+Open data
-Basic information
Entry | Database: PDB / ID: 5oga | ||||||||||||||||||||
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Title | Structure of minimal i-motif domain | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / i-motif / DNA non-canonical structure / minor groove tetrad | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | SOLUTION NMR / simulated annealing | Authors | Mir, B. / Serrano, I. / Buitrago, D. / Orozco, M. / Escaja, N. / Gonzalez, C. | Citation | Journal: J. Am. Chem. Soc. / Year: 2017 | Title: Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH. Authors: Mir, B. / Serrano, I. / Buitrago, D. / Orozco, M. / Escaja, N. / Gonzalez, C. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oga.cif.gz | 133.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oga.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 5oga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/5oga ftp://data.pdbj.org/pub/pdb/validation_reports/og/5oga | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 6275.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 0.5 mM LL3, 90% H2O/10% D2O / Label: LL3 / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.5 mM / Component: LL3 / Isotopic labeling: none |
Sample conditions | Ionic strength: 10 mM NaPi mM / Label: LL3 / pH: 7.0 / Pressure: 1 atm / Temperature: 278 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: simulated annealing / Software ordinal: 5 | ||||||||||||||||||
NMR representative | Selection criteria: null | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 |