[English] 日本語
![](img/lk-miru.gif)
- PDB-1g8u: MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURID... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1g8u | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / MODIFIED NUCLEOTIDE / FORMYLURIDINE / DNA DAMAGE / B-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Tsunoda, M. / Karino, N. / Ueno, Y. / Matsuda, A. / Takenaka, A. | ![]() ![]() Title: Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers? Authors: Tsunoda, M. / Karino, N. / Ueno, Y. / Matsuda, A. / Takenaka, A. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 24.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 15.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 319.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 319.5 KB | Display | |
Data in XML | ![]() | 1.3 KB | Display | |
Data in CIF | ![]() | 2.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g75C ![]() 1g8nC ![]() 1g8vC ![]() 355dS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 3677.376 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: MPD, spermine, sodium chloride, cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Mar 5, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 21907 / Num. obs: 6732 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.25 % / Rmerge(I) obs: 0.024 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.389 / % possible all: 97.6 |
Reflection | *PLUS Num. obs: 7779 / Num. measured all: 31872 / Rmerge(I) obs: 0.029 |
-
Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 355D Resolution: 1.85→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||
Refine analyze |
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
| ||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.029
| ||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.24 / Rfactor Rwork: 0.24 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.291 / Rfactor Rwork: 0.271 |