data_17563 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Glycyl-tRNA(GCC) anticodon stem-loop from Bacillus subtilis ; _BMRB_accession_number 17563 _BMRB_flat_file_name bmr17563.str _Entry_type original _Submission_date 2011-03-31 _Accession_date 2011-03-31 _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 Chang Andrew T. . 2 Nikonowicz Edward P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 108 "13C chemical shifts" 90 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-04-04 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17564 'Glycyl-tRNA(UCC)1B anticodon stem-loop' 17565 'Unmodified Glycyl-tRNA(UCC) anticodon stem-loop' stop_ _Original_release_date 2012-04-04 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure solution of three glycyl-tRNA anticodon stem-loops' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chang Andrew T. . 2 Nikonowicz Edward P. . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'glycyl-tRNA anticodon stem-loops' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*GP*GP*GP*CP*CP*UP*UP*GP*CP*CP*AP*AP*GP*GP*UP*CP*C)-3')' $glycyl-tRNA 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_glycyl-tRNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common glycyl-tRNA _Molecular_mass 5434.313 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence GGGCCUUGCCAAGGUCC loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 G 4 C 5 C 6 U 7 U 8 G 9 C 10 C 11 A 12 A 13 G 14 G 15 U 16 C 17 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 $glycyl-tRNA 'B. subtilis' 1423 Bacteria . Bacillus subtilis 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 $glycyl-tRNA 'enzymatic semisynthesis' . Bacillus subtilis . . 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 $glycyl-tRNA . mM 0.02 0.04 '[U-98% 13C; U-98% 15N]' D2O 100 % . . 'natural abundance' KH2PO4 10 mM . . 'natural abundance' K2HPO4 10 mM . . 'natural abundance' KCl 10 mM . . 'natural abundance' EDTA 0.2 mM . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $glycyl-tRNA . mM 0.02 0.04 'natural abundance' D2O 100 % . . 'natural abundance' KH2PO4 10 mM . . 'natural abundance' K2HPO4 10 mM . . 'natural abundance' KCl 10 mM . . 'natural abundance' EDTA 0.2 mM . . '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 'structure solution' stop_ _Details . save_ save_Felix _Saveframe_category software _Name FELIX _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'chemical shift assignment' processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _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 $sample_1 save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_3D_1H-13C_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY' _Sample_label $sample_1 save_ save_3D_HCCH-TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $sample_1 save_ save_2D_HCN_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCN' _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 'ionic strength' 10 . mM pH 6.2 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_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 water H 1 protons Hz 500 internal direct . . . 1.000000000 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' '2D 1H-1H COSY' '2D 1H-1H NOESY' '3D 1H-13C NOESY' '3D HCCH-TOCSY' '2D HCN' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $reference_1 _Mol_system_component_name 'RNA (5'-R(*GP*GP*GP*CP*CP*UP*UP*GP*CP*CP*AP*AP*GP*GP*UP*CP*C)-3')' _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 5.75 0.02 1 2 1 1 G H5' H 4.01 0.02 1 3 1 1 G H5'' H 3.92 0.02 1 4 1 1 G H8 H 8.05 0.02 1 5 1 1 G C8 C 140.13 0.05 1 6 2 2 G H1' H 5.90 0.02 1 7 2 2 G H2' H 4.56 0.02 1 8 2 2 G H3' H 4.59 0.02 1 9 2 2 G H5' H 4.47 0.02 1 10 2 2 G H5'' H 4.26 0.02 1 11 2 2 G H8 H 7.63 0.02 1 12 2 2 G C1' C 92.33 0.05 1 13 2 2 G C2' C 75.72 0.05 1 14 2 2 G C3' C 73.45 0.05 1 15 2 2 G C5' C 66.42 0.05 1 16 2 2 G C8 C 137.08 0.05 1 17 3 3 G H1' H 5.79 0.02 1 18 3 3 G H2' H 4.63 0.02 1 19 3 3 G H3' H 4.38 0.02 1 20 3 3 G H5' H 4.47 0.02 1 21 3 3 G H5'' H 4.26 0.02 1 22 3 3 G H8 H 7.31 0.02 1 23 3 3 G C1' C 93.25 0.05 1 24 3 3 G C2' C 75.17 0.05 1 25 3 3 G C3' C 72.95 0.05 1 26 3 3 G C5' C 66.02 0.05 1 27 3 3 G C8 C 136.75 0.05 1 28 4 4 C H1' H 5.50 0.02 1 29 4 4 C H2' H 4.31 0.02 1 30 4 4 C H3' H 4.42 0.02 1 31 4 4 C H5 H 5.38 0.02 1 32 4 4 C H5' H 4.48 0.02 1 33 4 4 C H5'' H 4.04 0.02 1 34 4 4 C H6 H 7.69 0.02 1 35 4 4 C C1' C 93.69 0.05 1 36 4 4 C C2' C 75.27 0.05 1 37 4 4 C C3' C 72.29 0.05 1 38 4 4 C C5 C 97.32 0.05 1 39 4 4 C C5' C 64.76 0.05 1 40 4 4 C C6 C 140.69 0.05 1 41 5 5 C H1' H 5.48 0.02 1 42 5 5 C H2' H 4.34 0.02 1 43 5 5 C H3' H 4.45 0.02 1 44 5 5 C H5 H 5.51 0.02 1 45 5 5 C H5' H 4.48 0.02 1 46 5 5 C H5'' H 4.05 0.02 1 47 5 5 C H6 H 7.71 0.02 1 48 5 5 C C1' C 94.46 0.05 1 49 5 5 C C2' C 75.57 0.05 1 50 5 5 C C3' C 71.89 0.05 1 51 5 5 C C5 C 97.88 0.05 1 52 5 5 C C5' C 63.96 0.05 1 53 5 5 C C6 C 141.23 0.05 1 54 6 6 U H1' H 5.57 0.02 1 55 6 6 U H2' H 4.32 0.02 1 56 6 6 U H3' H 4.49 0.02 1 57 6 6 U H5 H 5.60 0.02 1 58 6 6 U H5' H 4.52 0.02 1 59 6 6 U H5'' H 4.04 0.02 1 60 6 6 U H6 H 7.80 0.02 1 61 6 6 U C1' C 93.54 0.05 1 62 6 6 U C2' C 75.37 0.05 1 63 6 6 U C3' C 72.54 0.05 1 64 6 6 U C5 C 104.30 0.05 1 65 6 6 U C5' C 64.41 0.05 1 66 6 6 U C6 C 142.14 0.05 1 67 7 7 U H1' H 5.72 0.02 1 68 7 7 U H2' H 4.35 0.02 1 69 7 7 U H3' H 4.51 0.02 1 70 7 7 U H5 H 5.37 0.02 1 71 7 7 U H5' H 4.39 0.02 1 72 7 7 U H5'' H 4.07 0.02 1 73 7 7 U H6 H 7.79 0.02 1 74 7 7 U C1' C 92.23 0.05 1 75 7 7 U C2' C 76.02 0.05 1 76 7 7 U C3' C 74.41 0.05 1 77 7 7 U C5 C 103.30 0.05 1 78 7 7 U C5' C 65.57 0.05 1 79 7 7 U C6 C 142.14 0.05 1 80 8 8 G H1' H 5.50 0.02 1 81 8 8 G H2' H 4.59 0.02 1 82 8 8 G H3' H 4.38 0.02 1 83 8 8 G H5' H 4.22 0.02 1 84 8 8 G H5'' H 4.01 0.02 1 85 8 8 G H8 H 7.75 0.02 1 86 8 8 G C1' C 91.28 0.05 1 87 8 8 G C2' C 75.42 0.05 1 88 8 8 G C3' C 71.94 0.05 1 89 8 8 G C5' C 66.99 0.05 1 90 8 8 G C8 C 138.86 0.05 1 91 9 9 C H1' H 5.66 0.02 1 92 9 9 C H2' H 4.39 0.02 1 93 9 9 C H3' H 4.08 0.02 1 94 9 9 C H5 H 5.56 0.02 1 95 9 9 C H5' H 4.04 0.02 1 96 9 9 C H5'' H 3.92 0.02 1 97 9 9 C H6 H 7.49 0.02 1 98 9 9 C C1' C 90.62 0.05 1 99 9 9 C C2' C 76.43 0.05 1 100 9 9 C C3' C 71.12 0.05 1 101 9 9 C C5 C 98.23 0.05 1 102 9 9 C C5' C 67.18 0.05 1 103 9 9 C C6 C 142.75 0.05 1 104 10 10 C H1' H 5.70 0.02 1 105 10 10 C H2' H 4.23 0.02 1 106 10 10 C H3' H 4.31 0.02 1 107 10 10 C H5 H 5.84 0.02 1 108 10 10 C H5' H 3.91 0.02 1 109 10 10 C H5'' H 3.91 0.02 1 110 10 10 C H6 H 7.60 0.02 1 111 10 10 C C1' C 91.23 0.05 1 112 10 10 C C2' C 76.23 0.05 1 113 10 10 C C3' C 71.23 0.05 1 114 10 10 C C5 C 99.04 0.05 1 115 10 10 C C5' C 67.54 0.05 1 116 10 10 C C6 C 143.22 0.05 1 117 11 11 A H1' H 5.82 0.02 1 118 11 11 A H2 H 7.28 0.02 1 119 11 11 A H2' H 4.85 0.02 1 120 11 11 A H3' H 4.52 0.02 1 121 11 11 A H5' H 4.21 0.02 1 122 11 11 A H5'' H 4.16 0.02 1 123 11 11 A H8 H 8.29 0.02 1 124 11 11 A C1' C 89.01 0.05 1 125 11 11 A C2 C 153.35 0.05 1 126 11 11 A C2' C 74.82 0.05 1 127 11 11 A C3' C 71.38 0.05 1 128 11 11 A C5' C 68.50 0.05 1 129 11 11 A C8 C 141.30 0.05 1 130 12 12 A H1' H 5.84 0.02 1 131 12 12 A H2 H 7.54 0.02 1 132 12 12 A H2' H 4.64 0.02 1 133 12 12 A H3' H 4.49 0.02 1 134 12 12 A H5' H 4.42 0.02 1 135 12 12 A H5'' H 4.37 0.02 1 136 12 12 A H8 H 7.91 0.02 1 137 12 12 A C1' C 92.39 0.05 1 138 12 12 A C2 C 153.53 0.05 1 139 12 12 A C2' C 75.42 0.05 1 140 12 12 A C3' C 73.96 0.05 1 141 12 12 A C5' C 67.90 0.05 1 142 12 12 A C8 C 140.13 0.05 1 143 13 13 G H1' H 5.57 0.02 1 144 13 13 G H2' H 4.51 0.02 1 145 13 13 G H3' H 4.40 0.02 1 146 13 13 G H5' H 4.40 0.02 1 147 13 13 G H5'' H 4.08 0.02 1 148 13 13 G H8 H 7.13 0.02 1 149 13 13 G C1' C 92.43 0.05 1 150 13 13 G C2' C 75.37 0.05 1 151 13 13 G C3' C 72.90 0.05 1 152 13 13 G C5' C 65.93 0.05 1 153 13 13 G C8 C 135.76 0.05 1 154 14 14 G H1' H 5.69 0.02 1 155 14 14 G H2' H 4.53 0.02 1 156 14 14 G H3' H 4.34 0.02 1 157 14 14 G H5' H 4.53 0.02 1 158 14 14 G H5'' H 4.31 0.02 1 159 14 14 G H8 H 7.13 0.02 1 160 14 14 G C1' C 92.93 0.05 1 161 14 14 G C2' C 76.38 0.05 1 162 14 14 G C3' C 72.49 0.05 1 163 14 14 G C5' C 65.37 0.05 1 164 14 14 G C8 C 135.76 0.05 1 165 15 15 U H1' H 5.50 0.02 1 166 15 15 U H2' H 4.14 0.02 1 167 15 15 U H3' H 4.51 0.02 1 168 15 15 U H5 H 5.38 0.02 1 169 15 15 U H6 H 7.74 0.02 1 170 15 15 U C1' C 93.65 0.05 1 171 15 15 U C2' C 75.62 0.05 1 172 15 15 U C3' C 72.09 0.05 1 173 15 15 U C5 C 103.90 0.05 1 174 15 15 U C6 C 140.59 0.05 1 175 16 16 C H1' H 5.64 0.02 1 176 16 16 C H2' H 4.20 0.02 1 177 16 16 C H3' H 4.46 0.02 1 178 16 16 C H5 H 5.66 0.02 1 179 16 16 C H5' H 4.51 0.02 1 180 16 16 C H5'' H 4.03 0.02 1 181 16 16 C H6 H 7.95 0.02 1 182 16 16 C C1' C 93.85 0.05 1 183 16 16 C C2' C 75.57 0.05 1 184 16 16 C C3' C 72.19 0.05 1 185 16 16 C C5 C 97.44 0.05 1 186 16 16 C C5' C 64.56 0.05 1 187 16 16 C C6 C 142.61 0.05 1 188 17 17 C H1' H 5.71 0.02 1 189 17 17 C H2' H 3.95 0.02 1 190 17 17 C H3' H 4.11 0.02 1 191 17 17 C H5' H 4.45 0.02 1 192 17 17 C H5'' H 3.99 0.02 1 193 17 17 C H6 H 7.64 0.02 1 194 17 17 C C1' C 92.74 0.05 1 195 17 17 C C2' C 77.63 0.05 1 196 17 17 C C3' C 70.27 0.05 1 197 17 17 C C5' C 65.11 0.05 1 198 17 17 C C6 C 141.91 0.05 1 stop_ save_