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Yorodumi- PDB-1r9f: Crystal structure of p19 complexed with 19-bp small interfering RNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r9f | ||||||
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Title | Crystal structure of p19 complexed with 19-bp small interfering RNA | ||||||
Components |
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Keywords | Viral protein/RNA / Protein-RNA complex / Dimer / double helix / Viral protein-RNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Tomato bushy stunt virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Ye, K. / Malinina, L. / Patel, D.J. | ||||||
Citation | Journal: Nature / Year: 2003 Title: Recognition of small interfering RNA by a viral suppressor of RNA Authors: Ye, K. / Malinina, L. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r9f.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r9f.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 1r9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r9f_validation.pdf.gz | 463.6 KB | Display | wwPDB validaton report |
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Full document | 1r9f_full_validation.pdf.gz | 465.1 KB | Display | |
Data in XML | 1r9f_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1r9f_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/1r9f ftp://data.pdbj.org/pub/pdb/validation_reports/r9/1r9f | 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 on special symmetry positions |
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Details | The biological assemble is a p19 dimer in complex with one siRNA duplex generated from the protein monomer and half RNA (19-bp duplex in half occupancy) in the asymmetric unit by the operation: Y+2/3,X-2/3,-Z+1/3. The 2-fold symmetry operation generates another overlapping half RNA in opposite orientation, compensating the lack of symmetry in RNA duplex itself. |
-Components
#1: RNA chain | Mass: 6690.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-OH and 3'-OH | ||
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#2: RNA chain | Mass: 6666.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-OH and 3'-OH | ||
#3: Protein | Mass: 15751.966 Da / Num. of mol.: 1 / Fragment: Residues 27-158 / Mutation: L144M, L147M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tomato bushy stunt virus / Genus: Tombusvirus / Gene: p19 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11690 | ||
#4: Chemical | #5: 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: 2.05 Å3/Da / Density % sol: 39.86 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: ammonium sulfate, potassium chloride, HEPES-NaOH, dithiothreitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9791,0.9789,0.9562 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 18, 2003 | ||||||||||||
Radiation | Monochromator: DIAMOND (111) DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→50 Å / Num. obs: 39408 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 44.8 | ||||||||||||
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2 / % possible all: 93.2 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 50 Å / Num. obs: 20413 / % possible obs: 99.11 % / Num. measured all: 194486 / Rmerge(I) obs: 0.06 | ||||||||||||
Reflection shell | *PLUS % possible obs: 93.2 % / Num. unique obs: 1872 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→14.86 Å / Rfactor Rfree error: 0.005 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.85 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→14.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.214 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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