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- PDB-1tbk: NMR structure of the VS ribozyme stem-loop V RNA in the absence o... -

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Basic information

Entry
Database: PDB / ID: 1tbk
TitleNMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.
ComponentsVS ribozyme stem-loop V
KeywordsRNA / U-turn / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsCampbell, D.O. / Legault, P.
CitationJournal: Biochemistry / Year: 2005
Title: Nuclear Magnetic Resonance Structure of the Varkud Satellite Ribozyme Stem-Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping
Authors: Campbell, D.O. / Legault, P.
History
DepositionMay 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: 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

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: VS ribozyme stem-loop V


Theoretical massNumber of molelcules
Total (without water)5,4191
Polymers5,4191
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)11 / 61The submitted conformer models are the 10 structures with the lowest energy (MODEL 2 -- 11)
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain VS ribozyme stem-loop V


Mass: 5419.261 Da / Num. of mol.: 1 / Fragment: SL5 / Source method: obtained synthetically
Details: This sequence is derived from the Neurospora Varkud satellite ribozyme

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D flip-back WATERGATE NOESY
1222D 1H-15N CPMG-NOESY
2322D 1H-15N CPMG-NOESY
1422D HNN-CSOSY
1552D HNN-COSY
1633D 13C-edited HMQC-NOESY
174DQF-COSY
1833D (H)CCH E.COSY
1932D 1H-13C CT-TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1unlabeled SL510 mM d11-Tris, 50 mM NaCl, 0.2 mM EDTA, 0.05 mM NaN3, pH 7.0, 90% H2O and 10% D2O
215N Sl510 mM d11-Tris, 50 mM NaCl, 0.2 mM EDTA, 0.05 mM NaN3, pH 7.0, 90% H2O and 10% D2O
313C 15N Sl510 mM d11-Tris, 50 mM NaCl, 0.2 mM EDTA, 0.05 mM NaN3, pH 7.0, 100% D2O
4unlabeled SL510 mM d11-Tris, 50 mM NaCl, 0.2 mM EDTA, 0.05 mM NaN3, pH 7.0, 100% D2O
515N SL510 mM d11-Tris, 50 mM NaCl, 0.2 mM EDTA, 0.05 mM NaN3, pH 7.0, 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl 7ambient 298 K
250 mM NaCl 7ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH-2.0.6Brungerstructure solution
NMRPipe97.231.15.18Delaglioprocessing
NMRView5.0.3Johnsondata analysis
MOLMOL2K.2Koradidata analysis
Curves5.1Laverydata analysis
X-PLORNIH-2.0.6Brungerrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: The submitted conformer models are the 10 structures with the lowest energy (MODEL 2 -- 11)
Conformers calculated total number: 61 / Conformers submitted total number: 11

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