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- PDB-1yn2: Solution structure of the Neurospora VS ribozyme stem-loop V in t... -

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Basic information

Entry
Database: PDB / ID: 1yn2
TitleSolution structure of the Neurospora VS ribozyme stem-loop V in the presence of MgCl2 with modeling of bound manganese ions
ComponentsVS RIBOZYME STEM-LOOP V
KeywordsRNA / U-turn / hairpin / magnesium ions / manganese ions / paramagnetic
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
Model type detailsminimized average
AuthorsCampbell, D.O. / Legault, P.
Citation
Journal: Biochemistry / Year: 2006
Title: NMR structure of varkud satellite ribozyme stem-loop v in the presence of magnesium ions and localization of metal-binding sites
Authors: Campbell, D.O. / Bouchard, P. / Desjardins, G. / Legault, P.
#1: Journal: To be Published / Year: 2005
Title: NMR Structure of the VS Ribozyme Stem-Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping
Authors: Campbell, D.O. / Legault, P.
History
DepositionJan 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 STEM-LOOP V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6395
Polymers5,4191
Non-polymers2204
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 46structures with the lowest energy
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
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N CPMG-NOESY
1213D 13C-EDITED HMQC-NOESY
1312D HNN-COSY
1413D (H)CCH E.COSY
1512D 1H-13C CT-HSQC
1612D 1H-15N HSQC
1711D 31P
NMR detailsText: Bound manganese ions were modeled using distance restraints derived from Mn-induced paramagnetic line broadening

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Sample preparation

DetailsContents: 0.8 mM to 2.0 mM of unlabeled, 15N, or 13C/15N SL5
Solvent system: [10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 ...Solvent system: [10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 uM, 20 uM, 40 uM, or 80 uM MnCl2 were added.
Sample conditionsIonic strength: variable (see sample details) / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH-2.0.6Brunger, A.structure solution
NMRPipemost currentDelaglio, F.data analysis
NMRView5.0.3Johnson, B.data analysis
MOLMOL2K.2Koradi, R.data analysis
X-PLORNIH-2.0.6Brunger, A.refinement
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
Details: Conformer 1 represents the minimized average structure, the 10 following structures represent the ensemble of low-energy structures
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 46 / Conformers submitted total number: 11

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