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- PDB-2gbh: NMR structure of stem region of helix-35 of 23S E.coli ribosomal ... -

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Basic information

Entry
Database: PDB / ID: 2gbh
TitleNMR structure of stem region of helix-35 of 23S E.coli ribosomal RNA (residues 736-760)
Components5'-R(*(GMP)P*GP*GP*CP*UP*AP*AP*UP*GP*(PSU)P*UP*GP*AP*AP*AP*AP*AP*UP*UP*AP*GP*CP*CP*C)-3'
KeywordsRNA / RDC / rCSA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Cartesian simulated annealing
AuthorsBax, A. / Boisbouvier, J. / Bryce, D. / Grishaev, A. / Jaroniec, C. / Miclet, E. / Nikonovicz, E. / O'Neil-Cabello, E. / Ying, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Measurement of five dipolar couplings from a single 3D NMR multiplet applied to the study of RNA dynamics.
Authors: O'Neil-Cabello, E. / Bryce, D.L. / Nikonowicz, E.P. / Bax, A.
History
DepositionMar 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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(*(GMP)P*GP*GP*CP*UP*AP*AP*UP*GP*(PSU)P*UP*GP*AP*AP*AP*AP*AP*UP*UP*AP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,6381
Polymers7,6381
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)5 / 5all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

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


Mass: 7637.666 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence of this RNA naturally exists in 23S Ribosomal RNA of E.Coli.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: RDC measurement

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Sample preparation

DetailsContents: 1.5mM helix-35psi U-15N,13C; 17mM NaCl, 17mM phosphate buffer; 99% D2O
Solvent system: 99% D2O
Sample conditionsIonic strength: 17 mM NaCl, 17 mM phosphate / pH: 6.8 / Pressure: ambient / Temperature: 298 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
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR softwareName: Xplor-NIH / Version: 2.9.4 / Developer: Schwieters, Kuszewski, Tjandra, Clore / Classification: refinement
RefinementMethod: Cartesian simulated annealing / Software ordinal: 1
Details: Experimental restraints for the helix-35 stem are 277 RDCs, 13 31P anisotropic shifts, 41 dihedral angles and 188 NOEs. During the refinement the geometries of selected ribose rings were ...Details: Experimental restraints for the helix-35 stem are 277 RDCs, 13 31P anisotropic shifts, 41 dihedral angles and 188 NOEs. During the refinement the geometries of selected ribose rings were kept identical with the NCS restraint terms. Attractive non-bonded potentials were employed. No database-derived terms were used. The parameter file was modified with nucleotide type-specific values for distances, angles and improper torsions. Cross-validation statistics on the groups of 1/4 of ribose 1-bond C-H RDCs corresponds to an average Q-factor of 0.135.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 5 / Conformers submitted total number: 5

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