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Open data
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Basic information
Entry | Database: PDB / ID: 1k9l | ||||||||||||||||||
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Title | Solution Structure of DNA TATGAGCGCTCATA | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / Lac operator / double-helix / mutant | Function / homology | DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / simulated annealing, molecular dynamics, matrix relaxation | ![]() Kaluarachchi, K. / Gorenstein, D.G. / Luxon, B.A. | ![]() Journal: J.Biomol.Struct.Dyn. / Year: 2000 | Title: How Do Proteins Recognize DNA? Solution Structure and Local Conformational Dynamics of Lac Operators by 2D NMR Authors: Kaluarachchi, K. / Gorenstein, D.G. / Luxon, B.A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26.7 KB | Display | ![]() |
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PDB format | ![]() | 17.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 237.1 KB | Display | ![]() |
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Full document | ![]() | 236.8 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: DNA chain | Mass: 4279.804 Da / Num. of mol.: 2 / Mutation: G2A/C13T / Source method: obtained synthetically Details: This sequence is a G2A/C13T mutant of the symmetrized wild-type lac operator sequence. |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
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Sample preparation
Details | Contents: 3 mM oligonucleotide, 55 mM potassium phosphate, 150 mM KCl, 0.1 mM NaN3 Solvent system: 99.96% D2O |
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Sample conditions | Ionic strength: 150 mM KCl / pH: 7.4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics, matrix relaxation 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: 2 / Conformers submitted total number: 1 |