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- PDB-1jvc: Dimeric DNA Quadruplex Containing Major Groove-Aligned A.T.A.T an... -

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Entry
Database: PDB / ID: 1jvc
TitleDimeric DNA Quadruplex Containing Major Groove-Aligned A.T.A.T and G.C.G.C Tetrads Stabilized by Inter-Subunit Watson-Crick A:T and G:C Pairs
Components5'-D(*GP*AP*GP*CP*AP*GP*GP*T)-3'
KeywordsDNA / ATAT and GCGC tetrads / dimeric DNA quadruplex / hydrogen bond alignments / inter-subunit Watson-Crick pairs
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics with simulated annealing method in torsional space
AuthorsZhang, N. / Gorin, A. / Majumdar, A. / Kettani, A. / Chernichenko, N. / Skripkin, E. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Dimeric DNA quadruplex containing major groove-aligned A-T-A-T and G-C-G-C tetrads stabilized by inter-subunit Watson-Crick A-T and G-C pairs.
Authors: Zhang, N. / Gorin, A. / Majumdar, A. / Kettani, A. / Chernichenko, N. / Skripkin, E. / Patel, D.J.
History
DepositionAug 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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(*GP*AP*GP*CP*AP*GP*GP*T)-3'
B: 5'-D(*GP*AP*GP*CP*AP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)4,9832
Polymers4,9832
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)10 / 60back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*GP*AP*GP*CP*AP*GP*GP*T)-3'


Mass: 2491.654 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY, COSY, TOCSY

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Sample preparation

DetailsContents: 1M NaCl, 2mM phosphate / Solvent system: H2O, D2O
Sample conditionsIonic strength: 1M NaCl, 2mM phosphate / pH: 6.6 / Pressure: 1 atm / Temperature: 273 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR softwareName: X-PLOR / Version: 3.81 / Developer: A. Brunger / Classification: refinement
RefinementMethod: molecular dynamics with simulated annealing method in torsional space
Software ordinal: 1 / Details: described in the primary citation
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 60 / Conformers submitted total number: 10

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