data_15331 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR SOLUTION STRUCTURE OF THE ANTICODON OF E.coli TRNA-VAL3 WITH 2 MODIFICATIONS (cmo5U34 M6A37) ; _BMRB_accession_number 15331 _BMRB_flat_file_name bmr15331.str _Entry_type original _Submission_date 2007-06-26 _Accession_date 2007-06-26 _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" 122 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-03 update BMRB 'complete entry citation' 2007-08-01 update author 'chemical shift update' 2007-07-26 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 CMO5U E.coli M6A N6-methyladenosine 'RNA HAIRPIN' TRNA 'TRNA DOMAIN' 'URIDINE 5-OXYACETIC ACID' Valine stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name '(cmo5U34 M6A37)-ASL Val3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label ASLval $RNA_ASLval 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_ASLval _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_ASLval _Molecular_mass 5402.314 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence CCUCCCUXACXAGGAGG loop_ _Residue_seq_code _Residue_label 1 C 2 C 3 U 4 C 5 C 6 C 7 U 8 CMO 9 A 10 C 11 6MZ 12 A 13 G 14 G 15 A 16 G 17 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_ASLval . . . . . . 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_ASLval 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_(cmo5U34_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_ASLval . mM 1.5 2 'natural abundance' H2O 90 % . . . D2O 10 % . . . stop_ save_ save_(cmo5U34_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_ASLval . mM 1.5 2 'natural abundance' D2O 100 % . . . 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 $(cmo5U34_M6A37)-ASL_Val3_D2O save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $(cmo5U34_M6A37)-ASL_Val3_D2O save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $(cmo5U34_M6A37)-ASL_Val3_D2O save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $(cmo5U34_M6A37)-ASL_Val3_D2O save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $(cmo5U34_M6A37)-ASL_Val3_D2O save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $(cmo5U34_M6A37)-ASL_Val3_H2O save_ save_2D_1H-31P_HETCOR_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $(cmo5U34_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' stop_ loop_ _Sample_label $(cmo5U34_M6A37)-ASL_Val3_D2O $(cmo5U34_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 5.523 . 1 2 27 1 C H2' H 4.477 . 1 3 27 1 C H3' H 4.503 . 1 4 27 1 C H4' H 4.351 . 1 5 27 1 C H5 H 6.031 . 1 6 27 1 C H6 H 8.145 . 1 7 28 2 C H1' H 5.613 . 1 8 28 2 C H2' H 4.446 . 1 9 28 2 C H3' H 5.623 . 1 10 28 2 C H4' H 4.450 . 1 11 28 2 C H5 H 5.632 . 1 12 28 2 C H6 H 8.053 . 1 13 28 2 C H41 H 7.112 . 1 14 28 2 C H42 H 8.774 . 1 15 29 3 U H1' H 5.552 . 1 16 29 3 U H2' H 4.551 . 1 17 29 3 U H3 H 14.11 . 1 18 29 3 U H3' H 4.455 . 1 19 29 3 U H4' H 4.457 . 1 20 29 3 U H5 H 5.654 . 1 21 29 3 U H5' H 4.103 . 2 22 29 3 U H6 H 7.882 . 1 23 30 4 C H1' H 5.532 . 1 24 30 4 C H2' H 4.324 . 1 25 30 4 C H3' H 4.435 . 1 26 30 4 C H4' H 4.314 . 1 27 30 4 C H5 H 5.652 . 1 28 30 4 C H6 H 7.882 . 1 29 30 4 C H41 H 7.020 . 1 30 30 4 C H42 H 8.382 . 1 31 31 5 C H1' H 5.528 . 1 32 31 5 C H2' H 4.502 . 1 33 31 5 C H3' H 4.352 . 1 34 31 5 C H4' H 4.345 . 1 35 31 5 C H5 H 5.520 . 1 36 31 5 C H6 H 7.512 . 1 37 31 5 C H41 H 7.032 . 1 38 31 5 C H42 H 8.292 . 1 39 32 6 C H1' H 5.697 . 1 40 32 6 C H2' H 4.354 . 1 41 32 6 C H3' H 4.483 . 1 42 32 6 C H4' H 4.461 . 1 43 32 6 C H5 H 5.745 . 1 44 32 6 C H6 H 7.794 . 1 45 33 7 U H1' H 5.593 . 1 46 33 7 U H2' H 4.062 . 1 47 33 7 U H3' H 4.504 . 1 48 33 7 U H4' H 4.349 . 1 49 33 7 U H5 H 5.607 . 1 50 33 7 U H6 H 7.592 . 1 51 34 8 CMO H1' H 5.396 . 1 52 34 8 CMO H2' H 4.643 . 1 53 34 8 CMO H3' H 4.675 . 1 54 34 8 CMO H4' H 4.286 . 1 55 34 8 CMO H7 H 4.292 . 2 56 34 8 CMO H5' H 4.197 . 2 57 34 8 CMO H5'' H 4.398 . 2 58 34 8 CMO H6 H 7.316 . 1 59 35 9 A H1' H 5.890 . 1 60 35 9 A H2 H 7.865 . 1 61 35 9 A H2' H 4.505 . 1 62 35 9 A H3' H 4.364 . 1 63 35 9 A H4' H 4.268 . 1 64 35 9 A H8 H 8.162 . 1 65 36 10 C H1' H 5.421 . 1 66 36 10 C H2' H 4.437 . 1 67 36 10 C H3' H 4.369 . 1 68 36 10 C H4' H 4.534 . 1 69 36 10 C H5 H 5.385 . 1 70 36 10 C H6 H 7.282 . 1 71 37 11 6MZ H1' H 5.757 . 1 72 37 11 6MZ H2' H 4.426 . 1 73 37 11 6MZ H3' H 4.342 . 1 74 37 11 6MZ H4' H 4.338 . 1 75 37 11 6MZ H2 H 7.702 . 1 76 37 11 6MZ H8 H 7.975 . 1 77 37 11 6MZ H71 H 2.532 . 2 78 37 11 6MZ H72 H 2.532 . 2 79 37 11 6MZ H73 H 2.532 . 2 80 38 12 A H1' H 5.603 . 1 81 38 12 A H2 H 7.922 . 1 82 38 12 A H2' H 4.501 . 1 83 38 12 A H3' H 4.376 . 1 84 38 12 A H4' H 4.325 . 1 85 38 12 A H5' H 4.202 . 2 86 38 12 A H5'' H 4.197 . 2 87 38 12 A H8 H 7.766 . 1 88 39 13 G H1 H 12.63 . 1 89 39 13 G H1' H 4.964 . 1 90 39 13 G H2' H 4.475 . 1 91 39 13 G H3' H 4.342 . 1 92 39 13 G H8 H 6.942 . 1 93 39 13 G H21 H 6.222 . 1 94 39 13 G H22 H 8.282 . 1 95 40 14 G H1 H 12.45 . 1 96 40 14 G H1' H 5.743 . 1 97 40 14 G H2' H 4.537 . 1 98 40 14 G H3' H 4.569 . 1 99 40 14 G H8 H 7.162 . 1 100 40 14 G H21 H 5.946 . 1 101 40 14 G H22 H 8.049 . 1 102 41 15 A H1' H 5.946 . 1 103 41 15 A H2 H 7.492 . 1 104 41 15 A H2' H 4.464 . 1 105 41 15 A H3' H 4.535 . 1 106 41 15 A H8 H 7.671 . 1 107 41 15 A H61 H 7.868 . 1 108 41 15 A H62 H 6.652 . 1 109 42 16 G H1 H 13.17 . 1 110 42 16 G H1' H 5.538 . 1 111 42 16 G H2' H 4.455 . 1 112 42 16 G H3' H 4.288 . 1 113 42 16 G H8 H 6.985 . 1 114 42 16 G H21 H 6.127 . 1 115 42 16 G H22 H 8.531 . 1 116 43 17 G H1 H 13.45 . 1 117 43 17 G H1' H 5.842 . 1 118 43 17 G H2' H 4.054 . 1 119 43 17 G H3' H 4.182 . 1 120 43 17 G H5' H 3.980 . 2 121 43 17 G H5'' H 4.001 . 1 122 43 17 G H8 H 7.260 . 1 stop_ save_