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- PDB-1ksb: Relationship of Solution and Protein-Bound Structures of DNA Dupl... -

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Basic information

Entry
Database: PDB / ID: 1ksb
TitleRelationship of Solution and Protein-Bound Structures of DNA Duplexes with the Major Intrastrand Cross-Link Lesions Formed on Cisplatin Binding to DNA
Components
  • 5'-D(*AP*GP*GP*CP*CP*GP*GP*AP*G)-3'
  • 5'-D(*CP*TP*CP*CP*GP*GP*CP*CP*T)-3'
KeywordsDNA / Deoxyribonucleic acid / Cisplatin / Duplex / 9-mer / Intrastrand cross-link / model J
Function / homologyCisplatin / DNA
Function and homology information
MethodSOLUTION NMR / AMBER
AuthorsMarzilli, L.G. / Saad, J.S. / Kuklenyik, Z. / Keating, K.A. / Xu, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2001
Title: Relationship of solution and protein-bound structures of DNA duplexes with the major intrastrand cross-link lesions formed on cisplatin binding to DNA.
Authors: Marzilli, L.G. / Saad, J.S. / Kuklenyik, Z. / Keating, K.A. / Xu, Y.
History
DepositionJan 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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*TP*CP*CP*GP*GP*CP*CP*T)-3'
B: 5'-D(*AP*GP*GP*CP*CP*GP*GP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7743
Polymers5,4742
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)1 / -
Representative

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Components

#1: DNA chain 5'-D(*CP*TP*CP*CP*GP*GP*CP*CP*T)-3'


Mass: 2667.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Cisplatin intrastrand cross-link DNA
#2: DNA chain 5'-D(*AP*GP*GP*CP*CP*GP*GP*AP*G)-3'


Mass: 2805.849 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
1112D NOESY
121DQF-COSY
NMR detailsText: 2D 1H-31P phase-sensitive Reverse Chemical Shift Correlation (RCSC) and 1H-13C magnitude mode HMQC experiments were performed.

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Sample preparation

DetailsContents: Platinated 9-mer duplex dissolved in D2O/H2O / Solvent system: D2O or (90% H2O, 10% D2O)
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
GE OMEGAGEOMEGA6001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix97processing
DiscoverBiosym/MSIrefinement
Insight IIstructure solution
Curvesdata analysis
IRMABiosym/MSIrefinement
RefinementMethod: AMBER / Software ordinal: 1
Details: NOE-Restrained refinement (details can be found in the paper)
NMR ensembleConformers submitted total number: 1

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