data_5167 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop ; _BMRB_accession_number 5167 _BMRB_flat_file_name bmr5167.str _Entry_type new _Submission_date 2001-10-03 _Accession_date 2001-10-03 _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 Ulyanov N. B. . 2 Bauer W. R. . 3 James T. L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 252 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2002-09-26 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'High-resolution NMR Structure of an AT-rich DNA Sequence' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 21986769 _PubMed_ID 11991355 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ulyanov N. B. . 2 Bauer W. R. . 3 James T. L. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_volume 22 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 265 _Page_last 280 _Year 2002 _Details . loop_ _Keyword 'deoxyribonucleic acid' 'DNA oligonucleotide' stem-and-loop AT-rich 'GAA hairpin loop' 'pribnow box' stop_ save_ ################################## # Molecular system description # ################################## save_system_GAA-Hairpin _Saveframe_category molecular_system _Mol_system_name 'AT-Rich DNA with the GAA-Hairpin Loop' _Abbreviation_common 'GAA-Hairpin loop' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'AT-Rich DNA with the GAA-Hairpin Loop' $GAA-Hairpin 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_GAA-Hairpin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'GAA-Hairpin loop' _Abbreviation_common GAA-Hairpin _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; CCTAATTATAACGAAGTTAT AATTAGG ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DT 4 DA 5 DA 6 DT 7 DT 8 DA 9 DT 10 DA 11 DA 12 DC 13 DG 14 DA 15 DA 16 DG 17 DT 18 DT 19 DA 20 DT 21 DA 22 DA 23 DT 24 DT 25 DA 26 DG 27 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 _Details $GAA-Hairpin . . . . . . 'Not relevant: the molecule is engineered.' 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 $GAA-Hairpin '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 $GAA-Hairpin 2 mM . 'phosphate buffer' 30 mM . EDTA 1 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1 loop_ _Task collection stop_ _Details 'Varian Associates, Inc.' save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 1.8 loop_ _Task processing stop_ _Details 'Delaglio, F.' save_ save_Sparky _Saveframe_category software _Name Sparky _Version 3.1 loop_ _Task 'data analysis' stop_ _Details 'Goddard, T.D., Kneller, D.G.' save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version 3.2 loop_ _Task 'iterative matrix relaxation' stop_ _Details 'Borgias, B.A., Thomas, P.D., Liu, H., Kumar, A., Tonelli, M.' save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task refinement stop_ _Details 'Guntert, P.' save_ save_miniCarlo _Saveframe_category software _Name miniCarlo _Version 'alpha version' loop_ _Task refinement stop_ _Details 'Ulyanov, N.B., Gorler, A., Gorin, A.A., Zhurkin, V.B.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D-NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name 2D-NOESY _Sample_label . save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name 2D-NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-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_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 8.0 . n/a temperature 283 . K 'ionic strength' 30 . mM pressure 1 . atm 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 TSP H 1 'methyl protons' ppm 0.00 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_chemical_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 'AT-Rich DNA with the GAA-Hairpin Loop' _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 DC H1' H 6.010 0.003 1 2 . 1 DC H2'' H 2.579 0.002 1 3 . 1 DC H2' H 2.264 0.004 1 4 . 1 DC H3' H 4.694 0.003 1 5 . 1 DC H4' H 4.139 0.003 1 6 . 1 DC H41 H 7.881 0.005 1 7 . 1 DC H42 H 7.127 0.005 1 8 . 1 DC H5 H 5.977 0.006 1 9 . 1 DC H6 H 7.831 0.004 1 10 . 1 DC H5'' H 3.793 0.011 2 11 . 1 DC H5' H 3.793 0.011 2 12 . 2 DC H1' H 5.989 0.003 1 13 . 2 DC H2'' H 2.477 0.003 1 14 . 2 DC H2' H 2.127 0.007 1 15 . 2 DC H3' H 4.822 0.003 1 16 . 2 DC H4' H 4.191 0.004 1 17 . 2 DC H41 H 8.514 0.005 1 18 . 2 DC H42 H 7.093 0.005 1 19 . 2 DC H5 H 5.650 0.004 1 20 . 2 DC H6 H 7.668 0.004 1 21 . 3 DT H1' H 5.520 0.005 1 22 . 3 DT H2'' H 2.431 0.003 1 23 . 3 DT H2' H 2.137 0.005 1 24 . 3 DT H3 H 13.691 0.005 1 25 . 3 DT H3' H 4.874 0.004 1 26 . 3 DT H4' H 4.151 0.005 1 27 . 3 DT H6 H 7.420 0.002 1 28 . 3 DT H71 H 1.676 0.002 1 29 . 3 DT H72 H 1.676 0.002 1 30 . 3 DT H73 H 1.676 0.002 1 31 . 4 DA H1' H 5.968 0.005 1 32 . 4 DA H2 H 6.806 0.005 1 33 . 4 DA H2'' H 2.941 0.003 1 34 . 4 DA H2' H 2.791 0.003 1 35 . 4 DA H3' H 5.072 0.004 1 36 . 4 DA H4' H 4.447 0.002 1 37 . 4 DA H61 H 7.511 0.008 1 38 . 4 DA H62 H 6.364 0.005 1 39 . 4 DA H8 H 8.303 0.003 1 40 . 5 DA H1' H 6.153 0.004 1 41 . 5 DA H2 H 7.480 0.004 1 42 . 5 DA H2'' H 2.924 0.003 1 43 . 5 DA H2' H 2.585 0.006 1 44 . 5 DA H3' H 5.017 0.004 1 45 . 5 DA H4' H 4.495 0.002 1 46 . 5 DA H5'' H 4.258 0.007 1 47 . 5 DA H5' H 4.306 0.012 1 48 . 5 DA H61 H 7.199 0.007 1 49 . 5 DA H62 H 6.142 0.005 1 50 . 5 DA H8 H 8.190 0.002 1 51 . 6 DT H1' H 5.870 0.003 1 52 . 6 DT H2'' H 2.542 0.003 1 53 . 6 DT H2' H 1.995 0.004 1 54 . 6 DT H3 H 13.670 0.005 1 55 . 6 DT H3' H 4.818 0.003 1 56 . 6 DT H4' H 4.190 0.003 1 57 . 6 DT H6 H 7.141 0.002 1 58 . 6 DT H71 H 1.272 0.002 1 59 . 6 DT H72 H 1.272 0.002 1 60 . 6 DT H73 H 1.272 0.002 1 61 . 7 DT H1' H 5.933 0.004 1 62 . 7 DT H2'' H 2.628 0.004 1 63 . 7 DT H2' H 2.256 0.003 1 64 . 7 DT H3 H 13.409 0.001 1 65 . 7 DT H3' H 4.931 0.006 1 66 . 7 DT H4' H 4.264 0.004 1 67 . 7 DT H6 H 7.372 0.003 1 68 . 7 DT H71 H 1.556 0.003 1 69 . 7 DT H72 H 1.556 0.003 1 70 . 7 DT H73 H 1.556 0.003 1 71 . 8 DA H1' H 6.190 0.003 1 72 . 8 DA H2 H 6.898 0.003 1 73 . 8 DA H2'' H 2.953 0.002 1 74 . 8 DA H2' H 2.639 0.006 1 75 . 8 DA H3' H 5.033 0.006 1 76 . 8 DA H4' H 4.459 0.004 1 77 . 8 DA H61 H 7.425 0.005 1 78 . 8 DA H62 H 6.261 0.005 1 79 . 8 DA H8 H 8.291 0.003 1 80 . 9 DT H1' H 5.646 0.006 1 81 . 9 DT H2'' H 2.471 0.004 1 82 . 9 DT H2' H 2.070 0.005 1 83 . 9 DT H3 H 13.127 0.005 1 84 . 9 DT H3' H 4.898 0.004 1 85 . 9 DT H4' H 4.202 0.005 1 86 . 9 DT H6 H 7.141 0.004 1 87 . 9 DT H71 H 1.293 0.002 1 88 . 9 DT H72 H 1.293 0.002 1 89 . 9 DT H73 H 1.293 0.002 1 90 . 10 DA H1' H 5.956 0.006 1 91 . 10 DA H2 H 6.690 0.004 1 92 . 10 DA H2'' H 2.896 0.003 1 93 . 10 DA H2' H 2.691 0.007 1 94 . 10 DA H3' H 5.056 0.002 1 95 . 10 DA H4' H 4.417 0.003 1 96 . 10 DA H8 H 8.210 0.003 1 97 . 11 DA H1' H 6.047 0.003 1 98 . 11 DA H2 H 7.716 0.004 1 99 . 11 DA H2'' H 2.671 0.002 1 100 . 11 DA H2' H 2.309 0.004 1 101 . 11 DA H3' H 4.948 0.005 1 102 . 11 DA H4' H 4.377 0.002 1 103 . 11 DA H61 H 7.658 0.005 1 104 . 11 DA H62 H 6.025 0.005 1 105 . 11 DA H8 H 7.947 0.003 1 106 . 11 DA H5'' H 4.228 0.005 2 107 . 11 DA H5' H 4.228 0.005 2 108 . 12 DC H1' H 5.713 0.005 1 109 . 12 DC H2'' H 2.166 0.008 1 110 . 12 DC H2' H 1.572 0.011 1 111 . 12 DC H3' H 4.775 0.002 1 112 . 12 DC H4' H 4.134 0.002 1 113 . 12 DC H41 H 8.229 0.005 1 114 . 12 DC H42 H 6.712 0.005 1 115 . 12 DC H5 H 4.776 0.004 1 116 . 12 DC H6 H 6.804 0.004 1 117 . 12 DC H5'' H 4.060 0.003 2 118 . 12 DC H5' H 4.060 0.003 2 119 . 13 DG H1' H 5.228 0.005 1 120 . 13 DG H2'' H 2.481 0.003 1 121 . 13 DG H2' H 2.617 0.005 1 122 . 13 DG H3' H 4.851 0.002 1 123 . 13 DG H4' H 4.377 0.003 1 124 . 13 DG H8 H 8.047 0.003 1 125 . 13 DG H5'' H 4.024 0.005 2 126 . 13 DG H5' H 4.024 0.005 2 127 . 14 DA H1' H 5.942 0.006 1 128 . 14 DA H2'' H 2.267 0.005 1 129 . 14 DA H2' H 2.222 0.004 1 130 . 14 DA H3' H 4.560 0.002 1 131 . 14 DA H4' H 2.076 0.002 1 132 . 14 DA H5'' H 3.334 0.004 1 133 . 14 DA H5' H 2.909 0.004 1 134 . 14 DA H8 H 8.071 0.003 1 135 . 15 DA H1' H 6.279 0.004 1 136 . 15 DA H2 H 8.085 0.002 1 137 . 15 DA H3' H 4.833 0.003 1 138 . 15 DA H4' H 4.351 0.002 1 139 . 15 DA H5'' H 3.994 0.005 1 140 . 15 DA H5' H 3.824 0.005 1 141 . 15 DA H8 H 7.984 0.008 1 142 . 15 DA H2'' H 2.894 0.006 2 143 . 15 DA H2' H 2.894 0.006 2 144 . 16 DG H1 H 12.598 0.002 1 145 . 16 DG H1' H 5.521 0.004 1 146 . 16 DG H2'' H 2.577 0.007 1 147 . 16 DG H2' H 2.571 0.005 1 148 . 16 DG H3' H 4.905 0.004 1 149 . 16 DG H4' H 4.425 0.002 1 150 . 16 DG H5'' H 4.307 0.005 1 151 . 16 DG H5' H 4.140 0.005 1 152 . 16 DG H8 H 8.020 0.004 1 153 . 17 DT H1' H 6.154 0.003 1 154 . 17 DT H2'' H 2.576 0.003 1 155 . 17 DT H2' H 2.208 0.004 1 156 . 17 DT H3 H 13.871 0.001 1 157 . 17 DT H3' H 4.909 0.006 1 158 . 17 DT H4' H 4.324 0.004 1 159 . 17 DT H6 H 7.380 0.003 1 160 . 17 DT H71 H 1.295 0.003 1 161 . 17 DT H72 H 1.295 0.003 1 162 . 17 DT H73 H 1.295 0.003 1 163 . 18 DT H1' H 5.740 0.004 1 164 . 18 DT H2'' H 2.516 0.004 1 165 . 18 DT H2' H 2.201 0.005 1 166 . 18 DT H3 H 13.638 0.005 1 167 . 18 DT H3' H 4.908 0.004 1 168 . 18 DT H4' H 4.177 0.001 1 169 . 18 DT H6 H 7.438 0.004 1 170 . 18 DT H71 H 1.643 0.003 1 171 . 18 DT H72 H 1.643 0.003 1 172 . 18 DT H73 H 1.643 0.003 1 173 . 19 DA H1' H 6.185 0.002 1 174 . 19 DA H2 H 7.010 0.003 1 175 . 19 DA H2'' H 2.906 0.002 1 176 . 19 DA H2' H 2.632 0.003 1 177 . 19 DA H3' H 5.017 0.006 1 178 . 19 DA H4' H 4.432 0.005 1 179 . 19 DA H61 H 7.494 0.005 1 180 . 19 DA H62 H 6.368 0.005 1 181 . 19 DA H8 H 8.342 0.002 1 182 . 20 DT H1' H 5.547 0.006 1 183 . 20 DT H2'' H 2.451 0.004 1 184 . 20 DT H2' H 2.060 0.005 1 185 . 20 DT H3 H 13.136 0.005 1 186 . 20 DT H3' H 4.865 0.003 1 187 . 20 DT H4' H 4.176 0.005 1 188 . 20 DT H6 H 7.156 0.004 1 189 . 20 DT H71 H 1.401 0.002 1 190 . 20 DT H72 H 1.401 0.002 1 191 . 20 DT H73 H 1.401 0.002 1 192 . 21 DA H1' H 5.983 0.003 1 193 . 21 DA H2 H 6.373 0.005 1 194 . 21 DA H2'' H 2.947 0.003 1 195 . 21 DA H2' H 2.658 0.003 1 196 . 21 DA H3' H 5.046 0.006 1 197 . 21 DA H4' H 4.425 0.003 1 198 . 21 DA H8 H 8.171 0.003 1 199 . 22 DA H1' H 6.142 0.005 1 200 . 22 DA H2 H 7.453 0.005 1 201 . 22 DA H2'' H 2.943 0.006 1 202 . 22 DA H2' H 2.562 0.008 1 203 . 22 DA H3' H 5.026 0.007 1 204 . 22 DA H4' H 4.494 0.003 1 205 . 22 DA H61 H 7.106 0.005 1 206 . 22 DA H62 H 6.112 0.005 1 207 . 22 DA H8 H 8.123 0.002 1 208 . 23 DT H1' H 5.918 0.005 1 209 . 23 DT H2'' H 2.533 0.002 1 210 . 23 DT H2' H 1.989 0.004 1 211 . 23 DT H3 H 13.610 0.005 1 212 . 23 DT H3' H 4.856 0.004 1 213 . 23 DT H4' H 4.204 0.005 1 214 . 23 DT H6 H 7.146 0.005 1 215 . 23 DT H71 H 1.227 0.002 1 216 . 23 DT H72 H 1.227 0.002 1 217 . 23 DT H73 H 1.227 0.002 1 218 . 24 DT H1' H 5.737 0.005 1 219 . 24 DT H2'' H 2.417 0.003 1 220 . 24 DT H2' H 2.079 0.005 1 221 . 24 DT H3 H 13.650 0.005 1 222 . 24 DT H3' H 4.901 0.007 1 223 . 24 DT H4' H 4.192 0.005 1 224 . 24 DT H6 H 7.347 0.004 1 225 . 24 DT H71 H 1.600 0.002 1 226 . 24 DT H72 H 1.600 0.002 1 227 . 24 DT H73 H 1.600 0.002 1 228 . 25 DA H1' H 5.933 0.003 1 229 . 25 DA H2 H 7.369 0.004 1 230 . 25 DA H2'' H 2.847 0.003 1 231 . 25 DA H2' H 2.685 0.006 1 232 . 25 DA H3' H 5.040 0.003 1 233 . 25 DA H4' H 4.411 0.003 1 234 . 25 DA H61 H 7.888 0.005 1 235 . 25 DA H62 H 6.392 0.006 1 236 . 25 DA H8 H 8.212 0.003 1 237 . 26 DG H1 H 12.919 0.002 1 238 . 26 DG H1' H 5.589 0.003 1 239 . 26 DG H2'' H 2.653 0.003 1 240 . 26 DG H2' H 2.529 0.003 1 241 . 26 DG H3' H 4.962 0.005 1 242 . 26 DG H4' H 4.375 0.005 1 243 . 26 DG H8 H 7.679 0.004 1 244 . 27 DG H1 H 12.918 0.005 1 245 . 27 DG H1' H 6.127 0.003 1 246 . 27 DG H2'' H 2.327 0.005 1 247 . 27 DG H2' H 2.423 0.005 1 248 . 27 DG H3' H 4.606 0.002 1 249 . 27 DG H4' H 4.216 0.004 1 250 . 27 DG H8 H 7.705 0.002 1 251 . 27 DG H5'' H 4.106 0.004 2 252 . 27 DG H5' H 4.106 0.004 2 stop_ save_