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- PDB-2es5: Structure of the SRE RNA -

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Basic information

Entry
Database: PDB / ID: 2es5
TitleStructure of the SRE RNA
Components5'-R(*GP*GP*AP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP*UP*CP*C)-3'
KeywordsRNA / RNA structure / stem-loop / pentaloop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsAllain, F.H.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Shape-specific recognition in the structure of the Vts1p SAM domain with RNA.
Authors: Oberstrass, F.C. / Lee, A. / Stefl, R. / Janis, M. / Chanfreau, G. / Allain, F.H.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: 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_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP*UP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3721
Polymers7,3721
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 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7372.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA was prepared by in vitro transcription

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 1mM RNA
Sample conditionsIonic strength: 50mM NaCl, 50mM Phosphate-Buffer / pH: 6.5 / Temperature: 303 K

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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 AVANCEBrukerAVANCE9001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
SparkyGoddard, TDdata analysis
Amber7Case, DAstructure solution
Amber7Case, DArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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