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- PDB-1tqr: NMR Structure of DNA 17-mer GGAAAATCTCTAGCAGT corresponding to th... -

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Basic information

Entry
Database: PDB / ID: 1tqr
TitleNMR Structure of DNA 17-mer GGAAAATCTCTAGCAGT corresponding to the extremity of the U5 LTR of the HIV-1 genome
Components(DNA HIV-1 U5 LTR extremity) x 2
KeywordsDNA / double helix
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics including classical, RDC constraints
AuthorsRenisio, J.G. / Cosquer, S. / Cherrak, I. / El Antri, S. / Mauffret, O. / Fermandjian, S.
CitationJournal: NUCLEIC ACIDS RES. / Year: 2005
Title: Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase
Authors: Renisio, J.G. / Cosquer, S. / Cherrak, I. / El Antri, S. / Mauffret, O. / Fermandjian, S.
History
DepositionJun 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 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: DNA HIV-1 U5 LTR extremity
B: DNA HIV-1 U5 LTR extremity


Theoretical massNumber of molelcules
Total (without water)10,4132
Polymers10,4132
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)9 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA HIV-1 U5 LTR extremity


Mass: 5235.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Classical phosphoramidite chemistry
#2: DNA chain DNA HIV-1 U5 LTR extremity


Mass: 5177.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Classical phosphoramidite chemistry

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1412D HSQC 1H-13C

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Sample preparation

Details
Solution-IDContents
1phosphte buffer PH6.7
2plus phage Pf1 12mg/mL

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR softwareName: CNS / Version: 0.9a / Classification: refinement
RefinementMethod: torsion angle dynamics including classical, RDC constraints
Software ordinal: 1
Details: in the first stage the classical constraints were used with TAD at high temperature, in a second stage the RDC were gradually added with TAD at low temperature (200K)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 9

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