data_4400 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure and Mechanism of Formation of the H-y5 ismomer of an Intramolecular DNA Triple Helix. ; _BMRB_accession_number 4400 _BMRB_flat_file_name bmr4400.str _Entry_type new _Submission_date 1999-09-11 _Accession_date 1999-09-13 _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 'van Dongen' M. J.P. . 2 Doreleijers J. F. . 3 'van der Marel' G. A. . 4 'van Boom' J. H. . 5 Hilbers C. W. . 6 Wijmenga S. S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 247 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 1999-10-26 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; van Dongen, M. J.P., Doreleijers, J. F., van der Marel, G. A., van Boom, J. H., Hilbers, C. W., and Wijmenga, S. S., "Structure and Mechanism of Formation of the H-y5 isomer of an intramolecular DNA triple helix," Nat. Struct. Biol. 6, 854-859 (1999). ; _Citation_title ; Structure and Mechanism of Formation of the H-y5 isomer of an intramolecular DNA triple helix ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99396740 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 'van Dongen' M. J.P. . 2 Doreleijers J. F. . 3 'van der Marel' G. A. . 4 'van Boom' J. H. . 5 Hilbers C. W. . 6 Wijmenga S. S. . stop_ _Journal_abbreviation 'Nat. Struct. Biol.' _Journal_name_full 'Nature Structural Biology' _Journal_volume 6 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 854 _Page_last 859 _Year 1999 _Details . loop_ _Keyword H-DNA 'triple helix' DNA 'NMR structure' stop_ save_ ################################## # Molecular system description # ################################## save_system_h-y5 _Saveframe_category molecular_system _Mol_system_name 'H-y5 Triple Helix' _Abbreviation_common h-y5 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label h-y5 $h-y5 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_h-y5 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'H-y5 Triple Helix' _Abbreviation_common h-y5 _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; TCTTCCTTTTCCTTCTCCCG AGAAGGTTTT ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 17 DT 2 18 DC 3 19 DT 4 20 DT 5 21 DC 6 22 DC 7 23 DT 8 24 DT 9 25 DT 10 26 DT 11 1 DC 12 2 DC 13 3 DT 14 4 DT 15 5 DC 16 6 DT 17 7 DC 18 8 DC 19 9 DC 20 10 DG 21 11 DA 22 12 DG 23 13 DA 24 14 DA 25 15 DG 26 16 DG 27 27 DT 28 28 DT 29 29 DT 30 30 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 $h-y5 . . . . . . 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 $h-y5 chemically_synthesized . . . . . 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 $h-y5 . mM 2.0 4.0 . stop_ save_ ############################ # Computer software used # ############################ save_XEASY _Saveframe_category software _Name XEASY _Version . loop_ _Task 'assignment book keeping and cross peak integration' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ save_NMR_spectrometer2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unitry-Plus _Field_strength 750 _Details . save_ save_NMR_spectrometer3 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unitry-Plus _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label . save_ save_PE-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name PE-COSY _Sample_label . save_ save_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ save_31P-1H_4 _Saveframe_category NMR_applied_experiment _Experiment_name 31P-1H _Sample_label . save_ save_TOCSY-NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY-NOESY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name PE-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name 31P-1H _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY-NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 4.5 0.2 n/a temperature 298 0.5 K 'ionic strength' 100 . mM stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 0.0 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_chem_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name h-y5 _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 DT H1' H 6.114 0.002 . 2 . 1 DT H71 H 1.931 0.001 . 3 . 1 DT H72 H 1.931 0.001 . 4 . 1 DT H73 H 1.931 0.001 . 5 . 1 DT H6 H 7.874 0.001 . 6 . 1 DT H2' H 2.489 0.003 . 7 . 1 DT H2'' H 2.668 0.002 . 8 . 2 DC H4' H 4.348 0.001 . 9 . 2 DC H1' H 6.195 0.002 . 10 . 2 DC H5 H 5.853 0.002 . 11 . 2 DC H6 H 7.943 0.001 . 12 . 2 DC H2' H 2.397 0.002 . 13 . 2 DC H2'' H 2.722 0.003 . 14 . 2 DC H3' H 4.699 0.005 . 15 . 3 DT H4' H 4.344 0.002 . 16 . 3 DT H1' H 6.088 0.001 . 17 . 3 DT H71 H 1.721 0.001 . 18 . 3 DT H72 H 1.721 0.001 . 19 . 3 DT H73 H 1.721 0.001 . 20 . 3 DT H6 H 7.788 0.001 . 21 . 3 DT H2' H 2.445 0.001 . 22 . 3 DT H2'' H 2.677 0.003 . 23 . 3 DT H3' H 4.816 0.002 . 24 . 4 DT H1' H 6.054 0.002 . 25 . 4 DT H71 H 1.648 0.001 . 26 . 4 DT H72 H 1.648 0.001 . 27 . 4 DT H73 H 1.648 0.001 . 28 . 4 DT H6 H 7.716 0.001 . 29 . 4 DT H2' H 2.312 0.001 . 30 . 4 DT H2'' H 2.656 0.005 . 31 . 4 DT H3' H 4.827 0.001 . 32 . 5 DC H1' H 6.089 0.002 . 33 . 5 DC H5 H 5.809 0.002 . 34 . 5 DC H6 H 7.860 0.002 . 35 . 5 DC H2' H 2.091 0.003 . 36 . 5 DC H2'' H 2.586 0.001 . 37 . 5 DC H3' H 4.789 0.000 . 38 . 6 DC H4' H 4.132 0.003 . 39 . 6 DC H1' H 6.287 0.002 . 40 . 6 DC H5 H 5.939 0.002 . 41 . 6 DC H6 H 7.815 0.002 . 42 . 6 DC H2' H 2.384 0.001 . 43 . 6 DC H2'' H 2.541 0.002 . 44 . 6 DC H3' H 4.779 0.001 . 45 . 7 DT H5' H 4.026 0.000 . 46 . 7 DT H5'' H 3.995 0.000 . 47 . 7 DT H4' H 4.137 0.097 . 48 . 7 DT H1' H 6.132 0.003 . 49 . 7 DT H71 H 1.846 0.002 . 50 . 7 DT H72 H 1.846 0.002 . 51 . 7 DT H73 H 1.846 0.002 . 52 . 7 DT H6 H 7.630 0.002 . 53 . 7 DT H2' H 2.134 0.003 . 54 . 7 DT H2'' H 2.354 0.004 . 55 . 7 DT H3' H 4.772 0.005 . 56 . 8 DT H5' H 3.931 0.002 . 57 . 8 DT H4' H 4.240 0.002 . 58 . 8 DT H1' H 5.954 0.002 . 59 . 8 DT H71 H 1.558 0.003 . 60 . 8 DT H72 H 1.558 0.003 . 61 . 8 DT H73 H 1.558 0.003 . 62 . 8 DT H6 H 7.326 0.002 . 63 . 8 DT H2' H 1.917 0.002 . 64 . 8 DT H2'' H 2.204 0.003 . 65 . 8 DT H3' H 4.676 0.002 . 66 . 9 DT H5' H 3.969 0.004 . 67 . 9 DT H5'' H 3.882 0.002 . 68 . 9 DT H1' H 5.896 0.002 . 69 . 9 DT H71 H 1.463 0.001 . 70 . 9 DT H72 H 1.463 0.001 . 71 . 9 DT H73 H 1.463 0.001 . 72 . 9 DT H6 H 7.291 0.002 . 73 . 9 DT H2' H 2.013 0.003 . 74 . 9 DT H2'' H 2.344 0.003 . 75 . 9 DT H3' H 4.730 0.001 . 76 . 10 DT H4' H 4.184 0.003 . 77 . 10 DT H1' H 6.065 0.001 . 78 . 10 DT H71 H 1.797 0.002 . 79 . 10 DT H72 H 1.797 0.002 . 80 . 10 DT H73 H 1.797 0.002 . 81 . 10 DT H6 H 7.516 0.002 . 82 . 10 DT H2' H 2.197 0.003 . 83 . 10 DT H2'' H 2.511 0.004 . 84 . 10 DT H3' H 4.826 0.002 . 85 . 11 DC H4' H 4.247 0.002 . 86 . 11 DC H1' H 5.933 0.001 . 87 . 11 DC H5 H 5.812 0.002 . 88 . 11 DC H6 H 7.714 0.003 . 89 . 11 DC H2' H 2.380 0.003 . 90 . 11 DC H2'' H 2.508 0.003 . 91 . 11 DC H3' H 4.837 0.002 . 92 . 12 DC H5' H 4.188 0.000 . 93 . 12 DC H5'' H 4.248 0.000 . 94 . 12 DC H4' H 4.289 0.003 . 95 . 12 DC H1' H 6.056 0.000 . 96 . 12 DC H5 H 5.577 0.001 . 97 . 12 DC H6 H 7.551 0.002 . 98 . 12 DC H2' H 2.313 0.001 . 99 . 12 DC H2'' H 2.618 0.002 . 100 . 12 DC H3' H 4.567 0.002 . 101 . 13 DT H4' H 4.211 0.002 . 102 . 13 DT H1' H 6.037 0.002 . 103 . 13 DT H71 H 1.657 0.001 . 104 . 13 DT H72 H 1.657 0.001 . 105 . 13 DT H73 H 1.657 0.001 . 106 . 13 DT H6 H 7.622 0.001 . 107 . 13 DT H2' H 2.247 0.002 . 108 . 13 DT H2'' H 2.663 0.001 . 109 . 13 DT H3' H 4.847 0.001 . 110 . 14 DT H4' H 4.208 0.001 . 111 . 14 DT H1' H 6.032 0.001 . 112 . 14 DT H71 H 1.696 0.001 . 113 . 14 DT H72 H 1.696 0.001 . 114 . 14 DT H73 H 1.696 0.001 . 115 . 14 DT H6 H 7.607 0.002 . 116 . 14 DT H2' H 2.393 0.002 . 117 . 14 DT H2'' H 2.580 0.002 . 118 . 14 DT H3' H 4.877 0.001 . 119 . 15 DC H4' H 4.171 0.002 . 120 . 15 DC H1' H 5.867 0.002 . 121 . 15 DC H5 H 5.560 0.002 . 122 . 15 DC H6 H 7.573 0.003 . 123 . 15 DC H2' H 2.127 0.002 . 124 . 15 DC H2'' H 2.521 0.002 . 125 . 15 DC H3' H 4.554 0.001 . 126 . 16 DT H4' H 4.269 0.001 . 127 . 16 DT H1' H 6.064 0.002 . 128 . 16 DT H71 H 1.613 0.002 . 129 . 16 DT H72 H 1.613 0.002 . 130 . 16 DT H73 H 1.613 0.002 . 131 . 16 DT H6 H 7.649 0.001 . 132 . 16 DT H2' H 2.529 0.003 . 133 . 16 DT H2'' H 2.258 0.002 . 134 . 16 DT H3' H 4.819 0.002 . 135 . 17 DC H5' H 4.034 0.001 . 136 . 17 DC H5'' H 4.096 0.002 . 137 . 17 DC H4' H 4.283 0.001 . 138 . 17 DC H1' H 5.804 0.002 . 139 . 17 DC H5 H 5.637 0.001 . 140 . 17 DC H6 H 7.697 0.003 . 141 . 17 DC H2' H 2.103 0.002 . 142 . 17 DC H2'' H 2.349 0.003 . 143 . 17 DC H3' H 4.855 0.002 . 144 . 18 DC H5' H 4.257 0.004 . 145 . 18 DC H5'' H 4.029 0.001 . 146 . 18 DC H4' H 4.324 0.003 . 147 . 18 DC H1' H 6.140 0.001 . 148 . 18 DC H5 H 6.390 0.001 . 149 . 18 DC H6 H 8.305 0.001 . 150 . 18 DC H2' H 1.701 0.002 . 151 . 18 DC H2'' H 2.208 0.002 . 152 . 18 DC H3' H 4.606 0.002 . 153 . 19 DC H5' H 3.329 0.001 . 154 . 19 DC H5'' H 3.524 0.002 . 155 . 19 DC H4' H 3.139 0.003 . 156 . 19 DC H1' H 5.267 0.001 . 157 . 19 DC H5 H 5.743 0.002 . 158 . 19 DC H6 H 7.537 0.001 . 159 . 19 DC H2' H 1.649 0.001 . 160 . 19 DC H2'' H 2.057 0.001 . 161 . 19 DC H3' H 4.322 0.001 . 162 . 20 DG H5' H 4.253 0.001 . 163 . 20 DG H5'' H 4.191 0.001 . 164 . 20 DG H4' H 3.749 0.001 . 165 . 20 DG H1' H 5.838 0.002 . 166 . 20 DG H8 H 6.894 0.001 . 167 . 20 DG H2' H 3.625 0.003 . 168 . 20 DG H2'' H 2.566 0.003 . 169 . 20 DG H3' H 4.689 0.001 . 170 . 21 DA H5' H 3.992 0.002 . 171 . 21 DA H5'' H 4.099 0.001 . 172 . 21 DA H4' H 4.431 0.001 . 173 . 21 DA H1' H 6.284 0.001 . 174 . 21 DA H2 H 7.610 0.002 . 175 . 21 DA H8 H 8.101 0.002 . 176 . 21 DA H2' H 2.952 0.001 . 177 . 21 DA H2'' H 3.015 0.002 . 178 . 21 DA H3' H 5.061 0.001 . 179 . 22 DG H5' H 4.197 0.001 . 180 . 22 DG H5'' H 4.107 0.000 . 181 . 22 DG H4' H 4.464 0.001 . 182 . 22 DG H1' H 5.896 0.002 . 183 . 22 DG H8 H 7.216 0.002 . 184 . 22 DG H2' H 2.411 0.002 . 185 . 22 DG H2'' H 2.914 0.002 . 186 . 22 DG H3' H 4.935 0.002 . 187 . 23 DA H4' H 4.419 0.001 . 188 . 23 DA H1' H 5.875 0.002 . 189 . 23 DA H2 H 7.153 0.001 . 190 . 23 DA H8 H 7.212 0.001 . 191 . 23 DA H2' H 2.209 0.003 . 192 . 23 DA H2'' H 2.833 0.001 . 193 . 23 DA H3' H 4.825 0.002 . 194 . 24 DA H4' H 4.385 0.001 . 195 . 24 DA H1' H 5.904 0.002 . 196 . 24 DA H2 H 7.496 0.002 . 197 . 24 DA H8 H 7.515 0.002 . 198 . 24 DA H2' H 2.261 0.002 . 199 . 24 DA H2'' H 2.746 0.002 . 200 . 24 DA H3' H 4.816 0.002 . 201 . 25 DG H4' H 4.312 0.001 . 202 . 25 DG H1' H 5.732 0.002 . 203 . 25 DG H8 H 7.366 0.002 . 204 . 25 DG H2' H 2.333 0.002 . 205 . 25 DG H2'' H 2.662 0.003 . 206 . 25 DG H3' H 4.861 0.001 . 207 . 26 DG H4' H 4.231 0.073 . 208 . 26 DG H1' H 5.900 0.001 . 209 . 26 DG H8 H 7.378 0.003 . 210 . 26 DG H2' H 2.321 0.002 . 211 . 26 DG H2'' H 2.616 0.004 . 212 . 26 DG H3' H 4.804 0.001 . 213 . 27 DT H4' H 4.045 0.002 . 214 . 27 DT H1' H 5.902 0.002 . 215 . 27 DT H71 H 1.409 0.002 . 216 . 27 DT H72 H 1.409 0.002 . 217 . 27 DT H73 H 1.409 0.002 . 218 . 27 DT H6 H 7.035 0.001 . 219 . 27 DT H2' H 2.061 0.001 . 220 . 27 DT H2'' H 2.273 0.002 . 221 . 27 DT H3' H 4.774 0.002 . 222 . 28 DT H1' H 6.085 0.001 . 223 . 28 DT H71 H 1.713 0.002 . 224 . 28 DT H72 H 1.713 0.002 . 225 . 28 DT H73 H 1.713 0.002 . 226 . 28 DT H6 H 7.483 0.001 . 227 . 28 DT H2' H 2.187 0.002 . 228 . 28 DT H2'' H 2.390 0.002 . 229 . 28 DT H3' H 4.788 0.001 . 230 . 29 DT H4' H 4.221 0.000 . 231 . 29 DT H1' H 6.168 0.002 . 232 . 29 DT H71 H 1.775 0.003 . 233 . 29 DT H72 H 1.775 0.003 . 234 . 29 DT H73 H 1.775 0.003 . 235 . 29 DT H6 H 7.551 0.001 . 236 . 29 DT H2' H 2.259 0.000 . 237 . 29 DT H2'' H 2.433 0.001 . 238 . 29 DT H3' H 4.789 0.001 . 239 . 30 DT H4' H 4.056 0.002 . 240 . 30 DT H1' H 6.207 0.001 . 241 . 30 DT H71 H 1.797 0.002 . 242 . 30 DT H72 H 1.797 0.002 . 243 . 30 DT H73 H 1.797 0.002 . 244 . 30 DT H6 H 7.596 0.001 . 245 . 30 DT H2' H 2.270 0.002 . 246 . 30 DT H2'' H 2.283 0.000 . 247 . 30 DT H3' H 4.497 0.001 . stop_ save_