[English] 日本語
Yorodumi- PDB-2led: Unique structural features of interconverting monomeric and dimer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2led | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from intron of N-myc gene | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / monomer-dimer equilibrium / N-myc / intron | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Model details | lowest energy, model 1 | Authors | Trajkovski, M. / Plavec, J. / Webba da Silva, M. | Citation | Journal: J.Am.Chem.Soc. / Year: 2012 | Title: Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene. Authors: Trajkovski, M. / Webba da Silva, M. / Plavec, J. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2led.cif.gz | 245.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2led.ent.gz | 205.2 KB | Display | PDB format |
PDBx/mmJSON format | 2led.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2led_validation.pdf.gz | 406.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2led_full_validation.pdf.gz | 652.4 KB | Display | |
Data in XML | 2led_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 2led_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/2led ftp://data.pdbj.org/pub/pdb/validation_reports/le/2led | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 6064.922 Da / Num. of mol.: 2 / Source method: obtained synthetically |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 0.4-6.6 mM DNA (5'-D(*TP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*A)-3'), 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample | Units: mM Component: DNA (5'-D(*TP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*A)-3')-1 Conc. range: 0.4-6.6 |
Sample conditions | Ionic strength: 120 / pH: 6.5 / Pressure: ambient / Temperature: 298.15 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 |