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- PDB-7fhi: Interaction between a fluoroquinolone derivative and RNAs with a ... -

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Basic information

Entry
Database: PDB / ID: 7fhi
TitleInteraction between a fluoroquinolone derivative and RNAs with a single bulge
ComponentsRNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*AP*CP*UP*CP*AP*GP*CP*CP*AP*UP*CP*C)-3')
KeywordsRNA / Complex / fluoroquinolone
Function / homologyChem-53D / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / na
AuthorsNagano, K. / Kamimura, T. / Kawai, G.
CitationJournal: J.Biochem. / Year: 2022
Title: Interaction between a fluoroquinolone derivative and RNAs with a single bulge.
Authors: Nagano, K. / Kamimura, T. / Kawai, G.
History
DepositionJul 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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 (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*AP*CP*UP*CP*AP*GP*CP*CP*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7632
Polymers6,3201
Non-polymers4441
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*AP*CP*UP*CP*AP*GP*CP*CP*AP*UP*CP*C)-3')


Mass: 6319.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: Chemical ChemComp-53D / 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide


Mass: 443.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34FN5O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Nonpolymer detailsThe ligand is expected to have +3 charges in the neutral solution at the atoms N14/N17/N27.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D HOHAHA

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Sample preparation

DetailsType: solution
Contents: 0.3 mM RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*AP*CP*UP*CP*AP*GP*CP*CP*AP*UP*CP*C)-3'), 0.3 mM K22, 95% H2O/5% D2O
Label: sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMRNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*AP*CP*UP*CP*AP*GP*CP*CP*AP*UP*CP*C)-3')none1
0.3 mMK22none1
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddardpeak picking
RefinementMethod: na / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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