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- PDB-2rpt: Structure of the CC mismatch from the thymidylate synthase bindin... -

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Entry
Database: PDB / ID: 2rpt
TitleStructure of the CC mismatch from the thymidylate synthase binding site 1 hairpin and analysis of its interaction with paromomycin
ComponentsRNA (5'-R(*GP*GP*CP*CP*CP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*CP*GP*GP*CP*C)-3')
KeywordsRNA / NMR spectroscopy / RNA structure / paromomycin / aminoglycoside-RNA interaction
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
AuthorsTavares, T.J. / Johnson, P.E.
CitationJournal: Rna / Year: 2009
Title: Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin
Authors: Tavares, T.J. / Beribisky, A.V. / Johnson, P.E.
History
DepositionAug 23, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,4511
Polymers6,4511
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)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 6450.943 Da / Num. of mol.: 1 / Fragment: thymidylate synthase binding site 1 mRNA hairpin / Source method: obtained synthetically / Details: IN-VITRO TRANSCRIPTION USING T7 RNA POLYMERASE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-1H NOESY
2212D 1H-1H TOCSY
2312D 1H-1H COSY
2412D 1H-13C HSQC
2523D 1H-13C NOESY-HSQC
2623D (H)CCH-COSY
2723D (H)CCH-TOCSY
1822D 1H-15N HSQC
1923D 1H-15N NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
13-5 mg/ml RNA, 90% H2O/10% D2O and 100% D2O90% H2O/10% D2O and 100% D2O
23-5 mg/ml [U-100% 13C; U-100% 15N] RNA, 90% H2O/10% D2O and 100% D2O90% H2O/10% D2O and 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mg/mLRNA1
3 mg/mLRNA[U-100% 13C; U-100% 15N]2
Sample conditions
Conditions-IDTemperature (K)
1278 K
2293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER DRXBrukerDRX6001
VARIAN INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19SCHWIETERS, KUSZEWSKI, TJrefinement
XwinNMRBruker Biospinstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
NMR constraintsNA other-angle constraints total count: 55 / NA sugar pucker constraints total count: 20 / NOE constraints total: 260 / NOE intraresidue total count: 108 / NOE medium range total count: 43 / NOE sequential total count: 109
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Representative conformer: 1

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