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- PDB-1ju0: NMR solution structure of a DNA kissing complex -

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Basic information

Entry
Database: PDB / ID: 1ju0
TitleNMR solution structure of a DNA kissing complex
Components5'-D(*CP*TP*TP*GP*CP*TP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3'
KeywordsDNA / HIV / SL1 / kissing complex / loop-loop dimer
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing matrix relaxation chemical shift back calculation
AuthorsBarbault, F. / Huynh-Dinh, T. / Paoletti, J. / Lancelot, G.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2002
Title: A new peculiar DNA structure: NMR solution structure of a DNA kissing complex.
Authors: Barbault, F. / Huynh-Dinh, T. / Paoletti, J. / Lanceloti, G.
History
DepositionAug 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2002Provider: 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(*CP*TP*TP*GP*CP*TP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3'
B: 5'-D(*CP*TP*TP*GP*CP*TP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)14,1832
Polymers14,1832
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)16 / 16back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #5lowest energy

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Components

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


Mass: 7091.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA reverse transcripted sequence

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
232DQF-COSY
242HSQC 31P-1H

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Sample preparation

Details
Solution-IDContentsSolvent system
12.7mM oligonucleotides 10 mM phosphate bufferH2O 90% D2O10%
22.7mM oligonucleotides 10 mM phosphate bufferD2O 100%
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1without any salt 5.8ambient 278 K
2without any salt 5.8ambient 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMRcollection
VNMRprocessing
CNS1Brungerstructure solution
RELAZ1Lancelotiterative matrix relaxation
NUCHEMICSWijmengadata analysis
Curves5Laverydata analysis
CNS1Brungerrefinement
RefinementMethod: simulated annealing matrix relaxation chemical shift back calculation
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 16 / Conformers submitted total number: 16

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