[English] 日本語
![](img/lk-miru.gif)
- PDB-1n5c: Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1n5c | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B form double helix / 3 / N4-etheno-2'-cytidine modification opposite G | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Freisinger, E. / Fernandes, A. / Grollman, A.P. / Kisker, C.F. | ![]() ![]() Title: Crystallographic Characterization of an Exocyclic DNA Adduct: 3,N4-etheno-2'-deoxycytidine in the Dodecamer 5'-CGCGAATT(ethenoC)GCG-3' Authors: Freisinger, E. / Fernandes, A. / Grollman, A.P. / Kisker, C.F. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 19.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 11.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 379.3 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 4.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
Details | The second part of the biological assembly/double helix is generated by the two fold axis: -x+y+1, y, -z+3/2. |
-
Components
#1: DNA chain | Mass: 3687.414 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.11 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / pH: 7 Details: Drop: MPD, potassium chloride, spermine tetrahydrochloride, cacodylate; Reservoir: MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2000 |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 4113 / % possible obs: 99.4 % / Observed criterion σ(I): 5 / Redundancy: 4 % / Rsym value: 0.061 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.187 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.79 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.061 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: NDB ENTRY BD0032 Resolution: 1.79→20 Å / Num. parameters: 1327 / Num. restraintsaints: 1445 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET'S PRINCIPLE | |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 137 / Occupancy sum non hydrogen: 303.75 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→20 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.1612 / Rfactor Rfree: 0.2193 / Rfactor Rwork: 0.061 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|