[English] 日本語
Yorodumi- PDB-2k8t: Solution NMR structure of trans-4-hydroxynonenal derived dG adduc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k8t | ||||||
---|---|---|---|---|---|---|---|
Title | Solution NMR structure of trans-4-hydroxynonenal derived dG adduct of (6R,8S,11R)-configuration opposite dC | ||||||
Components |
| ||||||
Keywords | DNA / HNE-dG (6R / 8S / 11R) / HNE derived dG adduct / trans-4-hydroxynonenal | ||||||
Function / homology | (2S,5R)-5-pentyltetrahydrofuran-2-ol / DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Huang, H. / Wang, H. / Qi, N. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: The stereochemistry of trans-4-hydroxynonenal-derived exocyclic 1,N2-2'-deoxyguanosine adducts modulates formation of interstrand cross-links in the 5'-CpG-3' sequence. Authors: Huang, H. / Wang, H. / Qi, N. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2k8t.cif.gz | 23.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2k8t.ent.gz | 16.9 KB | Display | PDB format |
PDBx/mmJSON format | 2k8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/2k8t ftp://data.pdbj.org/pub/pdb/validation_reports/k8/2k8t | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA strand A |
---|---|
#2: DNA chain | Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA strand B |
#3: Chemical | ChemComp-HNB / ( |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|---|
NMR experiment | Type: 2D 1H-1H NOESY |
-Sample preparation
Details | Contents: 1 mM DNA (5'-D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'), 1 mM DNA (5'-D(*DGP*DGP*DAP*DCP*DTP*DCP*DGP*DCP*DTP*DAP*DGP*DC)-3'), 100% D2O Solvent system: 100% D2O | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Sample |
| |||||||||
Sample conditions | Ionic strength: 100 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
---|
-Processing
NMR software | Name: Amber / Version: 7 Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm Classification: refinement |
---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 10 / Conformers submitted total number: 1 |