+Open data
-Basic information
Entry | Database: PDB / ID: 1k9h | ||||||||||||||||||
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Title | NMR structure of DNA TGTGAGCGCTCACA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Lac operator / Double helix | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / molecular dynamics, matrix relaxation, simulated annealing | Authors | Kaluarachchi, K. / Gorenstein, D.G. / Luxon, B.A. | Citation | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k9h.cif.gz | 27 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k9h.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k9h_validation.pdf.gz | 237.1 KB | Display | wwPDB validaton report |
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Full document | 1k9h_full_validation.pdf.gz | 236.9 KB | Display | |
Data in XML | 1k9h_validation.xml.gz | 2.2 KB | Display | |
Data in CIF | 1k9h_validation.cif.gz | 2.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k9h ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k9h | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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: 4280.792 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence has been derived from the natural Lac Operator sequence by symmetrizing the minimum required length for lac repressor binding. |
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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 homonuclear techniques. |
-Sample preparation
Details | Contents: 3.6 mM oligonucleotide, 55 mM potassium phosphate, 150 mM KCl, 0.1mM 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: molecular dynamics, matrix relaxation, 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,structures with the lowest energy Conformers calculated total number: 2 / Conformers submitted total number: 1 |