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- PDB-2l5z: NMR structure of the A730 loop of the Neurospora VS ribozyme -

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Basic information

Entry
Database: PDB / ID: 2l5z
TitleNMR structure of the A730 loop of the Neurospora VS ribozyme
ComponentsRNA (26-MER)
KeywordsRNA / internal loop / VS ribozyme
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesNeurospora (fungus)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsminimized average, model 1
AuthorsDesjardins, G. / Bonneau, E. / Girard, N. / Boisbouvier, J. / Legault, P.
Citation
Journal: Nucleic Acids Res. / Year: 2011
Title: NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site.
Authors: Desjardins, G. / Bonneau, E. / Girard, N. / Boisbouvier, J. / Legault, P.
#1: Journal: To be Published
Title: NMR Structure of the A730 loop of the Neurospora VS Ribozyme: Insights into the Formation of the Active Site
Authors: Desjardins, G. / Bonneau, E. / Girard, N. / Boisbouvier, J. / Legault, P.
History
DepositionNov 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)8,4211
Polymers8,4211
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)21 / 500structures with the lowest energy
RepresentativeModel #1minimized average

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Components

#1: RNA chain RNA (26-MER)


Mass: 8421.106 Da / Num. of mol.: 1 / Fragment: A730 loop domain of the VS ribozyme / Source method: obtained synthetically / Source: (synth.) Neurospora (fungus)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2162D 1H-13C CT-HSQC
2262D 1H-13C HMQC
2362D 1H-15N MQ-(HC)N(C)H
2463D CT-(H)CCH-COSY
2563D (H)CCH-TOCSY
2663D 13C-edited HMQC-NOESY
1711D flip-back WATERGATE 1H
1812D flip-back WATERGATE NOESY
1932D imino- and amino-optimized 2D 1H-15N HSQC
11052D H(NCCC)H for uracil and cytosine residues
11152D H(NC)-TOCSY-(C)H for guanosine residues
11252D (H)N(C)-TOCSY-(C)H for adenosine residues
11332D 1H-15N CPMG-NOESY
21442D 1H 15N HMQC optimized for transfers via J=7.0 Hz and J=21 Hz
11532D HNN-COSY
21622D DQF-COSY
21763D (H)CCH-E.COSY
11872D imino-optimized 2D 1H-15N HSQC
2198Spin-state selective experiments
2206Spin-state selective experiments

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-1.8 mM VS ribozyme SVI RNA (26-MER)-1, 90% H2O/10% D2O90% H2O/10% D2O
20.4-1.8 mM VS ribozyme SVI RNA (26-MER)-2, 100% D2O100% D2O
30.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-3, 90% H2O/10% D2O90% H2O/10% D2O
40.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-4, 100% D2O100% D2O
50.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-5, 90% H2O/10% D2O90% H2O/10% D2O
60.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6, 100% D2O100% D2O
70.4 mM [U-15N] VS ribozyme SVI RNA (26-MER)-7, 90% H2O/10% D2O90% H2O/10% D2O
80.4 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMVS ribozyme SVI RNA (26-MER)-10.4-1.81
mMVS ribozyme SVI RNA (26-MER)-20.4-1.82
mMVS ribozyme SVI RNA (26-MER)-3[U-15N]0.4-1.83
mMVS ribozyme SVI RNA (26-MER)-4[U-15N]0.4-1.84
mMVS ribozyme SVI RNA (26-MER)-5[U-13C; U-15N]0.4-1.85
mMVS ribozyme SVI RNA (26-MER)-6[U-13C; U-15N]0.4-1.86
0.4 mMVS ribozyme SVI RNA (26-MER)-7[U-15N]7
0.4 mMVS ribozyme SVI RNA (26-MER)-8[U-13C; U-15N]8
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM KCl and 5 mM MgCl2 6.5 ambient atm288 K
250 mM KCl and 5 mM MgCl2 6.5 ambient atm288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
Module1(Module)data analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Curves+(CURVES) Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K.structure analysis
PyMOLPyMol (Schr dinger)structure display
PyMOLPyMol (Schr dinger)structure analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 21

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