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- PDB-2m4p: Solution structure of an intramolecular propeller-type G-quadrupl... -

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Basic information

Entry
Database: PDB / ID: 2m4p
TitleSolution structure of an intramolecular propeller-type G-quadruplex containing a single bulge
ComponentsDNA (5'-D(*TP*TP*GP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
KeywordsDNA / G-quadruplex / Bulges
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsMukundan, V.T. / Phan, A.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Bulges in G-Quadruplexes: Broadening the Definition of G-Quadruplex-Forming Sequences.
Authors: Mukundan, V.T. / Phan, A.T.
History
DepositionFeb 8, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 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 (5'-D(*TP*TP*GP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)6,0351
Polymers6,0351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*TP*TP*GP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')


Mass: 6034.862 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1412D 1H-13C JR-HMBC

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Sample preparation

DetailsContents: 0.1-2.0 mM DNA (5'-D(*TP*TP*GP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM
Component: DNA (5'-D(*TP*TP*GP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1
Conc. range: 0.1-2.0
Sample conditionsIonic strength: 0.05 / pH: 7 / Pressure: ambient / 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
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 340 / NOE intraresidue total count: 238 / NOE medium range total count: 32 / NOE sequential total count: 70
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.099 Å / Maximum upper distance constraint violation: 0.179 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.013 Å / Distance rms dev error: 0.002 Å

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