data_25534 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RNA structure determination by solid-state NMR spectroscopy ; _BMRB_accession_number 25534 _BMRB_flat_file_name bmr25534.str _Entry_type original _Submission_date 2015-03-12 _Accession_date 2015-03-12 _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 Marchanka Alexander . . 2 Simon Bernd . . 3 Althoff-Ospelt Gerhard . . 4 Carlomagno Teresa . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 173 "15N chemical shifts" 49 "31P chemical shifts" 9 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-08-29 update BMRB 'update entry citation' 2015-05-08 original author 'original release' stop_ _Original_release_date 2015-05-08 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title ; RNA structure determination by solid-state NMR spectroscopy ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25960310 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Marchanka Alexander . . 2 Simon Bernd . . 3 Althoff-Ospelt Gerhard . . 4 Carlomagno Teresa . . stop_ _Journal_abbreviation 'Nat. Commun.' _Journal_volume 6 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 7024 _Page_last 7024 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "26mer Box C/D RNA (5'-R(P*CP*UP*GP*AP*GP*CP*UP*CP*GP*AP*AP*AP*GP*AP*GP*CP*AP*AP*UP*GP*AP*UP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common '26mer Box C/D RNA' _Molecular_mass 7450.573 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 26 _Mol_residue_sequence ; GCUGAGCUCGAAAGAGCAAU GAUGUC ; loop_ _Residue_seq_code _Residue_label 1 G 2 C 3 U 4 G 5 A 6 G 7 C 8 U 9 C 10 G 11 A 12 A 13 A 14 G 15 A 16 G 17 C 18 A 19 A 20 U 21 G 22 A 23 U 24 G 25 U 26 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 $entity 'E. 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 $entity 'enzymatic semisynthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type microcrystalline _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 20 mg/mL 'nucleotide-type-selective [U-99% 13C; U-99% 15N]' H2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_(13C,15N-TEDOR)-13C,13C_PDSD_1 _Saveframe_category NMR_applied_experiment _Experiment_name '(13C,15N-TEDOR)-13C,13C PDSD' _Sample_label $sample_1 save_ save_13C-31P_TEDOR_2 _Saveframe_category NMR_applied_experiment _Experiment_name '13C-31P TEDOR' _Sample_label $sample_1 save_ save_CHHC_3 _Saveframe_category NMR_applied_experiment _Experiment_name CHHC _Sample_label $sample_1 save_ save_NHHC_4 _Saveframe_category NMR_applied_experiment _Experiment_name NHHC _Sample_label $sample_1 save_ save_CN-TEDOR_5 _Saveframe_category NMR_applied_experiment _Experiment_name CN-TEDOR _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 7.5 . pH temperature 260 . 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 adamantane C 13 'methyl carbons' ppm 38.48 external direct . . . 1 adamantane N 15 'methyl carbons' ppm 38.48 na indirect . . . 0.402980 adamantane P 31 'methyl carbons' ppm 38.48 na indirect . . . 1.609894 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 '(13C,15N-TEDOR)-13C,13C PDSD' '13C-31P TEDOR' 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 entity _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 2 2 C C2 C 158.1 0 1 2 3 3 U C1' C 93.7 0 1 3 3 3 U C2 C 154.1 0 1 4 3 3 U C2' C 75.6 0 1 5 3 3 U C3' C 71.9 0 1 6 3 3 U C4 C 165.7 0 1 7 3 3 U C4' C 82.9 0 1 8 3 3 U C5 C 104.7 0 1 9 3 3 U C5' C 64.0 0 1 10 3 3 U C6 C 139.3 0 1 11 3 3 U N1 N 145.5 0 1 12 3 3 U N3 N 157.1 0 1 13 4 4 G C1' C 90.1 0 1 14 4 4 G C2 C 156.6 0 1 15 4 4 G C2' C 76.0 0 1 16 4 4 G C3' C 79.6 0 1 17 4 4 G C4 C 155.3 0 1 18 4 4 G C4' C 88.3 0 1 19 4 4 G C5 C 116.7 0 1 20 4 4 G C5' C 67.8 0 1 21 4 4 G C6 C 160.3 0 1 22 4 4 G C8 C 139.0 0 1 23 4 4 G N1 N 145.0 0 1 24 4 4 G N2 N 81.4 0 1 25 4 4 G N9 N 167.0 0 1 26 4 4 G P P -3.8 0 1 27 5 5 A C1' C 88.1 0 1 28 5 5 A C2 C 156.0 0 1 29 5 5 A C2' C 78.4 0 1 30 5 5 A C3' C 80.0 0 1 31 5 5 A C4 C 150.9 0 1 32 5 5 A C4' C 83.4 0 1 33 5 5 A C5 C 118.8 0 1 34 5 5 A C5' C 70.3 0 1 35 5 5 A C6 C 156.6 0 1 36 5 5 A C8 C 139.8 0 1 37 5 5 A N6 N 81.4 0 1 38 5 5 A N9 N 166.9 0 1 39 5 5 A P P -0.7 0 1 40 6 6 G C1' C 92.6 0 1 41 6 6 G C2 C 158.2 0 1 42 6 6 G C2' C 75.8 0 1 43 6 6 G C3' C 77.3 0 1 44 6 6 G C4 C 152.2 0 1 45 6 6 G C4' C 83.4 0 1 46 6 6 G C5 C 119.5 0 1 47 6 6 G C5' C 70.9 0 1 48 6 6 G C6 C 157.9 0 1 49 6 6 G C8 C 139.0 0 1 50 6 6 G N1 N 148.9 0 1 51 6 6 G N2 N 75.8 0 1 52 6 6 G N9 N 171.1 0 1 53 6 6 G P P -3.8 0 1 54 7 7 C C1' C 93.9 0 1 55 7 7 C C2 C 159.3 0 1 56 7 7 C C2' C 75.4 0 1 57 7 7 C C3' C 72.1 0 1 58 7 7 C C4 C 168.1 0 1 59 7 7 C C4' C 82.0 0 1 60 7 7 C C5 C 97.1 0 1 61 7 7 C C5' C 64.3 0 1 62 7 7 C C6 C 142.2 0 1 63 7 7 C N1 N 152.2 0 1 64 7 7 C N3 N 196.3 0 1 65 7 7 C N4 N 100.1 0 1 66 8 8 U C1' C 93.7 0 1 67 8 8 U C2 C 152.8 0 1 68 8 8 U C2' C 75.5 0 1 69 8 8 U C3' C 72.1 0 1 70 8 8 U C4 C 169.4 0 1 71 8 8 U C4' C 82.1 0 1 72 8 8 U C5 C 103.2 0 1 73 8 8 U C5' C 64.3 0 1 74 8 8 U C6 C 142.3 0 1 75 8 8 U N1 N 145.5 0 1 76 8 8 U N3 N 163.6 0 1 77 9 9 C C1' C 93.2 0 1 78 9 9 C C2 C 158.2 0 1 79 9 9 C C2' C 75.9 0 1 80 9 9 C C3' C 71.4 0 1 81 9 9 C C4 C 168.1 0 1 82 9 9 C C4' C 81.2 0 1 83 9 9 C C5 C 98.2 0 1 84 9 9 C C5' C 64.2 0 1 85 9 9 C C6 C 140.2 0 1 86 9 9 C N1 N 151.7 0 1 87 9 9 C N3 N 197.7 0 1 88 9 9 C N4 N 99.1 0 1 89 10 10 G C1' C 94.0 0 1 90 10 10 G C2' C 75.7 0 1 91 10 10 G C3' C 71.5 0 1 92 10 10 G C4 C 155.5 0 1 93 10 10 G C4' C 81.8 0 1 94 10 10 G C5' C 64.4 0 1 95 10 10 G C6 C 161.7 0 1 96 10 10 G C8 C 136.3 0 1 97 10 10 G N1 N 146.2 0 1 98 10 10 G N2 N 75.5 0 1 99 10 10 G N9 N 171.3 0 1 100 14 14 G C1' C 92.6 0 1 101 14 14 G C2 C 157.5 0 1 102 14 14 G C2' C 74.6 0 1 103 14 14 G C4 C 151.9 0 1 104 14 14 G C5 C 119.2 0 1 105 14 14 G C5' C 69.5 0 1 106 14 14 G C8 C 137.4 0 1 107 14 14 G N1 N 148.2 0 1 108 14 14 G N2 N 75.4 0 1 109 14 14 G N9 N 170.1 0 1 110 15 15 A C1' C 92.9 0 1 111 15 15 A C2 C 153.0 0 1 112 15 15 A C2' C 75.5 0 1 113 15 15 A C3' C 72.3 0 1 114 15 15 A C4 C 148.6 0 1 115 15 15 A C4' C 81.8 0 1 116 15 15 A C5 C 120.6 0 1 117 15 15 A C5' C 65.2 0 1 118 15 15 A C6 C 157.6 0 1 119 15 15 A C8 C 139.5 0 1 120 15 15 A N1 N 222.1 0 1 121 15 15 A N9 N 171.5 0 1 122 16 16 G C1' C 92.5 0 1 123 16 16 G C2 C 157.0 0 1 124 16 16 G C2' C 75.8 0 1 125 16 16 G C3' C 72.0 0 1 126 16 16 G C4 C 151.6 0 1 127 16 16 G C4' C 81.7 0 1 128 16 16 G C5 C 119.0 0 1 129 16 16 G C5' C 64.3 0 1 130 16 16 G C6 C 160.9 0 1 131 16 16 G C8 C 135.6 0 1 132 16 16 G N1 N 148.0 0 1 133 16 16 G N2 N 74.6 0 1 134 16 16 G N9 N 170.9 0 1 135 17 17 C C1' C 93.6 0 1 136 17 17 C C2 C 158.5 0 1 137 17 17 C C2' C 75.7 0 1 138 17 17 C C3' C 71.7 0 1 139 17 17 C C4 C 167.6 0 1 140 17 17 C C4' C 81.6 0 1 141 17 17 C C5 C 97.9 0 1 142 17 17 C C5' C 64.1 0 1 143 17 17 C C6 C 139.0 0 1 144 17 17 C N1 N 150.5 0 1 145 17 17 C N3 N 195.9 0 1 146 17 17 C N4 N 99.0 0 1 147 18 18 A C1' C 94.1 0 1 148 18 18 A C2 C 156.0 0 1 149 18 18 A C2' C 76.6 0 1 150 18 18 A C3' C 72.5 0 1 151 18 18 A C4 C 150.6 0 1 152 18 18 A C4' C 81.6 0 1 153 18 18 A C5 C 121.6 0 1 154 18 18 A C5' C 64.6 0 1 155 18 18 A C6 C 157.7 0 1 156 18 18 A C8 C 138.6 0 1 157 18 18 A N6 N 80.7 0 1 158 18 18 A N7 N 230.9 0 1 159 18 18 A N9 N 173.2 0 1 160 18 18 A P P -4.2 0 1 161 19 19 A C1' C 89.7 0 1 162 19 19 A C2 C 154.5 0 1 163 19 19 A C2' C 72.2 0 1 164 19 19 A C3' C 78.5 0 1 165 19 19 A C4 C 150.5 0 1 166 19 19 A C4' C 85.1 0 1 167 19 19 A C5 C 121.8 0 1 168 19 19 A C5' C 67.4 0 1 169 19 19 A C6 C 156.4 0 1 170 19 19 A C8 C 145.8 0 1 171 19 19 A N6 N 76.3 0 1 172 19 19 A N7 N 228.2 0 1 173 19 19 A N9 N 164.7 0 1 174 19 19 A P P -1.8 0 1 175 20 20 U C1' C 89.4 0 1 176 20 20 U C2 C 154.2 0 1 177 20 20 U C2' C 75.4 0 1 178 20 20 U C3' C 80.5 0 1 179 20 20 U C4 C 167.9 0 1 180 20 20 U C4' C 84.2 0 1 181 20 20 U C5 C 105.7 0 1 182 20 20 U C5' C 69.5 0 1 183 20 20 U C6 C 146.8 0 1 184 20 20 U N1 N 147.4 0 1 185 20 20 U N3 N 158.5 0 1 186 20 20 U P P -5.3 0 1 187 21 21 G C1' C 87.5 0 1 188 21 21 G C2' C 77.5 0 1 189 21 21 G C3' C 80.0 0 1 190 21 21 G C4 C 155.7 0 1 191 21 21 G C4' C 87.5 0 1 192 21 21 G C5 C 117.6 0 1 193 21 21 G C5' C 68.3 0 1 194 21 21 G C6 C 160.3 0 1 195 21 21 G C8 C 139.1 0 1 196 21 21 G N1 N 145.6 0 1 197 21 21 G N2 N 81.0 0 1 198 21 21 G N9 N 168.8 0 1 199 21 21 G P P -6.0 0 1 200 22 22 A C1' C 92.4 0 1 201 22 22 A C2 C 156.0 0 1 202 22 22 A C2' C 75.7 0 1 203 22 22 A C3' C 72.4 0 1 204 22 22 A C4 C 147.5 0 1 205 22 22 A C4' C 82.9 0 1 206 22 22 A C5 C 120.8 0 1 207 22 22 A C5' C 65.8 0 1 208 22 22 A C6 C 157.1 0 1 209 22 22 A C8 C 140.0 0 1 210 22 22 A N6 N 81.2 0 1 211 22 22 A N9 N 170.2 0 1 212 22 22 A P P -0.1 0 1 213 23 23 U C1' C 93.0 0 1 214 23 23 U C2 C 151.0 0 1 215 23 23 U C2' C 74.6 0 1 216 23 23 U C3' C 72.1 0 1 217 23 23 U C4 C 167.6 0 1 218 23 23 U C4' C 82.3 0 1 219 23 23 U C5 C 103.8 0 1 220 23 23 U C5' C 63.1 0 1 221 23 23 U C6 C 140.0 0 1 222 23 23 U N1 N 144.7 0 1 223 23 23 U N3 N 155.7 0 1 224 23 23 U P P -4.2 0 1 225 24 24 G C1' C 92.6 0 1 226 24 24 G C2 C 157.4 0 1 227 24 24 G C4 C 152.9 0 1 228 24 24 G C5 C 118.1 0 1 229 24 24 G C8 C 136.2 0 1 230 24 24 G N2 N 76.5 0 1 231 24 24 G N9 N 172.4 0 1 stop_ save_