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Yorodumi- PDB-2m4p: Solution structure of an intramolecular propeller-type G-quadrupl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2m4p | ||||||||||||||||||||
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Title | Solution structure of an intramolecular propeller-type G-quadruplex containing a single bulge | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / Bulges | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics | Model details | lowest energy, model1 | Authors | Mukundan, V.T. / Phan, A.T. | Citation | Journal: J.Am.Chem.Soc. / Year: 2013 | Title: Bulges in G-Quadruplexes: Broadening the Definition of G-Quadruplex-Forming Sequences. Authors: Mukundan, V.T. / Phan, A.T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m4p.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m4p.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 2m4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/2m4p ftp://data.pdbj.org/pub/pdb/validation_reports/m4/2m4p | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 6034.862 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.1-2.0 mM DNA (5'-D(*TP*TP*GP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Units: mM Component: DNA (5'-D(*TP*TP*GP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1 Conc. range: 0.1-2.0 |
Sample conditions | Ionic strength: .05 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics Software ordinal: 1 | |||||||||
NMR constraints | NOE constraints total: 340 / NOE intraresidue total count: 238 / NOE medium range total count: 32 / NOE sequential total count: 70 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.099 Å / Maximum upper distance constraint violation: 0.179 Å / Representative conformer: 1 | |||||||||
NMR ensemble rms | Distance rms dev: 0.013 Å / Distance rms dev error: 0.002 Å |