data_17885 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of a DNA dodecamer containing the 7-aminomethyl-7-deaza-2'-deoxyguanosine adduct ; _BMRB_accession_number 17885 _BMRB_flat_file_name bmr17885.str _Entry_type original _Submission_date 2011-08-26 _Accession_date 2011-08-26 _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 Szulik Marta W. . 2 Ganguly Manjori . . 3 Wang Ruo-Wen . . 4 Gold Barry . . 5 Stone Michael P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 73 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-05-14 update BMRB 'update entry citation' 2012-08-27 original author 'original release' stop_ _Original_release_date 2011-09-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24131376 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Szulik Marta W. . 2 Voehler Markus W. . 3 Ganguly Manjori . . 4 Gold Barry . . 5 Stone Michael P. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 52 _Journal_issue 43 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 7659 _Page_last 7668 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name DNA_dodecamer _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(P*AP*GP*AP*CP*GP*CP*TP*CP*TP*C)-3')" $DNA_dodecamer 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_dodecamer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_dodecamer _Molecular_mass 3005.005 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; GAGAXCGCTCTC ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DA 3 DG 4 DA 5 2LA 6 DC 7 DG 8 DC 9 DT 10 DC 11 DT 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_2LA _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 2-amino-5-(aminomethyl)-7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one _BMRB_code . _PDB_code 2LA _Standard_residue_derivative . _Molecular_mass 375.274 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Sep 14 15:34:03 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? N9 N9 N . 0 . ? C1' C1' C . 0 . ? C10 C10 C . 0 . ? N11 N11 N . 0 . ? OP1 OP1 O . 0 . ? C2' C2' C . 0 . ? OP2 OP2 O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 0 . ? H1N1 H1N1 H . 0 . ? H8 H8 H . 0 . ? H10 H10 H . 0 . ? H10A H10A H . 0 . ? H1' H1' H . 0 . ? HN11 HN11 H . 0 . ? HN1A HN1A H . 0 . ? H12' H12' H . 0 . ? H22' H22' H . 0 . ? HN2 HN2 H . 0 . ? HN2A HN2A H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H15' H15' H . 0 . ? H25' H25' H . 0 . ? OP3 OP3 O . 0 . ? HOP2 HOP2 H . 0 . ? HO3' HO3' H . 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 DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING N1 C2 ? ? SING N1 C6 ? ? SING N1 H1N1 ? ? SING C2 N2 ? ? DOUB C2 N3 ? ? SING N2 HN2 ? ? SING N2 HN2A ? ? SING N3 C4 ? ? DOUB C4 C5 ? ? SING C4 N9 ? ? SING C5 C6 ? ? SING C5 C7 ? ? DOUB C6 O6 ? ? DOUB C7 C8 ? ? SING C7 C10 ? ? SING C8 N9 ? ? SING C8 H8 ? ? SING N9 C1' ? ? SING C1' C2' ? ? SING C1' O4' ? ? SING C1' H1' ? ? SING C10 N11 ? ? SING C10 H10 ? ? SING C10 H10A ? ? SING N11 HN11 ? ? SING N11 HN1A ? ? SING C2' C3' ? ? SING C2' H12' ? ? SING C2' H22' ? ? SING C3' O3' ? ? SING C3' C4' ? ? SING C3' H3' ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING C4' H4' ? ? SING C5' O5' ? ? SING C5' H15' ? ? SING C5' H25' ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING O3' HO3' ? ? SING OP3 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_dodecamer Human 9606 Eukaryota Metazoa Homo sapiens 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_dodecamer 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_7amG_sample _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_dodecamer 0.25 mM [U-2H] 'sodium phosphate' 10 mM 'natural abundance' 'sodium chloride' 200 mM 'natural abundance' 'sodium azide' 0.011 M 'natural abundance' 'sodium EDTA' 0.05 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.0.b.6 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . 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' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 10 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement 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 $7amG_sample save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $7amG_sample save_ ####################### # Sample conditions # ####################### save_7amG_sample_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.21 . M pH 7 . pH pressure 1 . atm temperature 273 . K 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 water H 1 protons ppm 4.7 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 $7amG_sample stop_ _Sample_conditions_label $7amG_sample_conditions _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name "DNA (5'-D(P*AP*GP*AP*CP*GP*CP*TP*CP*TP*C)-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 DG H1' H 5.495 . . 2 1 1 DG H2' H 2.389 . . 3 1 1 DG H2'' H 2.588 . 2 4 1 1 DG H3' H 4.765 . . 5 1 1 DG H8 H 7.802 . 1 6 2 2 DA H1' H 5.894 . . 7 2 2 DA H2 H 7.707 . 1 8 2 2 DA H2' H 2.699 . . 9 2 2 DA H2'' H 2.833 . 2 10 2 2 DA H3' H 4.981 . . 11 2 2 DA H8 H 8.127 . 1 12 3 3 DG H1' H 5.450 . . 13 3 3 DG H2' H 2.521 . . 14 3 3 DG H2'' H 2.640 . 2 15 3 3 DG H3' H 4.943 . . 16 3 3 DG H8 H 7.641 . 1 17 4 4 DA H1' H 6.143 . . 18 4 4 DA H2 H 7.726 . 1 19 4 4 DA H2' H 2.726 . . 20 4 4 DA H2'' H 2.669 . 2 21 4 4 DA H3' H 4.964 . . 22 4 4 DA H5' H 4.400 . . 23 4 4 DA H8 H 8.019 . 1 24 5 5 2LA H1' H 5.492 . . 25 5 5 2LA H10 H 3.638 . . 26 5 5 2LA H10A H 3.467 . . 27 5 5 2LA H2' H 2.229 . . 28 5 5 2LA H2'' H 2.214 . . 29 5 5 2LA H3' H 4.822 . . 30 5 5 2LA H8 H 6.507 . . 31 6 6 DC H1' H 5.781 . . 32 6 6 DC H2' H 1.856 . . 33 6 6 DC H2'' H 2.363 . 2 34 6 6 DC H3' H 4.771 . . 35 6 6 DC H5 H 5.149 . 1 36 6 6 DC H6 H 7.255 . 1 37 7 7 DG H1' H 5.863 . . 38 7 7 DG H2' H 2.595 . . 39 7 7 DG H2'' H 2.671 . 2 40 7 7 DG H3' H 4.914 . . 41 7 7 DG H8 H 7.797 . 1 42 8 8 DC H1' H 5.839 . . 43 8 8 DC H2' H 1.995 . . 44 8 8 DC H2'' H 2.464 . 2 45 8 8 DC H3' H 4.649 . . 46 8 8 DC H5 H 5.341 . 1 47 8 8 DC H6 H 7.347 . 1 48 9 9 DT H1' H 6.059 . . 49 9 9 DT H2' H 2.125 . . 50 9 9 DT H2'' H 2.246 . 2 51 9 9 DT H3' H 4.851 . . 52 9 9 DT H6 H 7.445 . 1 53 9 9 DT H71 H 1.514 . 1 54 9 9 DT H72 H 1.514 . 1 55 9 9 DT H73 H 1.514 . 1 56 10 10 DC H1' H 5.970 . . 57 10 10 DC H2' H 2.499 . . 58 10 10 DC H2'' H 2.491 . 2 59 10 10 DC H3' H 4.743 . . 60 10 10 DC H5 H 5.641 . 1 61 10 10 DC H6 H 7.587 . 1 62 11 11 DT H1' H 6.073 . . 63 11 11 DT H2' H 2.152 . . 64 11 11 DT H2'' H 2.243 . 2 65 11 11 DT H3' H 4.841 . . 66 11 11 DT H6 H 7.453 . 1 67 11 11 DT H71 H 1.703 . 1 68 11 11 DT H72 H 1.703 . 1 69 11 11 DT H73 H 1.703 . 1 70 12 12 DC H1' H 6.245 . . 71 12 12 DC H3' H 4.534 . . 72 12 12 DC H5 H 5.838 . 1 73 12 12 DC H6 H 7.646 . 1 stop_ save_