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Yorodumi- PDB-3sj2: A Crystal Structure of a Model of the Repeating r(CGG) Transcript... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sj2 | ||||||
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Title | A Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in Fragile X Syndrome | ||||||
Components |
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Keywords | RNA / Trinucleotide disorders / Fragile X-syndrome | ||||||
Function / homology | ACETATE ION / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Kumar, A. / Pengfei, F. / Park, H. / Nettles, K. / Guo, M. / Disney, M.D. | ||||||
Citation | Journal: Chembiochem / Year: 2011 Title: A Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in Fragile X Syndrome. Authors: Kumar, A. / Fang, P. / Park, H. / Guo, M. / Nettles, K.W. / Disney, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sj2.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sj2.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 3sj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sj2_validation.pdf.gz | 394.6 KB | Display | wwPDB validaton report |
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Full document | 3sj2_full_validation.pdf.gz | 394.6 KB | Display | |
Data in XML | 3sj2_validation.xml.gz | 7 KB | Display | |
Data in CIF | 3sj2_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/3sj2 ftp://data.pdbj.org/pub/pdb/validation_reports/sj/3sj2 | 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: RNA chain | Mass: 6156.689 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: RNA chain | Mass: 5544.357 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#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: 2.52 Å3/Da / Density % sol: 51.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Potassium Chloride, 0.01 M Magnesium Chloride, 0.05 M Tris.HCl, 30%(v/v)PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 6, 2011 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.36→27.56 Å / Num. all: 25014 / Num. obs: 24111 / % possible obs: 98.64 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.38 Å2 | ||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→27.543 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 18.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.225 Å2 / ksol: 0.411 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.36→27.543 Å
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Refine LS restraints |
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LS refinement shell |
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