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- PDB-1n53: SOLUTION STRUCTURE OF B. SUBTILIS T BOX ANTITERMINATOR RNA -

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Basic information

Entry
Database: PDB / ID: 1n53
TitleSOLUTION STRUCTURE OF B. SUBTILIS T BOX ANTITERMINATOR RNA
Components
  • RNA (5'-R(*GP*AP*GP*GP*GP*UP*GP*GP*AP*AP*CP*CP*GP*CP*GP*C)-3')
  • RNA (5'-R(*GP*CP*GP*UP*CP*CP*CP*UP*C)-3')
KeywordsRNA / T box / bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsGerdeman, M.S. / Henkin, T.M. / Hines, J.V.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Solution Structure of the Bacillus subtilis T-box Antiterminator RNA: Seven Nucleotide Bulge Characterized by Stacking and Flexibility
Authors: Gerdeman, M.S. / Henkin, T.M. / Hines, J.V.
History
DepositionNov 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 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 (5'-R(*GP*AP*GP*GP*GP*UP*GP*GP*AP*AP*CP*CP*GP*CP*GP*C)-3')
B: RNA (5'-R(*GP*CP*GP*UP*CP*CP*CP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)8,0152
Polymers8,0152
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)1 / 50The minimized average structure of the 9 lowest energy structures (all with favorable non-bond energy and the fewest number of constraint violations) is submitted.
RepresentativeModel #1

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Components

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


Mass: 5231.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized using T7 RNA polymerase
#2: RNA chain RNA (5'-R(*GP*CP*GP*UP*CP*CP*CP*UP*C)-3')


Mass: 2783.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized using T7 RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1413D 13C-separated NOESY
1512D HSQC
1612D 1H 31P HETCOR
NMR detailsText: This structure was determined using standard 2D and 3D homonuclear and heteronuclear NMR techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM (U-15N, U-13C) or 1.2 mM (unlabeled) T box model RNA (AM1A); 10 mM sodium phosphate buffer pH 6.5, 0.01 mM EDTA100% D2O
20.7 mM (U-15N, U-13C) or 1.2 mM (unlabeled) T box model RNA (AM1A); 10 mM sodium phosphate buffer pH 6.5, 0.01 mM EDTA90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM 6.5ambient 295 K
210 mM 6.5ambient 277 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX4002
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameVersionDeveloperClassification
Felix95,98processing
X-PLOR98.1Brungerstructure solution
XwinNMRprocessing
X-PLOR98.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: A total of 313 distance constraints and 59 dihedral angle constraints were used.
NMR ensembleConformer selection criteria: The minimized average structure of the 9 lowest energy structures (all with favorable non-bond energy and the fewest number of constraint violations) is submitted.
Conformers calculated total number: 50 / Conformers submitted total number: 1

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