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- PDB-2mn0: D loop of tRNA(Met) -

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Basic information

Entry
Database: PDB / ID: 2mn0
TitleD loop of tRNA(Met)
Components5'-R(*GP*GP*AP*GP*AP*GP*(H2U)P*GP*GP*AP*AP*CP*UP*CP*C)-3'
KeywordsRNA / tRNA / D arm / H2U
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model1
AuthorsLescrinier, E. / Dyubankova, N. / Herdewijn, P.
CitationJournal: Org.Biomol.Chem. / Year: 2015
Title: Contribution of dihydrouridine in folding of the D-arm in tRNA.
Authors: Dyubankova, N. / Sochacka, E. / Kraszewska, K. / Nawrot, B. / Herdewijn, P. / Lescrinier, E.
History
DepositionMar 25, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Mar 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*AP*GP*AP*GP*(H2U)P*GP*GP*AP*AP*CP*UP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,8731
Polymers4,8731
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain 5'-R(*GP*GP*AP*GP*AP*GP*(H2U)P*GP*GP*AP*AP*CP*UP*CP*C)-3'


Mass: 4872.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: D-arm of tRNA(Met) / Source: (synth.) Schizosaccharomyces pombe (fission yeast)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1412D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM D arm tRNA(Met), 100% D2O / Solvent system: 100% D2O
SampleConc.: 1 mM / Component: D arm tRNA(Met)-1
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospindata analysis
X-PLOR NIH3.851Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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