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- PDB-2kxm: Solution NMR Structure of the 27 nucleotide engineered neomycin s... -

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Basic information

Entry
Database: PDB / ID: 2kxm
TitleSolution NMR Structure of the 27 nucleotide engineered neomycin sensing riboswitch RNA-ribostmycin complex
ComponentsRNA (27-MER)
KeywordsRNA/Antibiotic / Riboswitches / RNA-ligand interaction / Aminoglycosides / RNA recognition / antibiotic / RNA-Antibiotic complex
Function / homologyRIBOSTAMYCIN / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 5
AuthorsDuchardt-Ferner, E. / Weigand, J.E. / Ohlenschlager, O. / Schmidtke, S.R. / Suess, B. / Wohnert, J.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Highly modular structure and ligand binding by conformational capture in a minimalistic riboswitch.
Authors: Duchardt-Ferner, E. / Weigand, J.E. / Ohlenschlager, O. / Schmidtke, S.R. / Suess, B. / Wohnert, J.
#1: Journal: BIOMOL.NMR ASSIGN. / Year: 2010
Title: NMR resonance assignments of an engineered neomycin-sensing riboswitch RNA bound to ribostamycin and tobramycin
Authors: Sina, S.R. / Elke, D. / Julia, W.E. / Beatrix, S. / Jens, W.
History
DepositionMay 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Structure summary
Revision 1.3Feb 5, 2014Group: Experimental preparation
Revision 1.4May 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)9,0122
Polymers8,5571
Non-polymers4541
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1closest to the average

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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-RIO / RIBOSTAMYCIN / 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL / (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside / Ribostamycin


Mass: 454.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34N4O10 / Comment: antibiotic*YM
Nonpolymer detailsTHE AMINO GROUPS ARE PROTONATED IN RIBOSTAMYCIN

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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-15N HSQC
2323D 1H-15N NOESY
3432D 1H-13C HSQC
2553D HNCO
2653D H(CCO)NH
3733D 1H-13C NOESY
3833D 1H-13C NOESY
3942D 1H-1H TOCSY
31042D DQF-COSY
31142D 1H-1H NOESY
21262D 1H-1H TOCSY
21362D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM RNA (27-MER)-1, 25 mM potassium phosphate-2, 50 mM potassium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 15N] RNA (27-MER)-4, 0.9 mM RIBOSTAMYCIN-5, 25 mM potassium phosphate-6, 50 mM potassium chloride-7, 90% H2O/10% D2O90% H2O/10% D2O
31.1 mM [U-100% 13C; U-100% 15N] RNA (27-MER)-8, 1.2 mM RIBOSTAMYCIN-9, 25 mM potassium phosphate-10, 50 mM potassium chloride-11, 100% D2O100% D2O
41.1 mM [U-13C; U-15N; U-2H] RNA (27-MER)-12, 1.2 mM RIBOSTAMYCIN-13, 25 mM potassium phosphate-14, 50 mM potassium chloride-15, 100% D2O100% D2O
51.1 mM [U-100% 13C; U-100% 15N] RNA (27-MER)-16, 1.2 mM RIBOSTAMYCIN-17, 25 mM potassium phosphate-18, 50 mM potassium chloride-19, 90% H2O/10% D2O90% H2O/10% D2O
61.1 mM [U-13C; U-15N; U-2H] RNA (27-MER)-20, 1.2 mM RIBOSTAMYCIN-21, 25 mM potassium phosphate-22, 50 mM potassium chloride-23, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMRNA (27-MER)-11
25 mMpotassium phosphate-21
50 mMpotassium chloride-31
0.8 mMRNA (27-MER)-4[U-100% 15N]2
0.9 mMRIBOSTAMYCIN-52
25 mMpotassium phosphate-62
50 mMpotassium chloride-72
1.1 mMRNA (27-MER)-8[U-100% 13C; U-100% 15N]3
1.2 mMRIBOSTAMYCIN-93
25 mMpotassium phosphate-103
50 mMpotassium chloride-113
1.1 mMRNA (27-MER)-12[U-13C; U-15N; U-2H]4
1.2 mMRIBOSTAMYCIN-134
25 mMpotassium phosphate-144
50 mMpotassium chloride-154
1.1 mMRNA (27-MER)-16[U-100% 13C; U-100% 15N]5
1.2 mMRIBOSTAMYCIN-175
25 mMpotassium phosphate-185
50 mMpotassium chloride-195
1.1 mMRNA (27-MER)-20[U-13C; U-15N; U-2H]6
1.2 mMRIBOSTAMYCIN-216
25 mMpotassium phosphate-226
50 mMpotassium chloride-236
Sample conditions
Conditions-IDpHTemperature (K)
16.2 267-298 K
26.2 283 K
36.2 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004
Bruker AvanceBrukerAVANCE9505

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.8.4.2Wuthrichchemical shift assignment
CARA1.8.4.2Wuthrichpeak picking
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
OPALLuginbuhl, Guntert, Billeter, Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 915 / NOE intraresidue total count: 362 / NOE long range total count: 120 / NOE sequential total count: 186 / Hydrogen bond constraints total count: 50
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å

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