
#1: Protein | Mass: 14513.208 Da / Num. of mol.: 2 / Fragment: UNP residues 27-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tomato bushy stunt virus / Gene: ORF4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P69517 #2: RNA chain | Mass: 6344.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: siRNA pG(CUG)6C #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 291 K / pH: 6 Details: 1.6 M ammonium sulfate, pH 8, potassium chloride, MES/NaOH, trace magnesium, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98035 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98035 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.95→20 Å / Num. all: 32588 / Num. obs: 32285 / % possible obs: 98.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.072 / Χ2: 1.051 / Net I/σ(I): 11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R9F Resolution: 1.95→19.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2369 / WRfactor Rwork: 0.2006 / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.8381 / SU B: 6.67 / SU ML: 0.109 / SU R Cruickshank DPI: 0.0421 / SU Rfree: 0.0352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.1 Å2 / Biso mean: 36.6245 Å2 / Biso min: 21.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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