data_17709 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution-state structures of monomeric and dimeric G-quadruplexes formed by a sequence from N-myc ; _BMRB_accession_number 17709 _BMRB_flat_file_name bmr17709.str _Entry_type original _Submission_date 2011-06-15 _Accession_date 2011-06-15 _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 Trajkovski Marko . . 2 Plavec Janez . . 3 'Webba da Silva' Mateus . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 115 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-03-09 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17708 'Solution-state structures of monomeric and dimeric G-quadruplexes adopted by a sequence from N-myc' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22303871 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Trajkovski Marko . . 2 'Webba da Silva' Mateus . . 3 Plavec Janez . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 134 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4132 _Page_last 4141 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name N-myc _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label N-myc $N-myc 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_N-myc _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common N-myc _Molecular_mass 6064.968 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence TAGGGCGGGAGGGAGGGAA loop_ _Residue_seq_code _Residue_label 1 DT 2 DA 3 DG 4 DG 5 DG 6 DC 7 DG 8 DG 9 DG 10 DA 11 DG 12 DG 13 DG 14 DA 15 DG 16 DG 17 DG 18 DA 19 DA 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 _Gene_mnemonic $N-myc humans 9606 Eukaryota Metazoa Homo sapiens N-myc 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 $N-myc '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $N-myc . mM 0.4 6.6 'natural abundance' D2O 10 % . . 'natural abundance' H2O" 90 % . . '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 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VNMRS _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VNMRS _Field_strength 600 _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-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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_JRHMBC_4 _Saveframe_category NMR_applied_experiment _Experiment_name JRHMBC _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 temperature 298.15 . K pH 6.5 . pH pressure 1 . atm 'ionic strength' 120 . mM 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 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-15N HSQC' '2D 1H-1H TOCSY' JRHMBC 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 N-myc _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 DT H1' H 5.770 0.001 1 2 1 1 DT H2' H 1.678 0.003 1 3 1 1 DT H2'' H 2.108 0.001 1 4 1 1 DT H3' H 4.434 0.000 1 5 1 1 DT H4' H 3.862 0.001 1 6 1 1 DT H5' H 3.426 0.002 1 7 1 1 DT H6 H 7.122 0.000 1 8 1 1 DT H71 H 1.558 0.002 1 9 1 1 DT H72 H 1.558 0.002 1 10 1 1 DT H73 H 1.558 0.002 1 11 2 2 DA H1' H 5.796 0.003 1 12 2 2 DA H2 H 7.814 0.000 1 13 2 2 DA H2' H 2.379 0.005 1 14 2 2 DA H2'' H 2.574 0.000 1 15 2 2 DA H3' H 4.803 0.000 1 16 2 2 DA H4' H 4.049 0.000 1 17 2 2 DA H8 H 7.942 0.002 1 18 3 3 DG H1 H 11.701 0.001 1 19 3 3 DG H1' H 6.010 0.001 1 20 3 3 DG H2' H 2.731 0.002 1 21 3 3 DG H2'' H 2.934 0.001 1 22 3 3 DG H3' H 4.948 0.000 1 23 3 3 DG H8 H 7.989 0.001 1 24 4 4 DG H1 H 11.382 0.002 1 25 4 4 DG H1' H 6.126 0.002 1 26 4 4 DG H2' H 2.539 0.004 1 27 4 4 DG H2'' H 2.873 0.002 1 28 4 4 DG H3' H 4.938 0.004 1 29 4 4 DG H8 H 7.600 0.000 1 30 5 5 DG H1 H 11.185 0.002 1 31 5 5 DG H1' H 6.418 0.001 1 32 5 5 DG H2' H 2.699 0.005 1 33 5 5 DG H2'' H 2.575 0.004 1 34 5 5 DG H3' H 5.088 0.009 1 35 5 5 DG H8 H 7.720 0.001 1 36 6 6 DC H1' H 6.438 0.003 1 37 6 6 DC H2' H 2.376 0.003 2 38 6 6 DC H2'' H 2.708 0.004 2 39 6 6 DC H3' H 5.057 0.002 1 40 6 6 DC H5 H 6.154 0.000 1 41 6 6 DC H6 H 7.991 0.007 1 42 7 7 DG H1 H 11.794 0.002 1 43 7 7 DG H1' H 6.146 0.002 1 44 7 7 DG H2' H 2.449 0.001 1 45 7 7 DG H2'' H 2.938 0.002 1 46 7 7 DG H3' H 5.130 0.002 1 47 7 7 DG H8 H 7.996 0.001 1 48 8 8 DG H1 H 11.492 0.002 1 49 8 8 DG H1' H 6.200 0.004 1 50 8 8 DG H2' H 2.661 0.000 1 51 8 8 DG H2'' H 2.929 0.000 1 52 8 8 DG H8 H 7.951 0.000 1 53 9 9 DG H1 H 11.404 0.001 1 54 9 9 DG H1' H 6.462 0.005 1 55 9 9 DG H2' H 2.693 0.003 1 56 9 9 DG H2'' H 2.570 0.002 1 57 9 9 DG H3' H 5.087 0.000 1 58 9 9 DG H8 H 7.829 0.000 1 59 10 10 DA H1' H 6.636 0.001 1 60 10 10 DA H2' H 2.877 0.000 1 61 10 10 DA H2'' H 2.877 0.000 1 62 10 10 DA H3' H 5.197 0.002 1 63 10 10 DA H8 H 8.495 0.001 1 64 11 11 DG H1 H 11.959 0.001 1 65 11 11 DG H1' H 6.173 0.000 1 66 11 11 DG H2' H 2.530 0.001 1 67 11 11 DG H2'' H 2.971 0.002 1 68 11 11 DG H3' H 5.168 0.001 1 69 11 11 DG H8 H 8.049 0.001 1 70 12 12 DG H1 H 11.341 0.003 1 71 12 12 DG H1' H 6.194 0.009 1 72 12 12 DG H2' H 2.662 0.000 1 73 12 12 DG H2'' H 2.918 0.000 1 74 12 12 DG H8 H 7.951 0.002 1 75 13 13 DG H1 H 11.215 0.002 1 76 13 13 DG H1' H 6.451 0.000 1 77 13 13 DG H2' H 2.680 0.000 1 78 13 13 DG H2'' H 2.575 0.000 1 79 13 13 DG H3' H 5.084 0.000 1 80 13 13 DG H8 H 7.796 0.000 1 81 14 14 DA H1' H 6.636 0.001 1 82 14 14 DA H2' H 2.877 0.000 1 83 14 14 DA H2'' H 2.877 0.000 1 84 14 14 DA H3' H 5.198 0.002 1 85 14 14 DA H8 H 8.494 0.000 1 86 15 15 DG H1 H 11.294 0.002 1 87 15 15 DG H1' H 6.029 0.002 1 88 15 15 DG H2' H 2.367 0.001 1 89 15 15 DG H2'' H 2.788 0.003 1 90 15 15 DG H3' H 5.117 0.001 1 91 15 15 DG H8 H 7.945 0.002 1 92 16 16 DG H1 H 11.302 0.004 1 93 16 16 DG H1' H 5.958 0.001 1 94 16 16 DG H2' H 2.641 0.003 1 95 16 16 DG H2'' H 2.713 0.003 1 96 16 16 DG H3' H 5.027 0.002 1 97 16 16 DG H8 H 7.927 0.002 1 98 17 17 DG H1 H 10.816 0.002 1 99 17 17 DG H1' H 5.877 0.003 1 100 17 17 DG H2' H 2.324 0.001 1 101 17 17 DG H2'' H 2.641 0.002 1 102 17 17 DG H3' H 4.925 0.001 1 103 17 17 DG H8 H 7.452 0.000 1 104 18 18 DA H1' H 5.814 0.001 1 105 18 18 DA H2 H 7.382 0.000 1 106 18 18 DA H2' H 2.255 0.002 1 107 18 18 DA H2'' H 2.392 0.002 1 108 18 18 DA H3' H 4.835 0.002 1 109 18 18 DA H8 H 7.906 0.001 1 110 19 19 DA H1' H 5.944 0.001 1 111 19 19 DA H2' H 2.395 0.004 1 112 19 19 DA H2'' H 2.261 0.001 1 113 19 19 DA H3' H 4.516 0.000 1 114 19 19 DA H4' H 3.997 0.000 1 115 19 19 DA H8 H 7.993 0.000 1 stop_ save_