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- PDB-2ldt: The 912-888 alternate conformation for helix 27 of E.coli 16S rRNA -

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Basic information

Entry
Database: PDB / ID: 2ldt
TitleThe 912-888 alternate conformation for helix 27 of E.coli 16S rRNA
ComponentsRNA (31-MER)
KeywordsRNA / rRNA / switch helix
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsSpano, M.N. / Walter, N.G.
CitationJournal: Biopolymers / Year: 2011
Title: Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA.
Authors: Spano, M.N. / Walter, N.G.
History
DepositionJun 2, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)10,0121
Polymers10,0121
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)13 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (31-MER)


Mass: 10012.048 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: transcribed using T7 RNA polymerase from a chemically synthesized double-stranded DNA template.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: ensemble of 13 low-energy nmr structures
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-15N HSQC
1412D 1H-13C HSQC
1512D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.8 - 1.6 mM [U-99% 13C; U-99% 15N] RNA (31-MER), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: RNA (31-MER)-1 / Isotopic labeling: [U-99% 13C; U-99% 15N] / Conc. range: 0.8-1.6
Sample conditionsIonic strength: 0.05 / pH: 6.4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 449
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 13

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