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Yorodumi- PDB-2n4y: Structure and possible function of a G-quadruplex in the long ter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n4y | ||||||||||||||||||||||
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Title | Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome | ||||||||||||||||||||||
Components | DNA_(5'-D(*Keywords | DNA / G-quadruplex / HIV-1 / Long Terminal Repeat | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | SOLUTION NMR / distance geometry, DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics | Model details | lowest energy, model1 | Authors | DeNicola, B. / Lech, C.J. / Heddi, B. / Regmi, S. / Frasson, I. / Perrone, R. / Richter, S.N. / Phan, A.T. | Citation | Journal: Nucleic Acids Res. / Year: 2016 | Title: Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome. Authors: De Nicola, B. / Lech, C.J. / Heddi, B. / Regmi, S. / Frasson, I. / Perrone, R. / Richter, S.N. / 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 | 2n4y.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n4y.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 2n4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/2n4y ftp://data.pdbj.org/pub/pdb/validation_reports/n4/2n4y | 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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NMR ensembles |
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-Components
#1: DNA chain | Mass: 6945.449 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 | Contents: 0.1-1 mM DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*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(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')-1 Conc. range: 0.1-1 |
Sample conditions | Ionic strength: 90 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry, DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics 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: 12 / NA delta-angle constraints total count: 0 / NA epsilon-angle constraints total count: 0 / NA gamma-angle constraints total count: 0 / NA other-angle constraints total count: 0 / NA sugar pucker constraints total count: 0 / NOE constraints total: 581 / NOE intraresidue total count: 406 / NOE long range total count: 70 / NOE medium range total count: 70 / NOE sequential total count: 105 / Hydrogen bond constraints total count: 2 | ||||||||||||||||||||||||||||||
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: 0.001 Å / Maximum upper distance constraint violation: 0.33 Å / Representative conformer: 1 | ||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.013 Å |