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- PDB-1jox: NMR Structure of the LP5.1 Hairpin from Bacillus RNase P RNA Refi... -

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Basic information

Entry
Database: PDB / ID: 1jox
TitleNMR Structure of the LP5.1 Hairpin from Bacillus RNase P RNA Refined with Residual Dipolar Couplings
Components5'-R(*GP*GP*CP*GP*GP*UP*GP*CP*UP*GP*AP*GP*AP*UP*GP*CP*CP*CP*GP*UP*C)-3'
KeywordsRNA / RIBONUCLEIC ACID / RNASE P / HAIRPIN / RESIDUAL DIPOLAR COUPLING REFINEMENT / UGNRAU
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLeeper, T.C. / Schmidt, F.J. / Van Doren, S.R.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action.
Authors: Leeper, T.C. / Martin, M.B. / Kim, H. / Cox, S. / Semenchenko, V. / Schmidt, F.J. / Van Doren, S.R.
History
DepositionJul 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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*GP*GP*UP*GP*CP*UP*GP*AP*GP*AP*UP*GP*CP*CP*CP*GP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,7761
Polymers6,7761
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)24 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 6776.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IN VITRO TRANSCRIPTION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-separated-NOESY (Mixing times of 200 and 250 ms)
121NOESY (Mixing times of 80 and 140 ms)
131(H)CCH-TOCSY
141(H)CCH-COSY
151IPAP-HSQC
16113C-HETERO-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM PL5.1 hairpin RNA U-15N,13C, 20mM phosphate buffer NA, 100% D2O100% D2O
21.0 mM PL5.1 hairpin RNA U-15N,13C, 20mM phosphate buffer NA, 8% H2O 92% D2O8% H2O 92% D2O
32.5 mM PL5.1 hairpin RNA U-15N,13C U and A residues only, 20mM phosphate buffer NA, 100% D2O100% D2O
41.8 mM PL5.1 hairpin RNA U-15N,13C A, C, and G residues only, 20mM phosphate buffer NA, 100% D2O100% D2O
51.8 mM PL5.1 hairpin RNA U-15N,13C A, C, and G residues only, 20mM phosphate buffer NA, 8% H2O 92% D2O8% H2O 92% D2O
61.8 mM PL5.1 hairpin RNA U-15N,13C A, C, and G residues only, 20mM phosphate buffer NA, 100% D2O with 5% PEG/Hexanol for orientation100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM Sodium Phosphate 5.5ambient 298 K
220 mM Sodium Phosphate 5.5ambient 277 K
320 mM Sodium Phosphate 5.5ambient 298 K
420 mM Sodium Phosphate 5.5ambient 298 K
520 mM Sodium Phosphate 5.5ambient 277 K
620 mM Sodium Phosphate 5.5ambient 298 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 DRXBrukerDRX5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger et. alrefinement
CNS1Brunger et. alstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: residual dipolar coupling refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 24

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