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- PDB-6neb: MYC Promoter G-Quadruplex with 1:6:1 loop length -

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Basic information

Entry
Database: PDB / ID: 6neb
TitleMYC Promoter G-Quadruplex with 1:6:1 loop length
ComponentsDNA (27-MER)
KeywordsDNA / G-quadruplex / Promoter / MYC
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / molecular dynamics
AuthorsDickerhoff, J. / Onel, B. / Chen, L. / Chen, Y. / Yang, D.
CitationJournal: Acs Omega / Year: 2019
Title: Solution Structure of a MYC Promoter G-Quadruplex with 1:6:1 Loop Length.
Authors: Dickerhoff, J. / Onel, B. / Chen, L. / Chen, Y. / Yang, D.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 1, 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 (27-MER)


Theoretical massNumber of molelcules
Total (without water)8,5641
Polymers8,5641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4890 Å2
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 (27-MER)


Mass: 8563.501 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
221isotropic12D 1H-1H NOESY
331isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC aromatic
151isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 1.5 mM DNA (27-MER), 90% H2O/10% D2O / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: DNA (27-MER) / Isotopic labeling: none
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mMconditions_171 atm298 K
2100 mMconditions_271 atm278 K
3100 mMconditions_371 atm313 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorerefinement
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
TopSpin3.5Bruker Biospinprocessing
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Refinement
MethodSoftware ordinalDetails
DGSA-distance geometry simulated annealing2
molecular dynamics1simulated annealing
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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