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- PDB-6ez0: Specific phosphorothioate substitution within domain 6 of a group... -

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Basic information

Entry
Database: PDB / ID: 6ez0
TitleSpecific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding
ComponentsRNA (27-MER)
KeywordsRNA / thiophosphate group II intron branch-adenosine hairpin tetraloop
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsErat, M.C. / Besic, E. / Oberhuber, M. / Johannsen, S. / Sigel, R.K.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: J. Biol. Inorg. Chem. / Year: 2018
Title: Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding.
Authors: Erat, M.C. / Besic, E. / Oberhuber, M. / Johannsen, S. / Sigel, R.K.O.
#1: Journal: Chembiochem / Year: 2007
Title: Solution structure of domain 6 from a self-splicing group II intron ribozyme: a Mg(2+) binding site is located close to the stacked branch adenosine.
Authors: Erat, M.C. / Zerbe, O. / Fox, T. / Sigel, R.K.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / 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_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)8,8011
Polymers8,8011
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2350 Å2
ΔGint4 kcal/mol
Surface area5110 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (27-MER)


Mass: 8800.562 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
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC aliphatic
141isotropic12D 1H-13C HSQC aromatic
252isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mM alpha-thio-D6-27, 100% D2Oalpha-thio-D6-27_D2O100% D2O
solution20.7 mM na alpha-thio-D6-27, 90% H2O/10% D2Oalpha-thio-D6-27_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMalpha-thio-D6-27natural abundance1
0.7 mMalpha-thio-D6-27na2
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
150 mMNon-exchangable6.7 pD0.11 atm303 K
250 mMExchangable6.7 1 atm275 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: Cryo TXI

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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