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- PDB-2m4q: NMR structure of E. coli ribosomela decoding site with apramycin -

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Basic information

Entry
Database: PDB / ID: 2m4q
TitleNMR structure of E. coli ribosomela decoding site with apramycin
ComponentsRNA (27-MER)
KeywordsRNA/antibiotic / RNA / antibiotic / decoding site / aminoglycoside / apramycin / RNA-antibiotic complex
Function / homologyAPRAMYCIN / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPuglisi, J.D. / Tsai, A. / Marshall, R. / Viani, E.
CitationJournal: Cell Rep / Year: 2013
Title: The impact of aminoglycosides on the dynamics of translation elongation.
Authors: Tsai, A. / Uemura, S. / Johansson, M. / Puglisi, E.V. / Marshall, R.A. / Aitken, C.E. / Korlach, J. / Ehrenberg, M. / Puglisi, J.D.
History
DepositionFeb 10, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 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 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
1: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1962
Polymers8,6561
Non-polymers5401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (27-MER)


Mass: 8656.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AM2 / APRAMYCIN / NEBRAMYCIN II / 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE


Mass: 539.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H41N5O11

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D DQF-COSY
1222D 1H-1H NOESY
1322D 1H-1H TOCSY
1412D 1H-15N HSQC
1512D 1H-13C HSQC
1612D 1H-13C HSQC aromatic
1713D (H)CCH-COSY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 13C; U-100% 15N] RNA, 0.5-1 mM APRAMYCIN, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM RNA, 0.5-1 mM APRAMYCIN, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA-1[U-100% 13C; U-100% 15N]0.5-11
mMAPRAMYCIN-20.5-11
mMRNA-30.5-12
mMAPRAMYCIN-40.5-12
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR softwareName: X-PLOR / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA beta-angle constraints total count: 16 / NA chi-angle constraints total count: 27 / NA epsilon-angle constraints total count: 19 / NA sugar pucker constraints total count: 26 / NOE constraints total: 626 / NOE intraresidue total count: 190
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10
NMR ensemble rmsDistance rms dev: 0.025 Å

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