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- PDB-5m1w: Structure of a stable G-hairpin -

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Basic information

Entry
Database: PDB / ID: 5m1w
TitleStructure of a stable G-hairpin
ComponentsDNA (5'-D(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3')
KeywordsDNA / G-hairpin G:G base pairs NMR spectroscopy conformational exchange
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsGajarsky, M. / Zivkovic, M.L. / Stadlbauer, P. / Pagano, B. / Fiala, R. / Amato, J. / Tomaska, L. / Sponer, J. / Plavec, J. / Trantirek, L.
Funding support Czech Republic, Slovenia, Italy, 8items
OrganizationGrant numberCountry
Czech Science Foundation13-28310S Czech Republic
Czech Science Foundation16-13721S Czech Republic
CEITEC 2020, Ministry of Education, Youth and Sports and National Programme for Sustainability IILQ1601 Czech Republic
European Organization for Molecular BiologyIG2535 Czech Republic
Marie-Curie grantECOPOD Czech Republic
Slovenian Research AgencyP1-242 Slovenia
Slovenian Research AgencyJ1-6733 Slovenia
Programma STAR 2014 of University of Naples Federico II14-CSP3-C03-141 Italy
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Structure of a Stable G-Hairpin.
Authors: Gajarsky, M. / Zivkovic, M.L. / Stadlbauer, P. / Pagano, B. / Fiala, R. / Amato, J. / Tomaska, L. / Sponer, J. / Plavec, J. / Trantirek, L.
History
DepositionOct 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2May 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 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,4761
Polymers3,4761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2140 Å2
MethodPISA
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(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3')


Mass: 3476.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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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
222isotropic22D 1H-1H NOESY
232isotropic22D 1H-1H TOCSY
242isotropic12D DQF-COSY
151isotropic52D 1H-1H ROESY
262isotropic52D 1H-1H ROESY
373isotropic41D 15N-edited HSQC
383isotropic41D 13C-edited HSQC
292isotropic3diffusion experiment
2102isotropic52D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.2 mM / SC11, 10 mM / potassium phosphate, 100 mM / potassium chloride, 90% H2O/10% D2OSC11_H2O90% H2O/10% D2O
solution20.2 mM / SC11, 10 mM / potassium phosphate, 100 mM / potassium chloride, 100% D2OSC11_D2O100% D2O
solution30.2 mM partial (12%) 15N, 13C residue-specific labelling SC11, 10 mM / potassium phosphate, 100 mM / potassium chloride, 90% H2O/10% D2OSC11_labelled90% H2O/10% D2Opartially (~12%) residue-specific 15N, 13C-labelled oligonucleotides
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMSC11/1
10 mMpotassium phosphate/1
100 mMpotassium chloride/1
0.2 mMSC11/2
10 mMpotassium phosphate/2
100 mMpotassium chloride/2
0.2 mMSC11partial (12%) 15N, 13C residue-specific labelling3
10 mMpotassium phosphate/3
100 mMpotassium chloride/3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mMSC11_H2O7.0 1 atm283 K
2100 mMSC11_D2O7.4 pD1 atm283 K
3100 mMSC11_labelled7.0 1 atm283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III7001room temperature inverse (1H-BB) probe
Bruker AVANCE IIIBrukerAVANCE III7005triple-resonance (1H-13C-15N) cryogenic probe
Bruker AVANCE IIIBrukerAVANCE III8502triple-resonance (1H-13C-15N) cryogenic probe
Bruker AVANCE IIIBrukerAVANCE III9503triple-resonance (1H-13C-15N) cryogenic probe
Varian Uniform NMR SystemVarianUniform NMR System6004DD2 console

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
TopSpin3.1Bruker Biospinprocessing
VNMRVarianprocessing
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
VNMRVarianchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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