data_34186 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Quadruplex with flipped tetrad formed by the c-myc promoter sequence ; _BMRB_accession_number 34186 _BMRB_flat_file_name bmr34186.str _Entry_type original _Submission_date 2017-10-18 _Accession_date 2017-10-18 _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 Karg B. . . 2 Weisz K. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 158 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-06-06 original BMRB . stop_ _Original_release_date 2018-06-06 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Loop Length Affects Syn-Anti Conformational Rearrangements in Parallel G-Quadruplexes. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29756658 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Karg B. . . 2 Weisz K. . . stop_ _Journal_abbreviation Chemistry _Journal_volume . _Journal_issue . _Journal_ISSN 1521-3765 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name cmbr-481317 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 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 entity_1 _Molecular_mass 7324.094 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; TGAXGGTXGGTAXGGTXGGT AA ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DG 3 DA 4 BGM 5 DG 6 DG 7 DT 8 BGM 9 DG 10 DG 11 DT 12 DA 13 BGM 14 DG 15 DG 16 DT 17 BGM 18 DG 19 DG 20 DT 21 DA 22 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_BGM _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE _BMRB_code BGM _PDB_code BGM _Standard_residue_derivative . _Molecular_mass 426.117 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C4 C4 C . 0 . ? N3 N3 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N1 N1 N . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? OP3 OP3 O . 0 . ? BR BR BR . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H1 H1 H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H3' H3' 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 P OP3 ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C1' N9 ? ? SING C1' C2' ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 BR ? ? SING N7 C5 ? ? DOUB C5 C4 ? ? SING C5 C6 ? ? SING C4 N3 ? ? DOUB N3 C2 ? ? SING C2 N2 ? ? SING C2 N1 ? ? SING N2 H21 ? ? SING N2 H22 ? ? SING N1 C6 ? ? SING N1 H1 ? ? DOUB C6 O6 ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C3' O3' ? ? SING C3' H3' ? ? 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 $entity_1 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '10 mM NA potassium phosphate, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 . mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '10 mM NA potassium phosphate, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 . mM 'natural abundance' 'potassium phosphate' 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 refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . 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_ ############################# # 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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _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 'ionic strength' 10 . mM pH 7 . pH* pressure 1 . atm temperature 303 . 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 water H 1 protons ppm 4.73 internal 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 $sample_2 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 DT H1' H 5.850 0.004 1 2 1 1 DT H2' H 1.785 0.005 2 3 1 1 DT H2'' H 2.121 0.002 2 4 1 1 DT H3' H 4.452 0.004 1 5 1 1 DT H5' H 3.521 0.008 2 6 1 1 DT H5'' H 3.855 0.003 2 7 1 1 DT H6 H 7.285 0.005 1 8 1 1 DT H71 H 1.674 0.005 1 9 1 1 DT H72 H 1.674 0.005 1 10 1 1 DT H73 H 1.674 0.005 1 11 2 2 DG H1' H 5.847 0.003 1 12 2 2 DG H2' H 2.537 0.004 1 13 2 2 DG H2'' H 2.436 0.002 1 14 2 2 DG H3' H 4.694 0.016 1 15 2 2 DG H4' H 4.138 0.003 1 16 2 2 DG H5' H 3.884 0.009 2 17 2 2 DG H5'' H 3.966 0.003 2 18 2 2 DG H8 H 7.628 0.006 1 19 3 3 DA H1' H 6.047 0.003 1 20 3 3 DA H2 H 7.552 0.0 1 21 3 3 DA H2' H 1.963 0.005 1 22 3 3 DA H2'' H 2.529 0.004 1 23 3 3 DA H3' H 4.678 . 1 24 3 3 DA H5' H 4.049 . 1 25 3 3 DA H5'' H 3.669 . 1 26 3 3 DA H8 H 7.850 0.002 1 27 4 4 BGM H1 H 11.326 0.002 1 28 4 4 BGM H1' H 6.196 0.003 1 29 4 4 BGM H2' H 3.970 0.006 1 30 4 4 BGM H2'' H 3.052 0.002 1 31 4 4 BGM H3' H 4.920 0.006 1 32 5 5 DG H1 H 11.511 0.001 1 33 5 5 DG H1' H 5.968 0.005 1 34 5 5 DG H2' H 2.444 0.005 1 35 5 5 DG H2'' H 2.898 0.002 1 36 5 5 DG H3' H 4.996 0.003 1 37 5 5 DG H8 H 8.010 0.004 1 38 6 6 DG H1 H 10.712 0.004 1 39 6 6 DG H1' H 6.420 0.013 1 40 6 6 DG H2' H 2.661 0.002 1 41 6 6 DG H2'' H 2.612 . 1 42 6 6 DG H3' H 5.118 0.006 1 43 6 6 DG H4' H 4.484 0.007 1 44 6 6 DG H8 H 7.636 0.003 1 45 7 7 DT H1' H 6.497 0.007 1 46 7 7 DT H2' H 2.387 0.011 1 47 7 7 DT H2'' H 2.768 0.006 1 48 7 7 DT H3' H 5.089 0.01 1 49 7 7 DT H4' H 4.343 0.005 1 50 7 7 DT H6 H 7.880 0.003 1 51 7 7 DT H71 H 1.982 0.004 1 52 7 7 DT H72 H 1.982 0.004 1 53 7 7 DT H73 H 1.982 0.004 1 54 8 8 BGM H1 H 11.398 0.002 1 55 8 8 BGM H1' H 5.971 0.007 1 56 8 8 BGM H2' H 3.659 . 1 57 8 8 BGM H2'' H 2.944 0.01 1 58 8 8 BGM H3' H 5.049 0.004 1 59 8 8 BGM H4' H 5.046 0.001 1 60 9 9 DG H1 H 11.879 0.001 1 61 9 9 DG H1' H 5.847 0.003 1 62 9 9 DG H2' H 2.599 0.004 1 63 9 9 DG H2'' H 2.780 0.003 1 64 9 9 DG H3' H 5.048 0.005 1 65 9 9 DG H8 H 8.226 0.002 1 66 10 10 DG H1 H 11.483 0.0 1 67 10 10 DG H1' H 6.427 0.009 1 68 10 10 DG H2' H 2.662 0.005 1 69 10 10 DG H2'' H 2.598 0.002 1 70 10 10 DG H3' H 5.079 0.003 1 71 10 10 DG H8 H 7.831 0.003 1 72 11 11 DT H1' H 6.211 0.003 1 73 11 11 DT H2' H 2.450 0.003 1 74 11 11 DT H3' H 5.090 . 1 75 11 11 DT H5' H 4.202 0.016 2 76 11 11 DT H5'' H 3.965 . 2 77 11 11 DT H6 H 7.632 0.001 1 78 11 11 DT H71 H 1.936 . 1 79 11 11 DT H72 H 1.936 . 1 80 11 11 DT H73 H 1.936 . 1 81 12 12 DA H1' H 6.649 0.004 1 82 12 12 DA H2 H 8.306 0.002 1 83 12 12 DA H2' H 3.069 0.005 1 84 12 12 DA H2'' H 2.951 0.001 1 85 12 12 DA H3' H 5.246 0.004 1 86 12 12 DA H4' H 4.617 . 1 87 12 12 DA H5'' H 4.177 . 1 88 12 12 DA H8 H 8.498 0.002 1 89 13 13 BGM H1 H 11.167 0.011 1 90 13 13 BGM H1' H 6.162 0.002 1 91 13 13 BGM H2' H 3.555 0.003 1 92 13 13 BGM H2'' H 3.090 0.003 1 93 13 13 BGM H3' H 5.051 0.003 1 94 14 14 DG H1 H 11.456 0.001 1 95 14 14 DG H1' H 5.980 0.005 1 96 14 14 DG H2' H 2.473 0.001 1 97 14 14 DG H2'' H 2.921 0.002 1 98 14 14 DG H3' H 5.005 0.004 1 99 14 14 DG H8 H 7.961 0.004 1 100 15 15 DG H1 H 10.868 0.007 1 101 15 15 DG H1' H 6.476 0.003 1 102 15 15 DG H2' H 2.675 0.003 1 103 15 15 DG H3' H 5.132 0.005 1 104 15 15 DG H4' H 4.339 0.017 1 105 15 15 DG H8 H 7.707 0.003 1 106 16 16 DT H1' H 6.497 0.007 1 107 16 16 DT H2' H 2.387 0.011 1 108 16 16 DT H2'' H 2.771 0.003 1 109 16 16 DT H3' H 5.104 0.01 1 110 16 16 DT H4' H 4.347 0.001 1 111 16 16 DT H6 H 7.880 0.003 1 112 16 16 DT H71 H 1.982 0.004 1 113 16 16 DT H72 H 1.982 0.004 1 114 16 16 DT H73 H 1.982 0.004 1 115 17 17 BGM H1 H 11.056 0.007 1 116 17 17 BGM H1' H 5.951 0.002 1 117 17 17 BGM H2' H 2.733 0.003 1 118 17 17 BGM H2'' H 2.823 0.006 1 119 17 17 BGM H3' H 5.050 0.002 1 120 17 17 BGM H4' H 5.045 . 1 121 18 18 DG H1 H 11.895 0.002 1 122 18 18 DG H1' H 5.741 0.003 1 123 18 18 DG H2' H 2.652 0.016 1 124 18 18 DG H2'' H 2.617 0.006 1 125 18 18 DG H3' H 5.047 0.003 1 126 18 18 DG H8 H 8.256 0.002 1 127 19 19 DG H1 H 11.190 0.007 1 128 19 19 DG H1' H 6.192 0.002 1 129 19 19 DG H2' H 2.482 0.003 1 130 19 19 DG H2'' H 2.757 0.007 1 131 19 19 DG H3' H 4.927 0.004 1 132 19 19 DG H8 H 7.600 0.002 1 133 20 20 DT H1' H 5.845 0.005 1 134 20 20 DT H2' H 1.803 0.003 1 135 20 20 DT H2'' H 2.246 0.002 1 136 20 20 DT H3' H 4.722 0.004 1 137 20 20 DT H5' H 4.149 0.006 2 138 20 20 DT H5'' H 4.049 0.005 2 139 20 20 DT H6 H 7.169 0.002 1 140 20 20 DT H71 H 1.597 0.002 1 141 20 20 DT H72 H 1.597 0.002 1 142 20 20 DT H73 H 1.597 0.002 1 143 21 21 DA H1' H 5.796 0.007 1 144 21 21 DA H2 H 7.366 0.003 1 145 21 21 DA H2' H 2.123 0.003 1 146 21 21 DA H2'' H 2.339 0.003 1 147 21 21 DA H3' H 4.611 . 1 148 21 21 DA H5' H 3.875 0.014 2 149 21 21 DA H5'' H 3.757 0.004 2 150 21 21 DA H8 H 7.851 0.01 1 151 22 22 DA H1' H 5.794 0.013 1 152 22 22 DA H2 H 7.492 0.007 1 153 22 22 DA H2' H 2.298 0.003 1 154 22 22 DA H2'' H 2.296 0.003 1 155 22 22 DA H3' H 4.386 0.002 1 156 22 22 DA H5' H 3.763 0.006 2 157 22 22 DA H5'' H 3.618 0.002 2 158 22 22 DA H8 H 7.680 0.01 1 stop_ save_