[English] 日本語
Yorodumi- PDB-2lfa: Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lfa | ||||||
---|---|---|---|---|---|---|---|
Title | Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine | ||||||
Components |
| ||||||
Keywords | DNA / (5'S)-8 / 5'-cyclo-2'-deoxyguanosine / cyclopurine / cyclo-dG | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Huang, H. / Das, R.S. / Basu, A. / Stone, M.P. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 Title: Structure of (5'S)-8,5'-Cyclo-2'-deoxyguanosine in DNA. Authors: Huang, H. / Das, R.S. / Basu, A.K. / Stone, M.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2lfa.cif.gz | 24.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2lfa.ent.gz | 15.8 KB | Display | PDB format |
PDBx/mmJSON format | 2lfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lfa_validation.pdf.gz | 342.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2lfa_full_validation.pdf.gz | 346.7 KB | Display | |
Data in XML | 2lfa_validation.xml.gz | 2.7 KB | Display | |
Data in CIF | 2lfa_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/2lfa ftp://data.pdbj.org/pub/pdb/validation_reports/lf/2lfa | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 3713.394 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: DNA chain | Mass: 3609.398 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.0 mM DNA (5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3'), 1.0 mM DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-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: 10 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 |