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- PDB-8xgw: Solution structure of d(CGATCG)2-Baicalein complex -

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Basic information

Entry
Database: PDB / ID: 8xgw
TitleSolution structure of d(CGATCG)2-Baicalein complex
ComponentsDNA (5'-D(*CP*AP*CP*GP*TP*G)-3')
KeywordsDNA / Oncogene / gene regulation / DNA-ligand complex / flavone
Function / homology5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / Distance restraints
AuthorsNair, M.S. / Kumar, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Solution structure of d(CACGTG)2-Baicalein complex.
Authors: Nair, M.S. / Kumar, S.
History
DepositionDec 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI
Revision 1.2Jun 26, 2024Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,8893
Polymers3,6182
Non-polymers2701
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Baicalein (5,6,7-trihydroxyflavone) / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-3WL / 5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one / Baicalein


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
214isotropic12D 1H-1H NOESY
224isotropic11D 1H

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Sample preparation

DetailsType: solution / Contents: 2.56 % w/v Hexamer DNA-Baicalein, 90% H2O/10% D2O
Details: Hexamer DNA-Baicalein in Phosphate buffer (20mM), 10 mM and NaCl, at 300K
Label: Hexamer DNA-Baicalein / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.56 % w/v / Component: Hexamer DNA-Baicalein / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 10 mM / Label: Condition_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.1Bruker Biospinchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
AmberTools18D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, Y. Huang, S. Izadi, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, J. Smith, R. SalomonFerrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2018), AMBER 2018, University of California, San Francisco.refinement
NMRFAM-SPARKYBioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopypeak picking
RefinementMethod: Distance restraints / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 8

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