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- PDB-2n60: G-quadruplexes with (4n-1) guanines in the G-tetrad core: formati... -

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Basic information

Entry
Database: PDB / ID: 2n60
TitleG-quadruplexes with (4n-1) guanines in the G-tetrad core: formation of a G-triad water complex and implication for small-molecule binding
ComponentsDNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
KeywordsDNA / G-quadruplex / Vacant site / 11 guanines / G-triad / K+ solution
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic (others)
MethodSOLUTION NMR / molecular dynamics, DGSA-distance geometry simulated annealing, simulated annealing
Model detailslowest energy, model1
AuthorsHeddi, B. / Martin-Pintado, N. / Serimbetov, Z. / Kari, T.M. / Phan, A.T.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triadwater complex and implication for small-molecule binding
Authors: Heddi, B. / Martin-Pintado, N. / Serimbetov, Z. / Kari, T.M. / Phan, A.T.
History
DepositionAug 8, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,7061
Polymers5,7061
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 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 5705.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1232D 1H-1H NOESY
1312D 1H-1H HMBC
1421D 15N-filtered 1H NMR
1541D 1H NMR
1611D 1H NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1-1.2 mM DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1, 90% H2O/10% D2O90% H2O/10% D2O
20.2-0.4 mM [U-4% 15N] DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2, 90% H2O/10% D2O90% H2O/10% D2O
30.6-1.2 mM DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-3, 100% D2O100% D2O
40.2-0.4 mM [U-100% 2H] DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-10.1-1.21
mMDNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2[U-4% 15N]0.2-0.42
mMDNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-30.6-1.23
mMDNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-4[U-100% 2H]0.2-0.44
Sample conditionsIonic strength: 45 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddardchemical shift calculation
SparkyGoddarddata analysis
TopSpinBruker Biospincollection
X-PLORSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLORSchwieters, Kuszewski, Tjandra and Clorerefinement
SpinWorkshttp://home.cc.umanitoba.ca/~wolowiec/spinworksdata analysis
RefinementMethod: molecular dynamics, DGSA-distance geometry simulated annealing, simulated annealing
Software ordinal: 1
NMR constraintsNA chi-angle constraints total count: 11 / NOE intraresidue total count: 91 / NOE medium range total count: 12 / NOE sequential total count: 45
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 10 / Representative conformer: 1

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