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- PDB-4bzv: The Solution Structure of the MLN 944-d(TACGCGTA)2 complex -

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Basic information

Entry
Database: PDB / ID: 4bzv
TitleThe Solution Structure of the MLN 944-d(TACGCGTA)2 complex
ComponentsDNA
KeywordsDNA / BIS(PHENAZINE-1-CARBOXAMIDES) / MLN 944 / INTERCALATION / DRUG DESIGN / ANTICANCER DRUG.
Function / homologyChem-XR2 / DNA
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodSOLUTION NMR / AMBER - MOLECULAR DYNAMICS
AuthorsSerobian, A. / Thomas, D.S. / Ball, G.E. / Denny, W.A. / Wakelin, L.P.G.
CitationJournal: Biopolymers / Year: 2014
Title: The Solution Structure of Bis(Phenazine-1-Carboxamide)-DNA Complexes: Mln 944 Binding Corrected and Extended.
Authors: Serobian, A. / Thomas, D.S. / Ball, G.E. / Denny, W.A. / Wakelin, L.P.G.
History
DepositionJul 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Structure summary
Revision 1.2Sep 3, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4443
Polymers4,8532
Non-polymers5911
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1DISTANCE RESTRAINTS
Representative

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Components

#1: DNA chain DNA /


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE DNA CONFORMATION IS IN THE FORM OF B-DNA. / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Chemical ChemComp-XR2 / 1-METHYL-9-[12-(9-METHYLPHENAZIN-10-IUM-1-YL)-12-OXO-2,11-DIAZA-5,8-DIAZONIADODEC-1-ANOYL]PHENAZIN-10-IUM


Mass: 590.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H38N8O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
14131P HSQC
15115N HSQC
NMR detailsText: AVERAGE ENERGY MINIMISED SOLUTION STRUCTURE FROM 10 NS OF MOLECULAR DYNAMICS

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 80 mM / pH: 5.0 / Pressure: 1.0 atm / Temperature: 288.0 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AMBERD.A.CASE,ET.AL.refinement
TOPSPIN3.1structure solution
RefinementMethod: AMBER - MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: DISTANCE RESTRAINTS / Conformers calculated total number: 1 / Conformers submitted total number: 1

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