[English] 日本語
![](img/lk-miru.gif)
- PDB-2dp7: Crystal Structure of D(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)c... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2dp7 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of D(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / modified nucleotide / 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine / B-DNA | Function / homology | (6-AMINOHEXYL)CARBAMIC ACID / : / DNA / DNA (> 10) | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 29.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 19.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 383.5 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dpbC ![]() 2dpcC ![]() 2dqoC ![]() 2dqpC ![]() 2dqqC ![]() 355dS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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 | ChemComp-MG / | #3: Chemical | #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.97 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20mM sodium cacodylate (pH 6.0), 40mM potassium chloride, 2.5mM magnesium chloride, 1.5mM spermine tetrahydrochloride and 5%(v/v) 2-methyl-2,4-pentanediol (MPD), equilibrated against 45%(v/v) ...Details: 20mM sodium cacodylate (pH 6.0), 40mM potassium chloride, 2.5mM magnesium chloride, 1.5mM spermine tetrahydrochloride and 5%(v/v) 2-methyl-2,4-pentanediol (MPD), equilibrated against 45%(v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→18.836 Å / Num. obs: 10074 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.047 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.55→1.63 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 355D Resolution: 1.55→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.
| |||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
|