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- PDB-6zte: Structure of a parallel c-myc modified with 5' duplex stem-loop a... -

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Basic information

Entry
Database: PDB / ID: 6zte
TitleStructure of a parallel c-myc modified with 5' duplex stem-loop and 3' diagonal snap-back loop
ComponentsDNA (36-MER)
KeywordsDNA / G-quadruplex / Duplex / Quadruplex-Duplex Junction
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsVianney, Y.M. / Weisz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WE 1933/15-1 Germany
CitationJournal: Chemistry / Year: 2020
Title: Quadruplex-Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands.
Authors: Vianney, Y.M. / Preckwinkel, P. / Mohr, S. / Weisz, K.
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 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 (36-MER)


Theoretical massNumber of molelcules
Total (without water)11,3401
Polymers11,3401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6160 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 (36-MER)


Mass: 11340.253 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
112isotropic12D 1H-13C HSQC aromatic
121isotropic12D 1H-1H NOESY
132isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.62 mM 0 nucleic acid, 90% H2O/10% D2Ocmycdup5-3sbl dissolved in 90% 10mM potassium phosphate buffer + 10% D2O, 0.62 mMSample1_0.62mm90% H2O/10% D2O
solution20.25 mM 0 nucleic acid, 90% H2O/10% D2Ocmycdup5-3sbl dissolved in 90% 10mM potassium phosphate buffer + 10% D2O, 0.25 mMSample1_0.25mm90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.62 mMnucleic acid01
0.25 mMnucleic acid02
Sample conditionsDetails: low salt buffer / Ionic strength: 10 mM / Label: mycdup5-3sbl_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 293 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
CcpNmr Analysis2.4.2CCPNchemical shift assignment
X-PLOR NIH2.52Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr Analysis2.4.2CCPNdata analysis
CcpNmr Analysis2.4.2CCPNpeak picking
TopSpin4.0.7Bruker Biospinprocessing
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
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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