data_19386 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; parallel-stranded G-quadruplex in DNA poly-G stretches ; _BMRB_accession_number 19386 _BMRB_flat_file_name bmr19386.str _Entry_type original _Submission_date 2013-07-24 _Accession_date 2013-07-24 _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 Sengar Anjali . . 2 Heddi Brahim . . 3 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" 164 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-12-01 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19381 'Locked nucleic acid into G-quadruplexes' 19389 'Stacked dimeric G-quadruplex' stop_ _Original_release_date 2014-12-01 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Formation of G-quadruplexes in poly-G sequences: Structure of a propeller-type parallel-stranded G-quadruplex formed by a G15 stretch' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25375976 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sengar Anjali . . 2 Heddi Brahim . . 3 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation Biochemistry _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'parallel-stranded G-quadruplex in DNA poly-G stretches' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*TP*TP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*T)-3')' $DNA 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*TP*TP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*T)-3') _Molecular_mass 5805.756 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence TTGGGGGGGGGGGGGGGT loop_ _Residue_seq_code _Residue_label 1 DT 2 DT 3 DG 4 DG 5 DG 6 DG 7 DG 8 DG 9 DG 10 DG 11 DG 12 DG 13 DG 14 DG 15 DG 16 DG 17 DG 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 $DNA . . . . . . 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 '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 $DNA . mM 0.1 2 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' KCl 5 mM . . 'natural abundance' KPi 5 mM . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.34 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'geometry optimization' refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 700 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_JRNOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H JRNOESY' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . 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 7.0 . pH pressure 1 . atm temperature 310 . 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 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 TOCSY' '2D 1H-1H NOESY' '2D 1H-1H JRNOESY' 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 'DNA (5'-D(*TP*TP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*T)-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 DT H1' H 5.860 0.01 1 2 1 1 DT H2' H 1.989 0.01 1 3 1 1 DT H2'' H 2.315 0.01 1 4 1 1 DT H3' H 4.562 0.01 1 5 1 1 DT H4' H 3.859 0.01 1 6 1 1 DT H5' H 3.552 0.01 2 7 1 1 DT H5'' H 3.552 0.01 2 8 1 1 DT H6 H 7.305 0.01 1 9 1 1 DT H71 H 1.566 0.01 2 10 1 1 DT H72 H 1.566 0.01 2 11 1 1 DT H73 H 1.566 0.01 2 12 2 2 DT H1' H 5.918 0.01 1 13 2 2 DT H2' H 1.986 0.01 1 14 2 2 DT H2'' H 2.383 0.01 1 15 2 2 DT H3' H 4.699 0.01 1 16 2 2 DT H4' H 4.021 0.01 1 17 2 2 DT H5' H 3.721 0.01 2 18 2 2 DT H5'' H 3.424 0.01 2 19 2 2 DT H6 H 7.364 0.01 1 20 2 2 DT H71 H 1.549 0.01 2 21 2 2 DT H72 H 1.549 0.01 2 22 2 2 DT H73 H 1.549 0.01 2 23 3 3 DG H1 H 11.983 0.01 1 24 3 3 DG H1' H 6.170 0.01 1 25 3 3 DG H2' H 2.847 0.01 1 26 3 3 DG H2'' H 3.098 0.01 1 27 3 3 DG H3' H 4.965 0.01 1 28 3 3 DG H4' H 4.467 0.01 1 29 3 3 DG H5' H 4.123 0.01 2 30 3 3 DG H5'' H 3.997 0.01 2 31 3 3 DG H8 H 8.145 0.01 1 32 4 4 DG H1 H 11.470 0.01 1 33 4 4 DG H1' H 6.249 0.01 1 34 4 4 DG H2' H 2.715 0.01 1 35 4 4 DG H2'' H 2.997 0.01 1 36 4 4 DG H3' H 5.040 0.01 1 37 4 4 DG H4' H 4.592 0.01 1 38 4 4 DG H5' H 4.452 0.01 2 39 4 4 DG H5'' H 4.334 0.01 2 40 4 4 DG H8 H 7.817 0.01 1 41 5 5 DG H1 H 11.339 0.01 1 42 5 5 DG H1' H 6.480 0.01 1 43 5 5 DG H2' H 2.708 0.01 1 44 5 5 DG H2'' H 2.588 0.01 1 45 5 5 DG H3' H 5.123 0.01 1 46 5 5 DG H4' H 4.683 0.01 1 47 5 5 DG H5' H 4.451 0.01 2 48 5 5 DG H5'' H 4.346 0.01 2 49 5 5 DG H8 H 7.800 0.01 1 50 6 6 DG H1' H 6.467 0.01 1 51 6 6 DG H2' H 2.937 0.01 1 52 6 6 DG H2'' H 2.821 0.01 1 53 6 6 DG H3' H 5.222 0.01 1 54 6 6 DG H4' H 4.680 0.01 1 55 6 6 DG H5' H 4.296 0.01 2 56 6 6 DG H5'' H 4.296 0.01 2 57 6 6 DG H8 H 8.154 0.01 1 58 7 7 DG H1 H 11.809 0.01 1 59 7 7 DG H1' H 6.183 0.01 1 60 7 7 DG H2' H 2.511 0.01 1 61 7 7 DG H2'' H 2.991 0.01 1 62 7 7 DG H3' H 5.194 0.01 1 63 7 7 DG H4' H 4.491 0.01 1 64 7 7 DG H5' H 4.389 0.01 2 65 7 7 DG H5'' H 4.285 0.01 2 66 7 7 DG H8 H 8.049 0.01 1 67 8 8 DG H1 H 11.494 0.01 1 68 8 8 DG H1' H 6.242 0.01 1 69 8 8 DG H2' H 2.696 0.01 1 70 8 8 DG H2'' H 2.960 0.01 1 71 8 8 DG H3' H 5.104 0.01 1 72 8 8 DG H4' H 4.597 0.01 1 73 8 8 DG H5' H 4.293 0.01 2 74 8 8 DG H5'' H 4.293 0.01 2 75 8 8 DG H8 H 7.984 0.01 1 76 9 9 DG H1 H 11.348 0.01 1 77 9 9 DG H1' H 6.485 0.01 1 78 9 9 DG H2' H 2.708 0.01 1 79 9 9 DG H2'' H 2.585 0.01 1 80 9 9 DG H3' H 5.125 0.01 1 81 9 9 DG H4' H 4.685 0.01 1 82 9 9 DG H5' H 4.443 0.01 2 83 9 9 DG H5'' H 4.347 0.01 2 84 9 9 DG H8 H 7.850 0.01 1 85 10 10 DG H1' H 6.467 0.01 1 86 10 10 DG H2' H 2.937 0.01 1 87 10 10 DG H2'' H 2.821 0.01 1 88 10 10 DG H3' H 5.222 0.01 1 89 10 10 DG H4' H 4.680 0.01 1 90 10 10 DG H5' H 4.296 0.01 2 91 10 10 DG H5'' H 4.296 0.01 2 92 10 10 DG H8 H 8.154 0.01 1 93 11 11 DG H1 H 11.894 0.01 1 94 11 11 DG H1' H 6.212 0.01 1 95 11 11 DG H2' H 2.552 0.01 1 96 11 11 DG H2'' H 3.011 0.01 1 97 11 11 DG H3' H 5.207 0.01 1 98 11 11 DG H4' H 4.497 0.01 1 99 11 11 DG H5' H 4.389 0.01 2 100 11 11 DG H5'' H 4.279 0.01 2 101 11 11 DG H8 H 8.060 0.01 1 102 12 12 DG H1 H 11.409 0.01 1 103 12 12 DG H1' H 6.247 0.01 1 104 12 12 DG H2' H 2.692 0.01 1 105 12 12 DG H2'' H 2.959 0.01 1 106 12 12 DG H3' H 5.108 0.01 1 107 12 12 DG H4' H 4.592 0.01 1 108 12 12 DG H5' H 4.315 0.01 2 109 12 12 DG H5'' H 4.283 0.01 2 110 12 12 DG H8 H 7.975 0.01 1 111 13 13 DG H1 H 11.095 0.01 1 112 13 13 DG H1' H 6.484 0.01 1 113 13 13 DG H2' H 2.708 0.01 1 114 13 13 DG H2'' H 2.587 0.01 1 115 13 13 DG H3' H 5.125 0.01 1 116 13 13 DG H4' H 4.675 0.01 1 117 13 13 DG H5' H 4.433 0.01 2 118 13 13 DG H5'' H 4.344 0.01 2 119 13 13 DG H8 H 7.820 0.01 1 120 14 14 DG H1' H 6.467 0.01 1 121 14 14 DG H2' H 2.937 0.01 1 122 14 14 DG H2'' H 2.821 0.01 1 123 14 14 DG H3' H 5.222 0.01 1 124 14 14 DG H4' H 4.680 0.01 1 125 14 14 DG H5' H 4.296 0.01 2 126 14 14 DG H5'' H 4.296 0.01 2 127 14 14 DG H8 H 8.154 0.01 1 128 15 15 DG H1 H 11.660 0.01 1 129 15 15 DG H1' H 6.146 0.01 1 130 15 15 DG H2' H 2.450 0.01 1 131 15 15 DG H2'' H 2.874 0.01 1 132 15 15 DG H3' H 5.184 0.01 1 133 15 15 DG H4' H 4.482 0.01 1 134 15 15 DG H5' H 4.375 0.01 2 135 15 15 DG H5'' H 4.286 0.01 2 136 15 15 DG H8 H 7.997 0.01 1 137 16 16 DG H1 H 11.549 0.01 1 138 16 16 DG H1' H 6.095 0.01 1 139 16 16 DG H2' H 2.753 0.01 1 140 16 16 DG H2'' H 2.753 0.01 1 141 16 16 DG H3' H 5.093 0.01 1 142 16 16 DG H4' H 4.512 0.01 1 143 16 16 DG H5' H 4.281 0.01 2 144 16 16 DG H5'' H 4.219 0.01 2 145 16 16 DG H8 H 8.019 0.01 1 146 17 17 DG H1 H 11.282 0.01 1 147 17 17 DG H1' H 6.266 0.01 1 148 17 17 DG H2' H 2.625 0.01 1 149 17 17 DG H2'' H 2.821 0.01 1 150 17 17 DG H3' H 4.931 0.01 1 151 17 17 DG H4' H 4.552 0.01 1 152 17 17 DG H5' H 4.314 0.01 2 153 17 17 DG H5'' H 4.277 0.01 2 154 17 17 DG H8 H 7.718 0.01 1 155 18 18 DT H1' H 5.947 0.01 1 156 18 18 DT H2' H 2.094 0.01 1 157 18 18 DT H3' H 4.452 0.01 1 158 18 18 DT H4' H 3.988 0.01 1 159 18 18 DT H5' H 4.260 0.01 2 160 18 18 DT H5'' H 4.087 0.01 2 161 18 18 DT H6 H 7.173 0.01 1 162 18 18 DT H71 H 1.528 0.01 2 163 18 18 DT H72 H 1.528 0.01 2 164 18 18 DT H73 H 1.528 0.01 2 stop_ save_