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- PDB-1k9h: NMR structure of DNA TGTGAGCGCTCACA -

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Basic information

Entry
Database: PDB / ID: 1k9h
TitleNMR structure of DNA TGTGAGCGCTCACA
Components5'-D(*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*A)-3'
KeywordsDNA / Lac operator / Double helix
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics, matrix relaxation, simulated annealing
AuthorsKaluarachchi, K. / Gorenstein, D.G. / Luxon, B.A.
CitationJournal: 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
DepositionOct 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*A)-3'
B: 5'-D(*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)8,5622
Polymers8,5622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 2back calculated data agree with experimental NOESY spectrum,structures with the lowest energy
Representativeclosest to the average

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Components

#1: DNA chain 5'-D(*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*A)-3'


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: This structure was determined using standard homonuclear techniques.

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Sample preparation

DetailsContents: 3.6 mM oligonucleotide, 55 mM potassium phosphate, 150 mM KCl, 0.1mM NaN3
Solvent system: 99.96% D2O
Sample conditionsIonic strength: 150 mM KCl / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS5001
Varian VXRSVarianVXRS6002

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Processing

NMR software
NameVersionDeveloperClassification
Amberversions 3-5Kollman. P.refinement
MORASS1Meadows. R.P.refinement
RefinementMethod: molecular dynamics, matrix relaxation, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer 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

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