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- PDB-1tjz: Solution Structure of the Active Site Stem-Loop of the VS Ribozyme -

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Basic information

Entry
Database: PDB / ID: 1tjz
TitleSolution Structure of the Active Site Stem-Loop of the VS Ribozyme
ComponentsVS Ribozyme
KeywordsRNA / RNA hairpin / RNA stem-loop / protonated adenine / GA base pair
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / The structure calculations utilized standard simulated annealing protocols.
AuthorsFlinders, J. / Dieckmann, T.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The solution structure of the VS ribozyme active site loop reveals a dynamic "hot-spot"
Authors: Flinders, J. / Dieckmann, T.
History
DepositionJun 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 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: VS Ribozyme


Theoretical massNumber of molelcules
Total (without water)7,1271
Polymers7,1271
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain VS Ribozyme


Mass: 7127.322 Da / Num. of mol.: 1 / Fragment: RNA Loop VI / Source method: obtained synthetically
Details: Synthesized enzymatically from a DNA template using T7 polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2232D NOESY
233DQF-COSY
2432D TOCSY
2543D 13C-separated NOESY
2652D NOESY
NMR detailsText: The structure was determined from restraints derived from homo- and heteronuclear experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM VSVI RNA, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM VSVI RNA U-15N,13C,90% H2O/10% D2O
31 mM VSVI RNA, 90% H2O, 10% D2O100% D2O
41 mM VSVI RNA U-15N,13C, 100% D2O100% D2O
51 mM VSVI RNA, 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)Ionic strength
16ambient 283 K
26ambient 293 K
36ambient 293 K10 mM MgCl2

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
XwinNMR3.5collection
Sparky3.106data analysis
CNS1.1structure solution
XwinNMR3.5processing
CNS1.1refinement
RefinementMethod: The structure calculations utilized standard simulated annealing protocols.
Software ordinal: 1
Details: The final structures are based on a total of 699 restraints: 582 NOE-derived restraints, 52 dihedral angle restraints, 9 planarity restraints, and 56 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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