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- PDB-2bq2: Solution Structure of the DNA Duplex ACGCGU-NA with a 2' Amido-Li... -

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Basic information

Entry
Database: PDB / ID: 2bq2
TitleSolution Structure of the DNA Duplex ACGCGU-NA with a 2' Amido-Linked Nalidixic Acid Residue at the 3' Terminal Nucleotide
Components5'-D(*AP*CP*GP*CP*GP*2AU)-3'
KeywordsDNA / NUCLEIC ACID / DEOXYRIBONUCLEIC ACID / DISRUPTED TERMINAL BASEPAIRS / QUINOLONE / SYNTHETIC HYBRID / DNA COMPLEX
Function / homologyNALIDIXIC ACID / DNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsSiegmund, K. / Maheshwary, S. / Narayanan, S. / Connors, W. / Richert, M.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it.
Authors: Siegmund, K. / Maheshwary, S. / Narayanan, S. / Connors, W. / Riedrich, M. / Printz, M. / Richert, C.
History
DepositionApr 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 2.0May 9, 2018Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_nmr_spectrometer
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_nmr_spectrometer.model
Revision 2.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _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: 5'-D(*AP*CP*GP*CP*GP*2AU)-3'
B: 5'-D(*AP*CP*GP*CP*GP*2AU)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0854
Polymers3,6202
Non-polymers4642
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 80LOWEST CALCULATED ENERGIES
Representative

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Components

#1: DNA chain 5'-D(*AP*CP*GP*CP*GP*2AU)-3'


Mass: 1810.206 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: NALIDIXIC ACID APPENDED TO THE AMINO FUNCTION OF 2'-AMINOURIDINE VIA AN AMIDE BOND
#2: Chemical ChemComp-NIX / NALIDIXIC ACID


Mass: 232.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141HSQC
NMR detailsText: NONE

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Sample preparation

DetailsContents: D2O AND 90% WATER/ 10%D2O
Sample conditionsIonic strength: 160 mM / pH: 7 / Pressure: 1.0 atm / Temperature: 283.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: SEE PRIMARY CITATION FOR DETAILS
NMR ensembleConformer selection criteria: LOWEST CALCULATED ENERGIES / Conformers calculated total number: 80 / Conformers submitted total number: 2

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