[English] 日本語
![](img/lk-miru.gif)
- PDB-456d: MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATCCGCG): THE WATSON... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 456d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATCCGCG): THE WATSON-CRICK TYPE N6-METHOXYADENOSINE/CYTIDINE BASE-PAIRS IN B-DNA | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / MODIFIED NUCLEOTIDE / MISMATCH / METHOXYADENOSINE / DNA DAMAGE / B-DNA / DOUBLE HELIX | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Chatake, T. / Ono, A. / Ueno, Y. / Matsuda, A. / Takenaka, A. | ![]() ![]() Title: Crystallographic studies on damaged DNAs. I. An N(6)-methoxyadenine residue forms a Watson-Crick pair with a cytosine residue in a B-DNA duplex. Authors: Chatake, T. / Ono, A. / Ueno, Y. / Matsuda, A. / Takenaka, A. #1: ![]() Title: Crystallization and preliminary analysis of a DNA dodecamer of d(CGCGmo6AATCCGCG) containing 2'-deoxy-N6-methoxyadenosine: change in crystal packing with different humidity Authors: Chatake, T. / Sunami, T. / Ono, A. / Ueno, Y. / Matsuda, A. / Takenaka, A. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 27.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 18 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 331.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 331.4 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 3.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 3678.407 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.89 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 1.6→100 Å / Num. all: 8017 / % possible obs: 87.1 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.06 | ||||||||||||||||||
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.152 / % possible all: 72.1 | ||||||||||||||||||
Reflection | *PLUS Num. obs: 8017 / Num. measured all: 32780 / Rmerge(I) obs: 0.06 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 72.1 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.6→5 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 5 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|