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Yorodumi- PDB-2l13: mini-haipin of AT basepairs having a C12-alkyl linker forming the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l13 | ||||||||||||||||||||
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Title | mini-haipin of AT basepairs having a C12-alkyl linker forming the loop region | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / mini-hairpin / alkyl chain / C12 / dodecyl / synthetic hybrid | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, matrix relaxation | Model details | minimized average, model 1 | Authors | Siegmund, K.H. / Hariharan, M. / Lewis, F.D. | Citation | Journal: J.Phys.Chem.B / Year: 2011 | Title: Conformation of a dodecane DNA hairpin linker. Multiple gauche bonds cover the bases. Authors: Siegmund, K. / Hariharan, M. / Lewis, F.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l13.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l13.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 2l13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/2l13 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/2l13 | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 3923.739 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: The C12-alkyl linker enables the short sequence to form a stable mini-hairpin. Ring-currents of the neighboring base-pair made assignment for all methylene protons possible. The position of ...Details: The C12-alkyl linker enables the short sequence to form a stable mini-hairpin. Ring-currents of the neighboring base-pair made assignment for all methylene protons possible. The position of the last terminal base-pair is not well defined due to end-fraying and the resulting lack of a sufficient number of constraints. | ||||||||||||||||||||||||||||
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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: 0.1 / pH: 7.2 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, matrix relaxation / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 80 / Conformers submitted total number: 11 |