data_19873 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; D loop of tRNA(Met) ; _BMRB_accession_number 19873 _BMRB_flat_file_name bmr19873.str _Entry_type original _Submission_date 2014-03-25 _Accession_date 2014-03-25 _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 Eveline Lescrinier . . 2 Natala Dyubankova . . 3 Piet Herdewijn . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 110 "13C chemical shifts" 94 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-04-13 original BMRB . stop_ _Original_release_date 2015-04-13 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Contribution of dihydrouridine in folding of the D-arm in tRNA ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25815904 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Eveline Lescrinier . . 2 Natalia Dyubankova . . 3 Piet Herdewijn . . stop_ _Journal_abbreviation 'Org. Biomol. Chem.' _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 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'D-arm of tRNA(Met)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'D-arm of tRNA(Met)' $D_arm_tRNA(Met) 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_D_arm_tRNA(Met) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common D_arm_tRNA(Met) _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence ; GGAGAGXGGAACUCCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 G 5 A 6 G 7 H2U 8 G 9 G 10 A 11 A 12 C 13 U 14 C 15 C 16 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_H2U _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE _BMRB_code H2U _PDB_code H2U _Standard_residue_derivative . _Molecular_mass 326.197 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C1' C1' C . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? HO2' HO2' H . 0 . ? HN3 HN3 H . 0 . ? H51 H51 H . 0 . ? H52 H52 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB P OP1 ? ? SING P OP2 ? ? SING P OP3 ? ? SING P O5' ? ? SING OP2 HOP2 ? ? SING OP3 HOP3 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C1' C2' ? ? SING C1' N1 ? ? SING C1' H1' ? ? SING C2' O2' ? ? SING C2' H2' ? ? SING O2' HO2' ? ? SING N1 C2 ? ? SING N1 C6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING N3 C4 ? ? SING N3 HN3 ? ? DOUB C4 O4 ? ? SING C4 C5 ? ? SING C5 C6 ? ? SING C5 H51 ? ? SING C5 H52 ? ? SING C6 H61 ? ? SING C6 H62 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $D_arm_tRNA(Met) . . . . . . 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 $D_arm_tRNA(Met) 'chemical synthesis' . . . . . 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 $D_arm_tRNA(Met) 1 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 3.851 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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 . 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 C 13 protons ppm 4.7 internal indirect . . . 0.251449530 water H 1 protons ppm 4.7 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 DQF-COSY' '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' '2D 1H-1H 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 'D-arm of tRNA(Met)' _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 H2' H 4.761 0.02 1 2 1 1 G H3' H 4.436 0.02 1 3 1 1 G H4' H 4.209 0.02 1 4 1 1 G H5' H 3.891 0.02 2 5 1 1 G H5'' H 3.802 0.02 2 6 1 1 G H8 H 7.847 0.02 1 7 1 1 G C2' C 72.339 0.30 1 8 1 1 G C3' C 71.154 0.30 1 9 1 1 G C4' C 81.690 0.30 1 10 1 1 G C5' C 59.630 0.30 1 11 1 1 G C8 C 135.790 0.30 1 12 2 2 G H1' H 5.785 0.02 1 13 2 2 G H2' H 4.574 0.02 1 14 2 2 G H3' H 4.449 0.02 1 15 2 2 G H4' H 4.415 0.02 1 16 2 2 G H5' H 4.469 0.02 2 17 2 2 G H5'' H 4.069 0.02 2 18 2 2 G H8 H 7.373 0.02 1 19 2 2 G C1' C 90.160 0.30 1 20 2 2 G C2' C 72.684 0.30 1 21 2 2 G C3' C 71.204 0.30 1 22 2 2 G C5' C 62.240 0.30 1 23 2 2 G C8 C 133.790 0.30 1 24 3 3 A H1' H 5.860 0.02 1 25 3 3 A H2 H 7.310 0.02 1 26 3 3 A H2' H 4.533 0.02 1 27 3 3 A H3' H 4.562 0.02 1 28 3 3 A H4' H 4.422 0.02 1 29 3 3 A H8 H 7.585 0.02 1 30 3 3 A C1' C 90.210 0.30 1 31 3 3 A C2 C 150.380 0.30 1 32 3 3 A C2' C 72.915 0.30 1 33 3 3 A C3' C 69.872 0.30 1 34 3 3 A C4' C 79.262 0.30 1 35 3 3 A C8 C 136.340 0.30 1 36 4 4 G H1' H 5.469 0.02 1 37 4 4 G H2' H 4.277 0.02 1 38 4 4 G H3' H 4.363 0.02 1 39 4 4 G H4' H 4.363 0.02 1 40 4 4 G H5' H 4.372 0.02 2 41 4 4 G H5'' H 3.964 0.02 2 42 4 4 G H8 H 6.922 0.02 1 43 4 4 G C1' C 89.939 0.30 1 44 4 4 G C2' C 72.892 0.30 1 45 4 4 G C3' C 70.064 0.30 1 46 4 4 G C4' C 79.640 0.30 1 47 4 4 G C5' C 62.844 0.30 1 48 4 4 G C8 C 133.092 0.30 1 49 5 5 A H1' H 5.690 0.02 1 50 5 5 A H2 H 7.908 0.02 1 51 5 5 A H2' H 4.283 0.02 1 52 5 5 A H3' H 4.559 0.02 1 53 5 5 A H4' H 4.313 0.02 1 54 5 5 A H5' H 4.026 0.02 2 55 5 5 A H5'' H 4.286 0.02 2 56 5 5 A H8 H 7.698 0.02 1 57 5 5 A C1' C 89.240 0.30 1 58 5 5 A C2 C 152.378 0.30 1 59 5 5 A C2' C 73.173 0.30 1 60 5 5 A C3' C 71.082 0.30 1 61 5 5 A C4' C 80.293 0.30 1 62 5 5 A C5' C 62.663 0.30 1 63 5 5 A C8 C 136.828 0.30 1 64 6 6 G H1' H 5.428 0.02 1 65 6 6 G H2' H 4.441 0.02 1 66 6 6 G H3' H 4.556 0.02 1 67 6 6 G H4' H 4.266 0.02 1 68 6 6 G H5' H 4.218 0.02 2 69 6 6 G H5'' H 3.991 0.02 2 70 6 6 G H8 H 7.522 0.02 1 71 6 6 G C1' C 87.428 0.30 1 72 6 6 G C2' C 72.632 0.30 1 73 6 6 G C3' C 73.439 0.30 1 74 6 6 G C4' C 81.840 0.30 1 75 6 6 G C5' C 63.940 0.30 1 76 6 6 G C8 C 136.142 0.30 1 77 7 7 H2U C1' C 86.007 0.30 1 78 7 7 H2U C2' C 69.138 0.30 1 79 7 7 H2U C3' C 74.946 0.30 1 80 7 7 H2U C4' C 81.380 0.30 1 81 7 7 H2U C5' C 65.310 0.30 1 82 7 7 H2U H1' H 5.587 0.02 1 83 7 7 H2U H2' H 3.978 0.02 1 84 7 7 H2U H3' H 4.265 0.02 1 85 7 7 H2U H4' H 4.021 0.02 1 86 7 7 H2U H5' H 3.758 0.02 2 87 7 7 H2U H5'' H 3.685 0.02 2 88 7 7 H2U H51 H 2.450 0.02 2 89 7 7 H2U H61 H 3.233 0.02 2 90 8 8 G H1' H 5.494 0.02 1 91 8 8 G H2' H 4.619 0.02 1 92 8 8 G H3' H 4.644 0.02 1 93 8 8 G H4' H 4.134 0.02 1 94 8 8 G H5' H 3.897 0.02 2 95 8 8 G H8 H 7.661 0.02 1 96 8 8 G C1' C 82.254 0.30 1 97 8 8 G C2' C 72.559 0.30 1 98 8 8 G C3' C 74.588 0.30 1 99 8 8 G C4' C 82.360 0.30 1 100 8 8 G C5' C 65.110 0.30 1 101 8 8 G C8 C 137.241 0.30 1 102 9 9 G H1' H 5.594 0.02 1 103 9 9 G H2' H 4.682 0.02 1 104 9 9 G H3' H 4.728 0.02 1 105 9 9 G H4' H 4.386 0.02 1 106 9 9 G H5' H 4.128 0.02 2 107 9 9 G H5'' H 4.035 0.02 2 108 9 9 G H8 H 7.803 0.02 1 109 9 9 G C1' C 87.414 0.30 1 110 9 9 G C2' C 72.605 0.30 1 111 9 9 G C3' C 74.449 0.30 1 112 9 9 G C4' C 82.348 0.30 1 113 9 9 G C5' C 65.260 0.30 1 114 9 9 G C8 C 139.040 0.30 1 115 10 10 A H1' H 5.773 0.02 1 116 10 10 A H2 H 7.770 0.02 1 117 10 10 A H2' H 4.720 0.02 1 118 10 10 A H3' H 4.554 0.02 1 119 10 10 A H4' H 4.413 0.02 1 120 10 10 A H5' H 4.243 0.02 2 121 10 10 A H5'' H 4.144 0.02 2 122 10 10 A H8 H 8.119 0.02 1 123 10 10 A C1' C 87.873 0.30 1 124 10 10 A C2 C 151.280 0.30 1 125 10 10 A C2' C 73.771 0.30 1 126 10 10 A C3' C 73.274 0.30 1 127 10 10 A C4' C 82.053 0.30 1 128 10 10 A C5' C 64.260 0.30 1 129 10 10 A C8 C 138.629 0.30 1 130 11 11 A H1' H 5.848 0.02 1 131 11 11 A H2 H 8.053 0.02 1 132 11 11 A H2' H 4.715 0.02 1 133 11 11 A H3' H 4.529 0.02 1 134 11 11 A H4' H 4.557 0.02 1 135 11 11 A H5' H 4.325 0.02 2 136 11 11 A H5'' H 4.165 0.02 2 137 11 11 A H8 H 8.172 0.02 1 138 11 11 A C1' C 87.848 0.30 1 139 11 11 A C2 C 152.453 0.30 1 140 11 11 A C2' C 73.305 0.30 1 141 11 11 A C3' C 69.925 0.30 1 142 11 11 A C4' C 81.627 0.30 1 143 11 11 A C5' C 64.600 0.30 1 144 11 11 A C8 C 138.002 0.30 1 145 12 12 C H1' H 5.166 0.02 1 146 12 12 C H2' H 4.266 0.02 1 147 12 12 C H3' H 4.358 0.02 1 148 12 12 C H4' H 4.316 0.02 1 149 12 12 C H5 H 5.700 0.02 1 150 12 12 C H5' H 4.286 0.02 2 151 12 12 C H5'' H 4.074 0.02 2 152 12 12 C H6 H 7.697 0.02 1 153 12 12 C C1' C 91.630 0.30 1 154 12 12 C C2' C 72.388 0.30 1 155 12 12 C C3' C 70.334 0.30 1 156 12 12 C C4' C 79.420 0.30 1 157 12 12 C C5 C 95.550 0.30 1 158 12 12 C C5' C 62.670 0.30 1 159 12 12 C C6 C 136.620 0.30 1 160 13 13 U H1' H 5.433 0.02 1 161 13 13 U H2' H 4.413 0.02 1 162 13 13 U H3' H 4.476 0.02 1 163 13 13 U H4' H 4.359 0.02 1 164 13 13 U H5 H 5.350 0.02 1 165 13 13 U H5' H 4.474 0.02 2 166 13 13 U H5'' H 4.016 0.02 2 167 13 13 U H6 H 7.904 0.02 1 168 13 13 U C1' C 91.043 0.30 1 169 13 13 U C2' C 72.376 0.30 1 170 13 13 U C3' C 69.322 0.30 1 171 13 13 U C4' C 79.349 0.30 1 172 13 13 U C5 C 100.340 0.30 1 173 13 13 U C5' C 61.570 0.30 1 174 13 13 U C6 C 135.654 0.30 1 175 14 14 C H1' H 5.478 0.02 1 176 14 14 C H2' H 4.132 0.02 1 177 14 14 C H3' H 4.393 0.02 1 178 14 14 C H4' H 4.331 0.02 1 179 14 14 C H5 H 5.570 0.02 1 180 14 14 C H5' H 4.458 0.02 2 181 14 14 C H5'' H 3.987 0.02 2 182 14 14 C H6 H 7.901 0.02 1 183 14 14 C C1' C 91.388 0.30 1 184 14 14 C C2' C 69.386 0.30 1 185 14 14 C C3' C 72.917 0.30 1 186 14 14 C C4' C 79.101 0.30 1 187 14 14 C C5 C 94.510 0.30 1 188 14 14 C C5' C 61.977 0.30 1 189 14 14 C C6 C 139.663 0.30 1 190 15 15 C H1' H 5.588 0.02 1 191 15 15 C H2' H 3.926 0.02 1 192 15 15 C H3' H 3.982 0.02 1 193 15 15 C H4' H 4.067 0.02 1 194 15 15 C H5 H 5.389 0.02 1 195 15 15 C H5' H 4.446 0.02 2 196 15 15 C H5'' H 3.931 0.02 2 197 15 15 C H6 H 7.555 0.02 1 198 15 15 C C1' C 90.128 0.30 1 199 15 15 C C2' C 74.670 0.30 1 200 15 15 C C3' C 69.131 0.30 1 201 15 15 C C4' C 80.570 0.30 1 202 15 15 C C5 C 95.289 0.30 1 203 15 15 C C5' C 62.310 0.30 1 204 15 15 C C6 C 138.975 0.30 1 stop_ save_