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- PDB-6r14: Structure of kiteplatinated dsDNA -

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Basic information

Entry
Database: PDB / ID: 6r14
TitleStructure of kiteplatinated dsDNA
Components
  • Kiteplatinated DNA oligomer, chain A
  • Kiteplatinated DNA oligomer, chain B
KeywordsDNA / kiteplatin
Function / homologyKiteplatin / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMargiotta, N. / Papadia, P. / Kubicek, K. / Krejcikova, M. / Gkionis, K. / Sponer, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education (Czech Republic)LQ1601 Czech Republic
CitationJournal: To Be Published
Title: Structural characterization of kiteplatinated DNA
Authors: Krejcikova, M. / Papadia, P. / Gkionis, K. / Plats, J. / Petruzzella, E. / Savino, S. / Hoeschelle, J.D. / Natile, G. / Sponer, J. / Kubicek, K. / Margiotta, N.
History
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kiteplatinated DNA oligomer, chain A
B: Kiteplatinated DNA oligomer, chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7083
Polymers7,3282
Non-polymers3801
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, besides mass spectrometry, the spectral features in NMR NOESY spectra exhibit characteristic abnormal shifts of crosslinked DNA for some residues
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1170 Å2
ΔGint-10 kcal/mol
Surface area4510 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain Kiteplatinated DNA oligomer, chain A


Mass: 3559.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain Kiteplatinated DNA oligomer, chain B


Mass: 3768.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-LN8 / Kiteplatin


Mass: 380.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14Cl2N2Pt / 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
111isotropic12D 1H-13C HSQC aliphatic
121isotropic32D 1H-1H NOESY
231isotropic22D DQF-COSY
251isotropic22D 1H-1H TOCSY
241isotropic22D 1H-15N HSQC
261isotropic32D 1H-1H NOESY
171isotropic22D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 1 mM NA- kiteplatin, 90% H2O/10% D2O / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: kiteplatin / Isotopic labeling: NA-
Sample conditions

Ionic strength: 100 mM / pH: 7 / Pressure: 1 atm

Conditions-IDLabelPH errTemperature (K)Temperature err
1condition_10.1273 K0.1
2condition_2298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001QCI cryoprobe
Bruker AVANCE IIIBrukerAVANCE III8502cryoprobe
Bruker AVANCE IIIBrukerAVANCE III9503cryoprobe

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: novel force-field for kitePt
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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