data_17980 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Monomer-dimer equilibrium for 5 -5 stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study ; _BMRB_accession_number 17980 _BMRB_flat_file_name bmr17980.str _Entry_type original _Submission_date 2011-10-07 _Accession_date 2011-10-07 _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 Do 'Ngoc Quang' . . 2 Phan 'Anh Tuan' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 159 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-01-17 update BMRB 'update entry citation' 2012-10-09 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title "Monomer-dimer equilibrium for the 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study." _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23019076 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Do 'Ngoc Quang' . . 2 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation Chemistry _Journal_name_full 'Chemistry (Weinheim an der Bergstrasse, Germany)' _Journal_volume 18 _Journal_issue 46 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 14752 _Page_last 14759 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name G-quadruplexes _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label G-quadruplexes $G-quadruplexes 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_G-quadruplexes _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')_ _Molecular_mass 5730.718 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence TTGGGTGGGTGGGTGGGT loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DT 3 3 DG 4 4 DG 5 5 DG 6 6 DT 7 7 DG 8 8 DG 9 9 DG 10 10 DT 11 11 DG 12 12 DG 13 13 DG 14 14 DT 15 15 DG 16 16 DG 17 17 DG 18 18 DT 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 $G-quadruplexes . . . . . . 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 $G-quadruplexes '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 $G-quadruplexes 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 16 . 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 0.00 internal direct . . . 1.000000000 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' 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 G-quadruplexes _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 5.868 0.001 1 2 1 1 DT H2' H 1.990 0.001 1 3 1 1 DT H2'' H 2.317 0.004 1 4 1 1 DT H3' H 4.565 0.002 1 5 1 1 DT H4' H 3.864 0.001 1 6 1 1 DT H5' H 3.555 0.001 4 7 1 1 DT H6 H 7.308 0.001 1 8 1 1 DT H71 H 1.575 0.001 2 9 1 1 DT H72 H 1.575 0.001 2 10 1 1 DT H73 H 1.575 0.001 2 11 2 2 DT H1' H 5.918 0.002 1 12 2 2 DT H2' H 1.987 0.002 3 13 2 2 DT H2'' H 2.380 0.001 3 14 2 2 DT H3' H 4.702 0.001 1 15 2 2 DT H4' H 4.019 0.001 1 16 2 2 DT H5' H 3.721 0.001 4 17 2 2 DT H5'' H 3.425 0.002 4 18 2 2 DT H6 H 7.365 0.001 1 19 2 2 DT H71 H 1.548 0.001 2 20 2 2 DT H72 H 1.548 0.001 2 21 2 2 DT H73 H 1.548 0.001 2 22 3 3 DG H1' H 6.171 0.001 1 23 3 3 DG H2' H 2.859 0.001 1 24 3 3 DG H2'' H 3.096 0.002 1 25 3 3 DG H3' H 4.970 0.001 1 26 3 3 DG H4' H 4.472 0.001 1 27 3 3 DG H5' H 4.123 0.001 4 28 3 3 DG H5'' H 4.001 0.001 4 29 3 3 DG H8 H 8.155 0.001 1 30 4 4 DG H1' H 6.244 0.001 1 31 4 4 DG H2' H 2.718 0.001 1 32 4 4 DG H2'' H 2.997 0.001 1 33 4 4 DG H3' H 5.038 0.001 1 34 4 4 DG H4' H 4.594 0.001 1 35 4 4 DG H5' H 4.340 0.001 4 36 4 4 DG H8 H 7.822 0.001 1 37 5 5 DG H1' H 6.479 0.001 1 38 5 5 DG H2' H 2.706 0.001 1 39 5 5 DG H2'' H 2.604 0.001 1 40 5 5 DG H3' H 5.137 0.001 1 41 5 5 DG H4' H 4.669 0.001 1 42 5 5 DG H5' H 4.446 0.001 4 43 5 5 DG H5'' H 4.337 0.001 4 44 5 5 DG H8 H 7.805 0.001 1 45 6 6 DT H1' H 6.557 0.001 1 46 6 6 DT H2' H 2.496 0.001 1 47 6 6 DT H2'' H 2.689 0.004 1 48 6 6 DT H3' H 5.163 0.002 1 49 6 6 DT H4' H 4.652 0.001 1 50 6 6 DT H5' H 4.365 0.002 4 51 6 6 DT H5'' H 4.325 0.001 4 52 6 6 DT H6 H 7.887 0.001 1 53 6 6 DT H71 H 2.003 0.001 2 54 6 6 DT H72 H 2.003 0.001 2 55 6 6 DT H73 H 2.003 0.001 2 56 7 7 DG H1' H 6.177 0.001 1 57 7 7 DG H2' H 2.505 0.001 1 58 7 7 DG H2'' H 2.977 0.001 1 59 7 7 DG H3' H 5.163 0.001 1 60 7 7 DG H4' H 4.478 0.001 1 61 7 7 DG H5' H 4.364 0.001 4 62 7 7 DG H5'' H 4.273 0.001 4 63 7 7 DG H8 H 8.044 0.001 1 64 8 8 DG H1' H 6.233 0.001 1 65 8 8 DG H2' H 2.693 0.001 1 66 8 8 DG H2'' H 2.965 0.008 1 67 8 8 DG H3' H 5.107 0.001 1 68 8 8 DG H4' H 4.596 0.001 1 69 8 8 DG H5' H 4.350 0.001 4 70 8 8 DG H5'' H 4.284 0.001 4 71 8 8 DG H8 H 7.997 0.001 1 72 9 9 DG H1' H 6.494 0.002 1 73 9 9 DG H2' H 2.716 0.001 1 74 9 9 DG H2'' H 2.600 0.001 1 75 9 9 DG H3' H 5.139 0.001 1 76 9 9 DG H4' H 4.675 0.001 1 77 9 9 DG H5' H 4.441 0.001 4 78 9 9 DG H5'' H 4.343 0.001 4 79 9 9 DG H8 H 7.858 0.001 1 80 10 10 DT H1' H 6.546 0.004 1 81 10 10 DT H2' H 2.491 0.007 1 82 10 10 DT H2'' H 2.721 0.017 1 83 10 10 DT H3' H 5.151 0.001 1 84 10 10 DT H4' H 4.653 0.006 1 85 10 10 DT H5' H 4.359 0.002 4 86 10 10 DT H5'' H 4.323 0.001 4 87 10 10 DT H6 H 7.885 0.002 1 88 10 10 DT H71 H 2.004 0.001 2 89 10 10 DT H72 H 2.004 0.001 2 90 10 10 DT H73 H 2.004 0.001 2 91 11 11 DG H1' H 6.207 0.001 1 92 11 11 DG H2' H 2.544 0.001 1 93 11 11 DG H2'' H 2.998 0.001 1 94 11 11 DG H3' H 5.175 0.001 1 95 11 11 DG H4' H 4.481 0.001 1 96 11 11 DG H5' H 4.363 0.001 1 97 11 11 DG H5'' H 4.266 0.002 1 98 11 11 DG H8 H 8.055 0.001 1 99 12 12 DG H1' H 6.233 0.002 1 100 12 12 DG H2' H 2.702 0.005 1 101 12 12 DG H2'' H 2.949 0.001 1 102 12 12 DG H3' H 5.111 0.001 1 103 12 12 DG H4' H 4.591 0.001 1 104 12 12 DG H5' H 4.335 0.001 4 105 12 12 DG H5'' H 4.284 0.001 4 106 12 12 DG H8 H 7.985 0.001 1 107 13 13 DG H1' H 6.490 0.001 1 108 13 13 DG H2' H 2.712 0.001 1 109 13 13 DG H2'' H 2.601 0.001 1 110 13 13 DG H3' H 5.137 0.001 1 111 13 13 DG H4' H 4.666 0.001 1 112 13 13 DG H5' H 4.433 0.001 4 113 13 13 DG H5'' H 4.323 0.001 4 114 13 13 DG H8 H 7.828 0.001 1 115 14 14 DT H1' H 6.540 0.001 1 116 14 14 DT H2' H 2.468 0.001 1 117 14 14 DT H2'' H 2.692 0.003 1 118 14 14 DT H3' H 5.144 0.001 1 119 14 14 DT H4' H 4.646 0.001 1 120 14 14 DT H5' H 4.364 0.001 4 121 14 14 DT H5'' H 4.319 0.004 4 122 14 14 DT H6 H 7.883 0.001 1 123 14 14 DT H71 H 1.996 0.001 2 124 14 14 DT H72 H 1.996 0.001 2 125 14 14 DT H73 H 1.996 0.001 2 126 15 15 DG H1' H 6.143 0.001 1 127 15 15 DG H2' H 2.441 0.001 1 128 15 15 DG H2'' H 2.869 0.001 1 129 15 15 DG H3' H 5.157 0.001 1 130 15 15 DG H4' H 4.472 0.001 1 131 15 15 DG H5' H 4.364 0.001 4 132 15 15 DG H5'' H 4.267 0.007 4 133 15 15 DG H8 H 7.995 0.001 1 134 16 16 DG H1' H 6.099 0.001 1 135 16 16 DG H2' H 2.748 0.001 1 136 16 16 DG H2'' H 2.762 0.001 1 137 16 16 DG H3' H 5.103 0.001 1 138 16 16 DG H4' H 4.516 0.001 1 139 16 16 DG H5' H 4.274 0.001 4 140 16 16 DG H5'' H 4.222 0.002 4 141 16 16 DG H8 H 8.030 0.001 1 142 17 17 DG H1' H 6.275 0.001 1 143 17 17 DG H2' H 2.632 0.003 1 144 17 17 DG H2'' H 2.832 0.002 1 145 17 17 DG H3' H 4.935 0.001 1 146 17 17 DG H4' H 4.560 0.001 1 147 17 17 DG H5' H 4.322 0.001 4 148 17 17 DG H5'' H 4.281 0.013 4 149 17 17 DG H8 H 7.726 0.001 1 150 18 18 DT H1' H 5.954 0.001 1 151 18 18 DT H2' H 2.104 0.001 1 152 18 18 DT H3' H 4.462 0.001 1 153 18 18 DT H4' H 3.996 0.001 1 154 18 18 DT H5' H 4.264 0.001 4 155 18 18 DT H5'' H 4.096 0.001 4 156 18 18 DT H6 H 7.178 0.001 1 157 18 18 DT H71 H 1.521 0.002 2 158 18 18 DT H72 H 1.521 0.002 2 159 18 18 DT H73 H 1.521 0.002 2 stop_ save_