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- PDB-6erl: Quadruplex with flipped tetrad formed by the c-myc promoter sequence -

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Basic information

Entry
Database: PDB / ID: 6erl
TitleQuadruplex with flipped tetrad formed by the c-myc promoter sequence
Componentscmbr-481317
KeywordsDNA / Quadruplex / G4 / 8-Bromo-Guanosine / tetrad flip
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / simulated annealing / molecular dynamics
AuthorsKarg, B. / Weisz, K.
CitationJournal: Chemistry / Year: 2018
Title: Loop Length Affects Syn-Anti Conformational Rearrangements in Parallel G-Quadruplexes.
Authors: Karg, B. / Weisz, K.
History
DepositionOct 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1May 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 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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: cmbr-481317


Theoretical massNumber of molelcules
Total (without water)7,3241
Polymers7,3241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2780 Å2
ΔGint22 kcal/mol
Surface area3300 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain cmbr-481317


Mass: 7324.094 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
132isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 mM NA potassium phosphate, 90% H2O/10% D2OA90% H2O/10% D2O
solution210 mM NA potassium phosphate, 100% D2OB100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMpotassium phosphateNA1
10 mMpotassium phosphateNA2
Sample conditionsIonic strength: 10 mM / Label: 1 / pH: 7 pH* / Pressure: 1 atm / Temperature: 303 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
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing2
simulated annealing1
molecular dynamics5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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