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- PDB-1v3p: Crystal structure of d(GCGAGAGC): the DNA octaplex structure with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v3p | ||||||
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Title | Crystal structure of d(GCGAGAGC): the DNA octaplex structure with I-motif of G-quartet | ||||||
![]() | 5'-D(* | ||||||
![]() | DNA / octaplex / quadruplex / G-quartet / I-motif / I-motif of G-quartet / base-intercalated duplex / base-intercalated motif / sheared G:A pair / deoxyribonucleic acid / X-ray analysis | ||||||
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 | ![]() | 21.9 KB | Display | ![]() |
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PDB format | ![]() | 13.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 327.1 KB | Display | ![]() |
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Full document | ![]() | 327.6 KB | Display | |
Data in XML | ![]() | 1.4 KB | Display | |
Data in CIF | ![]() | 2.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v3nSC ![]() 1v3oC S: Starting model for refinement C: citing same article ( |
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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 an octaplex generated from the duplex in the asymmetric unit by the operations: (x, y, z), (1-x, 1-y, z), (x,1-y,2-z) and (1-x, y, 2-z). |
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Components
#1: DNA chain | Mass: 2602.540 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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#2: Chemical | |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.7 % | ||||||||||||||||||||||||||||||||||||
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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: Nov 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 2014 / Num. obs: 1980 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.4 / Num. unique all: 199 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V3N Resolution: 2.3→9 Å / σ(F): 3 Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
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Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.29 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å
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