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Yorodumi- PDB-2lia: Solution NMR structure of a DNA dodecamer containing the 7-aminom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lia | ||||||||||||||||||||
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Title | Solution NMR structure of a DNA dodecamer containing the 7-aminomethyl-7-deaza-2'-deoxyguanosine adduct | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Model details | closest to the average, model 1 | Authors | Szulik, M.W. / Ganguly, M. / Wang, R. / Gold, B. / Stone, M.P. | Citation | Journal: Biochemistry / Year: 2013 | Title: Site-Specific Stabilization of DNA by a Tethered Major Groove Amine, 7-Aminomethyl-7-deaza-2'-deoxyguanosine. Authors: Szulik, M.W. / Voehler, M.W. / Ganguly, M. / Gold, B. / Stone, M.P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lia.cif.gz | 25.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lia.ent.gz | 16.5 KB | Display | PDB format |
PDBx/mmJSON format | 2lia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lia_validation.pdf.gz | 379 KB | Display | wwPDB validaton report |
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Full document | 2lia_full_validation.pdf.gz | 393 KB | Display | |
Data in XML | 2lia_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 2lia_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/2lia ftp://data.pdbj.org/pub/pdb/validation_reports/li/2lia | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3691.445 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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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: 0.25 mM [U-2H] DNA dodecamer, 10 mM [U-2H] sodium phosphate, 200 mM [U-2H] sodium chloride, 0.011 M [U-2H] sodium azide, 0.05 mM [U-2H] sodium EDTA, 100% D2O Solvent system: 100% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.21 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||
NMR constraints | NOE constraints total: 211 / NOE intraresidue total count: 114 / NOE sequential total count: 97 | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 42 / Conformers submitted total number: 1 | ||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.453 Å |