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Open data
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Basic information
Entry | Database: PDB / ID: 2fza | ||||||||||||||||||
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Title | Crystal structure of d(GCGGGAGC): the base-intercalated duplex | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / base-intercalated duplex / base-intercalated motif / sheared G:A pair / DNA hexaplex / deoxyribonucleic acid | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() ![]() Kondo, J. / Ciengshin, T. / Juan, E.C.M. / Mitomi, K. / Takenaka, A. | ![]() ![]() Title: Crystal structure of d(gcGXGAgc) with X=G: a mutation at X is possible to occur in a base-intercalated duplex for multiplex formation Authors: Kondo, J. / Ciengshin, T. / Juan, E.C.M. / Sato, Y. / Mitomi, K. / Shimizu, S. / Takenaka, A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 19.1 KB | Display | ![]() |
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PDB format | ![]() | 12 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 320.7 KB | Display | ![]() |
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Full document | ![]() | 322.2 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 2.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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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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Details | The biological assembly is a DNA hexaplex generate from the three DNA duplex (X,Y,Z),(-Y,X-Y,Z) and (-X+Y,-X,Z). |
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Components
#1: DNA chain | Mass: 2571.538 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized #2: Chemical | #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.96 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50mM sodium cacodylate, 10mM spermine tetrahydrochloride, 20mM calcium chloride, 100mM sodium chloride, 10%(v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MAC Science DIP-2040 / Detector: CCD / Date: Jun 3, 2003 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ROTATED-INCLINED SI(111) DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.605→31.496 Å / Num. obs: 525 / % possible obs: 93.6 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 3.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D52, 57-64 (1996).
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Solvent computation | Bsol: 300 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→10 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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