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- PDB-2b7g: Structure of the Smaug Recognition RNA Element -

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Entry
Database: PDB / ID: 2b7g
TitleStructure of the Smaug Recognition RNA Element
Components5'-R(*GP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP*C)-3'
KeywordsRNA / Protein-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsJohnson, P.E. / Donaldson, L.W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: RNA recognition by the Vts1p SAM domain
Authors: Johnson, P.E. / Donaldson, L.W.
History
DepositionOct 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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: 5'-R(*GP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0871
Polymers6,0871
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 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 6086.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Smaug Recognition Element

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian UNITYVarianUNITY8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR2.9.9Schweiters, C.D., Kuzewski, J.J., Tjandra, N. & Clore, G.M.structure solution
X-PLOR2.9.9Schweiters, C.D., Kuzewski, J.J., Tjandra, N. & Clore, G.M.refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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