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- PDB-2f88: Solution NMR structure of domain 5 from the Pyaiella littoralis (... -

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Basic information

Entry
Database: PDB / ID: 2f88
TitleSolution NMR structure of domain 5 from the Pyaiella littoralis (PL) group II intron
ComponentsD5-PL RNA RIBOZYME DOMAIN
KeywordsRNA / RNA hairpin / GNRA Tetraloop / Internal bulge / Mg Metal binding site
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / TORSION ANGLE MOLECULAR DYNAMICS CARTESIAN SPACE SIMULATED ANNEALING RESIDUAL DIPOLAR COUPLINGS REFINEMENT
AuthorsDayie, K.T.
CitationJournal: Rna / Year: 2006
Title: Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA
Authors: Seetharaman, M. / Eldho, N.V. / Padgett, R.A. / Dayie, K.T.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 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: D5-PL RNA RIBOZYME DOMAIN


Theoretical massNumber of molelcules
Total (without water)11,0101
Polymers11,0101
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)10 / 30structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain D5-PL RNA RIBOZYME DOMAIN


Mass: 11009.607 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was synthesized by in vitro transcription with T7 RNA polymerase'

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
2232D TOCSY
2313D 13C-separated NOESY
1413D 15N-separated NOESY
3513D 1H-13C-1H (H)CCH TOCSY
3613D 1H-13C-1H (H)CCH COSY
3713D 1H-13C-1H (H)CCH COSY TROSY
3813D HCCNH
2923D 13C-separated ROESY
410113C/15N HSQC
411113C/15N TROSY
NMR detailsText: The structure was determined using a battery of standard homonuclear and recently optimized triple-resonance NMR experiments

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM fully 13C/15N A,C,G,U labeled D5-PL, 100 mM KCl, 10 mM phosphate, 0-10 mM MgCl2, 92% H2O and 8% D2O or 99.999% D2O92% H2O and 8% D2O or 99.999% D2O
21 mM A-13C/15N Uracil labeled D5-PL, 100 mM KCl, 10 mM phosphate buffer, 0-10 mM MgCl2, 92% H2O and 8% D2O or 99.999% D2O92% H2O and 8% D2O or 99.999% D2O
31 mM unlabeled D5-PL, 100 mM KCl, 10 mM phosphate buffer, 0-10 mM MgCl2, 92% H2O and 8% D2O or 99.999% D2O92% H2O and 8% D2O or 99.999% D2O
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
1100 mM KCl 6.5278 K
2100 mM KCl 6.5298 K
3100 mM KCl 6.5308 K
4100 mM KCl 6.5318 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Bruker AVANCEBrukerAVANCE6003
Bruker AVANCEBrukerAVANCE8004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio, Baxprocessing
Sparky3Goddard & Knellerdata analysis
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: TORSION ANGLE MOLECULAR DYNAMICS CARTESIAN SPACE SIMULATED ANNEALING RESIDUAL DIPOLAR COUPLINGS REFINEMENT
Software ordinal: 1
Details: STRUCTURES BASED ON 549 NOE-DERIVED DISTANCE RESTRAINTS, 304 DIHEDRAL RESTRAINTS, 60 HYDROGEN BOND RESTRAINTS, AND 37 RESIDUAL DIPOLAR COUPLING RESTRAINTS
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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