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- PDB-2mkm: G-triplex structure and formation propensity -

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Basic information

Entry
Database: PDB / ID: 2mkm
TitleG-triplex structure and formation propensity
ComponentsDNA_(5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3')
KeywordsDNA / G-triplex / G-triad
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained Molecular Dynamics (rMD)
Model detailsclosest to the average, model1
AuthorsCerofolini, L. / Fragai, M. / Giachetti, A. / Limongelli, V. / Luchinat, C. / Novellino, E. / Parrinello, M. / Randazzo, A.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: G-triplex structure and formation propensity.
Authors: Cerofolini, L. / Amato, J. / Giachetti, A. / Limongelli, V. / Novellino, E. / Parrinello, M. / Fragai, M. / Randazzo, A. / Luchinat, C.
History
DepositionFeb 10, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Jun 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 1.3May 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(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,4761
Polymers3,4761
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 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA_(5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3')


Mass: 3476.254 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 DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-1H ROESY
1512D JR-HMBC
161E.COSY
1712D 31P-1H HSQC
1812D 31P-1H COSY
1912D 13C-1H HSQC
1101IPAP

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Sample preparation

DetailsContents: 0.7 mM DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3'), 70 mM potassium chloride, 10 mM potassium phosphate, 0.2 mM EDTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.7 mMDNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3')-11
70 mMpotassium chloride-21
10 mMpotassium phosphate-31
0.2 mMEDTA-41
Sample conditionsIonic strength: 0.08 / pH: 7 / Pressure: ambient / Temperature: 274 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004
Bruker DRXBrukerDRX5005
Bruker AvanceBrukerAVANCE9506

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmanrefinement
CARA2.1Keller and Wuthrichchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
RefinementMethod: restrained Molecular Dynamics (rMD) / Software ordinal: 1
NMR constraintsNA beta-angle constraints total count: 6 / NA chi-angle constraints total count: 11 / NA gamma-angle constraints total count: 9 / NA other-angle constraints total count: 11 / NA sugar pucker constraints total count: 30 / Hydrogen bond constraints total count: 22
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 10

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