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- PDB-2rpk: Solution Structure of Domain II of the Positive Polarity CCHMVD H... -

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Basic information

Entry
Database: PDB / ID: 2rpk
TitleSolution Structure of Domain II of the Positive Polarity CCHMVD Hammerhead Ribozyme
ComponentsRNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3')
KeywordsRNA / HAMMERHEAD RIBOZYME / VIROID / CCHMVD / HEXALOOP
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, restrained energy minimization
Model type detailsminimized average
AuthorsGallego, J. / Dufour, D. / de la Pena, M. / Gago, S. / Flores, R.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads
Authors: Dufour, D. / de la Pena, M. / Gago, S. / Flores, R. / Gallego, J.
History
DepositionMay 28, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 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: RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,4221
Polymers6,4221
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)1 / 60minimized average structure of 33 converged conformers with the least restraint violation energy and total energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3')


Mass: 6421.895 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
2322D 1H-1H TOCSY
2422D 1H-1H COSY
1532D 1H-15N HSQC
2642D 1H-13C HSQC
2743D 1H,13C HMQC-NOESY
2843D (H)CCH-COSY
2942D (H)CCH-TOCSY
21043D HCP
21143D 13C-ED-1H-31P HETCOR

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA, 100% D2O100% D2O
30.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
40.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMRNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3')1
10 mMsodium phosphate1
0.1 mMEDTA1
0.7 mMRNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3')2
10 mMsodium phosphate2
0.1 mMEDTA2
0.4 mMRNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3')[U-100% 13C; U-100% 15N]3
10 mMsodium phosphate3
0.1 mMEDTA3
0.4 mMRNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3')[U-100% 13C; U-100% 15N]4
10 mMsodium phosphate4
0.1 mMEDTA4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
112.46ambient 281 K
212.46ambient 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddarddata analysis
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing, restrained energy minimization / Software ordinal: 1
Details: minimized average structure of 33 converged conformers with the least restraint violation energy and total energy
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: minimized average structure of 33 converged conformers with the least restraint violation energy and total energy
Conformers calculated total number: 60 / Conformers submitted total number: 1 / Representative conformer: 1

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