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- PDB-1jur: Solution Structure of Helix III in Xenopus Oocyte 5S rRNA. -

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Entry
Database: PDB / ID: 1jur
TitleSolution Structure of Helix III in Xenopus Oocyte 5S rRNA.
Components5'-R(*GP*GP*CP*CP*UP*GP*AP*GP*GP*AP*GP*AP*CP*UP*CP*AP*GP*AP*AP*GP*CP*C)-3'
KeywordsRNA / 5 S rRNA / bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHuber, P.W. / Rife, J.P. / Moore, P.B.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The structure of helix III in Xenopus oocyte 5 S rRNA: an RNA stem containing a two-nucleotide bulge.
Authors: Huber, P.W. / Rife, J.P. / Moore, P.B.
History
DepositionAug 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: 5'-R(*GP*GP*CP*CP*UP*GP*AP*GP*GP*AP*GP*AP*CP*UP*CP*AP*GP*AP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,1351
Polymers7,1351
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)9 / 30structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 7135.346 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The stem of this hairpin occurs naturally in Xenopus Oocytes.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
232DQF-COSY
2422D 13C separated HMQC
2522D 31P separated COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM Helix III hairpin; 5mM Cacodylate buffer (pH 6.5); 100 mM KCl90% H2O/10% D2O
22mM Helix III hairpin; 5mM Cacodylate buffer (pH 6.5); 100 mM KCl100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM KCl 6.5ambient 10 K
2100 mM KCl 6.5ambient 30 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
Varian UNITYVarianUNITY5001
Varian UNITYPLUSVarianUNITYPLUS6002
Varian INOVAVarianINOVA8003
GE OMEGAGEOMEGA5004

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
Felix95Biosymprocessing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: In addition to the experimentally derived distance constraints and dihedral angle constraints, the structures were computed using 22 non-experimental constraints to ensure Watson-Crick Base ...Details: In addition to the experimentally derived distance constraints and dihedral angle constraints, the structures were computed using 22 non-experimental constraints to ensure Watson-Crick Base pairing and tetraloop formation.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 9

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