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- PDB-2lu0: NMR solution structure of the kappa-zeta region of S.cerevisiae g... -

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Basic information

Entry
Database: PDB / ID: 2lu0
TitleNMR solution structure of the kappa-zeta region of S.cerevisiae group II intron ai5(gamma)
ComponentsRNA (49-MER)
KeywordsRNA / Three-way junction / Metal ion / group II intron / ribozyme
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsDonghi, D. / Pechlaner, M. / Finazzo, C. / Knobloch, B. / Sigel, R.K.O.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: The structural stabilization of the kappa three-way junction by Mg(II) represents the first step in the folding of a group II intron.
Authors: Donghi, D. / Pechlaner, M. / Finazzo, C. / Knobloch, B. / Sigel, R.K.O.
History
DepositionJun 5, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (49-MER)


Theoretical massNumber of molelcules
Total (without water)15,8001
Polymers15,8001
Non-polymers00
Water0
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 (49-MER)


Mass: 15800.444 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence occurs naturally in S.cerevisiae and was synthesized in vitro using T7 polymerase and synthetic DNA oligonucleotides
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-1H NOESY
2442D 1H-1H NOESY
2552D 1H-15N HSQC
1632D 1H-13C HSQC
1713D 1H-13C NOESY aliphatic
2852D JNN HNN COSY
1932D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-1.0 mM RNA (49-MER), 60 mM potassium chloride, 10 uM EDTA, 0-12 mM magnesium chloride, 100% D2O100% D2O
20.3-1.0 mM [3',4',5',5 ,5-D5] RNA (49-MER), 60 mM potassium chloride, 10 uM EDTA, 0-12 mM magnesium chloride, 100% D2O100% D2O
30.3-1 mM 100% 13C; 100% 15N RNA (49-MER), 60 mM potassium chloride, 10 uM EDTA, 0-12 mM magnesium chloride, 100% D2O100% D2O
40.3-1.0 mM RNA (49-MER), 60 mM potassium chloride, 10 uM EDTA, 0-12 mM magnesium chloride, 90% H2O/10% D2O90% H2O/10% D2O
50.3-1.0 mM 100% 13C; 100% 15N RNA (49-MER), 60 mM potassium chloride, 10 uM EDTA, 0-12 mM magnesium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (49-MER)-10.3-1.01
60 mMpotassium chloride-21
10 uMEDTA-31
mMmagnesium chloride-40-121
mMRNA (49-MER)-5[3',4',5',5 ,5-D5]0.3-1.02
60 mMpotassium chloride-62
10 uMEDTA-72
mMmagnesium chloride-80-122
mMRNA (49-MER)-9100% 13C; 100% 15N0.3-13
60 mMpotassium chloride-103
10 uMEDTA-113
mMmagnesium chloride-120-123
mMRNA (49-MER)-130.3-1.04
60 mMpotassium chloride-144
10 uMEDTA-154
mMmagnesium chloride-160-124
mMRNA (49-MER)-17100% 13C; 100% 15N0.3-1.05
60 mMpotassium chloride-185
10 uMEDTA-195
mMmagnesium chloride-200-125
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
160 6.5-6.9 ambient 300 K
260 6.5-6.9 ambient 275-285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyGoddardpeak integration
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorestructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 848 / NOE intraresidue total count: 256 / NOE long range total count: 134 / NOE medium range total count: 38 / NOE sequential total count: 420
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.2 Å

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