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- PDB-5fhj: Extensive amphimorphism in DNA: Three stable conformations for th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fhj | ||||||||||||||||||||
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Title | Extensive amphimorphism in DNA: Three stable conformations for the decadeoxynucleotide d(GCATGCATGC) | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / amphimorphism / double-folded / B-type helix | Function / homology | : / DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Thirugnanasambandam, A. / Karthik, S. / Gautham, N. | ![]() ![]() Title: DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC). Authors: Thirugnanasambandam, A. / Karthik, S. / Artheswari, G. / Gautham, N. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36 KB | Display | ![]() |
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PDB format | ![]() | 24.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 396 KB | Display | ![]() |
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Full document | ![]() | 396 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 3045.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-CO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.2 % / Description: tetragonal prisms |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1mM DNA, 50 mM sodium cacodylate buffer, 10 mM cobalt chloride, 0.5 mM spermine, 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2013 / Details: Bent collimating mirror | |||||||||
Radiation | Monochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.68→29.44 Å / Num. obs: 15873 / % possible obs: 99.9 % / Redundancy: 28 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.8 | |||||||||
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 25.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.8 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→29.437 Å
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Refine LS restraints |
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LS refinement shell |
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