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- PDB-2k66: NMR solution structure of the d3'-stem closed by a GAAA tetraloop... -

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Basic information

Entry
Database: PDB / ID: 2k66
TitleNMR solution structure of the d3'-stem closed by a GAAA tetraloop of the group II intron Sc.ai5(gamma)
Components5'-R(*GP*GP*AP*GP*UP*AP*UP*GP*UP*GP*AP*AP*AP*GP*CP*AP*UP*AP*CP*UP*CP*C)-3'
KeywordsRNA / group II intron / ribozyme / splicing / d3'-stem / GAAA tetraloop / RNA 22-mer / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsKruschel, D. / Sigel, R.K.O.
CitationJournal: Rna / Year: 2014
Title: NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition.
Authors: Kruschel, D. / Skilandat, M. / Sigel, R.K.
History
DepositionJul 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Mar 12, 2014Group: Database references
Revision 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*GP*GP*AP*GP*UP*AP*UP*GP*UP*GP*AP*AP*AP*GP*CP*AP*UP*AP*CP*UP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,0821
Polymers7,0821
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 5'-R(*GP*GP*AP*GP*UP*AP*UP*GP*UP*GP*AP*AP*AP*GP*CP*AP*UP*AP*CP*UP*CP*C)-3'


Mass: 7082.274 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 1H-1H NOESY
2212D 1H-1H NOESY
1312D 1H-1H TOCSY
2412D 1H-1H TOCSY
3522D 1H-1H NOESY
4622D 1H-1H NOESY
5732D 1H-13C HSQC
6842D 1H-15N HSQC
7942D JNN HNN-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
20.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
41.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMRNA (22-MER)1
10 mMpotassium chloride1
10 uMEDTA1
0.9 mMRNA (22-MER)2
10 mMpotassium chloride2
10 uMEDTA2
1.0 mMRNA (22-MER)[U-100% 13C; U-100% 15N]3
10 mMpotassium chloride3
10 uMEDTA3
1.0 mMRNA (22-MER)[U-100% 13C; U-100% 15N]4
10 mMpotassium chloride4
10 uMEDTA4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1106.0-6.1 ambient 293 K
2106.0-6.1 ambient 303 K
3106.2ambient 278 K
4106.2ambient 293 K
5106.4ambient 303 K
6106.4ambient 278 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
TopSpin1.3, 2.0, 2.1Bruker Biospinprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddarddata analysis
Sparky3.1Goddardpeak picking
DYANA1.5Guntert, Braun and Wuthrichstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIH2.16Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 471 / NOE intraresidue total count: 157 / NOE long range total count: 86 / NOE medium range total count: 0 / NOE sequential total count: 228
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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