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Yorodumi- PDB-333d: THE CRYSTAL STRUCTURE OF AN RNA OLIGOMER INCORPORATING TANDEM ADE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 333d | |||||||||||||||||||||
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Title | THE CRYSTAL STRUCTURE OF AN RNA OLIGOMER INCORPORATING TANDEM ADENOSINE-INOSINE MISMATCHES | |||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / A-RNA / DOUBLE HELIX / INTERNAL LOOP / MISMATCHED | Function / homology | RNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | Authors | Carter, R.J. / Baeyens, K.J. / SantaLucia Jr., J. / Turner, D.H. / Holbrook, S.R. | Citation | Journal: Nucleic Acids Res. / Year: 1997 | Title: The crystal structure of an RNA oligomer incorporating tandem adenosine-inosine mismatches. Authors: Carter, R.J. / Baeyens, K.J. / SantaLucia, J. / Turner, D.H. / Holbrook, S.R. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 333d.cif.gz | 13.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb333d.ent.gz | 7.5 KB | Display | PDB format |
PDBx/mmJSON format | 333d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 333d_validation.pdf.gz | 378.4 KB | Display | wwPDB validaton report |
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Full document | 333d_full_validation.pdf.gz | 378.9 KB | Display | |
Data in XML | 333d_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 333d_validation.cif.gz | 2.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/33/333d ftp://data.pdbj.org/pub/pdb/validation_reports/33/333d | 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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-Components
#1: RNA chain | Mass: 2565.602 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-CA / |
#3: 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: 49.7 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 21, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.52→12 Å / Num. all: 5952 / Num. obs: 1014 / % possible obs: 91.8 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.079 |
Reflection | *PLUS Highest resolution: 2.52 Å / Lowest resolution: 25 Å / % possible obs: 91.8 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Num. measured all: 5952 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CGC:GCG FRAGMENT OF ARL048 Resolution: 2.52→12 Å / σ(F): 3 Details: NUCLEIC ACID RNA-DNA PARAMETER FILE: G. PARKINSON,ET AL. (1996) ACTA CRYST. D52, 57-64
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.52→12 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: TOPOL_BERMAN.RNA / Topol file: PARAM_BERMAN.RNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.52 Å / Lowest resolution: 12 Å / σ(F): 3 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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