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- PDB-2dqq: Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-am... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dqq | ||||||
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Title | Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine | ||||||
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![]() | DNA-RNA HYBRID / modified nucleotide / 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine / A-form RNA:DNA hybrid duplex | ||||||
Function / homology | (6-AMINOHEXYL)CARBAMIC ACID / DNA / RNA![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Juan, E.C.M. / Kondo, J. / Ito, T. / Ueno, Y. / Matsuda, A. / Takenaka, A. | ||||||
![]() | ![]() Title: Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules Authors: Juan, E.C.M. / Kondo, J. / Kurihara, T. / Ito, T. / Ueno, Y. / Matsuda, A. / 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 | ![]() | 22.2 KB | Display | ![]() |
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PDB format | ![]() | 14.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2dp7C ![]() 2dpbC ![]() 2dpcC ![]() 2dqoC ![]() 2dqpC ![]() 479dS 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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Unit cell |
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Components
#1: DNA chain | Mass: 2664.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: RNA chain | Mass: 2981.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.4 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25mM sodium cacodylate, pH 7.0, 5mM spermine tetrahydrochloride, 25mM lithium chloride and 7.5% MPD, equilibrated against 35% (v/v) MPD, 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: Dec 12, 2003 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.488 Å / Num. obs: 4587 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 479D Resolution: 2→10 Å / σ(F): 3 / Stereochemistry target values: Maximum Likelihood Details: The value of the item "Number reflections (observed) is the number of reflections used in refinement. This value excludes the reflections that have sigma(F) less than 3.0.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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