[English] 日本語
Yorodumi- PDB-6als: Solution structure of a DNA dodecamer with 5-methylcytosine at th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6als | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 9th position and 8-oxoguanine at the 4th position | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Drew-Dickerson / non-canonical / modified DNA / oxidized DNA / DNA damage / DNA adduct / lesion | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | SOLUTION NMR / simulated annealing | Authors | Gruber, D.R. / Shernyukov, A.V. / Endutkin, A.V. / Bagryanskaya, E.G. / Zharkov, D.O. / Smirnov, S.L. | Funding support | United States, 1items |
Citation | Journal: Nucleic Acids Res. / Year: 2018 | Title: Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation. Authors: Gruber, D.R. / Toner, J.J. / Miears, H.L. / Shernyukov, A.V. / Kiryutin, A.S. / Lomzov, A.A. / Endutkin, A.V. / Grin, I.R. / Petrova, D.V. / Kupryushkin, M.S. / Yurkovskaya, A.V. / Johnson, ...Authors: Gruber, D.R. / Toner, J.J. / Miears, H.L. / Shernyukov, A.V. / Kiryutin, A.S. / Lomzov, A.A. / Endutkin, A.V. / Grin, I.R. / Petrova, D.V. / Kupryushkin, M.S. / Yurkovskaya, A.V. / Johnson, E.C. / Okon, M. / Bagryanskaya, E.G. / Zharkov, D.O. / Smirnov, S.L. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6als.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6als.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 6als.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6als_validation.pdf.gz | 203 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6als_full_validation.pdf.gz | 245.9 KB | Display | |
Data in XML | 6als_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/6als ftp://data.pdbj.org/pub/pdb/validation_reports/al/6als | HTTPS FTP |
-Related structure data
Related structure data | 5l06C 5l2gC 5trnC 5uz1C 5uz2C 5uz3C 6altC 6aluC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 3627.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Type: solution Contents: 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*(DC5)P*GP*(DMC)P*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3'), 100% D2O Label: dd11 / Solvent system: 100% D2O | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||
Sample conditions |
|
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
---|
-Processing
NMR software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 18 / Conformers submitted total number: 11 |