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- PDB-2nq0: Solution Structures of a DNA Dodecamer Duplex with a Cisplatin 1,... -

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Basic information

Entry
Database: PDB / ID: 2nq0
TitleSolution Structures of a DNA Dodecamer Duplex with a Cisplatin 1,2-d(GG) Intrastrand Cross-Link
Components
  • 5'-D(*CP*CP*TP*CP*AP*GP*GP*CP*CP*TP*CP*C)-3'
  • 5'-D(*GP*GP*AP*GP*GP*CP*CP*TP*GP*AP*GP*G)-3'
KeywordsDNA / Deoxyribonucleic acid / cisplatin / duplex / dodecamer
Function / homologyCisplatin / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsWu, Y. / Bhattacharyya, D. / Chaney, S. / Campbell, S.
CitationJournal: Biochemistry / Year: 2007
Title: Solution Structures of a DNA Dodecamer Duplex with and without a Cisplatin 1,2-d(GG) Intrastrand Cross-Link: Comparison with the Same DNA Duplex Containing an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link
Authors: Wu, Y. / Bhattacharyya, D. / King, C.L. / Baskerville-Abraham, I. / Huh, S.-H. / Boysen, G. / Swenberg, J.A. / Temple, B. / Campbell, S.L. / Chaney, S.G.
History
DepositionOct 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*AP*GP*GP*CP*CP*TP*CP*C)-3'
B: 5'-D(*GP*GP*AP*GP*GP*CP*CP*TP*GP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6283
Polymers7,3282
Non-polymers3001
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 20structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3559.319 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*GP*AP*GP*GP*CP*CP*TP*GP*AP*GP*G)-3'


Mass: 3768.453 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
1222D TOCSY
132DQF-COSY
1412D NOESY
1522D 1H 31P HETCOR
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.9mM DEOXYRIBONUCLEIC ACID, OXALIPLATIN; DNA, DUPLEX, DODECAMER, 95% H2O, 5% D2O95% H2O/5% D2O
21.9mM DEOXYRIBONUCLEIC ACID, OXALIPLATIN, DNA, DUPLEX, DODECAMER, 100% D2O100% D2O
Sample conditionsIonic strength: 100mM NaCl, 5mM NaPi / pH: 7 / Pressure: 1 atm / 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 15

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