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- PDB-1hwq: SOLUTION STRUCTURE OF THE VS RIBOZYME SUBSTRATE STEM-LOOP -

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Entry
Database: PDB / ID: 1hwq
TitleSOLUTION STRUCTURE OF THE VS RIBOZYME SUBSTRATE STEM-LOOP
ComponentsVS RIBOZYME SUBSTRATE RNA
KeywordsRNA / VS RIBOZYME / STEM-LOOP / TANDEM GA / PROTONATED ADENINE / A+C BASE PAIR
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsFlinders, J.C. / Dieckmann, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA.
Authors: Flinders, J. / Dieckmann, T.
History
DepositionJan 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VS RIBOZYME SUBSTRATE RNA


Theoretical massNumber of molelcules
Total (without water)9,7061
Polymers9,7061
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain VS RIBOZYME SUBSTRATE RNA


Mass: 9705.832 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA samples were transcribed from synthetic DNA templates using T7 RNA polymerase.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
3333D 13C-separated NOESY
242DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM VS RNA90% H2O/10% D2O
21.5 mM VS RNA100% D2O
31.5 mM VS RNA, 13C, 15N labeled100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15 mM NaCl 6ambient 274 K
25 mM NaCl 6ambient 298 K
35 mM NaCl 6ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
XEASY1.3.13Bartels, C.data analysis
CNS1Brunger, A.structure solution
CNS1Brunger, A.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: These structures were calculated using a total of 568 restraints; including 335 NOE-derived distance constraints, 158 dihedral angle restraints, 12 planarity restraints, and 63 H-bond distance restraints.
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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