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Yorodumi- PDB-2kv0: 2-Aminopurine incorporation perturbs the dynamics and structure of DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kv0 | ||||||
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Title | 2-Aminopurine incorporation perturbs the dynamics and structure of DNA | ||||||
Components |
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Keywords | DNA / 2-Aminopurine / fluorophore / structure perturbation | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model type details | minimized average | ||||||
Authors | Dallmann, A. / Dehmel, L. / Peters, T. / Muegge, C. / Griesinger, C.P. / Tuma, J. / Ernsting, N.P. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010 Title: 2-Aminopurine incorporation perturbs the dynamics and structure of DNA. Authors: Dallmann, A. / Dehmel, L. / Peters, T. / Mugge, C. / Griesinger, C. / Tuma, J. / Ernsting, N.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kv0.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kv0.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 2kv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/2kv0 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/2kv0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3976.599 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3967.585 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-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 | pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AV / Manufacturer: Bruker / Model: AV / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Torsion angle dynamics,50K at 20,000K with subsequent gradual cooling to 25K in 154 steps of 0.5 ps length (34 steps to cool down to 3,000 K, followed by 120 steps to reach the end ...Details: Torsion angle dynamics,50K at 20,000K with subsequent gradual cooling to 25K in 154 steps of 0.5 ps length (34 steps to cool down to 3,000 K, followed by 120 steps to reach the end temperature) and a final minimization (3,000 steps). | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 333 / NOE intraresidue total count: 145 / NOE sequential total count: 188 / Hydrogen bond constraints total count: 78 | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 11 |