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- PDB-1syz: Solution structure of the S. Cerevisiae U6 intramolecular stem lo... -

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Basic information

Entry
Database: PDB / ID: 1syz
TitleSolution structure of the S. Cerevisiae U6 intramolecular stem loop (ISL) RNA at pH 5.7
ComponentsU6 INTRAMOLECULAR STEM-LOOP RNA
KeywordsRNA / Stem-loop / GNRA-like tetratloop / A-C Wobble pair / Internal loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / XPLOR-NIH 2.0.6.
AuthorsReiter, N.J. / Blad, H. / Abildgaard, F. / Butcher, S.E.
Citation
Journal: Biochemistry / Year: 2004
Title: Dynamics in the U6 RNA Intramolecular Stem-Loop: A Base Flipping Conformational Change.
Authors: Reiter, N.J. / Blad, H. / Abildgaard, F. / Butcher, S.E.
#1: Journal: To be Published
Title: Dynamics in the U6 RNA intramolecular stem loop structure: II. Analysis of conformational exchange and metal binding using 13C NMR relaxation
Authors: Blad, H. / Reiter, N.J. / Abildgaard, F. / Butcher, S.E.
History
DepositionApr 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)14 / 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. THE SEQUENCE IS FROM SACCHAROMYCES CEREVISIAE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
2322D TOCSY
2421H-13C HSQC
NMR detailsText: 13C, 15N Istopically labelled RNA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.2 mM RNA, 50 mM NaCl, pH 5.7H2O
20.8-1.2 mM RNA, 50 mM NaCl, pH 5.7D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl 5.7Ambient 285 K
250 mM NaCl 5.7Ambient 303 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. et al.structure solution
XPLORNIH2.0.6.Clore, G.M. et. al.refinement
X-PLOR2.6Bruker Biospincollection
Sparky3Goddard, T.D. et. al.data analysis
RefinementMethod: XPLOR-NIH 2.0.6. / Software ordinal: 1
Details: Method allowed for the incorporation of 29 residual dipolar couplings into the structure refinement process.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 14

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