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- PDB-1fl8: HYPERMODIFIED NUCLEOSIDES IN THE ANTICODON OF TRNALYS STABILIZE A... -

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Basic information

Entry
Database: PDB / ID: 1fl8
TitleHYPERMODIFIED NUCLEOSIDES IN THE ANTICODON OF TRNALYS STABILIZE A CANONICAL U-TURN STRUCTURE
ComponentsANTICODON DOMAIN OF TRNA(LYS)
KeywordsRNA / tRNA / anticodon / pseudouridine / mnm5s2U / t6a
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / used H5-H6 distances for distance calculations then simulated annealing, molecular dynamics in vacuo then restrained minimization in vacuo
AuthorsSundaram, M. / Durant, P.C. / Davis, D.R.
CitationJournal: Biochemistry / Year: 2000
Title: Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-turn structure.
Authors: Sundaram, M. / Durant, P.C. / Davis, D.R.
History
DepositionAug 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 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_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: ANTICODON DOMAIN OF TRNA(LYS)


Theoretical massNumber of molelcules
Total (without water)5,5541
Polymers5,5541
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)20 / 35structures with the lowest energy
RepresentativeModel #4closest to the average,lowest energy

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Components

#1: RNA chain ANTICODON DOMAIN OF TRNA(LYS)


Mass: 5554.438 Da / Num. of mol.: 1 / Fragment: 17-MER TRNA(LYS) ANTICODON DOMAIN / Mutation: G27U, U28C, U29A, A41U, A42G, U43A / Source method: obtained synthetically
Details: RESIDUES 30-40 (TRNA NUMBERING) ARE IDENTICAL TO THOSE FOUND IN THE ANTICODON DOMAIN OF E. COLI TRNA(LYS) INCLUDING MODIFIED NUCLEOSIDES

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
231DQF-COSY
2411H-31P-COSY
2511H-31P-HETERO-TOCSY-TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and standard 1H-31P 2D correlation experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM natural abundance RNA; 10mM phosphate buffer; 50mM KCl; 50mM NaCl; 10mM MgCl290% H2O/10% D2O
21.5mM natural abundance RNA; 10mM phosphate buffer; 50mM KCl; 50mM NaCl; 10mM MgCl299.99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1120mM 7 ambient 285 K
2120mM 7 ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian UNITYVarianUNITY5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
VNMR6.1BVarianprocessing
VNMR6.1BVariandata analysis
FelixMSIprocessing
FelixMSIdata analysis
DiscoverMSIstructure solution
DiscoverMSIrefinement
RefinementMethod: used H5-H6 distances for distance calculations then simulated annealing, molecular dynamics in vacuo then restrained minimization in vacuo
Software ordinal: 1
Details: 123 NOE-derived restraints, 15 hydrogen bond restraints, 102 lower/upper bound restraints, 161 dihedral restraints, 68 chiral restraints
NMR representativeSelection criteria: closest to the average,lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 35 / Conformers submitted total number: 20

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