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- PDB-2lbq: NMR structure of i6A37_tyrASL -

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Basic information

Entry
Database: PDB / ID: 2lbq
TitleNMR structure of i6A37_tyrASL
ComponentsRNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*UP*AP*(6IA)P*AP*UP*CP*CP*CP*C)-3')
KeywordsRNA / Tyrosyl-tRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, 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
DepositionApr 5, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*UP*AP*(6IA)P*AP*UP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,5121
Polymers5,5121
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 #1closest to the average

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Components

#1: RNA chain RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*UP*AP*(6IA)P*AP*UP*CP*CP*CP*C)-3')


Mass: 5512.433 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-13C HSQC
1312D (H)CCH-COSY
1412D 1H-13C Long Range HSQC
1513D 1H-13C NOESY
1612D (H)CCH-RELAY
1712D HCNC

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Sample preparation

DetailsContents: 2.0 mM [U-100% 13C; U-100% 15N] i6A tyrASL, 10 mM potassium phosphate, 10 mM potassium chloride, 0.02 mM EDTA, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMi6A tyrASL-1[U-100% 13C; U-100% 15N]1
10 mMpotassium phosphate-21
10 mMpotassium chloride-31
0.02 mMEDTA-41
Sample conditionspH: 6.3 / 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.data analysis
FelixAccelrys Software Inc.processing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Insight IIAccelrys Software Inc.data analysis
VnmrJVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 8

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