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- PDB-2kka: Human telomere DNA two-tetrad quadruplex structure in K+ solution -

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Basic information

Entry
Database: PDB / ID: 2kka
TitleHuman telomere DNA two-tetrad quadruplex structure in K+ solution
Components5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*IP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3'
KeywordsDNA / human telomere G-quadruplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsfewest violations, model 1
AuthorsZhang, Z. / Dai, J. / Yang, D.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution: insights into the interconversion of human telomeric G-quadruplex structures.
Authors: Zhang, Z. / Dai, J. / Veliath, E. / Jones, R.A. / Yang, D.
History
DepositionJun 16, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 17, 2014Group: Other / Structure summary
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*IP*GP*GP*TP*TP*AP*GP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,2731
Polymers7,2731
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)8 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 7272.676 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM DNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*(DI)P*GP*GP*TP*TP*AP*GP*GP*GP*T)-3')-1, 60 mM potassium chloride-2, 30 mM potassium phosphate-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMDNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*(DI)P*GP*GP*TP*TP*AP*GP*GP*GP*T)-3')-11
60 mMpotassium chloride-21
30 mMpotassium phosphate-31
Sample conditionsIonic strength: 90 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 8

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