[English] 日本語
Yorodumi- PDB-5izp: Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position -
+Open data
-Basic information
Entry | Database: PDB / ID: 5izp | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Drew-Dickerson / dodecamer / 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. / Hoppins, J.J. / Miears, H.L. / Kiryutin, A.S. / Kasymov, R.D. / Yurkovskaya, A.V. / Zharkov, D.O. / Smirnov, S.L. | Citation | Journal: Plos One / Year: 2016 | Title: 8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme. Authors: Hoppins, J.J. / Gruber, D.R. / Miears, H.L. / Kiryutin, A.S. / Kasymov, R.D. / Petrova, D.V. / Endutkin, A.V. / Popov, A.V. / Yurkovskaya, A.V. / Fedechkin, S.O. / Brockerman, J.A. / ...Authors: Hoppins, J.J. / Gruber, D.R. / Miears, H.L. / Kiryutin, A.S. / Kasymov, R.D. / Petrova, D.V. / Endutkin, A.V. / Popov, A.V. / Yurkovskaya, A.V. / Fedechkin, S.O. / Brockerman, J.A. / Zharkov, D.O. / Smirnov, S.L. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5izp.cif.gz | 234 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5izp.ent.gz | 190 KB | Display | PDB format |
PDBx/mmJSON format | 5izp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/5izp ftp://data.pdbj.org/pub/pdb/validation_reports/iz/5izp | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 3679.392 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 |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||
Sample conditions |
|
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 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: 15 |