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Yorodumi- PDB-4ktg: Crystal structure of double-helical GGC-repetitive RNA 19mer comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ktg | ||||||
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Title | Crystal structure of double-helical GGC-repetitive RNA 19mer complexed with RSS p19 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA silencing suppression / trinucleotide repeats / 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: 1.92 Å | ||||||
Authors | Tamjar, J. / Katorcha, E. / Popov, A.N. / Malinina, L. | ||||||
Citation | Journal: To be published Title: Structural insights into CNG-repetitive RNAs associated with human Trinucleotide Repeat Expansion Diseases (TREDs) Authors: Tamjar, J. / Katorcha, E. / Cabo, A. / Delgado, S. / 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 | 4ktg.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ktg.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ktg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ktg_validation.pdf.gz | 472.7 KB | Display | wwPDB validaton report |
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Full document | 4ktg_full_validation.pdf.gz | 477.1 KB | Display | |
Data in XML | 4ktg_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 4ktg_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/4ktg ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4ktg | HTTPS FTP |
-Related 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 / Refine code: 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.: 1 / Fragment: UNP residues 27-158 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 | ||||
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#2: RNA chain | Mass: 6233.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: siRNA pGC(GGC)5GC #3: Chemical | #4: 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: 2.19 Å3/Da / Density % sol: 43.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.8 M ammonium sulfate, 0.1 M MES, pH 6, VAPOR DIFFUSION, 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: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.92→40 Å / Num. obs: 18255 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.089 / Χ2: 1.118 / Net I/σ(I): 14.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2545 / WRfactor Rwork: 0.2113 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8376 / SU B: 4.101 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1722 / SU Rfree: 0.1559 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 108.98 Å2 / Biso mean: 51.363 Å2 / Biso min: 23.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5
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LS refinement shell | Resolution: 1.92→1.967 Å / Total num. of bins used: 20
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