data_26024 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RNA Bulge Loop that Specifically Binds Metal Ions ; _BMRB_accession_number 26024 _BMRB_flat_file_name bmr26024.str _Entry_type original _Submission_date 2016-04-08 _Accession_date 2016-04-08 _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 Gu Xiaobo . . 2 Schroeder Susan J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 184 "13C chemical shifts" 78 "15N chemical shifts" 11 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-09-22 original BMRB . stop_ _Original_release_date 2016-09-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27631837 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gu Xiaobo . . 2 Park Sun-Young . . 3 Tonelli Marco . . 4 Cornilescu Gabriel . . 5 Xia Tianbing . . 6 Zhong Dongping . . 7 Schroeder Susan J. . stop_ _Journal_abbreviation 'J. Phys. Chem. Lett.' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3841 _Page_last 3846 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RNA (28-MER)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (28-MER)' $RNA_(28-MER) stop_ _System_molecular_weight . _System_physical_state na _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RNA_(28-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(28-MER) _Molecular_mass 8970.434 _Mol_thiol_state 'not available' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; GGACGUUAAAAGGCUUCGGC CUACGUCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 C 5 G 6 U 7 U 8 A 9 A 10 A 11 A 12 G 13 G 14 C 15 U 16 U 17 C 18 G 19 G 20 C 21 C 22 U 23 A 24 C 25 G 26 U 27 C 28 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_(28-MER) bacteriophage 38018 Viruses . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name _Details $RNA_(28-MER) 'enzymatic semisynthesis' . . . . 'Transcription of RNA using T7 polymerase' 'Transcription of RNA using T7 polymerase' 'Transcription of RNA using T7 polymerase' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_AU_label _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(28-MER) 1.5 mM '[U-98% 13C; U-98% 15N]-A,U' 'cobalt hexamine' 1.5 mM 'natural abundance' 'sodium chloride' 10 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' stop_ save_ save_NO_label _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(28-MER) 1 mM 'natural abundance' 'cobalt hexamine' 1 mM 'natural abundance' 'sodium chloride' 10 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' stop_ save_ save_AU_label_RDC _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(28-MER) 1.5 mM '[U-98% 13C; U-98% 15N]-A,U' 'cobalt hexamine' 1.5 mM 'natural abundance' phage 5 mg/mL 'natural abundance' 'sodium chloride' 10 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VNMRS _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model INOVA _Field_strength 900 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model INOVA _Field_strength 800 _Details . save_ save_spectrometer_4 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model 'NMR System' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $AU_label save_ save_3D_HCCH-TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $AU_label save_ save_2D_NOESY13CHSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY13CHSQC' _Sample_label $AU_label save_ save_2D_HCNTROSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCNTROSY' _Sample_label $AU_label save_ save_2D_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $AU_label save_ save_2D_1H-13C_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $AU_label_RDC save_ save_2D_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $NO_label save_ save_2D_COSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D COSY' _Sample_label $NO_label save_ save_2D_1H-13C_HSQC_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $NO_label 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' 20 . mM pH 6 . pH pressure 1 . atm temperature 298 . 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' 20 . mM pH 6 . pH pressure 1 . bar temperature 274 . 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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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-13C HSQC' '3D HCCH-TOCSY' '2D NOESY13CHSQC' '2D HCNTROSY' stop_ loop_ _Sample_label $AU_label stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (28-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 5.891 . . 2 1 1 G H2' H 4.947 . . 3 1 1 G H3' H 4.577 . . 4 1 1 G H5' H 4.349 . . 5 1 1 G H8 H 8.265 . . 6 2 2 G H1' H 5.850 . . 7 2 2 G H2' H 4.576 . . 8 2 2 G H3' H 4.199 . . 9 2 2 G H8 H 7.654 . . 10 3 3 A H1' H 6.014 . . 11 3 3 A H2 H 7.778 . . 12 3 3 A H2' H 4.619 . . 13 3 3 A H3' H 4.630 . . 14 3 3 A H4' H 4.497 . . 15 3 3 A H5' H 5.032 . . 16 3 3 A H5'' H 4.098 . . 17 3 3 A H8 H 7.785 . . 18 3 3 A C1' C 92.708 . . 19 3 3 A C2 C 154.162 . . 20 3 3 A C2' C 72.493 . . 21 3 3 A C3' C 75.694 . . 22 3 3 A C4' C 81.960 . . 23 3 3 A C5' C 64.625 . . 24 3 3 A C8 C 139.492 . . 25 3 3 A N9 N 171.384 . . 26 4 4 C H1' H 5.411 . . 27 4 4 C H2' H 4.473 . . 28 4 4 C H3' H 4.428 . . 29 4 4 C H5 H 5.278 . . 30 4 4 C H6 H 7.572 . . 31 5 5 G H1' H 5.724 . . 32 5 5 G H2' H 4.433 . . 33 5 5 G H3' H 4.536 . . 34 5 5 G H5' H 4.099 . . 35 5 5 G H5'' H 4.027 . . 36 5 5 G H8 H 7.545 . . 37 6 6 U H1' H 5.692 . . 38 6 6 U H2' H 4.514 . . 39 6 6 U H3' H 4.546 . . 40 6 6 U H4' H 4.398 . . 41 6 6 U H5 H 5.073 . . 42 6 6 U H5' H 4.246 . . 43 6 6 U H5'' H 4.051 . . 44 6 6 U H6 H 7.878 . . 45 6 6 U C1' C 93.587 . . 46 6 6 U C2' C 75.329 . . 47 6 6 U C3' C 72.058 . . 48 6 6 U C4' C 82.049 . . 49 6 6 U C5 C 103.448 . . 50 6 6 U C5' C 64.298 . . 51 6 6 U C6 C 141.887 . . 52 6 6 U N1 N 147.021 . . 53 7 7 U H1' H 6.049 . . 54 7 7 U H2' H 4.908 . . 55 7 7 U H3' H 4.584 . . 56 7 7 U H4' H 4.631 . . 57 7 7 U H5 H 5.950 . . 58 7 7 U H5' H 4.283 . . 59 7 7 U H5'' H 4.377 . . 60 7 7 U H6 H 7.949 . . 61 7 7 U C1' C 94.720 . . 62 7 7 U C2' C 75.676 . . 63 7 7 U C4' C 84.343 . . 64 7 7 U C5' C 68.874 . . 65 7 7 U C6 C 143.478 . . 66 7 7 U N1 N 143.938 . . 67 8 8 A H1' H 6.086 . . 68 8 8 A H2 H 7.904 . . 69 8 8 A H2' H 4.541 . . 70 8 8 A H3' H 4.829 . . 71 8 8 A H4' H 4.527 . . 72 8 8 A H5' H 4.311 . . 73 8 8 A H5'' H 4.138 . . 74 8 8 A H8 H 8.434 . . 75 8 8 A C1' C 90.042 . . 76 8 8 A C2' C 75.466 . . 77 8 8 A C3' C 77.762 . . 78 8 8 A C4' C 84.961 . . 79 8 8 A C5' C 67.727 . . 80 8 8 A C8 C 142.115 . . 81 9 9 A H1' H 6.060 . . 82 9 9 A H2 H 8.057 . . 83 9 9 A H2' H 4.739 . . 84 9 9 A H3' H 4.689 . . 85 9 9 A H4' H 4.539 . . 86 9 9 A H5' H 4.518 . . 87 9 9 A H5'' H 4.270 . . 88 9 9 A H8 H 8.319 . . 89 9 9 A C1' C 92.563 . . 90 9 9 A C2 C 154.767 . . 91 9 9 A C2' C 73.699 . . 92 9 9 A C3' C 76.900 . . 93 9 9 A C4' C 82.824 . . 94 9 9 A C5' C 65.842 . . 95 9 9 A C8 C 142.367 . . 96 9 9 A N9 N 168.640 . . 97 10 10 A H1' H 5.683 . . 98 10 10 A H2 H 7.611 . . 99 10 10 A H2' H 4.556 . . 100 10 10 A H3' H 4.541 . . 101 10 10 A H4' H 4.533 . . 102 10 10 A H5' H 4.434 . . 103 10 10 A H5'' H 4.130 . . 104 10 10 A H8 H 7.602 . . 105 10 10 A C1' C 92.638 . . 106 10 10 A C2 C 153.357 . . 107 10 10 A C2' C 75.625 . . 108 10 10 A C4' C 82.444 . . 109 10 10 A C5' C 66.113 . . 110 10 10 A C8 C 139.460 . . 111 10 10 A N9 N 170.048 . . 112 11 11 A H1' H 5.923 . . 113 11 11 A H2 H 7.840 . . 114 11 11 A H2' H 4.284 . . 115 11 11 A H3' H 4.253 . . 116 11 11 A H4' H 4.211 . . 117 11 11 A H5' H 4.415 . . 118 11 11 A H5'' H 4.027 . . 119 11 11 A H8 H 7.983 . . 120 11 11 A C1' C 91.916 . . 121 11 11 A C2 C 153.855 . . 122 11 11 A C3' C 70.345 . . 123 11 11 A C4' C 83.959 . . 124 11 11 A C5' C 65.518 . . 125 11 11 A C8 C 140.341 . . 126 11 11 A N9 N 171.280 . . 127 12 12 G H1' H 5.733 . . 128 12 12 G H2' H 4.450 . . 129 12 12 G H3' H 4.492 . . 130 12 12 G H8 H 7.863 . . 131 13 13 G H1' H 5.825 . . 132 13 13 G H2' H 4.538 . . 133 13 13 G H3' H 4.508 . . 134 13 13 G H4' H 4.622 . . 135 13 13 G H5' H 4.070 . . 136 13 13 G H5'' H 4.104 . . 137 13 13 G H8 H 7.270 . . 138 14 14 C H1' H 5.544 . . 139 14 14 C H2' H 4.537 . . 140 14 14 C H3' H 4.246 . . 141 14 14 C H4' H 4.402 . . 142 14 14 C H5 H 5.204 . . 143 14 14 C H5' H 4.052 . . 144 14 14 C H5'' H 4.506 . . 145 14 14 C H6 H 7.473 . . 146 15 15 U H1' H 5.678 . . 147 15 15 U H2' H 3.813 . . 148 15 15 U H3' H 4.526 . . 149 15 15 U H4' H 4.386 . . 150 15 15 U H5 H 5.724 . . 151 15 15 U H5' H 4.323 . . 152 15 15 U H5'' H 4.163 . . 153 15 15 U H6 H 7.804 . . 154 15 15 U C1' C 94.644 . . 155 15 15 U C2' C 76.024 . . 156 15 15 U C3' C 73.234 . . 157 15 15 U C4' C 82.464 . . 158 15 15 U C5 C 105.007 . . 159 15 15 U C5' C 64.043 . . 160 15 15 U C6 C 140.773 . . 161 15 15 U N1 N 147.169 . . 162 16 16 U H1' H 6.105 . . 163 16 16 U H2' H 4.688 . . 164 16 16 U H3' H 4.031 . . 165 16 16 U H4' H 4.483 . . 166 16 16 U H5 H 5.872 . . 167 16 16 U H5' H 4.249 . . 168 16 16 U H5'' H 4.106 . . 169 16 16 U H6 H 8.041 . . 170 16 16 U C1' C 89.213 . . 171 16 16 U C2' C 74.630 . . 172 16 16 U C3' C 77.867 . . 173 16 16 U C4' C 83.713 . . 174 16 16 U C5 C 105.494 . . 175 16 16 U C5' C 67.870 . . 176 16 16 U C6 C 144.688 . . 177 16 16 U N1 N 143.878 . . 178 17 17 C H1' H 5.974 . . 179 17 17 C H2' H 4.127 . . 180 17 17 C H3' H 4.502 . . 181 17 17 C H4' H 3.814 . . 182 17 17 C H5 H 6.154 . . 183 17 17 C H5' H 3.627 . . 184 17 17 C H5'' H 2.738 . . 185 17 17 C H6 H 7.716 . . 186 18 18 G H1' H 5.974 . . 187 18 18 G H2' H 4.856 . . 188 18 18 G H3' H 5.630 . . 189 18 18 G H4' H 4.414 . . 190 18 18 G H5'' H 4.200 . . 191 18 18 G H8 H 7.868 . . 192 19 19 G H1' H 4.465 . . 193 19 19 G H2' H 4.402 . . 194 19 19 G H5' H 4.230 . . 195 19 19 G H8 H 8.302 . . 196 20 20 C H1' H 5.633 . . 197 20 20 C H2' H 4.466 . . 198 20 20 C H3' H 4.232 . . 199 20 20 C H5 H 5.202 . . 200 20 20 C H6 H 7.685 . . 201 21 21 C H1' H 5.543 . . 202 21 21 C H2' H 4.667 . . 203 21 21 C H3' H 4.399 . . 204 21 21 C H5 H 5.393 . . 205 21 21 C H6 H 7.698 . . 206 22 22 U H1' H 5.596 . . 207 22 22 U H2' H 4.654 . . 208 22 22 U H3' H 4.388 . . 209 22 22 U H4' H 4.496 . . 210 22 22 U H5 H 4.905 . . 211 22 22 U H5' H 4.487 . . 212 22 22 U H5'' H 4.174 . . 213 22 22 U H6 H 7.522 . . 214 22 22 U C1' C 93.315 . . 215 22 22 U C2' C 75.835 . . 216 22 22 U C3' C 73.501 . . 217 22 22 U C4' C 82.529 . . 218 22 22 U C5' C 65.642 . . 219 22 22 U C6 C 141.109 . . 220 22 22 U N1 N 145.854 . . 221 23 23 A H1' H 5.608 . . 222 23 23 A H2 H 8.042 . . 223 23 23 A H2' H 3.994 . . 224 23 23 A H3' H 4.141 . . 225 23 23 A H4' H 4.216 . . 226 23 23 A H5' H 4.296 . . 227 23 23 A H5'' H 3.991 . . 228 23 23 A H8 H 8.392 . . 229 23 23 A C1' C 92.142 . . 230 23 23 A C2 C 154.617 . . 231 23 23 A C2' C 77.348 . . 232 23 23 A C3' C 70.348 . . 233 23 23 A C4' C 84.221 . . 234 23 23 A C5' C 65.418 . . 235 23 23 A C8 C 139.414 . . 236 23 23 A N9 N 171.109 . . 237 24 24 C H1' H 5.610 . . 238 24 24 C H2' H 4.480 . . 239 24 24 C H3' H 4.287 . . 240 24 24 C H5 H 5.629 . . 241 24 24 C H6 H 7.708 . . 242 25 25 G H1' H 5.422 . . 243 25 25 G H2' H 4.437 . . 244 25 25 G H8 H 7.816 . . 245 26 26 U H1' H 5.625 . . 246 26 26 U H2' H 4.566 . . 247 26 26 U H3' H 4.364 . . 248 26 26 U H4' H 4.353 . . 249 26 26 U H5 H 5.089 . . 250 26 26 U H5' H 4.529 . . 251 26 26 U H5'' H 4.073 . . 252 26 26 U H6 H 7.853 . . 253 26 26 U C1' C 93.624 . . 254 26 26 U C2' C 75.880 . . 255 26 26 U C3' C 73.280 . . 256 26 26 U C4' C 82.752 . . 257 26 26 U C5 C 102.494 . . 258 26 26 U C5' C 64.805 . . 259 26 26 U C6 C 142.331 . . 260 26 26 U N1 N 147.180 . . 261 27 27 C H1' H 5.610 . . 262 27 27 C H2' H 4.357 . . 263 27 27 C H3' H 4.437 . . 264 27 27 C H4' H 4.094 . . 265 27 27 C H5 H 5.511 . . 266 27 27 C H5'' H 3.994 . . 267 27 27 C H6 H 7.667 . . 268 28 28 C H1' H 5.546 . . 269 28 28 C H2' H 4.487 . . 270 28 28 C H3' H 4.456 . . 271 28 28 C H5 H 5.543 . . 272 28 28 C H5' H 4.095 . . 273 28 28 C H6 H 7.933 . . stop_ save_