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- PDB-1sy4: Refined solution structure of the S. cerevisiae U6 INTRAMOLECULAR... -

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Basic information

Entry
Database: PDB / ID: 1sy4
TitleRefined solution structure of the S. cerevisiae U6 INTRAMOLECULAR STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR COUPLINGS (RDCS)
ComponentsU6 Intramolecular Stem-Loop RNA
KeywordsRNA / Stem-loop (GNRA-like tetraloop) / A-C wobble pair / internal loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / XPLOR-NIH 2.0.6 structure calculation which incorporates Residual dipolar couplings
AuthorsReiter, N.J. / Nikstad, L.J. / Allman, A.M. / Johnson, R.J. / Butcher, S.E.
Citation
Journal: RNA / Year: 2003
Title: Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.
Authors: Reiter, N.J. / Nikstad, L.J. / Allman, A.M. / Johnson, R.J. / Butcher, S.E.
#1: Journal: Nat.Struct.Biol. / Year: 2002
Title: Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure
Authors: Huppler, A. / Nikstad, L.J. / Allmann, A.M. / Brow, D.A. / Butcher, S.E.
History
DepositionMar 31, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionApr 6, 2004ID: 1NYZ
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U6 Intramolecular Stem-Loop RNA


Theoretical massNumber of molelcules
Total (without water)7,6691
Polymers7,6691
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)12 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain U6 Intramolecular Stem-Loop RNA


Mass: 7668.615 Da / Num. of mol.: 1 / Mutation: A62G / Source method: obtained synthetically / Details: in vitro T7 RNA polymerase transcription

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1312D 1H-13C HSQC
2422D NOESY
NMR detailsText: T7 RNA transcript from synthetic DNA (sequence from Saccharomyces cerevisiae)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.4 MM RNA, 50 MM NaCl, pH 7.0D2O
20.8-1.4 MM RNA, 50 MM NaCl, pH 7.0H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl 7ambient 303 K
250 mM NaCl 7ambient 285 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX3

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A. T. et. al.structure solution
XPLORNIH2.0.6.Clore, G.M. et. al.refinement
XwinNMR2.6Bruker Biospincollection
Sparky3Goddard, T. D. etl. al.data analysis
RefinementMethod: XPLOR-NIH 2.0.6 structure calculation which incorporates Residual dipolar couplings
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: 12

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