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- PDB-2n0r: RNA structure determination by solid-state NMR spectroscopy -

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Basic information

Entry
Database: PDB / ID: 2n0r
TitleRNA structure determination by solid-state NMR spectroscopy
ComponentsRNA (5'-R(*GP*CP*UP*GP*AP*GP*CP*UP*CP*GP*AP*AP*AP*GP*AP*GP*CP*AP*AP*UP*GP*AP*UP*GP*UP*C)-3')
KeywordsRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLID-STATE NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsMarchanka, A. / Simon, B. / Althoff-Ospelt, G. / Carlomagno, T.
CitationJournal: Nat Commun / Year: 2015
Title: RNA structure determination by solid-state NMR spectroscopy.
Authors: Marchanka, A. / Simon, B. / Althoff-Ospelt, G. / Carlomagno, T.
History
DepositionMar 12, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references / Source and taxonomy
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
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*CP*UP*GP*AP*GP*CP*UP*CP*GP*AP*AP*AP*GP*AP*GP*CP*AP*AP*UP*GP*AP*UP*GP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)8,4071
Polymers8,4071
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 / 300structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 8407.075 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111(13C,15N-TEDOR)-13C,13C PDSD
12113C-31P TEDOR
131CHHC
141NHHC
151CN-TEDOR

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Sample preparation

DetailsContents: 20 mg/mL nucleotide-type-selective [U-99% 13C; U-99% 15N] 26mer Box C/D RNA, 100% H2O
Solvent system: 100% H2O
SampleConc.: 20 mg/mL / Component: 26mer Box C/D RNA-1
Isotopic labeling: nucleotide-type-selective [U-99% 13C; U-99% 15N]
Sample conditionspH: 7.5 / Temperature: 260 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readdata analysis
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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