data_15319 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR SOLUTION STRUCTURE OF THE ANTICODON OF E.coli TRNA-VAL3 WITH NO MODIFICATIONS ; _BMRB_accession_number 15319 _BMRB_flat_file_name bmr15319.str _Entry_type new _Submission_date 2007-06-20 _Accession_date 2007-06-20 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR 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" 117 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-12 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title 'Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding' _Citation_status published _Citation_type journal _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 _Page_first 6117 _Page_last 6129 _Year 2008 save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Unmodified ASLval3' loop_ _Mol_system_component_name _Mol_label ASLval $RNA_ASLval stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no 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' ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence CCUCCCUUACAAGGAGG 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 A 12 38 A 13 39 G 14 40 G 15 41 A 16 42 G 17 43 G 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_Unmodified_ASLval3_H2O _Saveframe_category sample _Sample_type solution 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_Unmodified_ASLval3_D2O _Saveframe_category sample _Sample_type solution 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 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ save_ save_VNMR _Saveframe_category software _Name VNMR loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ 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_ save_ save_SPARKY _Saveframe_category software _Name SPARKY loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ 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_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $Unmodified_ASLval3_D2O save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $Unmodified_ASLval3_D2O save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $Unmodified_ASLval3_D2O save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $Unmodified_ASLval3_D2O save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $Unmodified_ASLval3_D2O save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $Unmodified_ASLval3_H2O save_ save_2D_1H-31P_HETCOR_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $Unmodified_ASLval3_D2O save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 295 . K pH 6.2 . pH pressure 1 . atm stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.2 . pH temperature 275 . K pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference 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 loop_ _Experiment_label '2D 1H-1H COSY' '2D DQF-COSY' '2D 1H-13C HSQC' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $Unmodified_ASLval3_D2O $Unmodified_ASLval3_H2O stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name ASLval 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 5.576 . 1 2 27 1 C H2' H 4.469 . 1 3 27 1 C H3' H 4.505 . 1 4 27 1 C H4' H 4.353 . 1 5 27 1 C H5 H 6.033 . 1 6 27 1 C H5' H 4.090 . 2 7 27 1 C H5'' H 3.938 . 2 8 27 1 C H6 H 8.177 . 1 9 28 2 C H1' H 5.626 . 1 10 28 2 C H2' H 4.438 . 1 11 28 2 C H3' H 4.635 . 1 12 28 2 C H4' H 4.453 . 1 13 28 2 C H5 H 5.575 . 1 14 28 2 C H6 H 7.375 . 1 15 28 2 C H41 H 7.126 . 1 16 28 2 C H42 H 8.791 . 1 17 29 3 U H1' H 5.575 . 1 18 29 3 U H2' H 4.563 . 1 19 29 3 U H3 H 14.11 . 1 20 29 3 U H3' H 4.427 . 1 21 29 3 U H4' H 4.462 . 1 22 29 3 U H5 H 5.462 . 1 23 29 3 U H6 H 7.975 . 1 24 30 4 C H1' H 5.540 . 1 25 30 4 C H2' H 4.427 . 1 26 30 4 C H3' H 4.448 . 1 27 30 4 C H4' H 4.327 . 1 28 30 4 C H5 H 5.663 . 1 29 30 4 C H6 H 7.903 . 1 30 30 4 C H41 H 7.122 . 1 31 30 4 C H42 H 8.795 . 1 32 31 5 C H1' H 5.380 . 1 33 31 5 C H2' H 4.326 . 1 34 31 5 C H3' H 4.488 . 1 35 31 5 C H4' H 4.352 . 1 36 31 5 C H5 H 5.400 . 1 37 31 5 C H6 H 7.540 . 1 38 31 5 C H41 H 7.012 . 1 39 31 5 C H42 H 8.405 . 1 40 32 6 C H1' H 5.643 . 1 41 32 6 C H2' H 4.363 . 1 42 32 6 C H3' H 4.519 . 1 43 32 6 C H4' H 4.463 . 1 44 32 6 C H5 H 5.683 . 1 45 32 6 C H6 H 7.794 . 1 46 33 7 U H1' H 5.611 . 1 47 33 7 U H2' H 4.197 . 1 48 33 7 U H3' H 4.549 . 1 49 33 7 U H4' H 4.351 . 1 50 33 7 U H5 H 5.613 . 1 51 33 7 U H6 H 7.640 . 1 52 34 8 U H1' H 5.479 . 1 53 34 8 U H2' H 4.552 . 1 54 34 8 U H3' H 4.628 . 1 55 34 8 U H4' H 4.151 . 1 56 34 8 U H5 H 5.641 . 1 57 34 8 U H6 H 7.719 . 1 58 35 9 A H1' H 5.850 . 1 59 35 9 A H2 H 7.926 . 1 60 35 9 A H2' H 4.571 . 1 61 35 9 A H3' H 4.360 . 1 62 35 9 A H4' H 4.151 . 1 63 35 9 A H5' H 4.240 . 2 64 35 9 A H5'' H 4.228 . 2 65 35 9 A H8 H 8.108 . 1 66 36 10 C H1' H 5.385 . 1 67 36 10 C H2' H 4.423 . 1 68 36 10 C H3' H 4.484 . 1 69 36 10 C H5 H 5.401 . 1 70 36 10 C H6 H 7.538 . 1 71 37 11 A H1' H 5.803 . 1 72 37 11 A H2 H 7.813 . 1 73 37 11 A H2' H 4.561 . 1 74 37 11 A H3' H 4.507 . 1 75 37 11 A H4' H 4.427 . 1 76 37 11 A H8 H 8.089 . 1 77 38 12 A H1' H 5.563 . 1 78 38 12 A H2 H 7.947 . 1 79 38 12 A H2' H 4.543 . 1 80 38 12 A H3' H 4.473 . 1 81 38 12 A H4' H 4.443 . 1 82 38 12 A H8 H 7.778 . 1 83 39 13 G H1 H 12.66 . 1 84 39 13 G H1' H 5.162 . 1 85 39 13 G H2' H 4.468 . 1 86 39 13 G H3' H 4.643 . 1 87 39 13 G H4' H 4.325 . 1 88 39 13 G H8 H 6.942 . 1 89 39 13 G H21 H 6.326 . 1 90 39 13 G H22 H 8.284 . 1 91 40 14 G H1 H 12.40 . 1 92 40 14 G H1' H 5.745 . 1 93 40 14 G H2' H 4.551 . 1 94 40 14 G H3' H 4.367 . 1 95 40 14 G H8 H 7.165 . 1 96 40 14 G H21 H 5.968 . 1 97 40 14 G H22 H 8.039 . 1 98 41 15 A H1' H 5.951 . 1 99 41 15 A H2 H 7.546 . 1 100 41 15 A H2' H 4.490 . 1 101 41 15 A H3' H 4.446 . 1 102 41 15 A H8 H 7.683 . 1 103 41 15 A H61 H 7.951 . 1 104 41 15 A H62 H 6.648 . 1 105 42 16 G H1 H 13.20 . 1 106 42 16 G H1' H 5.549 . 1 107 42 16 G H2' H 4.453 . 1 108 42 16 G H3' H 4.290 . 1 109 42 16 G H8 H 7.008 . 1 110 42 16 G H21 H 6.168 . 1 111 42 16 G H22 H 8.592 . 1 112 43 17 G H1 H 13.44 . 1 113 43 17 G H1' H 5.853 . 1 114 43 17 G H2' H 4.022 . 1 115 43 17 G H3' H 4.187 . 1 116 43 17 G H5'' H 3.990 . 2 117 43 17 G H8 H 7.260 . 1 stop_ save_