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- PDB-2mnb: Thiazotropsin B DNA recognition sequence d(CGACGCGTCG)2 -

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Basic information

Entry
Database: PDB / ID: 2mnb
TitleThiazotropsin B DNA recognition sequence d(CGACGCGTCG)2
Components5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3'
KeywordsDNA / THIAZOTROPSINS / DNA RECOGNITION / ISOTHERMAL TITRATION CALORIMETRY NMR / SELF-ASSEMBLY / MINOR GROOVE BINDER
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / na
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsAlniss, H.Y. / Salvia, M.-V. / Sadikov, M. / Golovchenko, I. / Anthony, N.G. / Khalaf, A.I. / Mackay, S.P. / Suckling, C.J. / Parkinson, J.A.
CitationJournal: Chembiochem / Year: 2014
Title: Recognition of the DNA minor groove by thiazotropsin analogues.
Authors: Alniss, H.Y. / Salvia, M.V. / Sadikov, M. / Golovchenko, I. / Anthony, N.G. / Khalaf, A.I. / MacKay, S.P. / Suckling, C.J. / Parkinson, J.A.
History
DepositionApr 2, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water00
1


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

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Components

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


Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-1H COSY

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Sample preparation

DetailsContents: 2 mM 5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3', 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: 5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3'-1
Sample conditionsIonic strength: 0.05 / pH: 7.4 / Pressure: ambient / Temperature: 298 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
NameDeveloperClassification
AmberBruker Biospincollection
AmberBruker Biospinchemical shift assignment
AmberBruker Biospinrefinement
AmberGoddardcollection
AmberGoddardchemical shift assignment
AmberGoddardrefinement
RefinementMethod: na / Software ordinal: 1
NMR constraintsNOE constraints total: 207 / NOE intraresidue total count: 137 / NOE sequential total count: 68
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1 / Conformers submitted total number: 1

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