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- PDB-2kar: HNE-dG adduct mismatched with dA in acidic solution -

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Basic information

Entry
Database: PDB / ID: 2kar
TitleHNE-dG adduct mismatched with dA in acidic solution
Components
  • 5'-D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'
  • 5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3'
KeywordsDNA / HNE-dG / mismatch / hydroxynonenal
Function / homology(4S)-nonane-1,4-diol / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsHuang, H. / Wang, H. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P.
CitationJournal: Chem.Res.Toxicol. / Year: 2009
Title: Conformational interconversion of the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N(2)-deoxyguanosine adduct when mismatched with deoxyadenosine in DNA
Authors: Huang, H. / Wang, H. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P.
History
DepositionNov 13, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _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(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'
B: 5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5113
Polymers7,3512
Non-polymers1601
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'


Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The DNA oligomer is chemically synthesized.
#2: DNA chain 5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3'


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The DNA oligomer is chemically synthesized.
#3: Chemical ChemComp-HND / (4S)-nonane-1,4-diol


Mass: 160.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O2
Nonpolymer detailsTHE LIGAND HND FORMS TWO COVALENT BONDS WITH THE DEOXY-GUANINE AT POSITION 7 OF CHAIN A. THIS ...THE LIGAND HND FORMS TWO COVALENT BONDS WITH THE DEOXY-GUANINE AT POSITION 7 OF CHAIN A. THIS LIGAND IS FORMED BY CHEMICAL REACTION OF ANOTHER LIGAND HNE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.0 mM DNA 5'-D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3', 1.0 mM 5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3', 1.0 mM (2E,4R)-4-HYDROXYNON-2-ENAL, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 / pH: 5.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: Amber
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 1

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