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- PDB-1mk6: SOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFL... -

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Basic information

Entry
Database: PDB / ID: 1mk6
TitleSOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT MISPAIRED WITH DEOXYADENOSINE
Components
  • 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'
  • 5'-D(*AP*GP*AP*TP*AP*GP*AP*TP*GP*T)-3'
KeywordsDNA / AFLATOXIN B1- Guanine Adduct Opposite an Adenine / mimicking GA Transition
Function / homology8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / distance geometry : MardiGras; simulated annealing, molecular dynamics : XPLOR; Average structure Calculation Addition of Solvent, and Counterions : AMBER; simulated annealing, Molecular Dynamics matrix relaxation : CORMA;
AuthorsGiri, I. / Johnston, D.S. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2002
Title: MISPAIRING OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT WITH DEOXYADENOSINE RESULTS IN EXTRUSION OF THE MISMATCHED DA TOWARD THE MAJOR GROOVE
Authors: Giri, I. / Johnston, D.S. / Stone, M.P.
History
DepositionAug 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / ndb_struct_conf_na / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_ref
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _ndb_struct_na_base_pair_step.roll / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_ref.pdbx_align_begin
Revision 2.1May 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
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.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'
B: 5'-D(*AP*GP*AP*TP*AP*GP*AP*TP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4423
Polymers6,1122
Non-polymers3301
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 20Final Calculated Structure is Being Submitted. Back Calculated Structure is in Agreement with NOESY data. The calculation was performed in Presence of solvent and counterions. Solvent, and Counterion co-ordinates are NOT being reported, only the Duplex DNA. Before Solvating and Addition of Counter IONS, 20 final structures were calculated using XPLOR. The final averaged energy minimized structure was solvated, and the counter Ions were added to it. Then MD was ran for 1.4 ns time scale to obtain final structure.
RepresentativeModel #1

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Components

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


Mass: 3003.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(*AP*GP*AP*TP*AP*GP*AP*TP*GP*T)-3'


Mass: 3108.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-AFN / 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1


Mass: 330.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
141P-COSY
151T1
NMR detailsText: 40 Structures were calculated starting from B and A form DNA. 20 closely convergent from both was averaged, and RMSD value was checked. The final averaged structure was calculated by averaging ...Text: 40 Structures were calculated starting from B and A form DNA. 20 closely convergent from both was averaged, and RMSD value was checked. The final averaged structure was calculated by averaging Final A and Final B, and after energy Minimization. This energy minimized structure was solvated, and explicit counterions were added. In all, 17 Na+ ions were added to neutralize the system using the Leap module in AMBER 6.0. The SHAKE algorithm constrained bonds involving protons to a tolerance of 0.0005 . A 1 fs time step was used. The rMD calculations were run for 1.4 ns, and coordinates were captured every 200 ps. The emergent structure from AMBER is Being reported

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Sample preparation

DetailsContents: 80 OD of d(ACATCAFBGATCT)d(AGATAGATGT) solution in NMR Buffer
Solvent system: For observation of nonexchangeable protons, the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved ...Solvent system: For observation of nonexchangeable protons, the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O. For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O. Most experiments were performed at 5 C. Spectra of exchangeable protons were obtained at 0 C.
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O 7.4 ATM 278 K
2For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O, buffer, containing 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.4 7.4 ATM 273 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
Felix97, 2000Accelyris, Inc., San Diego, CAprocessing
XwinNMR4Brukercollection
MARDIGRAS3.2Borgias, B. A., and James, T. L. (1990) J. Magn. Reson. 87, 475-487data analysis
X-PLOR3.1A.T.Brungerrefinement
Amber6Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) J. Phys. Chem. 40, 10269-10280structure solution
CORMA4Keepers, J. W., and James, T. L. (1984) J. Magn. Reson. 57, 404-426.data analysis
Insight II2000Accelyris, Inc., San Diego, CAstructure solution
GAUSSIAN 981998Frisch, M. J., Trucks, G. W., et al. (1998) Gaussian 98, Gaussian Inc., Pittsburgh, PA.processing
RefinementMethod: distance geometry : MardiGras; simulated annealing, molecular dynamics : XPLOR; Average structure Calculation Addition of Solvent, and Counterions : AMBER; simulated annealing, Molecular ...Method: distance geometry : MardiGras; simulated annealing, molecular dynamics : XPLOR; Average structure Calculation Addition of Solvent, and Counterions : AMBER; simulated annealing, Molecular Dynamics matrix relaxation : CORMA;
Software ordinal: 1
Details: There were 329 experimental distance restraints derived from nonexchangeable 1H NOEs by MARDIGRAS. These consisted of 181 intranucleotide restraints, 110 internucleotide restraints, and 38 adduct-DNA restraints
NMR ensembleConformer selection criteria: Final Calculated Structure is Being Submitted. Back Calculated Structure is in Agreement with NOESY data. The calculation was performed in Presence of solvent and ...Conformer selection criteria: Final Calculated Structure is Being Submitted. Back Calculated Structure is in Agreement with NOESY data. The calculation was performed in Presence of solvent and counterions. Solvent, and Counterion co-ordinates are NOT being reported, only the Duplex DNA. Before Solvating and Addition of Counter IONS, 20 final structures were calculated using XPLOR. The final averaged energy minimized structure was solvated, and the counter Ions were added to it. Then MD was ran for 1.4 ns time scale to obtain final structure.
Conformers calculated total number: 20 / Conformers submitted total number: 1

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