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- PDB-1kka: Solution Structure of the Unmodified Anticodon Stem-loop from E. ... -

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Basic information

Entry
Database: PDB / ID: 1kka
TitleSolution Structure of the Unmodified Anticodon Stem-loop from E. coli tRNA(Phe)
Componentsanticodon stem-loop of tRNA(PHE)
KeywordsRNA / RNA stem-loop / trinucleotide loop / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailstRNA(Phe)
AuthorsCabello-Villegas, J. / Winkler, M.E. / Nikonowicz, E.P.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Solution conformations of unmodified and A(37)N(6)-dimethylallyl modified anticodon stem-loops of Escherichia coli tRNA(Phe).
Authors: Cabello-Villegas, J. / Winkler, M.E. / Nikonowicz, E.P.
History
DepositionDec 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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:
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Assembly

Deposited unit
A: anticodon stem-loop of tRNA(PHE)


Theoretical massNumber of molelcules
Total (without water)5,4661
Polymers5,4661
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)8 / 60structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1

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Components

#1: RNA chain anticodon stem-loop of tRNA(PHE)


Mass: 5466.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 RNA polymerase in vitro transcription

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131DQF-COSY
141HNN-COSY
NMR detailsText: The structure was determined using 1H, 13C, 15N and 31P heteronuclear NMR spectroscopy.

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Sample preparation

DetailsContents: 2mM ACSL-Phe, 15N, 13C
Solvent system: 10 mM Potassium Phosphate, 10mM NaCl, 0.02mM EDTA. 90% H2O-10% D2O or 100% D2O.
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM KPi, 10mM NaCl 6.81 atm298 K
210 mM KPi, 10mM NaCl 6.81 atm288 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 spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.861Brunger, A.refinement
Felix98MSI-Biosymdata analysis
X-PLOR3.1Brungerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 294 NOE distance constraints, 36 base pair constraints, 70 torsion angle constraints. Global fold without torsion angle constraints. Refinement with torsion angle constraints.
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 8

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