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Yorodumi- PDB-247d: CRYSTAL STRUCTURES OF AN A-FORM DUPLEX WITH SINGLE-ADENOSINE BULG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 247d | |||||||||||||||||||||
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Title | CRYSTAL STRUCTURES OF AN A-FORM DUPLEX WITH SINGLE-ADENOSINE BULGES AND A CONFORMATIONAL BASIS FOR SITE SPECIFIC RNA SELF-CLEAVAGE | |||||||||||||||||||||
Components | DNA/RNA (5'-R(*Keywords | DNA/RNA / A-DNA/RNA / DOUBLE HELIX / BULGES / DNA-RNA complex | Function / homology | DNA/RNA hybrid / DNA/RNA hybrid (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | Authors | Portmann, S. / Grimm, S. / Workman, C. / Usman, N. / Egli, M. | Citation | Journal: Chem.Biol. / Year: 1996 | Title: Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage. Authors: Portmann, S. / Grimm, S. / Workman, C. / Usman, N. / Egli, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 247d.cif.gz | 15.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb247d.ent.gz | 9.2 KB | Display | PDB format |
PDBx/mmJSON format | 247d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/47/247d ftp://data.pdbj.org/pub/pdb/validation_reports/47/247d | 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
#1: DNA/RNA hybrid | Mass: 3454.211 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.29 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7.4 / Details: pH 7.40, VAPOR DIFFUSION | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.9 / Method: unknown | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM TEMPERATURE |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 13, 1994 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→23.57 Å / Num. all: 18394 / Num. obs: 1035 / % possible obs: 82 % / Rmerge(I) obs: 0.075 |
Reflection | *PLUS % possible obs: 82 % |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 3 Å / % possible obs: 50 % |
-Processing
Software |
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Refinement | Resolution: 2.8→10 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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