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- PDB-5m4w: Structure of DNA AGCGA-quadruplex adopted by 15-mer oligonucleoti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m4w | |||||||||||||||||||||||||||||||
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Title | Structure of DNA AGCGA-quadruplex adopted by 15-mer oligonucleotide found in regulatory region of the PLEKHG3 human gene with G11 to I11 mutation, d(GCGAGGGAGCIAGGG),VK34_I11 | |||||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / AGCGA-quadruplex / AGCGA-quadruplex family / G-G N1-carboniyl symmetric base pair / PLEKHG3 gene / inosine | Function / homology | DNA / DNA (> 10) | ![]() Biological species | ![]() Method | SOLUTION NMR / simulated annealing | ![]() Kocman, V. / Plavec, J. | Funding support | | ![]()
![]() ![]() Title: Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions. Authors: Kocman, V. / Plavec, J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 197.8 KB | Display | ![]() |
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PDB format | ![]() | 158.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 350.8 KB | Display | ![]() |
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Full document | ![]() | 459 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m1lC ![]() 5m2lC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 4750.071 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 100 mM / Label: VK34_I11_c1 / pH: 6 / Pressure: 1 atm / Temperature: 273 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 10 |