+Open data
-Basic information
Entry | Database: PDB / ID: 1k9l | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Solution Structure of DNA TATGAGCGCTCATA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Lac operator / double-helix / mutant | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, molecular dynamics, matrix relaxation | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1k9l.cif.gz | 26.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1k9l.ent.gz | 17.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k9l_validation.pdf.gz | 237.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1k9l_full_validation.pdf.gz | 236.8 KB | Display | |
Data in XML | 1k9l_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 1k9l_validation.cif.gz | 2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k9l ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k9l | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-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. |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||
NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
-Sample preparation
Details | Contents: 3 mM oligonucleotide, 55 mM potassium phosphate, 150 mM KCl, 0.1 mM NaN3 Solvent system: 99.96% D2O |
---|---|
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 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |