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- PDB-2awq: Solution Structure of pseudouridine-32 modified anticodon stem-lo... -

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Entry
Database: PDB / ID: 2awq
TitleSolution Structure of pseudouridine-32 modified anticodon stem-loop of E. coli tRNAPhe
Components5'-R(*GP*GP*GP*GP*AP*(PSU)P*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP*C)-3'
KeywordsRNA / tri-loop / Watson-Crick type psi32-A38 base pair
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle randomization simulated annealing, molecular dynamics
AuthorsCabello-Villegas, J. / Nikonowicz, E.P.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Solution structure of psi32-modified anticodon stem-loop of Escherichia coli tRNAPhe.
Authors: Cabello-Villegas, J. / Nikonowicz, E.P.
History
DepositionSep 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
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: 5'-R(*GP*GP*GP*GP*AP*(PSU)P*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP*C)-3'


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)10 / 75structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average,fewest violations

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Components

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


Mass: 5466.324 Da / Num. of mol.: 1 / Fragment: anticodon arm / Source method: obtained synthetically
Details: prepared by in vitro transcription and enzymatically pseudouridylated

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121(H)CCH-TOCSY
131CCH-RELAY
2423D 15N-separated NOESY
152DQF-COSY
162HP-HETCOR
NMR detailsText: pseudouridine assigned using CCH-RELAY type experiments. Base pairing determined from interresidue N-N scalar correlations. Distances derived from multiple mixing time NOESY experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.3 mM C-13 labeled RNA hairpin, 10 mM NaCl, 10 mM potassium phosphate, pH 6.8100% D2O
22.8 mM N-15 labeled RNA hairpin, 10 mM NaCl, 10 mM potassium phosphate, pH 6.890% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM NaCl, 10 mM potassium phosphate 6.8 ambient 298 K
210 mM NaCl, 10 mM potassium phosphate 6.8 ambient 285 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 AMXBrukerAMX5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerrefinement
Felix2000accelrysprocessing
RefinementMethod: torsion angle randomization simulated annealing, molecular dynamics
Software ordinal: 1
Details: structure determined using NOE derived distance constraints, and torsional angle restraints derived from J-couplings. Hydrogen bonds derived from NOESY and NN-COSY data.
NMR representativeSelection criteria: closest to the average,fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 75 / Conformers submitted total number: 10

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