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- PDB-2miy: Solution NMR structure of a preQ1 Class II riboswitch from Strept... -

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Basic information

Entry
Database: PDB / ID: 2miy
TitleSolution NMR structure of a preQ1 Class II riboswitch from Streptococcus pneumoniae
ComponentsRNA_(59-MER)
KeywordsRNA / preQ1 / riboswitch / classII / pseudoknot / Streptococcus pneumoniae
Function / homology7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKang, M. / Eichhorn, C.D. / Feigon, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural determinants for ligand capture by a class II preQ1 riboswitch.
Authors: Kang, M. / Eichhorn, C.D. / Feigon, J.
History
DepositionDec 20, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA_(59-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0822
Polymers18,9031
Non-polymers1791
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA_(59-MER)


Mass: 18903.258 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H TOCSY
2343D (H)CCH-TOCSY
2453D (H)CCH-TOCSY
2563D (H)CCH-TOCSY
2673D (H)CCH-TOCSY
1732D 1H-1H NOESY
1822D 1H-1H NOESY
1982D 1H-13C HSQC
11082D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM RNA (59-MER), 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE, 60 mM potassium chloride, 3 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE, 100% D2O100% D2O
31 mM (U-50%)-2H RNA (59-MER), 60 mM potassium chloride, 3 mM calcium Chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE, 100% D2O100% D2O
41.2 mM [U-13C; U-15N]-Ade RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE, 100% D2O100% D2O
51.2 mM [U-13C; U-15N]-Gua RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE, 100% D2O100% D2O
61.2 mM [U-13C; U-15N]-Cyt RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE, 100% D2O100% D2O
71.2 mM [U-13C; U-15N]-Ura RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE, 100% D2O100% D2O
81.2 mM [U-100% 13C; U-100% 15N] RNA (59-MER), 60 mM potassium chloride, 3 mM calcium chloride, 2 mM 7-DEAZA-7-AMINOMETHYL-GUANINE, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMRNA (59-MER)-11
2 mM7-DEAZA-7-AMINOMETHYL-GUANINE-21
60 mMpotassium chloride-31
3 mMcalcium chloride-41
1.2 mMRNA (59-MER)-52
60 mMpotassium chloride-62
3 mMcalcium chloride-72
2 mM7-DEAZA-7-AMINOMETHYL-GUANINE-82
1 mMRNA (59-MER)-9(U-50%)-2H3
60 mMpotassium chloride-103
3 mMcalcium Chloride-113
2 mM7-DEAZA-7-AMINOMETHYL-GUANINE-123
1.2 mMRNA (59-MER)-13[U-13C; U-15N]-Ade4
60 mMpotassium chloride-144
3 mMcalcium chloride-154
2 mM7-DEAZA-7-AMINOMETHYL-GUANINE-164
1.2 mMRNA (59-MER)-17[U-13C; U-15N]-Gua5
60 mMpotassium chloride-185
3 mMcalcium chloride-195
2 mM7-DEAZA-7-AMINOMETHYL-GUANINE-205
1.2 mMRNA (59-MER)-21[U-13C; U-15N]-Cyt6
60 mMpotassium chloride-226
3 mMcalcium chloride-236
2 mM7-DEAZA-7-AMINOMETHYL-GUANINE-246
1.2 mMRNA (59-MER)-25[U-13C; U-15N]-Ura7
60 mMpotassium chloride-267
3 mMcalcium chloride-277
2 mM7-DEAZA-7-AMINOMETHYL-GUANINE-287
1.2 mMRNA (59-MER)-29[U-100% 13C; U-100% 15N]8
60 mMpotassium chloride-308
3 mMcalcium chloride-318
2 mM7-DEAZA-7-AMINOMETHYL-GUANINE-328
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
166 6-6.3 ambient 300 K
266 6-6.3 ambient 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRDrawJohnson, One Moon Scientificpeak picking
Insight IIAccelrys Software Inc.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA sugar pucker constraints total count: 59 / NOE constraints total: 866 / NOE intraresidue total count: 306 / NOE long range total count: 44 / NOE medium range total count: 190 / NOE sequential total count: 326
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 18

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