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- PDB-6r9l: A quadruplex hybrid structure with lpp loop orientation and 5 syn... -

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Basic information

Entry
Database: PDB / ID: 6r9l
TitleA quadruplex hybrid structure with lpp loop orientation and 5 syn residues
ComponentsDNA (25-MER)
KeywordsDNA / G-quadruplex / hybrid structure / duplex moiety
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsKarg, B. / Weisz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundationdfg we 1933/15-1 Germany
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations.
Authors: Karg, B. / Mohr, S. / Weisz, K.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations.
Authors: Karg, B. / Mohr, S. / Weisz, K.
#2: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations
Authors: Karg, B. / Mohr, S. / Weisz, K.
History
DepositionApr 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_nmr_spectrometer.model
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Aug 21, 2019Group: Data collection / 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 1.4Jun 23, 2021Group: Data collection / Category: pdbx_nmr_spectrometer
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)8,0511
Polymers8,0511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1140 Å2
ΔGint9 kcal/mol
Surface area4330 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (25-MER)


Mass: 8050.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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
121isotropic12D DQF-COSY
131isotropic12D 1H-13C HSQC
142isotropic12D 1H-1H NOESY
152isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM MYC4t-5s, 90% H2O/10% D2OMYC4t-5s_H2O90% H2O/10% D2O
solution20.8 mM MYC4t-5s, 100% D2OMYC4t-5s_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMMYC4t-5snatural abundance1
0.8 mMMYC4t-5snatural abundance2
Sample conditionsIonic strength: 10 mM / Label: MYC4t-5s / pH: 7 pH* / Pressure: 1 atm / Temperature: 303 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
TopSpin3Bruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
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: 20 / Conformers submitted total number: 10

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