data_4750 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of the most conserved RNA motif in Srp RNA ; _BMRB_accession_number 4750 _BMRB_flat_file_name bmr4750.str _Entry_type original _Submission_date 2000-06-02 _Accession_date 2000-06-05 _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 Schmitz U. . . 2 James T. L. . 3 Lukavsky P. . . 4 Walter P. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 214 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-07-06 original author . stop_ _Original_release_date 2000-07-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of the Most Conserved internal loop in Srp RNA' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99332051 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schmitz U. . . 2 James T. L. . 3 Lukavsky P. . . 4 Walter P. . . stop_ _Journal_abbreviation 'Nat. Struct. Biol.' _Journal_volume 6 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 634 _Page_last 638 _Year 1999 _Details . loop_ _Keyword '4.5S RNA' 'COMPLETE RELAXATION MATRIX ANALYSIS' 'NMR OF RNA' 'RNA STRUCTURE' SRP stop_ save_ ################################## # Molecular system description # ################################## save_SRP _Saveframe_category molecular_system _Mol_system_name 'CONSERVED MOTIF IN SRP RNA' _Abbreviation_common SRP _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'SRP DOMAIN IV' $SRP_domain_IV stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SRP_domain_IV _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'SRP DOMAIN IV' _Abbreviation_common 'SRP domain IV' _Molecular_mass 8000 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; GGCGUCAGGUCCGGAAGGAA GCAGCGCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 41 G 2 42 G 3 43 C 4 44 G 5 45 U 6 46 C 7 47 A 8 48 G 9 49 G 10 50 U 11 51 C 12 52 C 13 53 G 14 54 G 15 55 A 16 56 A 17 57 G 18 58 G 19 59 A 20 60 A 21 61 G 22 62 C 23 63 A 24 64 G 25 65 C 26 66 G 27 67 C 28 68 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 $SRP_domain_IV 'Escherichia coli' 562 Eubacteria . 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 $SRP_domain_IV 'enzymatic semisynthesis' . Escherichia coli . . 'Prepared by in vitro transcription with T7 RNA polymerase' 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 _Isotopic_labeling $SRP_domain_IV 0.25 mM . stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 5.0 loop_ _Task REFINEMENT stop_ _Details 'PEARLMAN, KOLLMAN ET AL.' save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Task 'STRUCTURE CALCULATION' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Unity Plus' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY,_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY, _Sample_label . save_ save_COSY,_2 _Saveframe_category NMR_applied_experiment _Experiment_name COSY, _Sample_label . save_ save_SSNOESY,_3 _Saveframe_category NMR_applied_experiment _Experiment_name SSNOESY, _Sample_label . save_ save_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY, _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name COSY, _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name SSNOESY, _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details 'Sample was snapcooled before each NMR session, after which RNA was dialyzed to remove MG.' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 0.2 n/a temperature 303 0.5 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'SRP DOMAIN IV' _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 G H8 H 8.18 . . 2 . 1 G H1' H 5.93 . . 3 . 1 G H2' H 4.5 . . 4 . 1 G H3' H 4.66 . . 5 . 1 G H4' H 4.38 . . 6 . 1 G H1 H 13.27 . . 7 . 2 G H8 H 7.64 . . 8 . 2 G H1' H 5.72 . . 9 . 2 G H2' H 4.45 . . 10 . 2 G H3' H 4.67 . . 11 . 2 G H1 H 13.42 . . 12 . 3 C H6 H 7.71 . . 13 . 3 C H5 H 5.21 . . 14 . 3 C H1' H 5.53 . . 15 . 3 C H2' H 4.55 . . 16 . 3 C H3' H 4.6 . . 17 . 3 C H4' H 4.45 . . 18 . 3 C H41 H 8.47 . . 19 . 3 C H42 H 6.51 . . 20 . 4 G H8 H 7.39 . . 21 . 4 G H1' H 5.73 . . 22 . 4 G H2' H 4.5 . . 23 . 4 G H3' H 4.38 . . 24 . 4 G H4' H 4.46 . . 25 . 4 G H1 H 13.12 . . 26 . 4 G H21 H 7.82 . . 27 . 4 G H22 H 6.09 . . 28 . 5 U H6 H 7.58 . . 29 . 5 U H5 H 5.10 . . 30 . 5 U H1' H 5.58 . . 31 . 5 U H2' H 4.51 . . 32 . 5 U H3' H 4.38 . . 33 . 5 U H3 H 12.31 . . 34 . 6 C H6 H 7.38 . . 35 . 6 C H5 H 5.46 . . 36 . 6 C H1' H 5.11 . . 37 . 6 C H2' H 4.01 . . 38 . 6 C H3' H 4.64 . . 39 . 6 C H4' H 4.52 . . 40 . 6 C H41 H 6.9 . . 41 . 7 A H8 H 7.94 . . 42 . 7 A H2 H 8.11 . . 43 . 7 A H1' H 6.1 . . 44 . 7 A H2' H 4.91 . . 45 . 7 A H3' H 4.66 . . 46 . 7 A H4' H 4.55 . . 47 . 7 A H5' H 4.15 . . 48 . 7 A H5'' H 4.25 . . 49 . 7 A H61 H 5.62 . . 50 . 8 G H8 H 7.24 . . 51 . 8 G H1' H 4.78 . . 52 . 8 G H2' H 4.44 . . 53 . 8 G H3' H 4.53 . . 54 . 8 G H5' H 4.36 . . 55 . 8 G H1 H 10.31 . . 56 . 8 G H21 H 8.80 . . 57 . 8 G H22 H 6.00 . . 58 . 9 G H8 H 7.84 . . 59 . 9 G H1' H 5.39 . . 60 . 9 G H2' H 4.34 . . 61 . 9 G H3' H 4.44 . . 62 . 9 G H5' H 4.06 . . 63 . 9 G H5'' H 4.13 . . 64 . 9 G H1 H 13.60 . . 65 . 9 G H21 H 5.98 . . 66 . 10 U H6 H 7.39 . . 67 . 10 U H5 H 5.42 . . 68 . 10 U H1' H 5.52 . . 69 . 10 U H2' H 4.36 . . 70 . 10 U H3' H 4.45 . . 71 . 10 U H4' H 4.07 . . 72 . 10 U H3 H 12.4 . . 73 . 11 C H6 H 7.88 . . 74 . 11 C H5 H 5.62 . . 75 . 11 C H1' H 5.44 . . 76 . 11 C H2' H 4.12 . . 77 . 11 C H3' H 4.5 . . 78 . 11 C H4' H 4.16 . . 79 . 11 C H41 H 8.29 . . 80 . 11 C H42 H 6.98 . . 81 . 12 C H6 H 7.57 . . 82 . 12 C H5 H 5.31 . . 83 . 12 C H1' H 5.48 . . 84 . 12 C H2' H 4.41 . . 85 . 12 C H3' H 4.37 . . 86 . 12 C H4' H 4.5 . . 87 . 12 C H41 H 8.13 . . 88 . 12 C H42 H 6.47 . . 89 . 13 G H8 H 7.52 . . 90 . 13 G H1' H 5.64 . . 91 . 13 G H2' H 4.28 . . 92 . 13 G H3' H 4.67 . . 93 . 13 G H4' H 4.41 . . 94 . 13 G H5' H 4.11 . . 95 . 13 G H5'' H 4.34 . . 96 . 13 G H1 H 10.57 . . 97 . 14 G H8 H 7.98 . . 98 . 14 G H1' H 5.46 . . 99 . 14 G H2' H 4.72 . . 100 . 14 G H3' H 4.4 . . 101 . 14 G H4' H 4.2 . . 102 . 14 G H5' H 4.00 . . 103 . 14 G H5'' H 4.02 . . 104 . 14 G H1 H 12.74 . . 105 . 14 G H21 H 6.15 . . 106 . 15 A H8 H 7.97 . . 107 . 15 A H2 H 7.79 . . 108 . 15 A H1' H 5.61 . . 109 . 15 A H2' H 4.39 . . 110 . 15 A H3' H 4.61 . . 111 . 15 A H4' H 4.27 . . 112 . 15 A H5' H 3.91 . . 113 . 15 A H5'' H 3.94 . . 114 . 16 A H8 H 8.19 . . 115 . 16 A H2 H 8.16 . . 116 . 16 A H1' H 5.99 . . 117 . 16 A H2' H 4.65 . . 118 . 16 A H3' H 4.97 . . 119 . 16 A H4' H 4.46 . . 120 . 16 A H5' H 4.25 . . 121 . 16 A H5'' H 4.26 . . 122 . 17 G H8 H 7.93 . . 123 . 17 G H1' H 3.61 . . 124 . 17 G H2' H 4.44 . . 125 . 17 G H3' H 4.2 . . 126 . 17 G H4' H 4.21 . . 127 . 17 G H5' H 4.09 . . 128 . 17 G H5'' H 4.29 . . 129 . 17 G H1 H 12.38 . . 130 . 17 G H21 H 7.78 . . 131 . 17 G H22 H 6.27 . . 132 . 18 G H8 H 7.17 . . 133 . 18 G H1' H 5.72 . . 134 . 18 G H2' H 4.47 . . 135 . 18 G H3' H 4.43 . . 136 . 18 G H1 H 12.4 . . 137 . 18 G H21 H 7.79 . . 138 . 18 G H22 H 6.31 . . 139 . 19 A H8 H 7.78 . . 140 . 19 A H2 H 6.83 . . 141 . 19 A H1' H 5.8 . . 142 . 19 A H2' H 4.3 . . 143 . 19 A H3' H 4.45 . . 144 . 19 A H61 H 8.49 . . 145 . 19 A H62 H 6.54 . . 146 . 20 A H8 H 7.82 . . 147 . 20 A H2 H 8.14 . . 148 . 20 A H1' H 6.08 . . 149 . 20 A H2' H 4.65 . . 150 . 20 A H3' H 4.42 . . 151 . 20 A H4' H 4.51 . . 152 . 20 A H61 H 8.80 . . 153 . 20 A H62 H 5.98 . . 154 . 21 G H8 H 7.46 . . 155 . 21 G H1' H 4.71 . . 156 . 21 G H2' H 3.89 . . 157 . 21 G H3' H 4.75 . . 158 . 21 G H4' H 4.37 . . 159 . 21 G H1 H 11.30 . . 160 . 21 G H21 H 6.16 . . 161 . 22 C H6 H 8.04 . . 162 . 22 C H5 H 5.93 . . 163 . 22 C H1' H 5.85 . . 164 . 22 C H2' H 4.51 . . 165 . 22 C H3' H 4.43 . . 166 . 22 C H4' H 4.17 . . 167 . 22 C H5' H 4.16 . . 168 . 22 C H41 H 8.54 . . 169 . 23 A H8 H 7.6 . . 170 . 23 A H2 H 6.67 . . 171 . 23 A H1' H 5.94 . . 172 . 23 A H2' H 4.63 . . 173 . 23 A H3' H 4.39 . . 174 . 23 A H4' H 4.53 . . 175 . 23 A H5' H 4.19 . . 176 . 23 A H61 H 5.59 . . 177 . 24 G H8 H 7.21 . . 178 . 24 G H1' H 4.62 . . 179 . 24 G H2' H 4.54 . . 180 . 24 G H3' H 4.35 . . 181 . 24 G H4' H 4.33 . . 182 . 24 G H5' H 4.04 . . 183 . 24 G H1 H 10.59 . . 184 . 24 G H21 H 6.69 . . 185 . 25 C H6 H 7.64 . . 186 . 25 C H5 H 5.4 . . 187 . 25 C H1' H 5.37 . . 188 . 25 C H2' H 4.29 . . 189 . 25 C H3' H 4.41 . . 190 . 25 C H4' H 4.33 . . 191 . 25 C H5' H 4.05 . . 192 . 25 C H41 H 8.42 . . 193 . 25 C H42 H 6.73 . . 194 . 26 G H8 H 7.63 . . 195 . 26 G H1' H 5.72 . . 196 . 26 G H2' H 4.46 . . 197 . 26 G H3' H 4.40 . . 198 . 26 G H1 H 12.96 . . 199 . 26 G H21 H 8.27 . . 200 . 26 G H22 H 6.12 . . 201 . 27 C H6 H 7.64 . . 202 . 27 C H5 H 5.21 . . 203 . 27 C H1' H 5.52 . . 204 . 27 C H2' H 4.3 . . 205 . 27 C H3' H 4.17 . . 206 . 27 C H41 H 8.56 . . 207 . 27 C H42 H 6.74 . . 208 . 28 C H6 H 7.64 . . 209 . 28 C H5 H 5.25 . . 210 . 28 C H1' H 5.71 . . 211 . 28 C H2' H 4.00 . . 212 . 28 C H3' H 4.17 . . 213 . 28 C H41 H 8.62 . . 214 . 28 C H42 H 6.75 . . stop_ save_