[English] 日本語
Yorodumi- PDB-2lg2: Structure of the duplex containing HNE derived (6S,8R,11S) N2-dG ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lg2 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the duplex containing HNE derived (6S,8R,11S) N2-dG cyclic hemiacetal when placed opposite dT | ||||||
Components |
| ||||||
Keywords | DNA / trans-4-hydroxynonenal / N2-dG cyclic hemiacetal | ||||||
Function / homology | (2R,5S)-5-pentyltetrahydrofuran-2-ol / DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Huang, H. / Wang, H. / Kozekova, A. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P. | ||||||
Citation | Journal: To be Published Title: Ring-chain tautomerization of trans-4-hydroxynonenal derived (6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct when placed opposite 2'-deoxythymidine in duplex Authors: Huang, H. / Wang, H. / Kozekova, A. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2lg2.cif.gz | 23.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2lg2.ent.gz | 16.4 KB | Display | PDB format |
PDBx/mmJSON format | 2lg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/2lg2 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/2lg2 | 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 |
---|---|
#2: DNA chain | Mass: 3678.403 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-2LE / ( |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|---|
NMR experiment | Type: 2D 1H-1H NOESY |
-Sample preparation
Details | Contents: 1 mM DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'), 1 mM DNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3'), 1 mM (2E,4R)-4-HYDROXYNON-2-ENAL, 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 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 |