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Yorodumi- PDB-208d: HIGH-RESOLUTION STRUCTURE OF A DNA HELIX FORMING (C.G)*G BASE TRIPLETS -
+Open data
-Basic information
Entry | Database: PDB / ID: 208d | ||||||||||||||||||
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Title | HIGH-RESOLUTION STRUCTURE OF A DNA HELIX FORMING (C.G)*G BASE TRIPLETS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / BASE TRIPLET | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | Authors | Van Meervelt, L. / Vlieghe, D. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O. | Citation | Journal: Nature / Year: 1995 Title: High-resolution structure of a DNA helix forming (C.G)*G base triplets. Authors: Van Meervelt, L. / Vlieghe, D. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Formation of (C.G)*G Triplets in a B-DNA Duplex with Overhanging Bases Authors: Vlieghe, D. / Van Meervelt, L. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 208d.cif.gz | 21.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb208d.ent.gz | 13.3 KB | Display | PDB format |
PDBx/mmJSON format | 208d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 208d_validation.pdf.gz | 323 KB | Display | wwPDB validaton report |
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Full document | 208d_full_validation.pdf.gz | 326.2 KB | Display | |
Data in XML | 208d_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 208d_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/08/208d ftp://data.pdbj.org/pub/pdb/validation_reports/08/208d | 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
#1: DNA chain | Mass: 2755.823 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #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: 1.94 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 289.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 6 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 2, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. all: 22402 / Num. obs: 2824 / % possible obs: 87 % / Observed criterion σ(I): 3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.036 |
Reflection | *PLUS Highest resolution: 2.05 Å / % possible obs: 87 % / Observed criterion σ(I): 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BDL001 Resolution: 2.05→8 Å / σ(F): 4
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.05→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 8 Å / σ(F): 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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