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- PDB-1k5i: NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved C... -

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Entry
Database: PDB / ID: 1k5i
TitleNMR Structure of a Ribosomal RNA Hairpin Containing a Conserved CUCAA Pentaloop
Components5'-R(P*GP*GP*AP*CP*CP*CP*GP*GP*GP*CP*UP*CP*AP*AP*CP*CP*UP*GP*GP*GP*UP*CP*C)-3'
KeywordsRNA / CUCAA pentaloop / RNA hairpin / non standard base-base interaction
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Distance Geometry, Simulated Annealing, Restrained Molecular Dynamics
AuthorsNagaswamy, U. / Gao, X. / Martinis, S.A. / Fox, G.E.
CitationJournal: Nucleic Acids Res. / Year: 2001
Title: NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop.
Authors: Nagaswamy, U. / Gao, X. / Martinis, S.A. / Fox, G.E.
History
DepositionOct 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: 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(P*GP*GP*AP*CP*CP*CP*GP*GP*GP*CP*UP*CP*AP*AP*CP*CP*UP*GP*GP*GP*UP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3691
Polymers7,3691
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 / 33structures with the lowest energy
Representative

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Components

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


Mass: 7369.440 Da / Num. of mol.: 1 / Fragment: 16S ribosomal RNA fragment (612-628) / Source method: obtained synthetically
Details: The oligonucleotide was synthesized by T7 run-off transcription.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1311H-31P HETCOR
141COSY-35
151TOCSY
161

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.590% H2O/10% D2O
210 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.599.99 % D2O
Sample conditionsIonic strength: 10 mM Sodium Phosphate / pH: 6.5 / Pressure: ambient / Temperature: 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 spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: Brunger / Classification: refinement
RefinementMethod: Distance Geometry, Simulated Annealing, Restrained Molecular Dynamics
Software ordinal: 1
Details: A total of 300 structures were calculated using distance geometry utilizing 123 experimentally derived distance restraints for the loop and 918 (258-experimental distances, 660-A form ...Details: A total of 300 structures were calculated using distance geometry utilizing 123 experimentally derived distance restraints for the loop and 918 (258-experimental distances, 660-A form distances) distance restraints for the stem region and 143 dihedral angle restraints. Additionally, 50 distance restraints were used to maintain the Watson-Crick geometry of the base pairs in the stem region. Final refinement resulted in 10 lowest energy structures.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 33 / Conformers submitted total number: 10

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