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- PDB-2dpb: Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dpb | ||||||||||||||||||
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Title | Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine | ||||||||||||||||||
![]() | DNA (5'-D(*![]() ![]() ![]() Function / homology | (6-AMINOHEXYL)CARBAMIC ACID / : / | ![]() ![]() Method | ![]() ![]() ![]() ![]() Juan, E.C.M. / Kondo, J. / Kurihara, T. / 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 | ![]() | 30 KB | Display | ![]() |
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PDB format | ![]() | 19.4 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 ![]() 2dpcC ![]() 2dqoC ![]() 2dqpC ![]() 2dqqC ![]() 355dS C: citing same article ( S: Starting model for refinement |
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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: 3649.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This DNA dodecamer is a synthetic construct. #2: Chemical | #3: Chemical | ChemComp-K / | #4: 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: 44.23 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20mM sodium cacodylate, pH 6.0, 40mM potassium chloride, 6mM spermine tetrahydrochloride and 5%(v/v) 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: Jan 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→19.463 Å / Num. obs: 11296 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 355D Resolution: 1.5→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: 1.5→10 Å
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