data_15362 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR SOLUTION STRUCTURE OF THE ANTICODON OF E.coli TRNA-VAL3 WITH 1 MODIFICATION (M6A37) ; _BMRB_accession_number 15362 _BMRB_flat_file_name bmr15362.str _Entry_type original _Submission_date 2007-07-04 _Accession_date 2007-07-04 _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 Vendeix Franck 'A. P.' . 2 Dziergowska Agnieszka . . 3 Gustilo Estella M. . 4 Graham William D. . 5 Sproat Brian . . 6 Malkiewicz Andrzej . . 7 Agris Paul F. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 120 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-03 update BMRB 'complete entry citation' 2007-07-27 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18473483 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Vendeix Franck 'A. P.' . 2 Dziergowska Agnieszka . . 3 Gustilo Estella M. . 4 Graham William D. . 5 Sproat Brian . . 6 Malkiewicz Andrzej . . 7 Agris Paul F. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 47 _Journal_issue 23 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6117 _Page_last 6129 _Year 2008 _Details . loop_ _Keyword 'ANTICODON STEM LOOP' ASL E.coli M6A N6-methyladenosine 'RNA HAIRPIN' TRNA 'TRNA DOMAIN' Valine stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name '(M6A37)-ASL Val3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label ASLval $RNA_CCUCCCUUAC6MZAGGAGG 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_CCUCCCUUAC6MZAGGAGG _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_CCUCCCUUAC6MZAGGAGG _Molecular_mass 5402.314 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence CCUCCCUUACXAGGAGG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 27 C 2 28 C 3 29 U 4 30 C 5 31 C 6 32 C 7 33 U 8 34 U 9 35 A 10 36 C 11 37 6MZ 12 38 A 13 39 G 14 40 G 15 41 A 16 42 G 17 43 G stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_6MZ _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common N6-METHYLADENOSINE-5'-MONOPHOSPHATE _BMRB_code . _PDB_code 6MZ _Standard_residue_derivative 6MZ _Molecular_mass 361.248 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jun 21 17:08:43 2007 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1' C1' C N 0 . ? C2 C2 C N 0 . ? C2' C2' C N 0 . ? C3' C3' C N 0 . ? C4 C4 C N 0 . ? C4' C4' C N 0 . ? C5 C5 C N 0 . ? C5' C5' C N 0 . ? C6 C6 C N 0 . ? C8 C8 C N 0 . ? C9 C9 C N 0 . ? H1' H1' H N 0 . ? H1P H1P H N 0 . ? H2 H2 H N 0 . ? H2' H2' H N 0 . ? H3' H3' H N 0 . ? H3P H3P H N 0 . ? H4' H4' H N 0 . ? H5'1 H5'1 H N 0 . ? H5'2 H5'2 H N 0 . ? H6 H6 H N 0 . ? H8 H8 H N 0 . ? H9 H9 H N 0 . ? H9C1 H9C1 H N 0 . ? H9C2 H9C2 H N 0 . ? HA HA H N 0 . ? HB HB H N 0 . ? N1 N1 N N 0 . ? N3 N3 N N 0 . ? N6 N6 N N 0 . ? N7 N7 N N 0 . ? N9 N9 N N 0 . ? O1P O1P O N 0 . ? O2' O2' O N 0 . ? O2P O2P O N 0 . ? O3' O3' O N 0 . ? O3P O3P O N 0 . ? O4' O4' O N 0 . ? O5' O5' O N 0 . ? P P P N 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 SING C4 C5 ? ? SING C4 N9 ? ? SING C2 N3 ? ? DOUB C4 N3 ? ? DOUB C2 N1 ? ? DOUB C5 C6 ? ? SING N1 C6 ? ? SING C6 N6 ? ? SING N6 C9 ? ? SING C5 N7 ? ? SING N9 C8 ? ? DOUB N7 C8 ? ? SING O5' C5' ? ? SING C1' H1' ? ? SING C9 H9C1 ? ? SING C9 H9C2 ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C4' H4' ? ? SING C3' H3' ? ? SING C2' H2' ? ? SING O2' HA ? ? SING O3' HB ? ? SING O3P H3P ? ? SING C5' C4' ? ? SING C4' O4' ? ? SING N9 C1' ? ? SING O4' C1' ? ? SING C1' C2' ? ? SING C2' O2' ? ? SING C4' C3' ? ? SING C2' C3' ? ? SING C3' O3' ? ? SING O1P P ? ? DOUB O2P P ? ? SING O5' P ? ? SING P O3P ? ? SING C2 H2 ? ? SING O1P H1P ? ? SING C8 H8 ? ? SING N6 H6 ? ? SING C9 H9 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $RNA_CCUCCCUUAC6MZAGGAGG . . . . . . 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_CCUCCCUUAC6MZAGGAGG 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_(M6A37)-ASL_Val3_H2O _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_CCUCCCUUAC6MZAGGAGG . mM 1.5 2 'natural abundance' stop_ save_ save_(M6A37)-ASL_Val3_D2O _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_CCUCCCUUAC6MZAGGAGG . mM 1.5 2 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version 3.0 loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . 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 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-1H_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $(M6A37)-ASL_Val3_D2O save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $(M6A37)-ASL_Val3_D2O save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $(M6A37)-ASL_Val3_D2O save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $(M6A37)-ASL_Val3_D2O save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $(M6A37)-ASL_Val3_D2O save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $(M6A37)-ASL_Val3_H2O save_ save_2D_1H-31P_HETCOR_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $(M6A37)-ASL_Val3_D2O save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.2 . pH pressure 1 . atm temperature 295 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.2 . pH pressure 1 . atm temperature 275 . 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 ppm 4.776 na direct . . . 1 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-1H COSY' '2D DQF-COSY' '2D 1H-13C HSQC' '2D 1H-1H NOESY' '2D 1H-31P HETCOR' stop_ loop_ _Sample_label $(M6A37)-ASL_Val3_D2O $(M6A37)-ASL_Val3_H2O stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name ASLval _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 27 1 C H1' H 5.570 . 1 2 27 1 C H2' H 4.475 . 1 3 27 1 C H3' H 4.519 . 1 4 27 1 C H4' H 4.363 . 1 5 27 1 C H5 H 5.642 . 1 6 27 1 C H5' H 4.086 . 2 7 27 1 C H5'' H 3.925 . 2 8 27 1 C H6 H 8.174 . 1 9 28 2 C H1' H 5.627 . 1 10 28 2 C H2' H 4.421 . 1 11 28 2 C H3' H 4.616 . 1 12 28 2 C H4' H 4.441 . 1 13 28 2 C H5 H 5.643 . 1 14 28 2 C H6 H 8.060 . 1 15 28 2 C H41 H 7.125 . 1 16 28 2 C H42 H 8.804 . 1 17 29 3 U H1' H 5.557 . 1 18 29 3 U H2' H 4.579 . 1 19 29 3 U H3 H 14.13 . 1 20 29 3 U H3' H 4.452 . 1 21 29 3 U H4' H 4.455 . 1 22 29 3 U H5 H 5.661 . 1 23 29 3 U H6 H 7.966 . 1 24 30 4 C H1' H 5.521 . 1 25 30 4 C H2' H 4.328 . 1 26 30 4 C H3' H 4.442 . 1 27 30 4 C H4' H 4.430 . 1 28 30 4 C H5 H 5.661 . 1 29 30 4 C H6 H 7.885 . 1 30 30 4 C H41 H 7.054 . 1 31 30 4 C H42 H 8.298 . 1 32 31 5 C H1' H 5.392 . 1 33 31 5 C H2' H 4.526 . 1 34 31 5 C H3' H 4.347 . 1 35 31 5 C H4' H 4.365 . 1 36 31 5 C H5 H 5.390 . 1 37 31 5 C H6 H 7.516 . 1 38 31 5 C H41 H 7.054 . 1 39 31 5 C H42 H 8.291 . 1 40 32 6 C H1' H 5.682 . 1 41 32 6 C H2' H 4.343 . 1 42 32 6 C H3' H 4.519 . 1 43 32 6 C H4' H 4.485 . 1 44 32 6 C H5 H 5.714 . 1 45 32 6 C H6 H 7.782 . 1 46 33 7 U H1' H 5.603 . 1 47 33 7 U H2' H 4.117 . 1 48 33 7 U H3' H 4.496 . 1 49 33 7 U H4' H 4.372 . 1 50 33 7 U H5 H 5.614 . 1 51 33 7 U H6 H 7.581 . 1 52 34 8 U H1' H 5.385 . 1 53 34 8 U H2' H 4.196 . 1 54 34 8 U H3' H 4.464 . 1 55 34 8 U H4' H 4.221 . 1 56 34 8 U H5 H 5.585 . 1 57 34 8 U H5' H 4.147 . 2 58 34 8 U H5'' H 4.393 . 2 59 34 8 U H6 H 7.729 . 1 60 35 9 A H1' H 5.895 . 1 61 35 9 A H2 H 7.952 . 1 62 35 9 A H2' H 4.524 . 1 63 35 9 A H3' H 4.881 . 1 64 35 9 A H4' H 4.326 . 1 65 35 9 A H8 H 8.219 . 1 66 36 10 C H1' H 5.427 . 1 67 36 10 C H2' H 4.442 . 1 68 36 10 C H3' H 4.374 . 1 69 36 10 C H4' H 4.533 . 1 70 36 10 C H5 H 5.531 . 1 71 36 10 C H6 H 7.326 . 1 72 37 11 6MZ H1' H 5.763 . 1 73 37 11 6MZ H2 H 7.729 . 1 74 37 11 6MZ H2' H 4.455 . 1 75 37 11 6MZ H3' H 4.348 . 1 76 37 11 6MZ H4' H 4.493 . 1 77 37 11 6MZ H8 H 7.961 . 1 78 37 11 6MZ H71 H 2.534 . 2 79 37 11 6MZ H72 H 2.534 . 2 80 37 11 6MZ H73 H 2.534 . 2 81 38 12 A H1' H 5.605 . 1 82 38 12 A H2 H 7.981 . 1 83 38 12 A H2' H 4.598 . 1 84 38 12 A H3' H 4.376 . 1 85 38 12 A H4' H 4.327 . 1 86 38 12 A H8 H 7.983 . 1 87 39 13 G H1 H 12.67 . 1 88 39 13 G H1' H 4.956 . 1 89 39 13 G H2' H 4.462 . 1 90 39 13 G H3' H 4.332 . 1 91 39 13 G H8 H 6.881 . 1 92 39 13 G H21 H 6.225 . 1 93 39 13 G H22 H 8.294 . 1 94 40 14 G H1 H 12.48 . 1 95 40 14 G H1' H 5.745 . 1 96 40 14 G H2' H 4.533 . 1 97 40 14 G H3' H 4.561 . 1 98 40 14 G H8 H 7.173 . 1 99 40 14 G H21 H 5.982 . 1 100 40 14 G H22 H 8.053 . 1 101 41 15 A H1' H 5.944 . 1 102 41 15 A H2 H 7.504 . 1 103 41 15 A H2' H 4.557 . 1 104 41 15 A H3' H 4.532 . 1 105 41 15 A H5' H 3.983 . 2 106 41 15 A H8 H 7.672 . 1 107 41 15 A H61 H 7.966 . 1 108 41 15 A H62 H 6.645 . 1 109 42 16 G H1 H 13.22 . 1 110 42 16 G H1' H 5.568 . 1 111 42 16 G H2' H 4.472 . 1 112 42 16 G H3' H 4.291 . 1 113 42 16 G H8 H 6.997 . 1 114 42 16 G H21 H 6.155 . 1 115 42 16 G H22 H 8.583 . 1 116 43 17 G H1 H 13.46 . 1 117 43 17 G H1' H 5.856 . 1 118 43 17 G H2' H 4.021 . 1 119 43 17 G H3' H 4.189 . 1 120 43 17 G H8 H 7.253 . 1 stop_ save_