data_17564 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Glycyl-tRNA(UCC)1B anticodon stem-loop from Staphylococcus epidermidis ; _BMRB_accession_number 17564 _BMRB_flat_file_name bmr17564.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" 107 "13C chemical shifts" 87 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-04-04 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17563 'Glycyl-tRNA(GCC) 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-loop' _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 . . 2 Nikonowicz Edward . . 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(UCC)1B anticodon stem-loop' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Glycyl-tRNA(UCC)1B anticodon stem-loop' $RNA 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'Glycyl-tRNA(UCC)1B anticodon stem-loop' _Molecular_mass 5371.249 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence GGGACCUUCCCGGUCUC loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 G 4 A 5 C 6 C 7 U 8 U 9 C 10 C 11 C 12 G 13 G 14 U 15 C 16 U 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 $RNA 'S. epidermidis' 1282 Bacteria . Staphylococcus epidermidis 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 'enzymatic semisynthesis' . Staphylococcus epidermidis . . 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 . 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' MgCl2 10 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 $RNA . mM 0.02 0.04 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' KH2PO4 10 mM . . 'natural abundance' K2HPO4 10 mM . . 'natural abundance' KCl 10 mM . . 'natural abundance' EDTA 0.2 mM . . 'natural abundance' MgCl2 10 mM . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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_ 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_ ######################### # 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 'with 10mM Mg2+' 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_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 water H 1 protons Hz 500 internal direct . . . 1.0 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 $chemical_shift_reference_1 _Mol_system_component_name 'Glycyl-tRNA(UCC)1B anticodon stem-loop' _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 5.52 0.02 1 2 2 2 G H1' H 5.82 0.02 1 3 2 2 G H2' H 4.68 0.02 1 4 2 2 G H3' H 4.57 0.02 1 5 2 2 G H4' H 4.46 0.02 1 6 2 2 G H5' H 4.09 0.02 1 7 2 2 G H5'' H 4.51 0.02 1 8 2 2 G H8 H 7.31 0.02 1 9 2 2 G C1' C 92.92 0.05 1 10 2 2 G C2' C 75.22 0.05 1 11 2 2 G C3' C 72.24 0.05 1 12 2 2 G C4' C 81.89 0.05 1 13 2 2 G C5' C 69.90 0.05 1 14 2 2 G C8 C 137.72 0.05 1 15 3 3 G H1' H 5.67 0.02 1 16 3 3 G H2' H 4.45 0.02 1 17 3 3 G H3' H 4.61 0.02 1 18 3 3 G H4' H 4.45 0.02 1 19 3 3 G H5' H 4.10 0.02 1 20 3 3 G H5'' H 4.48 0.02 1 21 3 3 G H8 H 7.27 0.02 1 22 3 3 G C1' C 92.72 0.05 1 23 3 3 G C2' C 75.35 0.05 1 24 3 3 G C3' C 72.18 0.05 1 25 3 3 G C4' C 81.82 0.05 1 26 3 3 G C5' C 69.63 0.05 1 27 3 3 G C8 C 136.94 0.05 1 28 4 4 A H1' H 5.96 0.02 1 29 4 4 A H2 H 7.78 0.02 1 30 4 4 A H2' H 4.46 0.02 1 31 4 4 A H3' H 4.50 0.02 1 32 4 4 A H4' H 4.46 0.02 1 33 4 4 A H5' H 4.10 0.02 1 34 4 4 A H5'' H 4.56 0.02 1 35 4 4 A H8 H 7.84 0.02 1 36 4 4 A C1' C 92.71 0.05 1 37 4 4 A C2 C 151.98 0.05 1 38 4 4 A C2' C 75.54 0.05 1 39 4 4 A C3' C 72.37 0.05 1 40 4 4 A C4' C 81.82 0.05 1 41 4 4 A C5' C 69.74 0.05 1 42 4 4 A C8 C 139.50 0.05 1 43 5 5 C H1' H 5.35 0.02 1 44 5 5 C H2' H 4.16 0.02 1 45 5 5 C H3' H 4.28 0.02 1 46 5 5 C H4' H 4.36 0.02 1 47 5 5 C H5 H 5.18 0.02 1 48 5 5 C H5' H 4.00 0.02 1 49 5 5 C H5'' H 4.44 0.02 1 50 5 5 C H6 H 7.40 0.02 1 51 5 5 C C1' C 93.64 0.05 1 52 5 5 C C2' C 75.61 0.05 1 53 5 5 C C3' C 72.11 0.05 1 54 5 5 C C4' C 81.62 0.05 1 55 5 5 C C5 C 97.03 0.05 1 56 5 5 C C5' C 69.79 0.05 1 57 5 5 C C6 C 140.55 0.05 1 58 6 6 C H1' H 5.54 0.02 1 59 6 6 C H2' H 4.37 0.02 1 60 6 6 C H3' H 4.29 0.02 1 61 6 6 C H5 H 5.33 0.02 1 62 6 6 C H5' H 4.01 0.02 1 63 6 6 C H5'' H 4.47 0.02 1 64 6 6 C H6 H 7.53 0.02 1 65 6 6 C C1' C 93.64 0.05 1 66 6 6 C C2' C 75.61 0.05 1 67 6 6 C C3' C 72.16 0.05 1 68 6 6 C C5 C 97.92 0.05 1 69 6 6 C C5' C 69.63 0.05 1 70 6 6 C C6 C 141.06 0.05 1 71 7 7 U H1' H 5.64 0.02 1 72 7 7 U H2' H 4.18 0.02 1 73 7 7 U H3' H 4.42 0.02 1 74 7 7 U H4' H 4.29 0.02 1 75 7 7 U H5 H 5.61 0.02 1 76 7 7 U H5' H 4.06 0.02 1 77 7 7 U H5'' H 4.31 0.02 1 78 7 7 U H6 H 7.71 0.02 1 79 7 7 U C1' C 92.48 0.05 1 80 7 7 U C2' C 76.27 0.05 1 81 7 7 U C3' C 73.63 0.05 1 82 7 7 U C4' C 82.94 0.05 1 83 7 7 U C5 C 104.59 0.05 1 84 7 7 U C5' C 70.23 0.05 1 85 8 8 U H1' H 5.54 0.02 1 86 8 8 U H2' H 4.07 0.02 1 87 8 8 U H3' H 4.52 0.02 1 88 8 8 U H4' H 4.33 0.02 1 89 8 8 U H5 H 5.66 0.02 1 90 8 8 U H5' H 4.07 0.02 1 91 8 8 U H5'' H 4.52 0.02 1 92 8 8 U H6 H 7.95 0.02 1 93 8 8 U C1' C 94.24 0.05 1 94 8 8 U C2' C 75.48 0.05 1 95 8 8 U C3' C 72.05 0.05 1 96 8 8 U C4' C 82.02 0.05 1 97 8 8 U C5 C 104.59 0.05 1 98 8 8 U C5' C 64.17 0.05 1 99 8 8 U C6 C 141.41 0.05 1 100 9 9 C H1' H 5.75 0.02 1 101 9 9 C H2' H 3.96 0.02 1 102 9 9 C H3' H 4.16 0.02 1 103 9 9 C H4' H 4.10 0.02 1 104 9 9 C H5 H 5.70 0.02 1 105 9 9 C H5' H 4.00 0.02 1 106 9 9 C H5'' H 4.49 0.02 1 107 9 9 C H6 H 7.82 0.02 1 108 9 9 C C1' C 92.72 0.05 1 109 9 9 C C2' C 77.46 0.05 1 110 9 9 C C3' C 69.40 0.05 1 111 9 9 C C4' C 82.88 0.05 1 112 9 9 C C5 C 98.16 0.05 1 113 9 9 C C5' C 70.23 0.05 1 114 9 9 C C6 C 142.37 0.05 1 115 10 10 C H1' H 5.56 0.02 1 116 10 10 C H2' H 4.53 0.02 1 117 10 10 C H3' H 4.46 0.02 1 118 10 10 C H4' H 4.48 0.02 1 119 10 10 C H5 H 5.62 0.02 1 120 10 10 C H6 H 7.81 0.02 1 121 10 10 C C1' C 93.63 0.05 1 122 10 10 C C2' C 78.57 0.05 1 123 10 10 C C3' C 73.54 0.05 1 124 10 10 C C4' C 82.33 0.05 1 125 10 10 C C5 C 98.28 0.05 1 126 10 10 C C6 C 141.45 0.05 1 127 11 11 C H1' H 5.59 0.02 1 128 11 11 C H2' H 4.40 0.02 1 129 11 11 C H3' H 4.48 0.02 1 130 11 11 C H5 H 5.49 0.02 1 131 11 11 C H6 H 7.68 0.02 1 132 11 11 C C1' C 93.23 0.05 1 133 11 11 C C3' C 71.96 0.05 1 134 11 11 C C5 C 98.16 0.05 1 135 11 11 C C6 C 141.60 0.05 1 136 12 12 G H1' H 5.55 0.02 1 137 12 12 G H2' H 4.56 0.02 1 138 12 12 G H3' H 4.31 0.02 1 139 12 12 G H5' H 4.58 0.02 1 140 12 12 G H5'' H 4.74 0.02 1 141 12 12 G H8 H 7.80 0.02 1 142 12 12 G C1' C 94.03 0.05 1 143 12 12 G C2' C 75.26 0.05 1 144 12 12 G C3' C 72.16 0.05 1 145 12 12 G C5' C 69.69 0.05 1 146 12 12 G C8 C 138.45 0.05 1 147 13 13 G H1' H 5.87 0.02 1 148 13 13 G H2' H 4.44 0.02 1 149 13 13 G H3' H 4.55 0.02 1 150 13 13 G H4' H 4.48 0.02 1 151 13 13 G H5' H 4.08 0.02 1 152 13 13 G H5'' H 4.56 0.02 1 153 13 13 G H8 H 7.46 0.02 1 154 13 13 G C1' C 93.25 0.05 1 155 13 13 G C2' C 75.42 0.05 1 156 13 13 G C3' C 72.44 0.05 1 157 13 13 G C4' C 82.15 0.05 1 158 13 13 G C5' C 69.69 0.05 1 159 13 13 G C8 C 137.48 0.05 1 160 14 14 U H1' H 5.58 0.02 1 161 14 14 U H2' H 4.74 0.02 1 162 14 14 U H3' H 4.48 0.02 1 163 14 14 U H5 H 5.07 0.02 1 164 14 14 U H6 H 7.87 0.02 1 165 14 14 U C1' C 93.23 0.05 1 166 14 14 U C2' C 75.06 0.05 1 167 14 14 U C3' C 74.40 0.05 1 168 14 14 U C5 C 102.27 0.05 1 169 14 14 U C6 C 141.99 0.05 1 170 15 15 C H1' H 5.60 0.02 1 171 15 15 C H2' H 4.58 0.02 1 172 15 15 C H3' H 4.35 0.02 1 173 15 15 C H4' H 4.44 0.02 1 174 15 15 C H5' H 4.58 0.02 1 175 15 15 C H5'' H 4.07 0.02 1 176 15 15 C H6 H 7.70 0.02 1 177 15 15 C C1' C 93.22 0.05 1 178 15 15 C C2' C 75.79 0.05 1 179 15 15 C C3' C 73.01 0.05 1 180 15 15 C C4' C 82.07 0.05 1 181 15 15 C C5' C 64.36 0.05 1 182 16 16 U H1' H 5.62 0.02 1 183 16 16 U H2' H 4.28 0.02 1 184 16 16 U H3' H 4.42 0.02 1 185 16 16 U H5 H 5.75 0.02 1 186 16 16 U H6 H 7.76 0.02 1 187 16 16 U C1' C 92.28 0.05 1 188 16 16 U C5 C 104.65 0.05 1 189 16 16 U C6 C 143.08 0.05 1 190 17 17 C H1' H 5.62 0.02 1 191 17 17 C H2' H 4.25 0.02 1 192 17 17 C H3' H 4.33 0.02 1 193 17 17 C H6 H 7.72 0.02 1 194 17 17 C C1' C 92.95 0.05 1 stop_ save_