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- PDB-1xrw: Solution Structure of a Platinum-Acridine Modified Octamer -

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Basic information

Entry
Database: PDB / ID: 1xrw
TitleSolution Structure of a Platinum-Acridine Modified Octamer
Components
  • 5'-D(*CP*CP*TP*CP*GP*TP*CP*C)-3'
  • 5'-D(*GP*GP*AP*CP*GP*AP*GP*G)-3'
KeywordsDNA / platinum / acridine / dual binding mode / major groove / unwinding
Function / homologyChem-2PT / DNA
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation
Model type detailsminimized average
AuthorsBaruah, H. / Wright, M.W. / Bierbach, U.
CitationJournal: Biochemistry / Year: 2005
Title: Solution Structural Study of a DNA Duplex Containing the Guanine-N7 Adduct Formed by a Cytotoxic Platinum-Acridine Hybrid Agent
Authors: Baruah, H. / Wright, M.W. / Bierbach, U.
History
DepositionOct 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 20, 2016Group: Atomic model / Non-polymer description
Revision 1.4May 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 / 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 / _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(*CP*CP*TP*CP*GP*TP*CP*C)-3'
B: 5'-D(*GP*GP*AP*CP*GP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4363
Polymers4,8552
Non-polymers5811
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 / -
Representativeminimized average structure

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Components

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


Mass: 2338.543 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*GP*AP*CP*GP*AP*GP*G)-3'


Mass: 2516.667 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-2PT / 1-[2-(ACRIDIN-9-YLAMINO)ETHYL]-1,3-DIMETHYLTHIOUREA-PLATINUM(II)-ETHANE-1,2-DIAMINE


Mass: 580.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N6PtS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
1411H-31P COSY

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Sample preparation

DetailsContents: 3.5mM modified duplex, 10 mM phosphate buffer, 10mM NaCl, 100% D2O or 90% H2O/10% D2O
Solvent system: 100% D2O or 90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM NaH2PO4, 10 mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
Felix2000Accelrysprocessing
Felix2000Accelrysdata analysis
MARDIGRAS3.2James, T. L.iterative matrix relaxation
Discover2000Accelrysrefinement
CORMA5.2James, T. L.data analysis
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, matrix relaxation
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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