data_18639 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion ; _BMRB_accession_number 18639 _BMRB_flat_file_name bmr18639.str _Entry_type original _Submission_date 2012-08-03 _Accession_date 2012-08-03 _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 Zalianyak Tatiana . . 2 'de los Santos' Carlos . . 3 Lukin Mark . . 4 Attaluri Sivaprasad . . 5 Johnson Francis . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 150 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-18 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 18638 'Duplex DNA Containing a b-Carba-Fapy-dG Lesion' 18640 'Duplex DNA Containing a b-Carba-Fapy-dG Lesion' stop_ _Original_release_date 2013-02-18 save_ ############################# # Citation for this entry # ############################# save_citation1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22897814 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lukin Mark . . 2 Zalianyak Tatiana . . 3 Attaluri Sivaprasad . . 4 Johnson Francis . . 5 'de los Santos' Carlos . . stop_ _Journal_abbreviation 'Chem. Res. Toxicol.' _Journal_volume 25 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2423 _Page_last 2431 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Duplex DNA Containing a b-Carba-Fapy-dG Lesion' _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 . _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 LWM 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 . _Details . _Residue_count 11 _Mol_residue_sequence GCATGCGTACG loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DA 4 DT 5 DG 6 DC 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_LWM _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common '[(1R,2S,4R)-4-{[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]amino}-2-hydroxycyclopentyl]methyl dihydrogen phosphate' _BMRB_code LWM _PDB_code LWM _Standard_residue_derivative . _Molecular_mass 363.264 _Mol_paramagnetic NO _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C1' C1' C . 0 . ? C2 C2 C . 0 . ? C2' C2' C . 0 . ? C3 C3 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 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H3 H3 H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5 H5 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H6' H6' H . 0 . ? H6'' H6'' H . 0 . ? HN1 HN1 H . 0 . ? HN2A HN2A H . 0 . ? HN7 HN7 H . 0 . ? HN9 HN9 H . 0 . ? HO3' HO3' H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? N1 N1 N . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? N4 N4 N . 0 . ? N5 N5 N . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? O3' O3' O . 0 . ? O5' O5' O . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? P1 P1 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 P1 O5' ? ? DOUB P1 OP1 ? ? SING N1 HN1 ? ? SING C1 N1 ? ? SING C1 N2 ? ? SING N2 H3' ? ? DOUB N3 C1 ? ? SING C2 N3 ? ? DOUB C3 C2 ? ? SING C3 C4 ? ? SING C4 N1 ? ? DOUB C4 O1 ? ? SING N4 C3 ? ? SING C5 N4 ? ? DOUB C5 O2 ? ? SING N5 C2 ? ? SING C1' N5 ? ? SING C1' H1' ? ? SING OP3 P1 ? ? SING OP3 HOP3 ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING OP2 P1 ? ? SING OP2 HOP2 ? ? SING C3' C2' ? ? SING C3' C4' ? ? SING C3' O3' ? ? SING O3' HO3' ? ? SING C4' H4' ? ? SING C4' C6' ? ? SING C5' C4' ? ? SING C5' H5'' ? ? SING O5' C5' ? ? SING C6' C1' ? ? SING C6' H6' ? ? SING HN7 N4 ? ? SING HN9 C5 ? ? SING H5 N5 ? ? SING H5' C5' ? ? SING H2'' C2' ? ? SING HN2A N2 ? ? SING H3 C3' ? ? SING H6'' C6' ? ? 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 1.57 mM 'natural abundance' $11_mer_oligonucleotide-D 1.57 mM 'natural abundance' 'phosphate buffer' 25 mM 'natural abundance' NaCl 50 mM 'natural abundance' EDTA 0.5 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 1.57 mM 'natural abundance' $11_mer_oligonucleotide-D 1.57 mM 'natural abundance' 'phosphate buffer' 25 mM 'natural abundance' NaCl 50 mM 'natural abundance' EDTA 0.5 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' 'peak volume calc.' 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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _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_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_6 _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 . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 6.8 . pH pressure 1 . atm stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 6.8 . 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 . . . 1.00 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 5.739 . 1 2 1 1 DC H2' H 1.978 . 1 3 1 1 DC H2'' H 2.386 . 1 4 1 1 DC H3' H 4.657 . 1 5 1 1 DC H4' H 4.027 . 1 6 1 1 DC H5 H 5.846 . 1 7 1 1 DC H6 H 7.586 . 1 8 2 2 DG H1' H 5.945 . 1 9 2 2 DG H2' H 2.639 . 1 10 2 2 DG H2'' H 2.756 . 1 11 2 2 DG H3' H 4.935 . 1 12 2 2 DG H4' H 4.325 . 1 13 2 2 DG H5' H 3.978 . 1 14 2 2 DG H8 H 7.934 . 1 15 3 3 DT H1' H 5.726 . 1 16 3 3 DT H2' H 2.108 . 1 17 3 3 DT H2'' H 2.469 . 1 18 3 3 DT H3' H 4.852 . 1 19 3 3 DT H4' H 4.851 . 1 20 3 3 DT H6 H 7.226 . 1 21 3 3 DT H71 H 1.480 . 1 22 3 3 DT H72 H 1.480 . 1 23 3 3 DT H73 H 1.480 . 1 24 4 4 DA H1' H 6.211 . 1 25 4 4 DA H2 H 7.421 . 1 26 4 4 DA H2' H 2.643 . 1 27 4 4 DA H2'' H 2.861 . 1 28 4 4 DA H3' H 4.968 . 1 29 4 4 DA H4' H 4.398 . 1 30 4 4 DA H8 H 8.218 . 1 31 5 5 DC H1' H 5.891 . 1 32 5 5 DC H2' H 1.997 . 1 33 5 5 DC H2'' H 2.295 . 1 34 5 5 DC H3' H 4.761 . 1 35 5 5 DC H5 H 5.195 . 1 36 5 5 DC H6 H 7.269 . 1 37 6 6 LWM H1' H 3.834 . 1 38 6 6 LWM H2' H 1.722 . 1 39 6 6 LWM H2'' H 1.896 . 1 40 6 6 LWM H3 H 4.405 . 1 41 6 6 LWM H4' H 2.167 . 1 42 6 6 LWM H6' H 0.960 . 1 43 6 6 LWM H6'' H 2.066 . 1 44 6 6 LWM HN9 H 7.211 . 1 45 7 7 DC H1' H 5.858 . 1 46 7 7 DC H2' H 2.134 . 1 47 7 7 DC H2'' H 2.499 . 1 48 7 7 DC H3' H 4.853 . 1 49 7 7 DC H5 H 5.695 . 1 50 7 7 DC H6 H 7.542 . 1 51 8 8 DA H1' H 6.198 . 1 52 8 8 DA H2' H 2.641 . 1 53 8 8 DA H2'' H 2.901 . 1 54 8 8 DA H3' H 4.970 . 1 55 8 8 DA H4' H 4.351 . 1 56 8 8 DA H8 H 8.255 . 1 57 9 9 DT H1' H 5.723 . 1 58 9 9 DT H2' H 1.940 . 1 59 9 9 DT H2'' H 2.324 . 1 60 9 9 DT H3' H 4.824 . 1 61 9 9 DT H6 H 7.072 . 1 62 9 9 DT H71 H 1.369 . 1 63 9 9 DT H72 H 1.369 . 1 64 9 9 DT H73 H 1.369 . 1 65 10 10 DG H1' H 5.882 . 1 66 10 10 DG H2' H 2.547 . 1 67 10 10 DG H2'' H 2.648 . 1 68 10 10 DG H3' H 4.924 . 1 69 10 10 DG H4' H 4.315 . 1 70 10 10 DG H8 H 7.807 . 1 71 11 11 DC H1' H 6.128 . 1 72 11 11 DC H2' H 2.128 . 1 73 11 11 DC H2'' H 2.158 . 1 74 11 11 DC H3' H 4.443 . 1 75 11 11 DC H4' H 4.008 . 1 76 11 11 DC H5 H 5.331 . 1 77 11 11 DC H6 H 7.380 . 1 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 12 1 DG H1' H 5.924 . 1 2 12 1 DG H2' H 2.562 . 1 3 12 1 DG H2'' H 2.742 . 1 4 12 1 DG H3' H 4.797 . 1 5 12 1 DG H4' H 4.197 . 1 6 12 1 DG H8 H 7.892 . 1 7 13 2 DC H1' H 5.655 . 1 8 13 2 DC H2' H 2.119 . 1 9 13 2 DC H2'' H 2.442 . 1 10 13 2 DC H3' H 4.848 . 1 11 13 2 DC H4' H 4.172 . 1 12 13 2 DC H5 H 5.385 . 1 13 13 2 DC H6 H 7.422 . 1 14 14 3 DA H1' H 6.243 . 1 15 14 3 DA H2 H 7.680 . 1 16 14 3 DA H2' H 2.664 . 1 17 14 3 DA H2'' H 2.915 . 1 18 14 3 DA H3' H 4.994 . 1 19 14 3 DA H4' H 4.392 . 1 20 14 3 DA H8 H 8.295 . 1 21 15 4 DT H1' H 5.678 . 1 22 15 4 DT H2' H 1.983 . 1 23 15 4 DT H2'' H 2.353 . 1 24 15 4 DT H3' H 4.810 . 1 25 15 4 DT H6 H 7.052 . 1 26 15 4 DT H71 H 1.423 . 1 27 15 4 DT H72 H 1.423 . 1 28 15 4 DT H73 H 1.423 . 1 29 16 5 DG H1' H 5.869 . 1 30 16 5 DG H2' H 2.523 . 1 31 16 5 DG H2'' H 2.672 . 1 32 16 5 DG H3' H 4.876 . 1 33 16 5 DG H4' H 4.329 . 1 34 16 5 DG H8 H 7.690 . 1 35 17 6 DC H1' H 5.676 . 1 36 17 6 DC H2' H 2.103 . 1 37 17 6 DC H2'' H 2.404 . 1 38 17 6 DC H3' H 4.713 . 1 39 17 6 DC H5 H 5.283 . 1 40 17 6 DC H6 H 7.241 . 1 41 18 7 DG H1' H 5.862 . 1 42 18 7 DG H2' H 2.490 . 1 43 18 7 DG H2'' H 2.662 . 1 44 18 7 DG H3' H 4.772 . 1 45 18 7 DG H4' H 4.269 . 1 46 18 7 DG H8 H 7.576 . 1 47 19 8 DT H1' H 5.786 . 1 48 19 8 DT H2' H 2.110 . 1 49 19 8 DT H2'' H 2.478 . 1 50 19 8 DT H3' H 4.859 . 1 51 19 8 DT H6 H 7.298 . 1 52 19 8 DT H71 H 1.316 . 1 53 19 8 DT H72 H 1.316 . 1 54 19 8 DT H73 H 1.316 . 1 55 20 9 DA H1' H 6.169 . 1 56 20 9 DA H2 H 7.493 . 1 57 20 9 DA H2' H 2.627 . 1 58 20 9 DA H2'' H 2.807 . 1 59 20 9 DA H3' H 4.983 . 1 60 20 9 DA H4' H 4.367 . 1 61 20 9 DA H8 H 8.230 . 1 62 21 10 DC H1' H 5.630 . 1 63 21 10 DC H2' H 1.827 . 1 64 21 10 DC H2'' H 2.244 . 1 65 21 10 DC H3' H 4.746 . 1 66 21 10 DC H5 H 5.294 . 1 67 21 10 DC H6 H 7.241 . 1 68 22 11 DG H1' H 6.093 . 1 69 22 11 DG H2' H 2.541 . 1 70 22 11 DG H2'' H 2.320 . 1 71 22 11 DG H3' H 4.611 . 1 72 22 11 DG H4' H 4.124 . 1 73 22 11 DG H8 H 7.844 . 1 stop_ save_