[English] 日本語
Yorodumi- PDB-2lod: Solution-state structure of an intramolecular G-quadruplex with p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lod | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-QUADRUPLEX / LOOPS | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Model details | lowest energy, model 1 | Authors | Marusic, M. / Sket, P. / Bauer, L. / Viglasky, V. / Plavec, J. | Citation | Journal: Nucleic Acids Res. / Year: 2012 | Title: Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops. Authors: Marusic, M. / Sket, P. / Bauer, L. / Viglasky, V. / Plavec, J. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2lod.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2lod.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 2lod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lod_validation.pdf.gz | 320 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2lod_full_validation.pdf.gz | 380 KB | Display | |
Data in XML | 2lod_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 2lod_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/2lod ftp://data.pdbj.org/pub/pdb/validation_reports/lo/2lod | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 6972.491 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| |||||||||||||||
Sample conditions | Ionic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 0 / NA beta-angle constraints total count: 0 / NA chi-angle constraints total count: 22 / NA delta-angle constraints total count: 0 / NA epsilon-angle constraints total count: 21 / NA gamma-angle constraints total count: 0 / NA other-angle constraints total count: 36 / NA sugar pucker constraints total count: 22 / NOE constraints total: 316 / NOE intraresidue total count: 216 / NOE long range total count: 19 / NOE medium range total count: 11 / NOE sequential total count: 70 / Hydrogen bond constraints total count: 24 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 10 |