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Yorodumi- PDB-100d: CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 100d | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING | ||||||||||||||||||
Components | DNA/RNA (5'-R(*Keywords | DNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX | Function / homology | SPERMINE / DNA/RNA hybrid | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | Authors | Ban, C. / Ramakrishnan, B. / Sundaralingam, M. | Citation | Journal: Nucleic Acids Res. / Year: 1994 | Title: Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing. Authors: Ban, C. / Ramakrishnan, B. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 100d.cif.gz | 23 KB | Display | PDBx/mmCIF format |
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PDB format | pdb100d.ent.gz | 14.2 KB | Display | PDB format |
PDBx/mmJSON format | 100d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/00/100d ftp://data.pdbj.org/pub/pdb/validation_reports/00/100d | 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/RNA hybrid | Mass: 3078.980 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-SPM / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.89 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS 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: MACSCIENCE |
Detector | Type: SIEMENS-NICOLET / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.9 Å / Num. all: 9305 / Num. obs: 2365 |
Reflection | *PLUS Highest resolution: 1.9 Å / Rmerge(I) obs: 0.058 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.9→8 Å / σ(F): 1 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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