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- PDB-2khy: Specifier Domain of B. subtilis tyrS T box leader RNA -

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Basic information

Entry
Database: PDB / ID: 2khy
TitleSpecifier Domain of B. subtilis tyrS T box leader RNA
ComponentsRNA (38-MER)
KeywordsRNA / Specifier domain / Bacillus / S-turn / loop-E
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsWang, J. / Henkin, T.M.
Citation
Journal: Nucleic Acids Res. / Year: 2010
Title: NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA.
Authors: Wang, J. / Henkin, T.M. / Nikonowicz, E.P.
#1: Journal: J.Bacteriol. / Year: 1997
Title: Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination.
Authors: Grundy, F.J. / Hodil, S.E. / Rollins, S.M. / Henkin, T.M.
History
DepositionApr 14, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 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: RNA (38-MER)


Theoretical massNumber of molelcules
Total (without water)12,2241
Polymers12,2241
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 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (38-MER)


Mass: 12224.326 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-13C HSQC
1233D 1H-13C NOESY
1333D (H)CCH-COSY
1433D (H)CCH-TOCSY
1532D 1H-13C HSQC
1612D 1H-1H NOESY
1712D DQF-COSY
2822D 1H-15N HSQC
2923D 1H-15N NOESY
11033D (H)CCH-COSY
NMR detailsText: For anisotropic experiments, phage Pf1 at 21 mg/ml was used.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM Specifier Domain of tyrS T box leader RNA-1, 100% D2O100% D2O
21.6 mM [U-99% 13C; U-99% 15N] Specifier Domain of tyrS T box leader RNA-2, 93% H2O/7% D2O93% H2O/7% D2O
31.6 mM [U-99% 13C; U-99% 15N] Specifier Domain of tyrS T box leader RNA-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.8 mMSpecifier Domain of tyrS T box leader RNA-11
1.6 mMSpecifier Domain of tyrS T box leader RNA-2[U-99% 13C; U-99% 15N]2
1.6 mMSpecifier Domain of tyrS T box leader RNA-3[U-99% 13C; U-99% 15N]3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.026.8ambient 301 K
20.026.8ambient 287 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR softwareName: X-PLOR NIH / Developer: Schwieters, C. et al. / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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