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Yorodumi- PDB-4jrt: Crystal structure of an A-form RNA duplex containing three GU bas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jrt | ||||||
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Title | Crystal structure of an A-form RNA duplex containing three GU base pairs | ||||||
Components |
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Keywords | RNA / A-form RNA / ribose-zipper motif / GU base pair | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Kondo, J. / Dock-Bregeon, A.C. / Willkomm, D.K. / Hartmann, R.K. / Westhof, E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet Authors: Kondo, J. / Dock-Bregeon, A.C. / Willkomm, D.K. / Hartmann, R.K. / Westhof, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jrt.cif.gz | 23.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jrt.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jrt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/4jrt ftp://data.pdbj.org/pub/pdb/validation_reports/jr/4jrt | HTTPS FTP |
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-Related structure data
Related structure data | 353dS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 3979.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription |
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#2: RNA chain | Mass: 3723.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription |
#3: Water | ChemComp-HOH / |
Nonpolymer details | HOH (A 111) AND HOH (A 112) ARE CLOSED TO SYMMETRY-RELATED RNA MOLECULE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.92 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion / pH: 7 Details: Sodium Cacodylate, Lithium acetate, PEG3350, pH 7.0, vapor diffusion, temperature 310K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å |
Detector | Detector: CCD / Date: Jul 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20.7 Å / Num. obs: 2330 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 353D Resolution: 2.6→20.7 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 41.7378 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.1 Å2 / Biso mean: 76.1548 Å2 / Biso min: 41.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20.7 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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