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Yorodumi- PDB-421d: 5'-D(*TP*TP*CP*TP*TP*(BRO)CP*TP*TP*C)-3', 5'-R(*GP*AP*AP*GP*AP*AP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 421d | ||||||
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Title | 5'-D(*TP*TP*CP*TP*TP*(BRO)CP*TP*TP*C)-3', 5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3' | ||||||
Components |
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Keywords | DNA-RNA HYBRID / DNA:RNA HYBRID DUPLEX / DNA-RNA COMPLEX | ||||||
Function / homology | DNA / RNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Xiong, Y. / Sundaralingam, M. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Crystal structure and conformation of a DNA-RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)-r(GAAGAAGAA). Authors: Xiong, Y. / Sundaralingam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 421d.cif.gz | 22.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb421d.ent.gz | 15.2 KB | Display | PDB format |
PDBx/mmJSON format | 421d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/21/421d ftp://data.pdbj.org/pub/pdb/validation_reports/21/421d | HTTPS FTP |
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-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: DNA chain | Mass: 2726.641 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 2965.895 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#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: 2.51 Å3/Da / Density % sol: 51.06 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 263 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 15, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24.04 Å / Num. obs: 4948 / % possible obs: 89.3 % / Observed criterion σ(I): 1 / Redundancy: 3.46 % / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.355 / % possible all: 77.2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 24.04 Å / Observed criterion σ(I): 1 / Redundancy: 3.46 % |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: DNA-RNA.PARAM / Topol file: DNA-RNA.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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