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- PDB-6yep: LNA modified G-quadruplex with flipped G-tract and central tetrad -

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Basic information

Entry
Database: PDB / ID: 6yep
TitleLNA modified G-quadruplex with flipped G-tract and central tetrad
ComponentsDNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*G)-R(P*(LCG))-D(P*GP*GP*AP*CP*GP*GP*G)-3')
KeywordsDNA / G-quadruplex / LNA / tetrad flip / G-tract flip
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsWeisz, K. / Haase, L.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WE 1933/15-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design.
Authors: Haase, L. / Weisz, K.
History
DepositionMar 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*G)-R(P*(LCG))-D(P*GP*GP*AP*CP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,0011
Polymers7,0011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area540 Å2
ΔGint6 kcal/mol
Surface area3760 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 14structures with the lowest energy
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*G)-R(P*(LCG))-D(P*GP*GP*AP*CP*GP*GP*G)-3')


Mass: 7000.501 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
111isotropic11D 1H
121isotropic12D 1H-1H NOESY
132isotropic12D 1H-1H NOESY
142isotropic12D DQF-COSY
151isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM L15, 90% H2O/10% D2OL1590% H2O/10% D2O
solution20.4 mM L15, 100% D2OL15_ex100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mML15natural abundance1
0.4 mML15natural abundance2
Sample conditionsIonic strength: 15 mM / Label: 10mMKP-298K / 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
NameVersionDeveloperClassification
TopSpin4.0.4Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNchemical shift assignment
X-PLOR NIH2.49Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
simulated annealing3
simulated annealing4
molecular dynamics5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 14 / Conformers submitted total number: 10

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