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Yorodumi- PDB-2ktp: Structure of the 1,N2-ethenodeoxyguanosine lesion opposite a one-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ktp | ||||||
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Title | Structure of the 1,N2-ethenodeoxyguanosine lesion opposite a one-base deletion in duplex DNA | ||||||
Components |
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Keywords | DNA / Ethenoguanine / one-base deletion | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Shanmugam, G. / Kozekov, I.D. / Guengerich, P.F. / Rizzo, C.J. / Stone, M.P. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structure of the 1,N(2)-etheno-2'-deoxyguanosine lesion in the 3'-G(epsilon dG)T-5' sequence opposite a one-base deletion. Authors: Shanmugam, G. / Kozekov, I.D. / Guengerich, F.P. / Rizzo, C.J. / 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 | 2ktp.cif.gz | 24.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ktp.ent.gz | 15.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ktp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/2ktp ftp://data.pdbj.org/pub/pdb/validation_reports/kt/2ktp | 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: 3671.415 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3389.221 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 | Contents: 0.3 mM DNA (5'-D(P*GP*CP*AP*TP*GP*GP*AP*AP*TP*C)-3')-1, 100% D2O Solvent system: 100% D2O |
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Sample | Conc.: 0.3 mM / Component: DNA (5'-D(P*GP*CP*AP*TP*GP*GP*AP*AP*TP*C)-3')-1 |
Sample conditions | Ionic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software | Name: Amber Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollm Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
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: 20 / Conformers submitted total number: 1 |