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Yorodumi- PDB-3szx: Crystal Structure of the Triplet Repeat in Myotonic Dystrophy Rev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3szx | ||||||||||||||||||
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Title | Crystal Structure of the Triplet Repeat in Myotonic Dystrophy Reveals Heterogeneous 1x1 Nucleotide UU Internal Loop Conformations | ||||||||||||||||||
Components | RNA (5'-R(P*Keywords | RNA / CUG Repeat RNA | Function / homology | RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å | Authors | Kumar, A. / Park, H. / Pengfei, F. / Parkesh, R. / Guo, M. / Nettles, K.W. / Disney, M.D. | Citation | Journal: Biochemistry / Year: 2011 | Title: Crystal Structure of the Triplet Repeat in Myotonic Dystrophy Reveals Heterogeneous 1x1 Nucleotide UU Internal Loop Conformations Authors: Kumar, A. / Park, H. / Fang, P. / Parkesh, R. / 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 | 3szx.cif.gz | 41.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3szx.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 3szx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/3szx ftp://data.pdbj.org/pub/pdb/validation_reports/sz/3szx | HTTPS FTP |
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-Related structure data
-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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-Components
#1: RNA chain | Mass: 6039.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Polyribonucleotide #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: 1.94 Å3/Da / Density % sol: 36.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10 mM magnesium sulfate, 50 mM sodium cacodylate, 1.8 M lithium sulfate , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97855 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 9, 2011 / Details: Rh coated flat mirror, toroidal focusing mirror | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97855 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→33.41 Å / Num. all: 4571 / Num. obs: 4571 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.204→33.41 Å / SU ML: 0.32 / σ(F): 0.13 / Phase error: 35.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.097 Å2 / ksol: 0.462 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.204→33.41 Å
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Refine LS restraints |
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LS refinement shell |
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