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- PDB-1v3n: Crystal structure of d(GCGAGAGC): the DNA quadruplex structure sp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v3n | ||||||||||||||||||
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Title | Crystal structure of d(GCGAGAGC): the DNA quadruplex structure split from the octaplex | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / octaplex / quadruplex / G-duet / base-intercalated duplex / base-intercalated motif / sheared G:A pair / deoxyribonucleic acid / X-ray analysis / crystal struture | Function / homology | : / DNA | ![]() Method | ![]() ![]() ![]() ![]() Kondo, J. / Umeda, S. / Sunami, T. / Takenaka, A. | ![]() ![]() Title: Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats Authors: Kondo, J. / Adachi, W. / Umeda, S. / Sunami, T. / 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 | ![]() | 21.1 KB | Display | ![]() |
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PDB format | ![]() | 13.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 325.3 KB | Display | ![]() |
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Full document | ![]() | 325.3 KB | Display | |
Data in XML | ![]() | 1.4 KB | Display | |
Data in CIF | ![]() | 2.5 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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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 quadruplex generated from the duplex in the asymmetric unit by the operations: x, y, z and -x, y, -z. |
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Components
#1: DNA chain | Mass: 2555.539 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-K / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2-methyl-2,4-pentanediol, spermine tetrahydrochloride, sodium chloride, potassium chloride, sodium cacodylate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2001 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→32 Å / Num. all: 4553 / Num. obs: 4543 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 7.7 | ||||||||||||
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.6 / Num. unique all: 583 / Rsym value: 0.265 / % possible all: 88.6 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
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Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.32 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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