data_17682 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The 912-888 alternate conformation for helix 27 of E.coli 16S rRNA ; _BMRB_accession_number 17682 _BMRB_flat_file_name bmr17682.str _Entry_type original _Submission_date 2011-06-02 _Accession_date 2011-06-02 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'ensemble of 13 low-energy nmr structures' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Spano Meredith Newby . 2 Walter Nils G. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 157 "13C chemical shifts" 39 "15N chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-09-01 original author . stop_ _Original_release_date 2011-09-01 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21442607 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Spano 'Meredith Newby' . . 2 Walter Nils G. . stop_ _Journal_abbreviation Biopolymers _Journal_name_full Biopolymers _Journal_volume 95 _Journal_issue 10 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 653 _Page_last 668 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RNA (31-MER)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (31-MER)' $RNA_(31-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_(31-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(31-MER) _Molecular_mass 3775.495 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 31 _Mol_residue_sequence ; GGGGAGUACGGCCGCAAGGU UAAAACUCCCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 G 4 4 G 5 5 A 6 6 G 7 7 U 8 8 A 9 9 C 10 10 G 11 11 G 12 12 C 13 13 C 14 14 G 15 15 C 16 16 A 17 17 A 18 18 G 19 19 G 20 20 U 21 21 U 22 22 A 23 23 A 24 24 A 25 25 A 26 26 C 27 27 U 28 28 C 29 29 C 30 30 C 31 31 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_(31-MER) 'Escherichia coli' 562 Bacteria . Escherichia coli 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 _Details $RNA_(31-MER) 'enzymatic semisynthesis' . Escherichia coli . . 'transcribed using T7 RNA polymerase from a chemically synthesized double-stranded DNA template.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'Final RNA concentrations for the samples ranged from 0.8 to 1.6 mM, as quantified by UV absorption' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(31-MER) . mM 0.8 1.6 '[U-99% 13C; U-99% 15N]' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' NaPi 10 mM . . 'natural abundance' EDTA 0.1 mM . . 'natural abundance' NaCl 50 mM . . '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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details '(10 mM NaPi, pH 6.4, 0.1 mM EDTA, 50 mM NaCl' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' .05 . M pH 6.4 . 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 DSS C 13 'methyl carbon' ppm 0 external indirect . . . 0.251449530 DSS H 1 'methy protons' ppm 0 external indirect . . . 1 DSS N 15 nitrogen ppm 0 external 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' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (31-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 12.71 . . 2 1 1 G H1' H 5.810 . . 3 1 1 G H2' H 4.890 . . 4 1 1 G H8 H 8.107 . . 5 1 1 G C8 C 139.822 . . 6 2 2 G H1 H 12.54 . . 7 2 2 G H1' H 5.622 . . 8 2 2 G H2' H 4.407 . . 9 2 2 G H8 H 7.518 . . 10 2 2 G H21 H 8.410 . . 11 2 2 G C8 C 137.297 . . 12 3 3 G C8 C 136.443 . . 13 3 3 G H1 H 12.49 . . 14 3 3 G H1' H 5.786 . . 15 3 3 G H2' H 4.598 . . 16 3 3 G H3' H 4.457 . . 17 3 3 G H8 H 7.205 . . 18 3 3 G H22 H 5.345 . . 19 4 4 G C8 C 136.653 . . 20 4 4 G H1 H 13.35 . . 21 4 4 G H1' H 5.736 . . 22 4 4 G H2' H 4.592 . . 23 4 4 G H3' H 4.452 . . 24 4 4 G H8 H 7.109 . . 25 4 4 G H21 H 8.217 . . 26 4 4 G H22 H 5.682 . . 27 5 5 A H1' H 5.936 . . 28 5 5 A H2 H 7.449 . . 29 5 5 A H2' H 4.407 . . 30 5 5 A H8 H 7.631 . . 31 5 5 A H61 H 7.787 . . 32 5 5 A H62 H 5.483 . . 33 5 5 A C8 C 139.792 . . 34 5 5 A C2 C 155.124 . . 35 5 5 A N1 N 155.124 . . 36 6 6 G C8 C 136.341 . . 37 6 6 G H1 H 12.19 . . 38 6 6 G H1' H 5.545 . . 39 6 6 G H2' H 4.330 . . 40 6 6 G H3' H 4.301 . . 41 6 6 G H8 H 7.049 . . 42 6 6 G H21 H 7.868 . . 43 6 6 G H22 H 5.715 . . 44 7 7 U C6 C 141.716 . . 45 7 7 U H1' H 5.587 . . 46 7 7 U H2' H 4.231 . . 47 7 7 U H3' H 4.319 . . 48 7 7 U H5 H 5.001 . . 49 8 8 A C8 C 142.176 . . 50 8 8 A C2 C 154.956 . . 51 8 8 A N1 N 154.956 . . 52 8 8 A H1' H 5.749 . . 53 8 8 A H2 H 7.567 . . 54 8 8 A H2' H 4.617 . . 55 8 8 A H3' H 4.354 . . 56 8 8 A H8 H 8.098 . . 57 9 9 C C6 C 143.436 . . 58 9 9 C H1' H 5.881 . . 59 9 9 C H2' H 4.493 . . 60 9 9 C H3' H 4.820 . . 61 9 9 C H5 H 5.686 . . 62 9 9 C H6 H 7.779 . . 63 10 10 G C8 C 138.888 . . 64 10 10 G H1' H 5.668 . . 65 10 10 G H2' H 4.894 . . 66 10 10 G H8 H 7.894 . . 67 11 11 G C8 C 137.228 . . 68 11 11 G H1 H 11.57 . . 69 11 11 G H1' H 5.620 . . 70 11 11 G H2' H 4.195 . . 71 11 11 G H8 H 7.517 . . 72 11 11 G H21 H 6.458 . . 73 11 11 G H22 H 5.286 . . 74 12 12 C C6 C 140.756 . . 75 12 12 C H1' H 5.507 . . 76 12 12 C H2' H 4.154 . . 77 12 12 C H5 H 5.346 . . 78 12 12 C H6 H 7.547 . . 79 12 12 C H41 H 8.421 . . 80 12 12 C H42 H 6.960 . . 81 13 13 C C6 C 141.082 . . 82 13 13 C H1' H 5.725 . . 83 13 13 C H2' H 4.234 . . 84 13 13 C H3' H 3.978 . . 85 13 13 C H5 H 5.461 . . 86 13 13 C H6 H 7.662 . . 87 13 13 C H41 H 8.240 . . 88 14 14 G C8 C 136.984 . . 89 14 14 G H1 H 10.60 . . 90 14 14 G H2' H 4.512 . . 91 14 14 G H8 H 7.601 . . 92 15 15 C C6 C 143.834 . . 93 15 15 C H1' H 5.554 . . 94 15 15 C H2' H 4.372 . . 95 15 15 C H3' H 4.216 . . 96 15 15 C H5 H 5.624 . . 97 15 15 C H6 H 7.754 . . 98 16 16 A C2 C 155.314 . . 99 16 16 A N1 N 155.214 . . 100 16 16 A C8 C 141.687 . . 101 16 16 A H1' H 5.578 . . 102 16 16 A H2 H 7.888 . . 103 16 16 A H2' H 4.285 . . 104 16 16 A H8 H 7.995 . . 105 17 17 A C2 C 155.617 . . 106 17 17 A N1 N 155.617 . . 107 17 17 A C8 C 142.101 . . 108 17 17 A H1' H 6.028 . . 109 17 17 A H2 H 8.007 . . 110 17 17 A H2' H 4.512 . . 111 17 17 A H3' H 4.454 . . 112 17 17 A H8 H 8.226 . . 113 18 18 G C8 C 137.802 . . 114 18 18 G H1 H 12.46 . . 115 18 18 G H1' H 3.834 . . 116 18 18 G H2' H 4.392 . . 117 18 18 G H3' H 4.154 . . 118 18 18 G H8 H 7.756 . . 119 18 18 G H21 H 8.455 . . 120 19 19 G C8 C 136.477 . . 121 19 19 G H1 H 13.35 . . 122 19 19 G H1' H 5.730 . . 123 19 19 G H2' H 4.358 . . 124 19 19 G H3' H 4.572 . . 125 19 19 G H8 H 7.123 . . 126 20 20 U C6 C 140.781 . . 127 20 20 U H1' H 5.405 . . 128 20 20 U H2' H 4.254 . . 129 20 20 U H3 H 11.77 . . 130 20 20 U H5 H 5.339 . . 131 20 20 U H6 H 7.591 . . 132 21 21 U C6 C 142.980 . . 133 21 21 U H1' H 5.616 . . 134 21 21 U H2' H 4.133 . . 135 21 21 U H3' H 4.638 . . 136 21 21 U H5 H 5.541 . . 137 21 21 U H6 H 7.804 . . 138 22 22 A C2 C 154.931 . . 139 22 22 A N1 N 154.931 . . 140 22 22 A C8 C 141.612 . . 141 22 22 A H1' H 5.652 . . 142 22 22 A H2 H 7.388 . . 143 22 22 A H2' H 4.419 . . 144 22 22 A H3' H 4.599 . . 145 22 22 A H8 H 8.044 . . 146 23 23 A C2 C 154.214 . . 147 23 23 A N1 N 154.214 . . 148 23 23 A C8 C 141.223 . . 149 23 23 A H1' H 5.409 . . 150 23 23 A H2 H 7.510 . . 151 23 23 A H2' H 4.423 . . 152 23 23 A H8 H 7.851 . . 153 24 24 A C2 C 155.727 . . 154 24 24 A N1 N 155.727 . . 155 24 24 A C8 C 141.123 . . 156 24 24 A H1' H 5.780 . . 157 24 24 A H2 H 8.049 . . 158 24 24 A H2' H 4.280 . . 159 24 24 A H8 H 8.261 . . 160 25 25 A C2 C 153.868 . . 161 25 25 A N1 N 153.868 . . 162 25 25 A C8 C 141.140 . . 163 25 25 A H1' H 5.755 . . 164 25 25 A H2 H 7.496 . . 165 25 25 A H2' H 4.341 . . 166 25 25 A H8 H 7.954 . . 167 26 26 C C6 C 141.615 . . 168 26 26 C H1' H 5.373 . . 169 26 26 C H2' H 4.195 . . 170 26 26 C H5 H 5.225 . . 171 26 26 C H6 H 7.532 . . 172 26 26 C H41 H 8.300 . . 173 26 26 C H42 H 6.845 . . 174 27 27 U C6 C 142.325 . . 175 27 27 U H1' H 5.524 . . 176 27 27 U H2' H 4.456 . . 177 27 27 U H3 H 14.07 . . 178 27 27 U H5 H 5.303 . . 179 27 27 U H6 H 7.902 . . 180 28 28 C C6 C 142.764 . . 181 28 28 C H1' H 5.558 . . 182 28 28 C H2' H 4.305 . . 183 28 28 C H5 H 5.622 . . 184 28 28 C H6 H 7.897 . . 185 29 29 C C6 C 142.035 . . 186 29 29 C H1' H 5.418 . . 187 29 29 C H2' H 4.503 . . 188 29 29 C H3' H 4.459 . . 189 29 29 C H5 H 5.439 . . 190 29 29 C H6 H 7.805 . . 191 29 29 C H41 H 8.322 . . 192 29 29 C H42 H 6.833 . . 193 30 30 C C6 C 141.086 . . 194 30 30 C H1' H 5.615 . . 195 30 30 C H2' H 4.098 . . 196 30 30 C H3' H 4.344 . . 197 30 30 C H5 H 5.374 . . 198 30 30 C H6 H 7.646 . . 199 31 31 C C6 C 142.333 . . 200 31 31 C H1' H 5.507 . . 201 31 31 C H2' H 4.510 . . 202 31 31 C H3' H 4.285 . . 203 31 31 C H5 H 5.603 . . 204 31 31 C H6 H 7.674 . . stop_ save_