data_17877 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of a shortened antiterminator hairpin from a Mg2+ riboswitch ; _BMRB_accession_number 17877 _BMRB_flat_file_name bmr17877.str _Entry_type original _Submission_date 2011-08-22 _Accession_date 2011-08-22 _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 Korth Maximiliane 'M. T.' . 2 Sigel Roland 'K. O.' . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 232 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-26 update BMRB 'update entry citation' 2012-08-22 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Unusually high-affinity Mg(2+) binding at the AU-rich sequence within the antiterminator hairpin of a Mg(2+) riboswitch.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22976989 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Korth Maximiliane M.T. . 2 Sigel Roland K.O. . stop_ _Journal_abbreviation 'Chem. Biodivers.' _Journal_name_full 'Chemistry & biodiversity' _Journal_volume 9 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2035 _Page_last 2049 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RNA (32-MER)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (32-MER)' $RNA_(32-MER) 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_RNA_(32-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(32-MER) _Molecular_mass 10304.251 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 32 _Mol_residue_sequence ; GGACCGAUAAGGUAGAAAUG CCUUAUCGGUCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 C 5 C 6 G 7 A 8 U 9 A 10 A 11 G 12 G 13 U 14 A 15 G 16 A 17 A 18 A 19 U 20 G 21 C 22 C 23 U 24 U 25 A 26 U 27 C 28 G 29 G 30 U 31 C 32 C 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 $RNA_(32-MER) 'Yersinia enterocolitica' 630 Bacteria . Yersinia enterocolitica 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 $RNA_(32-MER) 'cell free synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'YE loop C short' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'potassium chloride' 50 mM 'natural abundance' EDTA 10 uM 'natural abundance' $RNA_(32-MER) 0.24 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'YE loop C short' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'potassium chloride' 50 mM 'natural abundance' EDTA 10 uM 'natural abundance' $RNA_(32-MER) 0.6 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details 'YE loop C short, partially deuterated' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'potassium chloride' 50 mM 'natural abundance' EDTA 10 uM 'natural abundance' $RNA_(32-MER) 0.8 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details 'YE loop C short' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'potassium chloride' 50 mM 'natural abundance' EDTA 10 uM 'natural abundance' $RNA_(32-MER) 0.5 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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_SPARKY _Saveframe_category software _Name SPARKY _Version 3.1 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version '1.3, 2.1, 3.0a' loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 2.24 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_3 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_4 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' 0.05 . M pH 6.8 . pH pressure 1 . atm temperature 303 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.05 . M pH 6.8 . pH pressure 1 . atm temperature 278 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.05 . M pH 6.8 . pH pressure 1 . atm temperature 293 . 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 TMS H 1 'methyl protons' ppm 0 external indirect . . . 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 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (32-MER)' _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 G H1' H 5.804 0.001 1 2 1 1 G H2' H 4.925 0.000 1 3 1 1 G H3' H 4.541 0.000 1 4 1 1 G H4' H 4.473 0.000 1 5 1 1 G H5' H 4.396 0.000 1 6 1 1 G H5'' H 4.278 0.000 1 7 1 1 G H8 H 8.134 0.003 1 8 2 2 G H1' H 5.881 0.001 1 9 2 2 G H2' H 4.646 0.001 1 10 2 2 G H3' H 4.579 0.002 1 11 2 2 G H4' H 4.490 0.000 1 12 2 2 G H5' H 4.316 0.000 1 13 2 2 G H5'' H 4.296 0.000 1 14 2 2 G H8 H 7.599 0.002 1 15 3 3 A H1' H 6.007 0.003 1 16 3 3 A H2 H 7.802 0.003 1 17 3 3 A H2' H 4.581 0.003 1 18 3 3 A H3' H 4.620 0.002 1 19 3 3 A H4' H 4.433 0.000 1 20 3 3 A H5'' H 4.233 0.000 1 21 3 3 A H8 H 7.905 0.003 1 22 4 4 C H1' H 5.359 0.002 1 23 4 4 C H2' H 4.249 0.001 1 24 4 4 C H3' H 4.294 0.003 1 25 4 4 C H4' H 4.486 0.000 1 26 4 4 C H5 H 5.219 0.003 1 27 4 4 C H5' H 4.393 0.000 1 28 4 4 C H5'' H 4.028 0.000 1 29 4 4 C H6 H 7.378 0.003 1 30 5 5 C H1' H 5.501 0.002 1 31 5 5 C H2' H 4.579 0.002 1 32 5 5 C H3' H 4.486 0.000 1 33 5 5 C H4' H 4.351 0.002 1 34 5 5 C H5 H 5.439 0.003 1 35 5 5 C H5' H 4.122 0.000 1 36 5 5 C H5'' H 4.058 0.000 1 37 5 5 C H6 H 7.649 0.003 1 38 6 6 G H1' H 5.652 0.001 1 39 6 6 G H2' H 4.648 0.001 1 40 6 6 G H3' H 4.518 0.000 1 41 6 6 G H4' H 4.112 0.000 1 42 6 6 G H5' H 4.256 0.000 1 43 6 6 G H5'' H 4.038 0.000 1 44 6 6 G H8 H 7.496 0.003 1 45 7 7 A H1' H 5.916 0.003 1 46 7 7 A H2 H 7.602 0.002 1 47 7 7 A H2' H 4.482 0.002 1 48 7 7 A H3' H 4.585 0.001 1 49 7 7 A H4' H 4.495 0.002 1 50 7 7 A H5'' H 4.129 0.000 1 51 7 7 A H8 H 7.786 0.003 1 52 8 8 U H1' H 5.395 0.001 1 53 8 8 U H2' H 4.415 0.001 1 54 8 8 U H3' H 4.391 0.001 1 55 8 8 U H4' H 4.102 0.000 1 56 8 8 U H5 H 5.018 0.003 1 57 8 8 U H5' H 4.082 0.000 1 58 8 8 U H5'' H 4.064 0.000 1 59 8 8 U H6 H 7.505 0.002 1 60 9 9 A H1' H 5.885 0.003 1 61 9 9 A H2 H 6.371 0.001 1 62 9 9 A H2' H 4.534 0.001 1 63 9 9 A H3' H 4.698 0.002 1 64 9 9 A H4' H 4.218 0.000 1 65 9 9 A H5' H 4.159 0.001 1 66 9 9 A H5'' H 4.146 0.002 1 67 9 9 A H8 H 8.020 0.003 1 68 10 10 A H1' H 5.817 0.001 1 69 10 10 A H2 H 7.323 0.001 1 70 10 10 A H2' H 4.558 0.000 1 71 10 10 A H3' H 4.604 0.001 1 72 10 10 A H4' H 4.475 0.000 1 73 10 10 A H5' H 4.149 0.000 1 74 10 10 A H5'' H 4.120 0.000 1 75 10 10 A H8 H 7.736 0.002 1 76 11 11 G H1' H 5.531 0.001 1 77 11 11 G H2' H 4.502 0.001 1 78 11 11 G H3' H 4.385 0.001 1 79 11 11 G H4' H 4.415 0.001 1 80 11 11 G H5' H 4.036 0.000 1 81 11 11 G H5'' H 4.030 0.000 1 82 11 11 G H8 H 7.059 0.002 1 83 12 12 G H1' H 5.699 0.002 1 84 12 12 G H2' H 4.564 0.000 1 85 12 12 G H3' H 4.421 0.002 1 86 12 12 G H4' H 4.340 0.000 1 87 12 12 G H5' H 4.327 0.000 1 88 12 12 G H5'' H 4.027 0.000 1 89 12 12 G H8 H 7.087 0.002 1 90 13 13 U H1' H 5.472 0.002 1 91 13 13 U H2' H 4.206 0.001 1 92 13 13 U H3' H 4.597 0.001 1 93 13 13 U H4' H 4.310 0.000 1 94 13 13 U H5 H 5.411 0.003 1 95 13 13 U H5' H 4.070 0.002 1 96 13 13 U H5'' H 4.061 0.002 1 97 13 13 U H6 H 7.663 0.002 1 98 14 14 A H1' H 5.982 0.002 1 99 14 14 A H2 H 7.307 0.001 1 100 14 14 A H2' H 4.601 0.001 1 101 14 14 A H3' H 4.459 0.000 1 102 14 14 A H4' H 4.443 0.002 1 103 14 14 A H5' H 4.393 0.000 1 104 14 14 A H5'' H 4.168 0.000 1 105 14 14 A H8 H 8.179 0.001 1 106 15 15 G H1' H 5.449 0.001 1 107 15 15 G H2' H 4.318 0.001 1 108 15 15 G H3' H 4.578 0.000 1 109 15 15 G H5'' H 4.333 0.000 1 110 15 15 G H8 H 7.164 0.003 1 111 16 16 A H1' H 5.680 0.001 1 112 16 16 A H2 H 7.756 0.001 1 113 16 16 A H2' H 4.716 0.001 1 114 16 16 A H3' H 4.434 0.001 1 115 16 16 A H4' H 4.220 0.001 1 116 16 16 A H5' H 3.936 0.001 1 117 16 16 A H5'' H 3.923 0.000 1 118 16 16 A H8 H 8.290 0.002 1 119 17 17 A H1' H 5.442 0.003 1 120 17 17 A H2 H 7.652 0.001 1 121 17 17 A H2' H 4.371 0.000 1 122 17 17 A H3' H 4.574 0.002 1 123 17 17 A H4' H 4.324 0.000 1 124 17 17 A H5'' H 3.923 0.000 1 125 17 17 A H8 H 7.900 0.002 1 126 18 18 A H1' H 6.005 0.002 1 127 18 18 A H2 H 8.189 0.002 1 128 18 18 A H2' H 4.491 0.001 1 129 18 18 A H3' H 4.877 0.001 1 130 18 18 A H4' H 4.267 0.000 1 131 18 18 A H5' H 4.427 0.000 1 132 18 18 A H5'' H 4.233 0.000 1 133 18 18 A H8 H 8.138 0.002 1 134 19 19 U H1' H 3.816 0.002 1 135 19 19 U H2' H 4.357 0.001 1 136 19 19 U H3' H 4.432 0.000 1 137 19 19 U H4' H 4.220 0.001 1 138 19 19 U H5 H 5.944 0.002 1 139 19 19 U H5' H 4.114 0.000 1 140 19 19 U H5'' H 4.194 0.001 1 141 19 19 U H6 H 7.940 0.003 1 142 20 20 G H1' H 5.821 0.002 1 143 20 20 G H2' H 4.555 0.001 1 144 20 20 G H3' H 4.415 0.000 1 145 20 20 G H4' H 4.463 0.000 1 146 20 20 G H5' H 4.191 0.000 1 147 20 20 G H5'' H 4.062 0.002 1 148 20 20 G H8 H 7.722 0.002 1 149 21 21 C H1' H 5.406 0.001 1 150 21 21 C H2' H 4.276 0.003 1 151 21 21 C H3' H 4.445 0.001 1 152 21 21 C H5 H 5.362 0.002 1 153 21 21 C H5' H 4.223 0.000 1 154 21 21 C H5'' H 4.175 0.000 1 155 21 21 C H6 H 7.717 0.003 1 156 22 22 C H1' H 5.468 0.002 1 157 22 22 C H2' H 4.392 0.001 1 158 22 22 C H3' H 4.430 0.000 1 159 22 22 C H5 H 5.475 0.003 1 160 22 22 C H6 H 7.737 0.002 1 161 23 23 U H1' H 5.504 0.001 1 162 23 23 U H2' H 4.481 0.001 1 163 23 23 U H3' H 4.497 0.002 1 164 23 23 U H4' H 4.431 0.000 1 165 23 23 U H5 H 5.386 0.003 1 166 23 23 U H5'' H 4.082 0.000 1 167 23 23 U H6 H 7.869 0.003 1 168 24 24 U H1' H 5.571 0.002 1 169 24 24 U H2' H 4.512 0.002 1 170 24 24 U H3' H 4.626 0.001 1 171 24 24 U H5 H 5.608 0.003 1 172 24 24 U H5'' H 4.151 0.000 1 173 24 24 U H6 H 7.994 0.003 1 174 25 25 A H1' H 5.931 0.001 1 175 25 25 A H2 H 6.974 0.002 1 176 25 25 A H2' H 4.422 0.001 1 177 25 25 A H3' H 4.654 0.003 1 178 25 25 A H4' H 4.638 0.001 1 179 25 25 A H5' H 4.229 0.000 1 180 25 25 A H5'' H 4.179 0.000 1 181 25 25 A H8 H 8.188 0.002 1 182 26 26 U H1' H 5.402 0.002 1 183 26 26 U H2' H 4.277 0.003 1 184 26 26 U H3' H 4.390 0.000 1 185 26 26 U H5 H 4.954 0.001 1 186 26 26 U H5'' H 4.065 0.000 1 187 26 26 U H6 H 7.610 0.003 1 188 27 27 C H1' H 5.541 0.001 1 189 27 27 C H2' H 4.493 0.002 1 190 27 27 C H3' H 4.589 0.000 1 191 27 27 C H4' H 4.234 0.000 1 192 27 27 C H5 H 5.508 0.001 1 193 27 27 C H5' H 4.089 0.000 1 194 27 27 C H5'' H 4.028 0.000 1 195 27 27 C H6 H 7.740 0.003 1 196 28 28 G H1' H 5.656 0.003 1 197 28 28 G H2' H 4.655 0.000 1 198 28 28 G H3' H 4.431 0.001 1 199 28 28 G H4' H 4.382 0.000 1 200 28 28 G H5'' H 4.076 0.000 1 201 28 28 G H8 H 7.511 0.003 1 202 29 29 G H1' H 5.718 0.001 1 203 29 29 G H2' H 4.457 0.002 1 204 29 29 G H3' H 4.502 0.000 1 205 29 29 G H4' H 4.490 0.002 1 206 29 29 G H5' H 4.073 0.000 1 207 29 29 G H5'' H 4.052 0.000 1 208 29 29 G H8 H 7.238 0.002 1 209 30 30 U H1' H 5.566 0.001 1 210 30 30 U H2' H 4.518 0.001 1 211 30 30 U H3' H 4.429 0.001 1 212 30 30 U H4' H 4.276 0.000 1 213 30 30 U H5 H 5.040 0.003 1 214 30 30 U H5' H 4.167 0.000 1 215 30 30 U H5'' H 4.082 0.000 1 216 30 30 U H6 H 7.773 0.002 1 217 31 31 C H1' H 5.603 0.003 1 218 31 31 C H2' H 4.258 0.001 1 219 31 31 C H3' H 4.351 0.000 1 220 31 31 C H4' H 4.280 0.000 1 221 31 31 C H5 H 5.654 0.001 1 222 31 31 C H5' H 4.120 0.000 1 223 31 31 C H5'' H 4.069 0.000 1 224 31 31 C H6 H 7.891 0.002 1 225 32 32 C H1' H 5.732 0.000 1 226 32 32 C H2' H 3.982 0.001 1 227 32 32 C H3' H 4.167 0.002 1 228 32 32 C H4' H 4.146 0.000 1 229 32 32 C H5 H 5.534 0.002 1 230 32 32 C H5' H 4.099 0.000 1 231 32 32 C H5'' H 4.021 0.001 1 232 32 32 C H6 H 7.680 0.003 1 stop_ save_