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- PDB-2kf7: Structure of a two-G-tetrad basket-type intramolecular G-quadrupl... -

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Basic information

Entry
Database: PDB / ID: 2kf7
TitleStructure of a two-G-tetrad basket-type intramolecular G-quadruplex formed by human telomeric repeats in K+ solution (with G7-to-BRG substitution)
ComponentsHUMAN TELOMERE DNA
KeywordsDNA / anticancer targets / human telomere / intramolecular G-quadruplexes
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / matrix relaxation, molecular dynamics, DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsLim, K.W. / Amrane, S. / Bouaziz, S. / Xu, W. / Mu, Y. / Patel, D.J. / Luu, K.N. / Phan, A.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers
Authors: Lim, K.W. / Amrane, S. / Bouaziz, S. / Xu, W. / Mu, Y. / Patel, D.J. / Luu, K.N. / Phan, A.T.
History
DepositionFeb 12, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN TELOMERE DNA


Theoretical massNumber of molelcules
Total (without water)7,0531
Polymers7,0531
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 / 100back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

#1: DNA chain HUMAN TELOMERE DNA


Mass: 7053.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-13C HSQC
1222D 1H-1H TOCSY
1322D 1H-1H COSY
1412D 1H-1H NOESY
1522D 1H-1H NOESY
2622D 1H-1H NOESY
1712D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-2.5mM DNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-1, 70mM potassium chloride-2, 20mM potassium phosphate-3, 90% H2O/10% D2O90% H2O/10% D2O
20.5-2.5mM DNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-4, 70mM potassium chloride-5, 20mM potassium phosphate-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMDNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-11
70 mMpotassium chloride-21
20 mMpotassium phosphate-31
0.5 mMDNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*(BGM)P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-42
70 mMpotassium chloride-52
20 mMpotassium phosphate-62
Sample conditions
Conditions-IDpHTemperature (K)
17298 K
25283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
Felix2007Felix NMR, Inc.peak picking
TopSpinBruker Biospinprocessing
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra, Clorestructure solution
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: matrix relaxation, molecular dynamics, DGSA-distance geometry simulated annealing
Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 0 / NA beta-angle constraints total count: 0 / NA chi-angle constraints total count: 8 / NA delta-angle constraints total count: 0 / NA epsilon-angle constraints total count: 4 / NA gamma-angle constraints total count: 0 / NA other-angle constraints total count: 8 / NA sugar pucker constraints total count: 0 / NOE constraints total: 580 / NOE intraresidue total count: 272 / NOE long range total count: 40 / NOE medium range total count: 49 / NOE sequential total count: 219 / Hydrogen bond constraints total count: 42
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.193 Å / Maximum upper distance constraint violation: 0.239 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.018 Å / Distance rms dev error: 0.002 Å

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