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- PDB-2la9: NMR structure of Pseudouridine_ASL_Tyr -

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Basic information

Entry
Database: PDB / ID: 2la9
TitleNMR structure of Pseudouridine_ASL_Tyr
ComponentsRNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*UP*AP*AP*AP*(PSU)P*CP*CP*CP*C)-3')
KeywordsRNA / Tyrosyl-tRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsDenmon, A.P. / Wang, J. / Nikonowicz, E.P.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Conformation Effects of Base Modification on the Anticodon Stem-Loop of Bacillus subtilis tRNA(Tyr).
Authors: Denmon, A.P. / Wang, J. / Nikonowicz, E.P.
History
DepositionMar 9, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn
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_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 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:
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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*UP*AP*AP*AP*(PSU)P*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,4421
Polymers5,4421
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 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 5442.300 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
1112D Natural Abundance HSQC
1212D 1H-1H NOESY
1312D 31P-1H

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Sample preparation

DetailsContents: 2.0 mM Pseudouridine_ASL_Tyr, 10 mM potassium chloride, 10 mM potassium phosphate, 0.02 mM EDTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2.0 mMPseudouridine_ASL_Tyr-11
10 mMpotassium chloride-21
10 mMpotassium phosphate-31
0.02 mMEDTA-41
Sample conditionspH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
FelixAccelrys Software Inc.peak picking
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.processing
Insight IIAccelrys Software Inc.data analysis
VNMRVariancollection
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 8

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