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- PDB-5mjx: 2'F-ANA/DNA Chimeric TBA Quadruplex structure -

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Basic information

Entry
Database: PDB / ID: 5mjx
Title2'F-ANA/DNA Chimeric TBA Quadruplex structure
ComponentsDNA (5'-D(*GP*GP*(FT)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
KeywordsDNA / 2'F-ANA/DNA TBA Structure / Structure from MOLMOL
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsLietard, J. / Abou Assi, H. / Gomez-Pinto, I. / Gonzalez, C. / Somoza, M.M. / Damha, M.J.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Mapping the affinity landscape of Thrombin-binding aptamers on 2 F-ANA/DNA chimeric G-Quadruplex microarrays.
Authors: Lietard, J. / Abou Assi, H. / Gomez-Pinto, I. / Gonzalez, C. / Somoza, M.M. / Damha, M.J.
History
DepositionDec 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*(FT)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,7611
Polymers4,7611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area310 Å2
ΔGint2 kcal/mol
Surface area2930 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 15structures with the lowest energy
RepresentativeModel #10minimized average structure

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Components

#1: DNA chain DNA (5'-D(*GP*GP*(FT)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')


Mass: 4761.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic22D DQF-COSY
131isotropic22D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.0 mg/mL DNA (5'-D(*GP*GP*(FT)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'), 90% H2O/10% D2O
Label: 1H_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mg/mL
Component: DNA (5'-D(*GP*GP*(FT)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
Isotopic labeling: natural abundance
Sample conditionsDetails: 10mM NaPi, 25mM KCl / Ionic strength: 10mM NaPi, 25mM KCl mM / Label: condicions_1 / pH: 7 / Pressure: 1 atm / Temperature: 279.6 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
DYANAGuntert, Braun and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 15 / Conformers submitted total number: 10

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