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- PDB-2lbl: Unmodified Glycyl-tRNA(UCC) anticodon stem-loop from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2lbl
TitleUnmodified Glycyl-tRNA(UCC) anticodon stem-loop from Bacillus subtilis
ComponentsRNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*UP*CP*CP*AP*AP*GP*UP*CP*UP*C)-3')
KeywordsRNA / anticodon stem-loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 3
AuthorsChang, A.T. / Nikonowicz, E.P.
CitationJournal: Biochemistry / Year: 2012
Title: Solution Nuclear Magnetic Resonance Analyses of the Anticodon Arms of Proteinogenic and Nonproteinogenic tRNA(Gly).
Authors: Chang, A.T. / Nikonowicz, E.P.
History
DepositionMar 31, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,3791
Polymers5,3791
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 lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 5379.237 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 1H-13C HSQC
1212D 1H-1H COSY
1322D 1H-1H NOESY
1413D (H)CCH-TOCSY
1513D 1H-13C NOESY
1612D HCN

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Sample preparation

Details
Solution-IDContentsSolvent system
10.02-0.04 mM [U-95% 13C; U-95% 15N] RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*UP*CP*CP*AP*AP*GP*UP*CP*UP*C)-3'), 100% D2O100% D2O
20.02-0.04 mM RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*UP*CP*CP*AP*AP*GP*UP*CP*UP*C)-3'), 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*UP*CP*CP*AP*AP*GP*UP*CP*UP*C)-3')-1[U-95% 13C; U-95% 15N]0.02-0.041
mMRNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*UP*CP*CP*AP*AP*GP*UP*CP*UP*C)-3')-20.02-0.042
Sample conditionsIonic strength: 10 / pH: 6.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.chemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 8

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