data_30335 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA- Sequence ; _BMRB_accession_number 30335 _BMRB_flat_file_name bmr30335.str _Entry_type original _Submission_date 2017-08-24 _Accession_date 2017-08-24 _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 Harika N. K. . 2 Boykin D. W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 131 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-01-25 original BMRB . stop_ _Original_release_date 2017-08-28 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA- Sequence ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Harika N. K. . 2 Boykin D. W. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 entity_2 $entity_2 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common "DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3')" _Molecular_mass 2748.838 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence ; CCAAGATAG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DC 3 3 DA 4 4 DA 5 5 DG 6 6 DA 7 7 DT 8 8 DA 9 9 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common "DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3')" _Molecular_mass 2721.796 _Mol_thiol_state . _Details . _Residue_count 9 _Mol_residue_sequence ; CTATCTTGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DT 3 3 DA 4 4 DT 5 5 DC 6 6 DT 7 7 DT 8 8 DG 9 9 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 . 32630 . . . . $entity_2 . 32630 . . . . 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 $entity_1 'chemical synthesis' . . . . . $entity_2 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.54 mM 'natural abundance' $entity_2 0.54 mM 'natural abundance' DSS 0.4 mM 'natural abundance' EDTA 0.14 mM 'natural abundance' 'Tris-d11 buffer' 10 mM 'natural abundance' 'sodium chloride' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address 'Goddard,T.D.; Kneller,D.G.' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 850 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_100MS_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 100MS' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_100MS_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 100MS' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_50MS_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 50MS' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_50MS_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 50MS' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_150MS_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 150MS' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_300MS_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 300MS' _Sample_label $sample_1 save_ save_2D_1H-1H_CONSTANT_TIME_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H CONSTANT TIME NOESY' _Sample_label $sample_1 save_ save_1D_31P_8 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 31P' _Sample_label $sample_1 save_ save_1H,_31P-correlated_2D_spectra_(HPCOR)_9 _Saveframe_category NMR_applied_experiment _Experiment_name '1H, 31P-correlated 2D spectra (HPCOR)' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.5 . mM pH 6.3 . pH* pressure 1 . atm temperature 285 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 0.000 internal direct . . . 1.0 'phosphoric acid (85%)' P 31 phosphorus ppm 0.000 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_chemical_shifts_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY 100MS' '2D 1H-1H NOESY 50MS' '2D 1H-1H NOESY 150MS' '2D 1H-1H NOESY 300MS' '2D 1H-1H CONSTANT TIME NOESY' '1D 31P' '1H, 31P-correlated 2D spectra (HPCOR)' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 5.972 0.005 1 2 1 1 DC H2' H 2.062 0.005 1 3 1 1 DC H2'' H 2.503 0.002 1 4 1 1 DC H3' H 4.667 0.004 1 5 1 1 DC H4' H 4.112 0.000 1 6 1 1 DC H5 H 5.960 0.000 1 7 1 1 DC H6 H 7.767 0.002 1 8 2 2 DC H1' H 5.279 0.004 1 9 2 2 DC H2' H 2.058 0.003 1 10 2 2 DC H2'' H 2.310 0.004 1 11 2 2 DC H3' H 4.821 0.008 1 12 2 2 DC H4' H 4.214 0.000 1 13 2 2 DC H5 H 5.711 0.006 1 14 2 2 DC H6 H 7.561 0.005 1 15 3 3 DA H1' H 5.806 0.004 1 16 3 3 DA H2 H 7.383 0.002 1 17 3 3 DA H2' H 2.783 0.005 1 18 3 3 DA H2'' H 2.867 0.004 1 19 3 3 DA H3' H 5.055 0.009 1 20 3 3 DA H4' H 4.373 0.004 1 21 3 3 DA H8 H 8.267 0.002 1 22 4 4 DA H1' H 5.924 0.003 1 23 4 4 DA H2 H 7.445 0.001 1 24 4 4 DA H2' H 2.619 0.013 1 25 4 4 DA H2'' H 2.837 0.003 1 26 4 4 DA H3' H 5.045 0.006 1 27 4 4 DA H4' H 4.415 0.007 1 28 4 4 DA H8 H 8.098 0.001 1 29 5 5 DG H1' H 5.569 0.003 1 30 5 5 DG H2' H 2.517 0.010 1 31 5 5 DG H2'' H 2.678 0.006 1 32 5 5 DG H3' H 4.956 0.010 1 33 5 5 DG H4' H 4.377 0.013 1 34 5 5 DG H8 H 7.589 0.014 1 35 6 6 DA H1' H 6.161 0.004 1 36 6 6 DA H2 H 7.670 0.003 1 37 6 6 DA H2' H 2.533 0.010 1 38 6 6 DA H2'' H 2.892 0.012 1 39 6 6 DA H3' H 4.954 0.007 1 40 6 6 DA H4' H 4.434 0.007 1 41 6 6 DA H8 H 8.053 0.006 1 42 7 7 DT H1' H 5.616 0.004 1 43 7 7 DT H2' H 1.989 0.014 1 44 7 7 DT H2'' H 2.368 0.024 1 45 7 7 DT H3' H 4.838 0.007 1 46 7 7 DT H4' H 4.415 0.000 1 47 7 7 DT H6 H 7.146 0.009 1 48 7 7 DT H71 H 1.339 0.001 1 49 7 7 DT H72 H 1.339 0.001 1 50 7 7 DT H73 H 1.339 0.001 1 51 8 8 DA H1' H 6.052 0.003 1 52 8 8 DA H2 H 7.321 0.004 1 53 8 8 DA H2' H 2.612 0.010 1 54 8 8 DA H2'' H 2.845 0.005 1 55 8 8 DA H3' H 5.038 0.006 1 56 8 8 DA H4' H 4.401 0.008 1 57 8 8 DA H8 H 8.127 0.004 1 58 9 9 DG H1' H 5.802 0.012 1 59 9 9 DG H2' H 2.363 0.004 1 60 9 9 DG H2'' H 2.387 0.014 1 61 9 9 DG H3' H 4.751 0.002 1 62 9 9 DG H4' H 4.369 0.000 1 63 9 9 DG H8 H 7.562 0.010 1 stop_ save_ save_assigned_chemical_shifts_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY 100MS' '2D 1H-1H NOESY 50MS' '2D 1H-1H NOESY 150MS' '2D 1H-1H NOESY 300MS' '2D 1H-1H CONSTANT TIME NOESY' '1D 31P' '1H, 31P-correlated 2D spectra (HPCOR)' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_2 _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 10 1 DC H1' H 5.866 0.014 1 2 10 1 DC H2' H 2.181 0.004 1 3 10 1 DC H2'' H 2.544 0.008 1 4 10 1 DC H3' H 4.693 0.010 1 5 10 1 DC H4' H 4.207 0.000 1 6 10 1 DC H5 H 5.882 0.006 1 7 10 1 DC H6 H 7.734 0.002 1 8 11 2 DT H1' H 5.837 0.009 1 9 11 2 DT H2' H 2.283 0.019 1 10 11 2 DT H2'' H 2.606 0.013 1 11 11 2 DT H3' H 4.925 0.010 1 12 11 2 DT H4' H 4.205 0.004 1 13 11 2 DT H6 H 7.538 0.023 1 14 11 2 DT H71 H 1.693 0.001 1 15 11 2 DT H72 H 1.693 0.001 1 16 11 2 DT H73 H 1.693 0.001 1 17 12 3 DA H1' H 6.315 0.002 1 18 12 3 DA H2' H 2.739 0.005 1 19 12 3 DA H2'' H 2.994 0.009 1 20 12 3 DA H3' H 5.049 0.009 1 21 12 3 DA H4' H 4.414 0.005 1 22 12 3 DA H8 H 8.411 0.001 1 23 13 4 DT H1' H 5.907 0.005 1 24 13 4 DT H2' H 2.155 0.007 1 25 13 4 DT H2'' H 2.509 0.005 1 26 13 4 DT H3' H 4.876 0.011 1 27 13 4 DT H4' H 4.255 0.003 1 28 13 4 DT H6 H 7.221 0.003 1 29 13 4 DT H71 H 1.406 0.004 1 30 13 4 DT H72 H 1.406 0.004 1 31 13 4 DT H73 H 1.406 0.004 1 32 14 5 DC H1' H 6.045 0.053 1 33 14 5 DC H2' H 2.143 0.008 1 34 14 5 DC H2'' H 2.523 0.016 1 35 14 5 DC H3' H 4.786 0.001 1 36 14 5 DC H4' H 4.110 0.000 1 37 14 5 DC H5 H 5.536 0.005 1 38 14 5 DC H6 H 7.602 0.002 1 39 15 6 DT H1' H 6.008 0.006 1 40 15 6 DT H2' H 2.114 0.002 1 41 15 6 DT H2'' H 2.535 0.008 1 42 15 6 DT H3' H 4.858 0.053 1 43 15 6 DT H4' H 4.185 0.005 1 44 15 6 DT H6 H 7.473 0.006 1 45 15 6 DT H71 H 1.647 0.004 1 46 15 6 DT H72 H 1.647 0.004 1 47 15 6 DT H73 H 1.647 0.004 1 48 16 7 DT H1' H 5.659 0.007 1 49 16 7 DT H2' H 1.976 0.006 1 50 16 7 DT H2'' H 2.283 0.006 1 51 16 7 DT H3' H 4.835 0.007 1 52 16 7 DT H4' H 4.177 0.000 1 53 16 7 DT H6 H 7.351 0.007 1 54 16 7 DT H71 H 1.721 0.008 1 55 16 7 DT H72 H 1.721 0.008 1 56 16 7 DT H73 H 1.721 0.008 1 57 17 8 DG H1' H 5.659 0.011 1 58 17 8 DG H2' H 2.687 0.009 1 59 17 8 DG H2'' H 2.728 0.004 1 60 17 8 DG H3' H 4.977 0.007 1 61 17 8 DG H4' H 4.354 0.002 1 62 17 8 DG H8 H 7.881 0.008 1 63 18 9 DG H1' H 6.153 0.007 1 64 18 9 DG H2' H 2.337 0.001 1 65 18 9 DG H2'' H 2.515 0.003 1 66 18 9 DG H3' H 4.645 0.003 1 67 18 9 DG H4' H 4.206 0.005 1 68 18 9 DG H8 H 7.826 0.007 1 stop_ save_