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- PDB-2mxs: Solution NMR-structure of the neomycin sensing riboswitch RNA bou... -

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Basic information

Entry
Database: PDB / ID: 2mxs
TitleSolution NMR-structure of the neomycin sensing riboswitch RNA bound to paromomycin
ComponentsRNA (27-MER)
KeywordsRNA / Riboswitch / Aminoglycoside
Function / homologyPAROMOMYCIN / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, energy minimization
Model detailslowest energy, model1
AuthorsSchmidtke, S. / Duchardt-Ferner, E. / Ohlenschlaeger, O. / Gottstein, D. / Wohnert, J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch.
Authors: Duchardt-Ferner, E. / Gottstein-Schmidtke, S.R. / Weigand, J.E. / Ohlenschlager, O. / Wurm, J.P. / Hammann, C. / Suess, B. / Wohnert, J.
History
DepositionJan 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1732
Polymers8,5571
Non-polymers6161
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 RNA (27-MER)


Mass: 8557.031 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM

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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-15N HSQC
1322D 1H-13C HNCO
1422D 1H-15N H56C56C4N3H
1522D 1H-15N HSQC NH2 only
2632D 1H-13C HSQC aromatic
2732D 1H-13C HSQC aliphatic
2842D 1H-13C HSQC aliphatic
2933D 1H-13C NOESY-HSQC aliphatic
21033D 1H-13C NOESY-HMQC aromatic
21133D (H)CCH-COSY
21233D (H)CCH-TOCSY
21332D 1H-15N lrHSQC
21432D DQF-COSY
21532D 1H-31P HCP
21633D (H)CCH-TOCSY-E.COSY
21732D 13C filter NOESY
21832D 13C filter TOCSY
21932D quant 31P coupled 1H, 13C HSQC
22032D quant 31P coupled 1H-13C HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.64 mM RNA (27-MER), 0.64 mM Paromomycin, 90% H2O/10% D2O90% H2O/10% D2O
20.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin, 90% H2O/10% D2O90% H2O/10% D2O
30.89 mM 13C; 15N RNA (27-MER), 0.89 mM Paromomycin, 100% D2O100% D2O
40.62 mM G-]13C; 15N] RNA (27-MER), 0.62 mM Paromomycin, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.64 mMRNA (27-MER)-11
0.64 mMParomomycin-21
0.89 mMRNA (27-MER)-313C; 15N2
0.89 mMParomomycin-42
0.89 mMRNA (27-MER)-513C; 15N3
0.89 mMParomomycin-63
0.62 mMRNA (27-MER)-7G-]13C; 15N]4
0.62 mMParomomycin-84
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.2 ambient 283 K
26.2 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE8004
Bruker AvanceBrukerAVANCE9005
Bruker AvanceBrukerAVANCE9506

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
SparkyGoddardpeak integration
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, energy minimization / Software ordinal: 1
NMR constraintsNOE constraints total: 1117 / NOE intraresidue total count: 587 / NOE long range total count: 94 / NOE sequential total count: 204
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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