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- PDB-1feq: NMR SOLUTION STRUCTURE OF THE ANTICODON OF TRNA(LYS3) WITH T6A MO... -

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Entry
Database: PDB / ID: 1feq
TitleNMR SOLUTION STRUCTURE OF THE ANTICODON OF TRNA(LYS3) WITH T6A MODIFICATION AT POSITION 37
Components5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*UP*UP*(T6A)P*AP*UP*CP*UP*GP*C)-3'
KeywordsRNA / TRNA / Anticodon STEM LOOP / TRNA DOMAIN / RNA HAIRPIN / T6A
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / global fold by distance geometry. Refinement by simulated annealing using the AMBER forcefield
AuthorsStuart, J.W. / Gdaniec, Z. / Guenther, R.H. / Marszalek, M. / Sochacka, E. / Malkiewicz, A. / Agris, P.F.
CitationJournal: Biochemistry / Year: 2000
Title: Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A.
Authors: Stuart, J.W. / Gdaniec, Z. / Guenther, R. / Marszalek, M. / Sochacka, E. / Malkiewicz, A. / Agris, P.F.
History
DepositionJul 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*UP*UP*(T6A)P*AP*UP*CP*UP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,5101
Polymers5,5101
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)11 / 50structures with the lowest energy
RepresentativeModel #1minimized average structure of family a (struct 2-5)

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Components

#1: RNA chain 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*UP*UP*(T6A)P*AP*UP*CP*UP*GP*C)-3'


Mass: 5510.319 Da / Num. of mol.: 1
Fragment: ANTICODON (RESIDUES 27-43) OF TRNA(LYS3) WITH T6A MODIFICATION AT POSITION 37
Source method: obtained synthetically
Details: sequence of tRNA(Lys3) with terminal base pair replaced with GC to enhance synthesis yield and stability

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 1.2 mM RNA, 10 mM cacodylate buffer, pH 5.6, 0.1 mM EDTA
Solvent system: 94% H2O, 6% D2O
Sample conditionspH: 5.6 / Pressure: 1 atm / Temperature: 289 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix98msidata analysis
Discover98msirefinement
RefinementMethod: global fold by distance geometry. Refinement by simulated annealing using the AMBER forcefield
Software ordinal: 1
Details: 272 restraints, 207 NOE-derived, 13 h-bond, 52 dihedral angle. Chi torsion was left unrestrained although likely anti for all residues.
NMR representativeSelection criteria: minimized average structure of family a (struct 2-5)
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 11

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