data_16223 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Aflatoxin Formamidopyrimidine alpha anomer in single strand DNA ; _BMRB_accession_number 16223 _BMRB_flat_file_name bmr16223.str _Entry_type original _Submission_date 2009-03-24 _Accession_date 2009-03-24 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Brown Kyle L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 46 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-16 update BMRB 'update DNA residue label to two-letter code' 2009-11-23 orignal author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 16222 5'-D(*DCP*DTP*DAP*DTP*(FAG)P*DAP*DTP*DTP*DCP*DA)-3' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural perturbations induced by the alpha-anomer of the aflatoxin B(1) formamidopyrimidine adduct in duplex and single-strand DNA.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19831353 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Brown Kyle L. . 2 Voehler Markus W. . 3 Magee Shane M. . 4 Harris Constance M. . 5 Harris Thomas M. . 6 Stone Michael P. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 131 _Journal_issue 44 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 16096 _Page_last 16107 _Year 2009 _Details . loop_ _Keyword Aflatoxin DNA Formamidopyrimidine stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 5'-D(*DCP*DTP*(FAG)P*DA)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*DCP*DTP*(FAG)P*DA)-3')' $DNA_(5'-D(*DCP*DTP*(FAG)P*DA)-3') stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_(5'-D(*DCP*DTP*(FAG)P*DA)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*DCP*DTP*(FAG)P*DA)-3') _Molecular_mass 1537.133 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence CTXA loop_ _Residue_seq_code _Residue_label 1 DC 2 DT 3 FAG 4 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_FAG _Saveframe_category polymer_residue _Mol_type 'DNA linking' _Name_common '[1',2'-DIDEOXY[2-AMINO-5-([9-HYDROXY-AFLATOXINB2-8-YL]-FORMYL-AMINO)-6-OXO-1,6-IHYDRO-PYRIMIDIN-4-YLAMINO]-RIBOFURANOSE]-5-MONOPHOSPHATE GROUP' _BMRB_code . _PDB_code FAG _Standard_residue_derivative . _Molecular_mass 693.509 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Nov 18 19:04:00 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C3A C3A C . 0 . ? C3 C3 C . 0 . ? C2A C2A C . 0 . ? C1 C1 C . 0 . ? O1 O1 O . 0 . ? P P P . 0 . ? O1P O1P O . 0 . ? O2P O2P O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C4 C4 C . 0 . ? N3 N3 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N1 N1 N . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? C5 C5 C . 0 . ? N7 N7 N . 0 . ? C8 C8 C . 0 . ? O8 O8 O . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C8A C8A C . 0 . ? C9 C9 C . 0 . ? O9 O9 O . 0 . ? C9A C9A C . 0 . ? C9B C9B C . 0 . ? O7 O7 O . 0 . ? C6A C6A C . 0 . ? O6A O6A O . 0 . ? C5M C5M C . 0 . ? C5B C5B C . 0 . ? C4B C4B C . 0 . ? O4 O4 O . 0 . ? CM CM C . 0 . ? C4A C4A C . 0 . ? CAA CAA C . 0 . ? O10 O10 O . 0 . ? C11 C11 C . 0 . ? O11 O11 O . 0 . ? CBA CBA C . 0 . ? H31 H31 H . 0 . ? H32 H32 H . 0 . ? H2A1 H2A1 H . 0 . ? H2A2 H2A2 H . 0 . ? HOP2 HOP2 H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? HN9 HN9 H . 0 . ? HN21 HN21 H . 0 . ? HN22 HN22 H . 0 . ? H1 H1 H . 0 . ? H8 H8 H . 0 . ? H2'1 H2'1 H . 0 . ? H2'2 H2'2 H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H8A H8A H . 0 . ? H9 H9 H . 0 . ? HO9 HO9 H . 0 . ? H9A H9A H . 0 . ? H6A H6A H . 0 . ? H5B H5B H . 0 . ? HM1 HM1 H . 0 . ? HM2 HM2 H . 0 . ? HM3 HM3 H . 0 . ? O3P O3P O . 0 . ? HOP3 HOP3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING C3A C3 ? ? SING C3A C4A ? ? DOUB C3A CBA ? ? SING C3 C2A ? ? SING C3 H31 ? ? SING C3 H32 ? ? SING C2A C1 ? ? SING C2A H2A1 ? ? SING C2A H2A2 ? ? DOUB C1 O1 ? ? SING C1 CBA ? ? DOUB P O1P ? ? SING P O2P ? ? SING P O5' ? ? SING O2P HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C1' N9 ? ? SING C1' C2' ? ? SING C1' H1' ? ? SING N9 C4 ? ? SING N9 HN9 ? ? SING C4 N3 ? ? DOUB C4 C5 ? ? DOUB N3 C2 ? ? SING C2 N2 ? ? SING C2 N1 ? ? SING N2 HN21 ? ? SING N2 HN22 ? ? SING N1 C6 ? ? SING N1 H1 ? ? DOUB C6 O6 ? ? SING C6 C5 ? ? SING C5 N7 ? ? SING N7 C8 ? ? SING N7 C8A ? ? DOUB C8 O8 ? ? SING C8 H8 ? ? SING C2' C3' ? ? SING C2' H2'1 ? ? SING C2' H2'2 ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C8A C9 ? ? SING C8A O7 ? ? SING C8A H8A ? ? SING C9 O9 ? ? SING C9 C9A ? ? SING C9 H9 ? ? SING O9 HO9 ? ? SING C9A C9B ? ? SING C9A C6A ? ? SING C9A H9A ? ? DOUB C9B C5M ? ? SING C9B CAA ? ? SING O7 C6A ? ? SING C6A O6A ? ? SING C6A H6A ? ? SING O6A C5M ? ? SING C5M C5B ? ? DOUB C5B C4B ? ? SING C5B H5B ? ? SING C4B O4 ? ? SING C4B C4A ? ? SING O4 CM ? ? SING CM HM1 ? ? SING CM HM2 ? ? SING CM HM3 ? ? DOUB C4A CAA ? ? SING CAA O10 ? ? SING O10 C11 ? ? DOUB C11 O11 ? ? SING C11 CBA ? ? SING P O3P ? ? SING O3P HOP3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA_(5'-D(*DCP*DTP*(FAG)P*DA)-3') . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $DNA_(5'-D(*DCP*DTP*(FAG)P*DA)-3') 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*DCP*DTP*(FAG)P*DA)-3') 0.4 mM 'natural abundance' D2O 100 % 'natural abundance' 'Sodium Phosphate' 20 mM 'natural abundance' NaCl 0.1 M 'natural abundance' NaN3 10 uM 'natural abundance' Na2EDTA 50 uM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*DCP*DTP*(FAG)P*DA)-3') 0.4 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' 'Sodium Phosphate' 20 mM 'natural abundance' NaCl 0.1 M 'natural abundance' NaN3 10 uM 'natural abundance' Na2EDTA 50 uM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address 'Borgias, B.A. & James, T.L.' . . stop_ loop_ _Task 'restraint generation' stop_ _Details . save_ save_CORMA _Saveframe_category software _Name CORMA _Version . loop_ _Vendor _Address _Electronic_address 'James T.L.' . . stop_ loop_ _Task 'structure validation' stop_ _Details . save_ save_CURVES _Saveframe_category software _Name CURVES _Version . loop_ _Vendor _Address _Electronic_address 'Lavery, R. and Sklenar, H' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Advance _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details '0.1 M NaCl, 10 uM NaN3, 50 uM Na2EDTA, 20 mM Sodium Phosphate' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 278 . K pH 8.7 . pH pressure 1 . atm 'ionic strength' 0.1 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio TSP H 1 'methyl protons' ppm 0 internal direct . . . 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (5'-D(*DCP*DTP*(FAG)P*DA)-3')' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 DC H1' H 5.808 0.004 1 2 1 1 DC H2' H 2.016 0.002 1 3 1 1 DC H2'' H 2.402 0.007 1 4 1 1 DC H3' H 4.531 0.003 1 5 1 1 DC H4' H 3.924 0.004 1 6 1 1 DC H5 H 5.544 0.000 1 7 1 1 DC H5' H 3.576 0.003 1 8 1 1 DC H6 H 7.477 0.003 1 9 2 2 DT H1' H 6.194 0.001 1 10 2 2 DT H2' H 2.212 0.002 1 11 2 2 DT H2'' H 2.370 0.015 1 12 2 2 DT H3' H 4.707 0.002 1 13 2 2 DT H4' H 4.275 0.004 1 14 2 2 DT H5' H 3.915 0.010 1 15 2 2 DT H5'' H 3.885 0.002 1 16 2 2 DT H6 H 7.543 0.002 1 17 2 2 DT H71 H 1.704 0.000 1 18 2 2 DT H72 H 1.704 0.000 1 19 2 2 DT H73 H 1.704 0.000 1 20 3 3 FAG H1' H 5.620 0.002 1 21 3 3 FAG H2' H 2.300 0.005 1 22 3 3 FAG H2'' H 1.878 0.001 1 23 3 3 FAG H3' H 4.541 0.003 1 24 3 3 FAG H4' H 4.108 0.002 1 25 3 3 FAG H5' H 3.820 0.000 1 26 3 3 FAG H5'' H 3.737 0.005 1 27 3 3 FAG H8 H 8.272 0.000 1 28 3 3 FAG H2a H 1.756 0.001 1 29 3 3 FAG H2b H 1.840 0.000 1 30 3 3 FAG H3a H 2.571 0.000 1 31 3 3 FAG H3b H 3.189 0.001 1 32 3 3 FAG H5 H 5.723 0.000 1 33 3 3 FAG H5B H 5.708 0.001 1 34 3 3 FAG H6a H 6.130 0.006 1 35 3 3 FAG H8A H 5.657 0.002 1 36 3 3 FAG H9 H 6.157 0.000 1 37 3 3 FAG H9a H 3.655 0.006 1 38 3 3 FAG Me H 3.757 0.001 1 39 4 4 DA H1' H 6.268 0.001 1 40 4 4 DA H2' H 2.694 0.008 1 41 4 4 DA H2'' H 2.510 0.003 1 42 4 4 DA H3' H 4.623 0.002 1 43 4 4 DA H4' H 4.174 0.003 1 44 4 4 DA H5' H 4.002 0.001 1 45 4 4 DA H5'' H 3.958 0.000 1 46 4 4 DA H8 H 8.294 0.001 1 stop_ save_