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- PDB-2mnd: Recognition complex of DNA d(CGACGCGTCG)2 with thiazotropsin B -

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Basic information

Entry
Database: PDB / ID: 2mnd
TitleRecognition complex of DNA d(CGACGCGTCG)2 with thiazotropsin B
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 / homologythiazotropsin B / DNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsminimized average structure, model 1
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 3, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
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 / _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

Downloads & links

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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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2094
Polymers6,0922
Non-polymers1,1172
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 least restraint violations
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
#2: Chemical ChemComp-3BF / thiazotropsin B / 3-({[2-({[4-({[4-(acetylamino)-1-methyl-1H-imidazol-2-yl]carbonyl}amino)-1-methyl-1H-pyrrol-2-yl]carbonyl}amino)-5-(propan-2-yl)-1,3-thiazol-4-yl]carbonyl}amino)-N,N-dimethylpropan-1-aminium


Mass: 558.676 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H36N9O4S

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 2 mM Thiazotropsin B, 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
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mMThiazotropsin B-11
2 mM5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3'-21
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
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
SYBYLTriposgeometry optimization
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmangeometry optimization
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
MARDIGRASTriposstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 740 / NOE intraresidue total count: 318 / NOE sequential total count: 141
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1 / Conformers submitted total number: 1

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