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- PDB-2h49: The NMR Structure of an Internal Loop from 23S Ribosomal RNA of D... -

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Basic information

Entry
Database: PDB / ID: 2h49
TitleThe NMR Structure of an Internal Loop from 23S Ribosomal RNA of Deinococcus radiodurans Differs from the Structure in the Crystal of the Ribosomal Subunit
Components
  • 5'-R(*GP*GP*CP*UP*AP*AP*GP*AP*C)-3'
  • 5'-R(*GP*UP*CP*GP*AP*AP*GP*CP*C)-3'
KeywordsRNA / RNA INTERNAL LOOP 5'cUAAg3'/3'gAAGc5' / COMPARISON BETWEEN CRYSTAL STRUCTURE AND NMR STRUCTURE / THERMODYNAMICS OF INTERNAL LOOP
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsShankar, N.
CitationJournal: Biochemistry / Year: 2006
Title: The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits.
Authors: Shankar, N. / Kennedy, S.D. / Chen, G. / Krugh, T.R. / Turner, D.H.
History
DepositionMay 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 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_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 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: 5'-R(*GP*GP*CP*UP*AP*AP*GP*AP*C)-3'
B: 5'-R(*GP*UP*CP*GP*AP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,7662
Polymers5,7662
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 2894.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized on a DNA/RNA synthesizer
#2: RNA chain 5'-R(*GP*UP*CP*GP*AP*AP*GP*CP*C)-3'


Mass: 2870.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized on a DNA/RNA synthesizer

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM TOTAL DUPLEX CONCENTRATION; 80MM NACL, 10MM SODIUM PHOSPHATE, 0.5MM NA2EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
22mM TOTAL DUPLEX CONCENTRATION; 80MM NACL, 10MM SODIUM PHOSPHATE, 0.5MM NA2EDTA, 100% D2O100% D2O
Sample conditionspH: 6.5 / Temperature units: 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

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.11T. D. Goddard and D. G. Knellerdata analysis
NMRDraw2.3F. Delaglioprocessing
Discover98Molecular Simulations Inc.refinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
Details: SILICON GRAPHICS OCTANE COMPUTER,AMBER 95 FORCE FIELD
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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