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- PDB-2m8y: Structure of d[CGCGAAGCATTCGCG] hairpin -

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Basic information

Entry
Database: PDB / ID: 2m8y
TitleStructure of d[CGCGAAGCATTCGCG] hairpin
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / hairpin / duplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, Distance-restrained molecular dynamics
Model detailslowest energy, model1
AuthorsLim, K.W. / Phan, A.T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Structural basis of DNA quadruplex-duplex junction formation.
Authors: Lim, K.W. / Phan, A.T.
History
DepositionMay 30, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,5951
Polymers4,5951
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(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3')


Mass: 4594.986 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
1122D 1H-1H NOESY
2212D 1H-1H JR NOESY
1322D 1H-1H COSY
1422D 1H-1H TOCSY
1522D 1H-13C HSQC
1612D 1H-13C JR HMBC
1722D 1H-31P HSQC
182H-D EXCHANGE
19315N-FILTERED
1104D-LABELED

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-2.0 mM DNA-1, 90% H2O/10% D2O90% H2O/10% D2O
20.5-2.0 mM DNA-2, 100% D2O100% D2O
30.5-2.0 mM [U-2% 15N] DNA-3, 90% H2O/10% D2O90% H2O/10% D2O
40.2-1.0 mM [U-100% 2H] DNA-4, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDNA-10.5-2.01
mMDNA-20.5-2.02
mMDNA-3[U-2% 15N]0.5-2.03
mMDNA-4[U-100% 2H]0.2-1.04
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
140 mM K+ 7ambient 278 K
240 mM K+ 7ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE4001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospinprocessing
Felix2007Felix NMR, Inc.peak picking
X-PLOR NIH2.29Schwieters, Kuszewski, Tjandra and Cloreprocessing
X-PLOR NIH2.29Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing, Distance-restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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