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- PDB-6tc8: 2'-F-arabinoguanosine and 2'-F-riboguanosine modified hybrid type... -

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Basic information

Entry
Database: PDB / ID: 6tc8
Title2'-F-arabinoguanosine and 2'-F-riboguanosine modified hybrid type G-quadruplex with V-loop
ComponentsDNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*(GFL)P*(GF2)P*GP*GP*AP*CP*GP*GP*G)-3')
KeywordsDNA / G-quadruplex / V-loop
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsHaase, L. / Weisz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationDFG WE 1933/15-1 Germany
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Switching the type of V-loop in sugar-modified G-quadruplexes through altered fluorine interactions.
Authors: Haase, L. / Weisz, K.
History
DepositionNov 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 15, 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: DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*(GFL)P*(GF2)P*GP*GP*AP*CP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,0081
Polymers7,0081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area560 Å2
ΔGint5 kcal/mol
Surface area3880 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*(GFL)P*(GF2)P*GP*GP*AP*CP*GP*GP*G)-3')


Mass: 7008.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN

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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
162isotropic12D 1H-1H NOESY
122isotropic12D DQF-COSY
132isotropic12D TOCSY
141isotropic12D 1H-13C HSQC aromatic
171isotropic12D 19F-1H HOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM A14F15, 90% H2O/10% D2OA14F1590% H2O/10% D2O
solution20.4 mM A14F15, 100% D2OA14F15_ex100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMA14F15natural abundance1
0.4 mMA14F15natural abundance2
Sample conditionsDetails: 10 mM potassium phosphate buffer / Ionic strength: 20 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing4
molecular dynamics5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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