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- PDB-2hns: Structure of the AAGU tetraloop -

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Basic information

Entry
Database: PDB / ID: 2hns
TitleStructure of the AAGU tetraloop
Components5'-R(*GP*GP*CP*GP*UP*GP*AP*UP*CP*AP*AP*GP*UP*GP*AP*UP*CP*GP*CP*GP*CP*C)-3'
KeywordsRNA / tetraloop / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsGaudin, C. / Fourmy, F. / Yoshizawa, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of an AAGU Tetraloop and its Contribution to Substrate Selection by yeast RNase III.
Authors: Gaudin, C. / Ghazal, G. / Yoshizawa, S. / Elela, S.A. / Fourmy, D.
History
DepositionJul 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 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_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(*GP*GP*CP*GP*UP*GP*AP*UP*CP*AP*AP*GP*UP*GP*AP*UP*CP*GP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,0891
Polymers7,0891
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7089.266 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
2322D TOCSY
242DQF-COSY
2532D HMQC
2633D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM RNA, 10mM phosphate buffer pH 6.4, 90% H2O, 10% D2O90% H2O/10% D2O
21mM RNA; 10mM phosphate buffer pH 6.4, 100% D2O100% D2O
31mM RNA A-15N,13C; 10mM phosphate buffer pH 6.4, 100% D2O100% D2O
41mM RNA c-15N,13C; 10mM phosphate buffer pH 6.4, 100% D2O100% D2O
51mM RNA G-15N,13C; 10mM phosphate buffer pH 6.4, 100% D2O100% D2O
61mM RNA U-15N,13C; 10mM phosphate buffer pH 6.4, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM sodium phosphate 6.4ambient 288 K
210mM sodium phosphate 6.4ambient 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 DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1collection
Gifa4M.A. DELSUCdata analysis
Sparky3.11data analysis
CNS1.1BRUNGER Astructure solution
CNS1.1BRUNGER Arefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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