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- PDB-1xwu: Solution structure of ACAUAGA loop -

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Basic information

Entry
Database: PDB / ID: 1xwu
TitleSolution structure of ACAUAGA loop
Components5'-R(*CP*GP*AP*AP*AP*CP*AP*UP*AP*GP*AP*UP*UP*CP*GP*A)-3'
KeywordsRNA / hairpin loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsSakamoto, T. / Oguro, A. / Kawai, G. / Ohtsu, T. / Nakamura, Y.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A
Authors: Sakamoto, T. / Oguro, A. / Kawai, G. / Ohtsu, T. / Nakamura, Y.
History
DepositionNov 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4May 29, 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(*CP*GP*AP*AP*AP*CP*AP*UP*AP*GP*AP*UP*UP*CP*GP*A)-3'


Theoretical massNumber of molelcules
Total (without water)5,1291
Polymers5,1291
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)1 / -
Representativeminimized average structure

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Components

#1: RNA chain 5'-R(*CP*GP*AP*AP*AP*CP*AP*UP*AP*GP*AP*UP*UP*CP*GP*A)-3' / ACAUAGA hepta-nucleotide loop


Mass: 5129.143 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1322D TOCSY
142DQF-COSY
152HP-COSY
164HCP
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM RNA; 20mM phosphate buffer NA, 50mM NaCl; 95% H2O, 5% D2O95% H2O/5% D2O
20.5mM RNA; 20mM phosphate buffer NA, 50mM NaCl; 100% D2O100% D2O
31mM RNA U-15N,13C; 20mM phosphate buffer NA, 50mM NaCl; 95% H2O, 5% D2O95% H2O/5% D2O
41mM RNA U-15N,13C; 20mM phosphate buffer NA, 50mM NaCl; 100% D2O100% D2O
Sample conditionsIonic strength: 70 mM / pH: 6.5 / Pressure: ambient / Temperature: 283 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 DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionClassification
XwinNMR2.6collection
XwinNMR2.6processing
Felix97data analysis
Discover97structure solution
Discover97refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure is based on a total of 292 restraints, 228 are NOE-derived distance constraints, 46 dihedral angle restraints, 13 distance restraints from hydrogen bonds, 5 base planarity restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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