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Yorodumi- PDB-241d: EXTENSION OF THE FOUR-STRANDED INTERCALATED CYTOSINE MOTIF BY ADE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 241d | ||||||||||||||||||
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Title | EXTENSION OF THE FOUR-STRANDED INTERCALATED CYTOSINE MOTIF BY ADENINE.ADENINE BASE PAIRING IN THE CRYSTAL STRUCTURE OF D(CCCAAT) | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / U-DNA / QUADRUPLE HELIX / ARALLEL-STRANDED TETRAPLEX / BASE INTERCALATED / MISMATCHED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.85 Å | Authors | Berger, I. / Kang, C. / Fredian, A. / Ratliff, R. / Moyzis, R. / Rich, A. | Citation | Journal: Nat.Struct.Biol. / Year: 1995 | Title: Extension of the four-stranded intercalated cytosine motif by adenine.adenine base pairing in the crystal structure of d(CCCAAT). Authors: Berger, I. / Kang, C. / Fredian, A. / Ratliff, R. / Moyzis, R. / Rich, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 241d.cif.gz | 15.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb241d.ent.gz | 10.2 KB | Display | PDB format |
PDBx/mmJSON format | 241d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 241d_validation.pdf.gz | 311.6 KB | Display | wwPDB validaton report |
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Full document | 241d_full_validation.pdf.gz | 320.8 KB | Display | |
Data in XML | 241d_validation.xml.gz | 2.4 KB | Display | |
Data in CIF | 241d_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/41/241d ftp://data.pdbj.org/pub/pdb/validation_reports/41/241d | 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: DNA chain | Mass: 1753.194 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.03 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.85→10 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |