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Yorodumi- PDB-1kkv: NMR Solution Structure of d(CCACGCGTGG)2, parent to G-T mismatch ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kkv | ||||||||||||||||||
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Title | NMR Solution Structure of d(CCACGCGTGG)2, parent to G-T mismatch structure | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / g-t mismatch / dynamics / spin relaxation / order parameter / helical parameter / sequence dependent structure / sequence dependent dynamics | Function / homology | DNA | Function and homology information Method | SOLUTION NMR / simulated annealing | Authors | Isaacs, R.J. / Spielmann, H.P. | Citation | Journal: J.Mol.Biol. / Year: 2002 | Title: Structural differences in the NOE-derived structure of G-T mismatched DNA relative to normal DNA are correlated with differences in (13)C relaxation-based internal dynamics. Authors: Isaacs, R.J. / Rayens, W.S. / Spielmann, H.P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kkv.cif.gz | 251.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kkv.ent.gz | 207.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kkv_validation.pdf.gz | 309.2 KB | Display | wwPDB validaton report |
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Full document | 1kkv_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 1kkv_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1kkv_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kkv ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kkv | HTTPS FTP |
-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: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized from phosphoramadites on solid support |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
-Sample preparation
Details | Contents: 4 mM double strand DNA / Solvent system: 99.96% D2O |
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Sample conditions | Ionic strength: 200 mM NaCl, 20 mM NaPO4, 10 mM NaN3, 0.1 mM EDTA pH: 7 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted, back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 20 / Conformers submitted total number: 20 |