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- PDB-2li4: Solution structure of a shortened antiterminator hairpin from a M... -

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Basic information

Entry
Database: PDB / ID: 2li4
TitleSolution structure of a shortened antiterminator hairpin from a Mg2+ riboswitch
ComponentsRNA (32-MER)
KeywordsRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKorth, M.M.T. / Sigel, R.K.O.
CitationJournal: To be Published
Title: Solution structure of a shortened antiterminator hairpin from a Mg2+ riboswitch
Authors: Korth, M.M.T. / Sigel, R.K.O.
History
DepositionAug 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (32-MER)


Theoretical massNumber of molelcules
Total (without water)10,3041
Polymers10,3041
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (32-MER)


Mass: 10304.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Yersinia enterocolitica (bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
1332D 1H-1H NOESY
3442D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM potassium chloride, 10 uM EDTA, 0.24 mM RNA (32-MER), 100% D2O100% D2O
250 mM potassium chloride, 10 uM EDTA, 0.6 mM RNA (32-MER), 90% H2O/10% D2O90% H2O/10% D2O
350 mM potassium chloride, 10 uM EDTA, 0.8 mM RNA (32-MER), 100% D2O100% D2O
450 mM potassium chloride, 10 uM EDTA, 0.5 mM RNA (32-MER), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMpotassium chloride-11
10 uMEDTA-21
0.24 mMRNA (32-MER)-31
50 mMpotassium chloride-42
10 uMEDTA-52
0.6 mMRNA (32-MER)-62
50 mMpotassium chloride-73
10 uMEDTA-83
0.8 mMRNA (32-MER)-93
50 mMpotassium chloride-104
10 uMEDTA-114
0.5 mMRNA (32-MER)-124
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.05 6.8 ambient 303 K
20.05 6.8 ambient 278 K
30.05 6.8 ambient 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddarddata analysis
Sparky3.1Goddardpeak picking
TopSpin1.3, 2.1, 3.0aBruker Biospinprocessing
X-PLOR2.24Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR2.24Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 569
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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