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Yorodumi- PDB-1jb8: The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jb8 | ||||||
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Title | The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation | ||||||
Components |
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Keywords | DNA/RNA / DNA/DNA intercalation / RNA/DNA hybrid / RNA/DNA polypurine tract / DNA-RNA COMPLEX | ||||||
Function / homology | DNA / RNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Han, G.W. / Kopka, M.L. / Langs, D. / Dickerson, R.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Crystal structure of an RNADNA hybrid reveals intermolecular intercalation: Dimer formation by base-pair swapping Authors: Han, G.W. / Kopka, M.L. / Langs, D. / Sawaya, M.R. / Dickerson, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jb8.cif.gz | 21.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jb8.ent.gz | 13.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jb8 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jb8 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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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: 3255.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA/DNA hybrid of PPT sequence of HIV |
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#2: DNA chain | Mass: 2991.961 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthesized by the solid-phase phosphoramidate method on an Eppendorf ECOSYN D300 Synthesizer. |
#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: 2.38 Å3/Da / Density % sol: 48.24 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: MPD, magnesium acetate, spermidine, Na cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 5.8 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→10 Å / Num. all: 18386 / Num. obs: 2814 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.053 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.78 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: P2(1)2(1)2(1) structure of the same sequence of RNA/DNA hybrid Resolution: 2.38→10 Å / Isotropic thermal model: Isotropic / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.38→10 Å
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Refine LS restraints |
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LS refinement shell |
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