data_11438 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DNA oligomer containing ethylene cross-linked cyclic 2'-deoxyuridylate dimer ; _BMRB_accession_number 11438 _BMRB_flat_file_name bmr11438.str _Entry_type original _Submission_date 2011-03-24 _Accession_date 2011-03-24 _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 Furuita Kyoko . . 2 Murata Shunpei . . 3 Jee JunGoo . . 4 Ichikawa Satoshi . . 5 Matsuda Akira . . 6 Kojima Chojiro . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 211 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-06-22 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 11437 "DNA oligomer containing propylene cross-linked cyclic 2' -deoxyuridylate dimer" stop_ _Original_release_date 2011-06-22 save_ ############################# # Citation for this entry # ############################# save_citation1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural Feature of Bent DNA Recognized by HMGB1' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21443191 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Furuita Kyoko . . 2 Murata Shunpei . . 3 Jee JunGoo . . 4 Ichikawa Satoshi . . 5 Matsuda Akira . . 6 Kojima Chojiro . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 133 _Journal_issue . _Journal_ASTM JACSAT _Journal_ISSN 0002-7863 _Journal_CSD 0004 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5788 _Page_last 5790 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Protein _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Ethylene-DNA $Ethylene-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_Ethylene-DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common Ethylene-DNA _Molecular_mass 111.103 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; CCTTCATTACATCCGGATGT AATGAAGG ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DT 4 DT 5 DC 6 DA 7 DT 8 DT 9 DA 10 DC 11 DA 12 DT 13 DC 14 DC 15 DG 16 DG 17 DA 18 DT 19 DG 20 DT 21 DA 22 DA 23 DT 24 DG 25 DA 26 DA 27 DG 28 DG 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 $Ethylene-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 $Ethylene-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 _Isotopic_labeling $Ethylene-DNA 0.7 mM 'natural abundance' 'sodium phosphate' 50 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Ethylene-DNA 0.7 mM 'natural abundance' 'sodium phosphate' 50 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address 'Brandan, A. Borgias, Paul D. Thomas, He Liu and Anil Kumar' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 800 _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-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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 pH 6.8 . pH temperature 283 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . pH temperature 303 . 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 external direct . . . 1 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 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name Ethylene-DNA _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 DC H1' H 5.948 0.001 1 2 1 1 DC H2'' H 2.531 0.008 1 3 1 1 DC H2' H 2.220 0.006 1 4 1 1 DC H3' H 4.639 0.002 1 5 1 1 DC H41 H 7.058 0.001 2 6 1 1 DC H42 H 8.351 0.001 2 7 1 1 DC H5 H 5.922 0.007 1 8 1 1 DC H6 H 7.776 0.007 1 9 2 2 DC H1' H 6.036 0.004 1 10 2 2 DC H2'' H 2.509 0.006 1 11 2 2 DC H2' H 2.194 0.004 1 12 2 2 DC H3' H 4.813 0.002 1 13 2 2 DC H41 H 7.048 0.000 2 14 2 2 DC H42 H 8.352 0.001 2 15 2 2 DC H5 H 5.617 0.001 1 16 2 2 DC H6 H 7.650 0.006 1 17 3 3 DT H1' H 6.072 0.005 1 18 3 3 DT H2'' H 2.589 0.005 1 19 3 3 DT H2' H 2.180 0.007 1 20 3 3 DT H3 H 14.060 0.001 1 21 3 3 DT H3' H 4.851 0.003 1 22 3 3 DT H6 H 7.477 0.009 1 23 3 3 DT H71 H 1.600 0.003 2 24 3 3 DT H72 H 1.600 0.003 2 25 3 3 DT H73 H 1.600 0.003 2 26 4 4 DT H1' H 5.994 0.005 1 27 4 4 DT H2'' H 2.460 0.006 1 28 4 4 DT H2' H 2.094 0.005 1 29 4 4 DT H3 H 13.890 0.002 1 30 4 4 DT H3' H 4.844 0.003 1 31 4 4 DT H6 H 7.404 0.007 1 32 4 4 DT H71 H 1.612 0.003 2 33 4 4 DT H72 H 1.612 0.003 2 34 4 4 DT H73 H 1.612 0.003 2 35 5 5 DC H1' H 5.327 0.003 1 36 5 5 DC H2'' H 2.259 0.003 1 37 5 5 DC H2' H 2.011 0.004 1 38 5 5 DC H3' H 4.790 0.003 1 39 5 5 DC H41 H 6.901 0.002 2 40 5 5 DC H42 H 8.461 0.001 2 41 5 5 DC H5 H 5.667 0.002 1 42 5 5 DC H6 H 7.491 0.004 1 43 6 6 DA H1' H 6.104 0.003 1 44 6 6 DA H2 H 7.541 0.001 1 45 6 6 DA H2'' H 2.729 0.004 1 46 6 6 DA H2' H 2.684 0.008 1 47 6 6 DA H3' H 4.938 0.002 1 48 6 6 DA H61 H 6.447 0.005 2 49 6 6 DA H62 H 7.665 0.001 2 50 6 6 DA H8 H 8.264 0.004 1 51 7 7 DT H71 H 2.726 0.004 2 52 7 7 DT H72 H 1.934 0.005 2 53 7 7 DT H73 H 1.934 0.005 2 54 7 7 DT H1' H 5.974 0.004 1 55 7 7 DT H2'' H 2.368 0.003 1 56 7 7 DT H2' H 1.939 0.006 1 57 7 7 DT H3 H 12.854 0.004 1 58 7 7 DT H3' H 4.650 0.004 1 59 7 7 DT H6 H 6.889 0.006 1 60 8 8 DT H71 H 2.252 0.003 2 61 8 8 DT H72 H 2.724 0.003 2 62 8 8 DT H73 H 2.724 0.003 2 63 8 8 DT H1' H 5.157 0.002 1 64 8 8 DT H2'' H 2.193 0.003 1 65 8 8 DT H2' H 1.995 0.003 1 66 8 8 DT H3 H 13.414 0.000 1 67 8 8 DT H3' H 4.654 0.003 1 68 8 8 DT H6 H 7.163 0.007 1 69 9 9 DA H1' H 6.168 0.004 1 70 9 9 DA H2 H 7.594 0.001 1 71 9 9 DA H2'' H 2.816 0.005 1 72 9 9 DA H2' H 2.610 0.004 1 73 9 9 DA H3' H 4.942 0.003 1 74 9 9 DA H61 H 6.276 0.000 2 75 9 9 DA H62 H 7.808 0.000 2 76 9 9 DA H8 H 8.194 0.003 1 77 10 10 DC H1' H 5.424 0.003 1 78 10 10 DC H2'' H 2.337 0.004 1 79 10 10 DC H2' H 2.056 0.004 1 80 10 10 DC H3' H 4.786 0.003 1 81 10 10 DC H41 H 6.546 0.000 2 82 10 10 DC H42 H 8.146 0.002 2 83 10 10 DC H5 H 5.225 0.001 1 84 10 10 DC H6 H 7.264 0.004 1 85 11 11 DA H1' H 6.188 0.002 1 86 11 11 DA H2 H 7.552 0.004 1 87 11 11 DA H2'' H 2.887 0.004 1 88 11 11 DA H2' H 2.614 0.006 1 89 11 11 DA H3' H 4.941 0.001 1 90 11 11 DA H61 H 6.205 0.001 2 91 11 11 DA H62 H 7.635 0.001 2 92 11 11 DA H8 H 8.214 0.005 1 93 12 12 DT H1' H 5.890 0.003 1 94 12 12 DT H2'' H 2.435 0.005 1 95 12 12 DT H2' H 2.030 0.005 1 96 12 12 DT H3 H 13.592 0.001 1 97 12 12 DT H3' H 4.811 0.005 1 98 12 12 DT H6 H 7.180 0.006 1 99 12 12 DT H71 H 1.329 0.002 2 100 12 12 DT H72 H 1.329 0.002 2 101 12 12 DT H73 H 1.329 0.002 2 102 13 13 DC H1' H 5.977 0.003 1 103 13 13 DC H2'' H 2.433 0.002 1 104 13 13 DC H2' H 2.154 0.002 1 105 13 13 DC H3' H 4.773 0.003 1 106 13 13 DC H41 H 6.904 0.001 2 107 13 13 DC H42 H 8.388 0.001 2 108 13 13 DC H5 H 5.609 0.005 1 109 13 13 DC H6 H 7.530 0.005 1 110 14 14 DC H1' H 6.177 0.002 1 111 14 14 DC H2'' H 2.211 0.001 1 112 14 14 DC H2' H 2.210 0.001 1 113 14 14 DC H3' H 4.517 0.001 1 114 14 14 DC H41 H 7.121 0.001 2 115 14 14 DC H42 H 8.216 0.000 2 116 14 14 DC H5 H 5.701 0.008 1 117 14 14 DC H6 H 7.599 0.003 1 118 15 15 DG H1' H 5.605 0.006 1 119 15 15 DG H2'' H 2.652 0.051 1 120 15 15 DG H2' H 2.495 0.006 1 121 15 15 DG H3' H 4.780 0.003 1 122 15 15 DG H8 H 7.810 0.001 1 123 16 16 DG H1 H 12.764 0.001 1 124 16 16 DG H1' H 5.620 0.010 1 125 16 16 DG H2'' H 2.771 0.005 1 126 16 16 DG H2' H 2.667 0.004 1 127 16 16 DG H3' H 4.988 0.003 1 128 16 16 DG H8 H 7.809 0.002 1 129 17 17 DA H1' H 6.255 0.003 1 130 17 17 DA H2 H 7.806 0.002 1 131 17 17 DA H2'' H 2.945 0.006 1 132 17 17 DA H2' H 2.630 0.004 1 133 17 17 DA H3' H 5.013 0.003 1 134 17 17 DA H61 H 5.962 0.001 2 135 17 17 DA H8 H 8.218 0.004 1 136 18 18 DT H1' H 5.708 0.003 1 137 18 18 DT H2'' H 2.391 0.006 1 138 18 18 DT H2' H 2.020 0.004 1 139 18 18 DT H3 H 13.412 0.001 1 140 18 18 DT H3' H 4.849 0.005 1 141 18 18 DT H6 H 7.072 0.006 1 142 18 18 DT H71 H 1.337 0.002 2 143 18 18 DT H72 H 1.337 0.002 2 144 18 18 DT H73 H 1.337 0.002 2 145 19 19 DG H1 H 12.376 0.000 1 146 19 19 DG H1' H 5.868 0.004 1 147 19 19 DG H2'' H 2.666 0.005 1 148 19 19 DG H2' H 2.548 0.005 1 149 19 19 DG H3' H 4.922 0.005 1 150 19 19 DG H8 H 7.809 0.005 1 151 20 20 DT H1' H 5.708 0.002 1 152 20 20 DT H2'' H 2.191 0.005 1 153 20 20 DT H2' H 1.697 0.006 1 154 20 20 DT H3 H 13.552 0.003 1 155 20 20 DT H3' H 4.809 0.003 1 156 20 20 DT H6 H 7.089 0.008 1 157 20 20 DT H71 H 1.437 0.003 2 158 20 20 DT H72 H 1.437 0.003 2 159 20 20 DT H73 H 1.437 0.003 2 160 21 21 DA H1' H 5.950 0.001 1 161 21 21 DA H2 H 6.963 0.002 1 162 21 21 DA H2'' H 2.570 0.005 1 163 21 21 DA H2' H 2.348 0.005 1 164 21 21 DA H3' H 5.069 0.003 1 165 21 21 DA H8 H 8.190 0.002 1 166 22 22 DA H1' H 6.022 0.010 1 167 22 22 DA H2 H 7.515 0.003 1 168 22 22 DA H2'' H 2.749 0.004 1 169 22 22 DA H2' H 2.589 0.004 1 170 22 22 DA H3' H 4.917 0.001 1 171 22 22 DA H8 H 8.177 0.003 1 172 23 23 DT H1' H 5.511 0.002 1 173 23 23 DT H2'' H 2.178 0.005 1 174 23 23 DT H2' H 1.823 0.004 1 175 23 23 DT H3 H 13.301 0.002 1 176 23 23 DT H3' H 4.747 0.003 1 177 23 23 DT H6 H 7.001 0.006 1 178 23 23 DT H71 H 1.226 0.003 2 179 23 23 DT H72 H 1.226 0.003 2 180 23 23 DT H73 H 1.226 0.003 2 181 24 24 DG H1 H 12.408 0.001 1 182 24 24 DG H1' H 5.310 0.005 1 183 24 24 DG H2'' H 2.651 0.004 1 184 24 24 DG H2' H 2.595 0.003 1 185 24 24 DG H3' H 4.920 0.004 1 186 24 24 DG H8 H 7.796 0.003 1 187 25 25 DA H1' H 5.802 0.006 1 188 25 25 DA H2 H 7.234 0.002 1 189 25 25 DA H2'' H 2.794 0.006 1 190 25 25 DA H2' H 2.625 0.004 1 191 25 25 DA H3' H 5.003 0.002 1 192 25 25 DA H61 H 5.809 0.003 2 193 25 25 DA H8 H 8.115 0.005 1 194 26 26 DA H1' H 5.830 0.004 1 195 26 26 DA H2 H 7.546 0.003 1 196 26 26 DA H2'' H 2.718 0.005 1 197 26 26 DA H2' H 2.485 0.004 1 198 26 26 DA H3' H 4.960 0.004 1 199 26 26 DA H61 H 5.949 0.000 2 200 26 26 DA H8 H 7.984 0.003 1 201 27 27 DG H1 H 12.890 0.001 1 202 27 27 DG H1' H 5.521 0.004 1 203 27 27 DG H2'' H 2.575 0.005 1 204 27 27 DG H2' H 2.413 0.005 1 205 27 27 DG H3' H 4.871 0.002 1 206 27 27 DG H8 H 7.531 0.003 1 207 28 28 DG H1' H 6.059 0.002 1 208 28 28 DG H2'' H 2.268 0.002 1 209 28 28 DG H2' H 2.361 0.004 1 210 28 28 DG H3' H 4.546 0.002 1 211 28 28 DG H8 H 7.610 0.003 1 stop_ save_