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- PDB-6f4z: 2'F-araG modified quadruplex with flipped G-tract and central tetrad -

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Basic information

Entry
Database: PDB / ID: 6f4z
Title2'F-araG modified quadruplex with flipped G-tract and central tetrad
ComponentsDNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*(GFL)P*GP*GP*AP*CP*GP*GP*G)-3')
KeywordsDNA / G-QUADRUPLEX / 2'F-ANA
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / molecular dynamics
AuthorsDickerhoff, J. / Weisz, K.
CitationJournal: Chembiochem / Year: 2018
Title: Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway.
Authors: Dickerhoff, J. / Weisz, K.
History
DepositionNov 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 1.3May 15, 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*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*(GFL)P*GP*GP*AP*CP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,9901
Polymers6,9901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area560 Å2
ΔGint6 kcal/mol
Surface area4110 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*GP*(GFL)P*GP*GP*AP*CP*GP*GP*G)-3')


Mass: 6990.482 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
121isotropic12D 1H-13C HSQC aromatic
132isotropic12D DQF-COSY
142isotropic12D 1H-1H TOCSY
152isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.37 mM DNA, 10 mM potassium phosphate, 90% H2O/10% D2Osample_H2O90% H2O/10% D2O
solution20.37 mM DNA, 10 mM potassium phosphate, 100% D2Osample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.37 mMDNAnatural abundance1
10 mMpotassium phosphatenatural abundance1
0.37 mMDNAnatural abundance2
10 mMpotassium phosphatenatural abundance2
Sample conditionsIonic strength: 10 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing1
molecular dynamics2
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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