data_18430 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure and Stability of Duplex DNA Containing (5 S) 5 ,8-Cyclo-2 -Deoxyadenosine: An Oxidative Lesion Repair by NER. ; _BMRB_accession_number 18430 _BMRB_flat_file_name bmr18430.str _Entry_type original _Submission_date 2012-04-30 _Accession_date 2012-04-30 _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 Zaliznyak Tatiana . . 2 'de los Santos' Carlos . . 3 Lukin Mark . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 149 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-03-11 update BMRB 'update entry citation' 2012-09-10 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure and stability of duplex DNA containing (5'S)-5',8-cyclo-2'-deoxyadenosine: an oxidatively generated lesion repaired by NER.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22928555 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zaliznyak Tatiana . . 2 Lukin Mark . . 3 'de los Santos' Carlos . . stop_ _Journal_abbreviation 'Chem. Res. Toxicol.' _Journal_name_full 'Chemical research in toxicology' _Journal_volume 25 _Journal_issue 10 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2103 _Page_last 2111 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Duplex DNA Containing (5 S) 5 ,8-Cyclo-2 -Deoxyadenosine' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 11_mer_oligonucleotide_B $11_mer_oligonucleotide_B 11_mer_oligonucleotide_D $11_mer_oligonucleotide_D 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_11_mer_oligonucleotide_B _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 11_mer_oligonucleotide_B _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence CGTACXCATGC loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DT 4 DA 5 DC 6 02I 7 DC 8 DA 9 DT 10 DG 11 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_11_mer_oligonucleotide_D _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 11_mer_oligonucleotide_D _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 11 _Mol_residue_sequence GCATGTGTACG loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DA 4 DT 5 DG 6 DT 7 DG 8 DT 9 DA 10 DC 11 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_02I _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common '(6S,7S,8S,10R)-4-amino-8-hydroxy-7,8,9,10-tetrahydro-6H-7,10-epoxyazepino[1,2-e]purin-6-yl dihydrogen phosphate' _BMRB_code 02I _PDB_code 02I _Standard_residue_derivative . _Molecular_mass 329.206 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1' C1' C . 0 . ? C2 C2 C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4 C4 C . 0 . ? C4' C4' C . 0 . ? C5 C5 C . 0 . ? C5' C5' C . 0 . ? C6 C6 C . 0 . ? C8 C8 C . 0 . ? H1' H1' H . 0 . ? H12' H12' H . 0 . ? H1N6 H1N6 H . 0 . ? H2 H2 H . 0 . ? H22' H22' H . 0 . ? H2N6 H2N6 H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5' H5' H . 0 . ? HO3' HO3' H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? N1 N1 N . 0 . ? N3 N3 N . 0 . ? N6 N6 N . 0 . ? N7 N7 N . 0 . ? N9 N9 N . 0 . ? O3' O3' O . 0 . ? O4' O4' O . 0 . ? O5' O5' O . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? P P P . 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 P O5' ? ? SING P OP3 ? ? SING N1 C6 ? ? DOUB C2 N1 ? ? SING N3 C2 ? ? DOUB N3 C4 ? ? SING C4 C5 ? ? DOUB C5 C6 ? ? SING C5 N7 ? ? SING C6 N6 ? ? SING N6 H2N6 ? ? DOUB C8 N7 ? ? SING C8 C5' ? ? SING N9 C4 ? ? SING N9 C8 ? ? SING C1' N9 ? ? SING C1' C2' ? ? SING OP3 HOP3 ? ? SING C2' C3' ? ? SING C2' H12' ? ? SING OP2 P ? ? SING OP2 HOP2 ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C4' C3' ? ? SING C4' C5' ? ? SING O4' C1' ? ? SING O4' C4' ? ? SING C5' O5' ? ? SING H2 C2 ? ? SING H1N6 N6 ? ? SING H1' C1' ? ? SING H22' C2' ? ? SING H4' C4' ? ? SING H5' C5' ? ? DOUB P OP1 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $11_mer_oligonucleotide_B . . . . . . $11_mer_oligonucleotide_D . . . . . . 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 $11_mer_oligonucleotide_B 'chemical synthesis' . . . . . $11_mer_oligonucleotide_D '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 $11_mer_oligonucleotide_B 0.7 mM 'natural abundance' $11_mer_oligonucleotide_D 0.7 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $11_mer_oligonucleotide_B 0.7 mM 'natural abundance' $11_mer_oligonucleotide_D 0.7 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'geometry optimization' refinement 'structure solution' stop_ _Details . save_ save_HYPER _Saveframe_category software _Name HYPER _Version . loop_ _Vendor _Address _Electronic_address 'Tejero, Monleon, Celda, Powers and Montelione' . . stop_ loop_ _Task 'geometry optimization' 'data analysis' stop_ _Details . save_ save_InsightII _Saveframe_category software _Name InsightII _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 400 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _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 '25 mM sodium phosphate, 50 mM sodium chloride' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 6.7 . pH pressure 1 . atm 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 DSS H 1 'methyl protons' ppm 0 internal direct . . . 1.0 TMP P 31 'Phosphade phasphorus' ppm 0 external direct . . . 1.0 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' 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 11_mer_oligonucleotide_B _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 5.833 . . 2 1 1 DC H2' H 2.060 . . 3 1 1 DC H2'' H 2.470 . . 4 1 1 DC H3' H 4.743 . . 5 1 1 DC H5 H 5.946 . . 6 1 1 DC H6 H 7.678 . . 7 2 2 DG H1' H 6.022 . . 8 2 2 DG H2' H 2.723 . . 9 2 2 DG H2'' H 2.833 . . 10 2 2 DG H3' H 5.019 . . 11 2 2 DG H4' H 4.403 . . 12 2 2 DG H8 H 8.018 . . 13 3 3 DT H1' H 5.766 . . 14 3 3 DT H2' H 2.133 . . 15 3 3 DT H2'' H 2.497 . . 16 3 3 DT H3' H 4.928 . . 17 3 3 DT H6 H 7.287 . . 18 3 3 DT H71 H 1.555 . . 19 3 3 DT H72 H 1.555 . . 20 3 3 DT H73 H 1.555 . . 21 4 4 DA H1' H 6.277 . . 22 4 4 DA H2 H 7.421 . . 23 4 4 DA H2' H 2.714 . . 24 4 4 DA H2'' H 2.951 . . 25 4 4 DA H3' H 5.064 . . 26 4 4 DA H4' H 4.463 . . 27 4 4 DA H8 H 8.291 . . 28 5 5 DC H1' H 5.893 . . 29 5 5 DC H2' H 2.247 . . 30 5 5 DC H2'' H 3.228 . . 31 5 5 DC H3' H 5.035 . . 32 5 5 DC H4' H 4.388 . . 33 5 5 DC H5 H 5.426 . . 34 5 5 DC H6 H 7.489 . . 35 6 6 02I H1' H 6.320 . . 36 6 6 02I H12' H 2.313 . . 37 6 6 02I H2 H 7.712 . . 38 6 6 02I H22' H 2.464 . . 39 6 6 02I H3' H 4.827 . . 40 6 6 02I H4' H 5.239 . . 41 6 6 02I H5' H 5.688 . . 42 7 7 DC H1' H 5.758 . . 43 7 7 DC H2' H 2.168 . . 44 7 7 DC H2'' H 2.571 . . 45 7 7 DC H3' H 4.852 . . 46 7 7 DC H4' H 4.285 . . 47 7 7 DC H5 H 5.569 . . 48 7 7 DC H5' H 4.051 . . 49 7 7 DC H6 H 7.618 . . 50 8 8 DA H1' H 6.268 . . 51 8 8 DA H2 H 7.559 . . 52 8 8 DA H2' H 2.668 . . 53 8 8 DA H2'' H 2.969 . . 54 8 8 DA H3' H 5.026 . . 55 8 8 DA H4' H 4.411 . . 56 8 8 DA H8 H 8.270 . . 57 9 9 DT H1' H 5.793 . . 58 9 9 DT H2' H 1.996 . . 59 9 9 DT H2'' H 2.386 . . 60 9 9 DT H3' H 4.902 . . 61 9 9 DT H6 H 7.145 . . 62 9 9 DT H71 H 1.472 . . 63 9 9 DT H72 H 1.472 . . 64 9 9 DT H73 H 1.472 . . 65 10 10 DG H1' H 5.959 . . 66 10 10 DG H2' H 2.642 . . 67 10 10 DG H2'' H 2.734 . . 68 10 10 DG H3' H 5.004 . . 69 10 10 DG H4' H 4.389 . . 70 10 10 DG H8 H 7.901 . . 71 11 11 DC H1' H 6.245 . . 72 11 11 DC H3' H 4.532 . . 73 11 11 DC H5 H 5.527 . . 74 11 11 DC H6 H 7.523 . . stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' 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 11_mer_oligonucleotide_D _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 DG H1' H 6.031 . . 2 1 1 DG H2' H 2.649 . . 3 1 1 DG H2'' H 2.834 . . 4 1 1 DG H3' H 4.889 . . 5 1 1 DG H4' H 4.272 . . 6 1 1 DG H8 H 7.991 . . 7 2 2 DC H1' H 5.724 . . 8 2 2 DC H2' H 2.220 . . 9 2 2 DC H2'' H 2.530 . . 10 2 2 DC H3' H 4.938 . . 11 2 2 DC H4' H 4.265 . . 12 2 2 DC H5 H 5.496 . . 13 2 2 DC H6 H 7.518 . . 14 3 3 DA H1' H 6.355 . . 15 3 3 DA H2 H 7.733 . . 16 3 3 DA H2' H 2.782 . . 17 3 3 DA H2'' H 3.040 . . 18 3 3 DA H3' H 5.091 . . 19 3 3 DA H4' H 4.492 . . 20 3 3 DA H8 H 8.393 . . 21 4 4 DT H1' H 5.841 . . 22 4 4 DT H2' H 2.079 . . 23 4 4 DT H2'' H 2.477 . . 24 4 4 DT H3' H 4.905 . . 25 4 4 DT H6 H 7.130 . . 26 4 4 DT H71 H 1.522 . . 27 4 4 DT H72 H 1.522 . . 28 4 4 DT H73 H 1.522 . . 29 5 5 DG H1' H 5.969 . . 30 5 5 DG H2' H 2.419 . . 31 5 5 DG H2'' H 2.766 . . 32 5 5 DG H3' H 4.974 . . 33 5 5 DG H4' H 4.347 . . 34 5 5 DG H8 H 7.698 . . 35 6 6 DT H1' H 5.637 . . 36 6 6 DT H2' H 2.214 . . 37 6 6 DT H2'' H 2.454 . . 38 6 6 DT H3' H 4.883 . . 39 6 6 DT H6 H 7.187 . . 40 6 6 DT H71 H 1.545 . . 41 6 6 DT H72 H 1.545 . . 42 6 6 DT H73 H 1.545 . . 43 7 7 DG H1' H 5.926 . . 44 7 7 DG H2' H 2.551 . . 45 7 7 DG H2'' H 2.767 . . 46 7 7 DG H3' H 4.940 . . 47 7 7 DG H4' H 4.366 . . 48 7 7 DG H8 H 7.843 . . 49 8 8 DT H1' H 5.709 . . 50 8 8 DT H2' H 2.171 . . 51 8 8 DT H2'' H 2.521 . . 52 8 8 DT H3' H 4.923 . . 53 8 8 DT H6 H 7.244 . . 54 8 8 DT H71 H 1.351 . . 55 8 8 DT H72 H 1.351 . . 56 8 8 DT H73 H 1.351 . . 57 9 9 DA H1' H 6.226 . . 58 9 9 DA H2 H 7.602 . . 59 9 9 DA H2' H 2.699 . . 60 9 9 DA H2'' H 2.877 . . 61 9 9 DA H3' H 5.057 . . 62 9 9 DA H4' H 4.439 . . 63 9 9 DA H8 H 8.287 . . 64 10 10 DC H1' H 5.712 . . 65 10 10 DC H2' H 1.901 . . 66 10 10 DC H2'' H 2.326 . . 67 10 10 DC H3' H 4.830 . . 68 10 10 DC H5 H 5.379 . . 69 10 10 DC H6 H 7.318 . . 70 11 11 DG H1' H 6.179 . . 71 11 11 DG H2' H 2.621 . . 72 11 11 DG H2'' H 2.399 . . 73 11 11 DG H3' H 4.694 . . 74 11 11 DG H4' H 4.207 . . 75 11 11 DG H8 H 7.936 . . stop_ save_