data_25785 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Assignment and structure of CssA5 (middle region) of CssA thermometer from Neisseria meningitidis ; _BMRB_accession_number 25785 _BMRB_flat_file_name bmr25785.str _Entry_type original _Submission_date 2015-08-31 _Accession_date 2015-08-31 _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 Barnwal Ravi P. . 2 Godin Kate S. . 3 Varani Gabriele . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 204 "13C chemical shifts" 32 "15N chemical shifts" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-03-21 update BMRB 'update entry citation' 2016-07-26 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25780 'CssA4 (bottom stem) of CssA thermometer' 25781 'CssA3 (top stem) of CssA thermometer' 25784 'CssA Thermometer from Neisseria meningitidis' stop_ _Original_release_date 2016-07-26 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27369378 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Barnwal Ravi P. . 2 Loh Edmund . . 3 Godin Kate S. . 4 Yip Jordan . . 5 Lavender Hayley . . 6 Tang Christoph M. . 7 Varani Gabriele . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 44 _Journal_issue 19 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9426 _Page_last 9437 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'CssA5 (middle region) of CssA thermometer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (43-MER)' $RNA_(43-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_(43-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common CssA5_RNA_(43-MER) _Molecular_mass 13741.223 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 43 _Mol_residue_sequence ; GGUGAGUACGUAGAGUAUAC UUCGGUAUACUUAUAUACUU ACC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 U 4 4 G 5 5 A 6 6 G 7 7 U 8 8 A 9 9 C 10 10 G 11 11 U 12 12 A 13 13 G 14 14 A 15 15 G 16 16 U 17 17 A 18 18 U 19 19 A 20 20 C 21 21 U 22 22 U 23 23 C 24 24 G 25 25 G 26 26 U 27 27 A 28 28 U 29 29 A 30 30 C 31 31 U 32 32 U 33 33 A 34 34 U 35 35 A 36 36 U 37 37 A 38 38 C 39 39 U 40 40 U 41 41 A 42 42 C 43 43 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_(43-MER) b-proteobacteria 487 Bacteria . Neisseria meningitidis 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_(43-MER) 'in vitro transcription' . . . . . 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(43-MER) . mM 0.4 1.1 'natural abundance' $RNA_(43-MER) . mM 0.4 1.1 '13C/15N-uniformly labeled' $RNA_(43-MER) . mM 0.4 1.1 '13C/15N-AU labeled' $RNA_(43-MER) . mM 0.4 1.1 'partially deuterated' H2O 95 % . . 'natural abundance' D2O 5 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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 'structure solution' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _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-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 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-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_3D_1H-13C_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY' _Sample_label $sample_1 save_ save_3D_HCCH-TOCSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 . pH pressure 1 . atm temperature 273 . 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 DSS P 31 'methyl protons' ppm 0.00 na indirect . . . 0.404808636 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-15N HSQC' '2D 1H-13C HSQC' '2D 1H-1H NOESY' '3D 1H-13C 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 (43-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 5.782 0.05 . 2 1 1 G HO2' H 4.887 0.05 . 3 1 1 G H8 H 8.064 0.05 . 4 2 2 G H1 H 13.300 0.05 . 5 2 2 G H1' H 5.885 0.05 . 6 2 2 G H2' H 4.482 0.05 . 7 2 2 G H8 H 7.520 0.05 . 8 2 2 G C8 C 134.009 0.12 . 9 2 2 G N1 N 148.855 0.12 . 10 3 3 U H1' H 5.626 0.05 . 11 3 3 U H2' H 4.632 0.05 . 12 3 3 U H3 H 13.826 0.05 . 13 3 3 U H5 H 5.107 0.05 . 14 3 3 U H6 H 7.642 0.05 . 15 3 3 U N3 N 163.194 0.12 . 16 4 4 G H1 H 9.909 0.05 . 17 4 4 G H1' H 5.666 0.05 . 18 4 4 G H2' H 4.712 0.05 . 19 4 4 G H8 H 7.618 0.05 . 20 4 4 G C8 C 134.297 0.12 . 21 4 4 G N1 N 142.616 0.12 . 22 5 5 A H1' H 5.796 0.05 . 23 5 5 A H2 H 7.495 0.05 . 24 5 5 A H2' H 4.647 0.05 . 25 5 5 A H8 H 7.561 0.05 . 26 5 5 A C2 C 150.235 0.12 . 27 5 5 A C8 C 136.154 0.12 . 28 6 6 G H1 H 13.295 0.05 . 29 6 6 G H1' H 5.508 0.05 . 30 6 6 G H2' H 4.407 0.05 . 31 6 6 G H8 H 6.966 0.05 . 32 6 6 G C8 C 132.878 0.12 . 33 6 6 G N1 N 148.827 0.12 . 34 7 7 U H1' H 5.486 0.05 . 35 7 7 U H2' H 4.654 0.05 . 36 7 7 U H3 H 13.411 0.05 . 37 7 7 U H5 H 5.000 0.05 . 38 7 7 U H6 H 7.601 0.05 . 39 7 7 U N3 N 162.548 0.12 . 40 8 8 A H1' H 5.879 0.05 . 41 8 8 A H2 H 7.046 0.05 . 42 8 8 A H2' H 4.650 0.05 . 43 8 8 A H8 H 7.946 0.05 . 44 8 8 A C2 C 150.017 0.12 . 45 8 8 A C8 C 136.413 0.12 . 46 9 9 C H1' H 5.237 0.05 . 47 9 9 C H2' H 4.170 0.05 . 48 9 9 C H5 H 5.393 0.05 . 49 9 9 C H6 H 7.527 0.05 . 50 10 10 G H1' H 5.531 0.05 . 51 10 10 G H2' H 4.491 0.05 . 52 10 10 G H8 H 7.612 0.05 . 53 10 10 G C8 C 135.355 0.12 . 54 11 11 U H1' H 5.432 0.05 . 55 11 11 U H2' H 4.139 0.05 . 56 11 11 U H5 H 5.257 0.05 . 57 11 11 U H6 H 7.462 0.05 . 58 11 11 U C6 C 138.729 0.12 . 59 12 12 A H1' H 5.922 0.05 . 60 12 12 A H2 H 7.245 0.05 . 61 12 12 A H2' H 4.687 0.05 . 62 12 12 A H8 H 8.074 0.05 . 63 12 12 A C2 C 150.356 0.12 . 64 13 13 G H1' H 5.689 0.05 . 65 13 13 G H2' H 4.606 0.05 . 66 13 13 G H8 H 7.758 0.05 . 67 13 13 G C8 C 135.506 0.12 . 68 14 14 A H1' H 5.869 0.05 . 69 14 14 A H2 H 7.489 0.05 . 70 14 14 A H2' H 4.731 0.05 . 71 14 14 A H8 H 7.808 0.05 . 72 14 14 A C2 C 150.287 0.12 . 73 15 15 G H1 H 13.253 0.05 . 74 15 15 G H1' H 5.608 0.05 . 75 15 15 G H2' H 4.460 0.05 . 76 15 15 G H8 H 7.176 0.05 . 77 15 15 G C8 C 133.349 0.12 . 78 15 15 G N1 N 148.750 0.12 . 79 16 16 U H1' H 5.514 0.05 . 80 16 16 U H2' H 4.572 0.05 . 81 16 16 U H3 H 13.489 0.05 . 82 16 16 U H5 H 5.059 0.05 . 83 16 16 U H6 H 7.670 0.05 . 84 16 16 U N3 N 162.640 0.12 . 85 17 17 A H1' H 5.959 0.05 . 86 17 17 A H2 H 6.994 0.05 . 87 17 17 A H2' H 4.423 0.05 . 88 17 17 A H8 H 8.111 0.05 . 89 17 17 A C2 C 150.032 0.12 . 90 18 18 U H1' H 5.379 0.05 . 91 18 18 U H2' H 4.313 0.05 . 92 18 18 U H3 H 13.199 0.05 . 93 18 18 U H5 H 5.022 0.05 . 94 18 18 U H6 H 7.615 0.05 . 95 18 18 U N3 N 162.297 0.12 . 96 19 19 A H1' H 5.951 0.05 . 97 19 19 A H2 H 7.098 0.05 . 98 19 19 A H2' H 4.488 0.05 . 99 19 19 A H8 H 8.070 0.05 . 100 19 19 A C2 C 150.203 0.12 . 101 20 20 C H1' H 5.268 0.05 . 102 20 20 C H2' H 4.251 0.05 . 103 20 20 C H5 H 5.107 0.05 . 104 20 20 C H6 H 7.226 0.05 . 105 20 20 C H41 H 8.438 0.05 . 106 20 20 C H42 H 6.927 0.05 . 107 20 20 C C6 C 137.134 0.12 . 108 21 21 U H1' H 5.573 0.05 . 109 21 21 U HO2' H 6.642 0.05 . 110 21 21 U H2' H 3.702 0.05 . 111 21 21 U H3 H 11.672 0.05 . 112 21 21 U H4' H 4.265 0.05 . 113 21 21 U H5 H 5.572 0.05 . 114 21 21 U H6 H 7.661 0.05 . 115 21 21 U N3 N 160.441 0.12 . 116 22 22 U H1' H 6.060 0.05 . 117 22 22 U H2' H 4.604 0.05 . 118 22 22 U H3 H 11.012 0.05 . 119 22 22 U H3' H 3.955 0.05 . 120 22 22 U H5 H 6.163 0.05 . 121 22 22 U H6 H 7.962 0.05 . 122 22 22 U C6 C 141.530 0.12 . 123 22 22 U N3 N 158.940 0.12 . 124 23 23 C H1' H 5.897 0.05 . 125 23 23 C H2' H 4.037 0.05 . 126 23 23 C H4' H 3.727 0.05 . 127 23 23 C H5 H 5.988 0.05 . 128 23 23 C H5' H 3.530 0.05 . 129 23 23 C H5'' H 2.607 0.05 . 130 23 23 C H6 H 7.630 0.05 . 131 23 23 C H41 H 7.159 0.05 . 132 23 23 C H42 H 6.158 0.05 . 133 24 24 G H1 H 10.020 0.05 . 134 24 24 G H1' H 5.905 0.05 . 135 24 24 G H2' H 4.777 0.05 . 136 24 24 G H3' H 5.573 0.05 . 137 24 24 G H4' H 4.339 0.05 . 138 24 24 G H5' H 4.325 0.05 . 139 24 24 G H5'' H 4.101 0.05 . 140 24 24 G H8 H 7.798 0.05 . 141 24 24 G H21 H 6.114 0.05 . 142 24 24 G N1 N 144.029 0.12 . 143 25 25 G H1 H 13.344 0.05 . 144 25 25 G H1' H 4.399 0.05 . 145 25 25 G H8 H 8.267 0.05 . 146 25 25 G H21 H 8.614 0.05 . 147 25 25 G C8 C 136.026 0.12 . 148 25 25 G N1 N 148.683 0.12 . 149 26 26 U H1' H 5.484 0.05 . 150 26 26 U H2' H 4.588 0.05 . 151 26 26 U H3 H 13.489 0.05 . 152 26 26 U H5 H 5.124 0.05 . 153 26 26 U H6 H 7.746 0.05 . 154 26 26 U C6 C 138.661 0.12 . 155 26 26 U N3 N 162.640 0.12 . 156 27 27 A H1' H 5.960 0.05 . 157 27 27 A H2 H 6.973 0.05 . 158 27 27 A H2' H 4.427 0.05 . 159 27 27 A H8 H 8.115 0.05 . 160 27 27 A C2 C 149.958 0.12 . 161 28 28 U H1' H 5.341 0.05 . 162 28 28 U H2' H 4.330 0.05 . 163 28 28 U H3 H 13.201 0.05 . 164 28 28 U H5 H 5.027 0.05 . 165 28 28 U H6 H 7.560 0.05 . 166 28 28 U C6 C 138.046 0.12 . 167 28 28 U N3 N 162.296 0.12 . 168 29 29 A H1' H 5.912 0.05 . 169 29 29 A H2 H 7.065 0.05 . 170 29 29 A H2' H 4.475 0.05 . 171 29 29 A H8 H 8.039 0.05 . 172 29 29 A C2 C 150.203 0.12 . 173 30 30 C H1' H 5.286 0.05 . 174 30 30 C H2' H 4.168 0.05 . 175 30 30 C H5 H 5.140 0.05 . 176 30 30 C H6 H 7.369 0.05 . 177 30 30 C H41 H 8.243 0.05 . 178 30 30 C H42 H 6.908 0.05 . 179 30 30 C C6 C 137.567 0.12 . 180 31 31 U H1' H 5.538 0.05 . 181 31 31 U H2' H 4.416 0.05 . 182 31 31 U H3 H 13.841 0.05 . 183 31 31 U H5 H 5.276 0.05 . 184 31 31 U H6 H 7.669 0.05 . 185 31 31 U N3 N 162.413 0.12 . 186 32 32 U H1' H 5.429 0.05 . 187 32 32 U H2' H 4.341 0.05 . 188 32 32 U H5 H 5.628 0.05 . 189 32 32 U H6 H 7.824 0.05 . 190 33 33 A H1' H 5.798 0.05 . 191 33 33 A H2 H 7.244 0.05 . 192 33 33 A H2' H 4.472 0.05 . 193 33 33 A H8 H 8.047 0.05 . 194 33 33 A C2 C 150.359 0.12 . 195 34 34 U H1' H 5.456 0.05 . 196 34 34 U H2' H 4.316 0.05 . 197 34 34 U H5 H 5.364 0.05 . 198 34 34 U H6 H 7.519 0.05 . 199 35 35 A H1' H 5.896 0.05 . 200 35 35 A H2 H 7.885 0.05 . 201 35 35 A H2' H 4.618 0.05 . 202 35 35 A H8 H 8.335 0.05 . 203 35 35 A C2 C 144.568 0.12 . 204 35 35 A C8 C 139.905 0.12 . 205 36 36 U H1' H 5.263 0.05 . 206 36 36 U H2' H 4.329 0.05 . 207 36 36 U H3 H 13.556 0.05 . 208 36 36 U H5 H 5.321 0.05 . 209 36 36 U H6 H 7.586 0.05 . 210 36 36 U C6 C 137.946 0.12 . 211 36 36 U N3 N 162.873 0.12 . 212 37 37 A H1' H 5.956 0.05 . 213 37 37 A H2 H 7.117 0.05 . 214 37 37 A H2' H 4.508 0.05 . 215 37 37 A H8 H 8.083 0.05 . 216 37 37 A C2 C 150.329 0.12 . 217 38 38 C H1' H 5.309 0.05 . 218 38 38 C H2' H 4.181 0.05 . 219 38 38 C H5 H 5.171 0.05 . 220 38 38 C H6 H 7.391 0.05 . 221 38 38 C H41 H 8.268 0.05 . 222 38 38 C H42 H 6.918 0.05 . 223 38 38 C C6 C 137.651 0.12 . 224 39 39 U H1' H 5.484 0.05 . 225 39 39 U H2' H 4.632 0.05 . 226 39 39 U H3 H 13.825 0.05 . 227 39 39 U H5 H 5.275 0.05 . 228 39 39 U H6 H 7.676 0.05 . 229 39 39 U N3 N 162.413 0.12 . 230 40 40 U H1' H 5.461 0.05 . 231 40 40 U H2' H 4.257 0.05 . 232 40 40 U H3 H 11.526 0.05 . 233 40 40 U H5 H 5.757 0.05 . 234 40 40 U H6 H 7.872 0.05 . 235 40 40 U C6 C 138.200 0.12 . 236 40 40 U N3 N 158.730 0.12 . 237 41 41 A H1' H 5.840 0.05 . 238 41 41 A H2 H 7.371 0.05 . 239 41 41 A H2' H 4.552 0.05 . 240 41 41 A H8 H 8.358 0.05 . 241 41 41 A C8 C 137.728 0.12 . 242 42 42 C H1' H 5.366 0.05 . 243 42 42 C H2' H 4.103 0.05 . 244 42 42 C H5 H 5.150 0.05 . 245 42 42 C H6 H 7.459 0.05 . 246 42 42 C H41 H 8.430 0.05 . 247 42 42 C H42 H 6.956 0.05 . 248 42 42 C C6 C 137.804 0.12 . 249 43 43 C H1' H 5.706 0.05 . 250 43 43 C H2' H 3.960 0.05 . 251 43 43 C H5 H 5.422 0.05 . 252 43 43 C H6 H 7.604 0.05 . 253 43 43 C H41 H 8.303 0.05 . 254 43 43 C H42 H 6.970 0.05 . stop_ save_