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- PDB-1r2p: Solution structure of domain 5 from the ai5(gamma) group II intron -

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Basic information

Entry
Database: PDB / ID: 1r2p
TitleSolution structure of domain 5 from the ai5(gamma) group II intron
Components34-MER
KeywordsRNA / RNA HAIRPIN / TETRALOOP / BULGE / METAL ION / MAGNESIUM
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / TORSION ANGLE MOLECULAR DYNAMICS CARTESIAN SPACE SIMULATED ANNEALING, MOLECULAR DYNAMICS RESIDUAL DIPOLAR COUPLINGS
AuthorsSigel, R.K.O. / Sashital, D.G. / Abramovitz, D.L. / Palmer III, A.G. / Butcher, S.E. / Pyle, A.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.
Authors: Sigel, R.K. / Sashital, D.G. / Abramovitz, D.L. / Palmer, A.G. / Butcher, S.E. / Pyle, A.M.
History
DepositionSep 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_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 1.4May 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: 34-MER


Theoretical massNumber of molelcules
Total (without water)10,9711
Polymers10,9711
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 34-MER


Mass: 10970.567 Da / Num. of mol.: 1 / Fragment: DOMAIN 5 OF THE AI5(GAMMA) GROUP II INTRON / Source method: obtained synthetically
Details: SEQUENCE OCCURS NATURALLY IN Saccharomyces CEREVISIAE (Baker's yeast) AND WAS SYNTHESIZED IN VITRO USING T7 RNA POLYMERASE AND SYNTHETIC DNA OLIGONUCLEOTIDES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
3222D NOESY
4322D NOESY
2443D 13C-separated NOESY
2542D 1H-13C HSQC
2622D 1H-1H TOCSY
2743D 1H-13C-1H (H)CCH TOCSY
2843D 1H-13C-1H (H)CCH COSY
2932D 2JHN HNN-COSY
NMR detailsText: RESIDUAL DIPOLAR COUPLINGS WERE MEASURED USING 1H-13C HSQC COUPLED IN EITHER THE PROTON OR THE CARBON DIMENSION

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 - 0.7 mM D5 RNA; 0 - 200mM KCl, 0 - 20 mM MgCl2, 0.01 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
20.5 - 0.7 mM D5 RNA; 0 - 200mM KCl, 0 - 20 mM MgCl2, 0.01 mM EDTA, 99.999% D2O99.999% D2O
30.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
40.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA, 99.999% D2O99.999% D2O
50.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA, 17 mg/mL Pf1 FILAMENTOUS BACTERIOPHAGE, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
1100mM KCl 6.5 278 K
2100mM KCl 6.5 298 K
3100mM KCl 6.5 308 K
4100mM KCl 6.5 291 K
5100mM KCl 6.5 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker AVANCEBrukerAVANCE6001
Bruker DMXBrukerDMX5002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger et. al.structure solution
DYANAGuntert, Mumenthaler, Wuthrichdata analysis
Sparky3Goddard and Knellerdata analysis
XwinNMR2.6Brukerprocessing
CNS1.1Brunger et. al.refinement
RefinementMethod: TORSION ANGLE MOLECULAR DYNAMICS CARTESIAN SPACE SIMULATED ANNEALING, MOLECULAR DYNAMICS RESIDUAL DIPOLAR COUPLINGS
Software ordinal: 1
Details: STRUCTURES BASED ON 678 NOE-DERIVED DISTANCE RESTRAINTS, 261 DIHEDRAL RESTRAINTS, 72 HYDROGEN BOND RESTRAINTS, AND 24 RESIDUAL DIPOLAR COUPLING RESTRAINTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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