data_15342 ####################### # 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 (cmo5U34) ; _BMRB_accession_number 15342 _BMRB_flat_file_name bmr15342.str _Entry_type original _Submission_date 2007-06-28 _Accession_date 2007-06-28 _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" 124 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-03 update BMRB 'complete entry citation' 2007-07-30 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 '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)-ASL Val3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label ASLval $RNA_CCUCCCUXACAAGGAGG 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_CCUCCCUXACAAGGAGG _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_CCUCCCUXACAAGGAGG _Molecular_mass 5402.314 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence CCUCCCUXACAAGGAGG 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 CM0 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_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_CM0 _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common '5-(CARBOXYMETHOXY) URIDINE-5'-MONOPHOSPHATE' _BMRB_code . _PDB_code CM0 _Standard_residue_derivative CM0 _Molecular_mass 398.217 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jun 21 19:09:27 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 . ? C7 C7 C N 0 . ? C8 C8 C N 0 . ? H1' H1' H N 0 . ? H2' H2' H N 0 . ? H2P H2P H N 0 . ? H3 H3 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 . ? H7C1 H7C1 H N 0 . ? H7C2 H7C2 H N 0 . ? H8 H8 H N 0 . ? HA HA H N 0 . ? HB HB H N 0 . ? N1 N1 N N 0 . ? N3 N3 N N 0 . ? O1P O1P O N 0 . ? O2 O2 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 . ? O4' O4' O N 0 . ? O5 O5 O N 0 . ? O5' O5' O N 0 . ? O8 O8 O N 0 . ? O9 O9 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 P O5' ? ? SING P O3P ? ? SING O5' C5' ? ? DOUB P O1P ? ? SING P O2P ? ? SING C3' C4' ? ? SING C5' C4' ? ? SING N1 C2 ? ? SING C4' O4' ? ? SING C3' C2' ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING C5 C4 ? ? SING N3 C4 ? ? DOUB C4 O4 ? ? DOUB C5 C6 ? ? SING N1 C6 ? ? SING C7 C8 ? ? SING C5 O5 ? ? SING C7 O5 ? ? SING C8 O8 ? ? SING N1 C1' ? ? SING C2' C1' ? ? SING O4' C1' ? ? SING C2' O2' ? ? DOUB C8 O9 ? ? SING C3' O3' ? ? SING O2P H2P ? ? SING O3P H3P ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C4' H4' ? ? SING C3' H3' ? ? SING C1' H1' ? ? SING C2' H2' ? ? SING C6 H6 ? ? SING N3 H3 ? ? SING C7 H7C1 ? ? SING C7 H7C2 ? ? SING O8 H8 ? ? SING O2' HA ? ? SING O3' HB ? ? 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_CCUCCCUXACAAGGAGG . . . . . . 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_CCUCCCUXACAAGGAGG 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_(cmo5U34)-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_CCUCCCUXACAAGGAGG . mM 1.5 2 'natural abundance' stop_ save_ save_(cmo5U34)-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_CCUCCCUXACAAGGAGG . 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 $(cmo5U34)-ASL_Val3_D2O save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $(cmo5U34)-ASL_Val3_D2O save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $(cmo5U34)-ASL_Val3_D2O save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $(cmo5U34)-ASL_Val3_D2O save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $(cmo5U34)-ASL_Val3_D2O save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $(cmo5U34)-ASL_Val3_H2O save_ save_2D_1H-31P_HETCOR_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $(cmo5U34)-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 1H-1H NOESY' stop_ loop_ _Sample_label $(cmo5U34)-ASL_Val3_D2O $(cmo5U34)-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 . . 2 27 1 C H2' H 4.474 . . 3 27 1 C H3' H 4.501 . . 4 27 1 C H4' H 4.352 . . 5 27 1 C H5 H 6.033 . . 6 27 1 C H5' H 4.076 . . 7 27 1 C H5'' H 4.915 . . 8 27 1 C H6 H 8.147 . . 9 28 2 C H1' H 5.621 . . 10 28 2 C H2' H 4.434 . . 11 28 2 C H3' H 4.628 . . 12 28 2 C H4' H 4.442 . . 13 28 2 C H5 H 5.633 . . 14 28 2 C H6 H 8.055 . . 15 28 2 C H41 H 7.137 . . 16 28 2 C H42 H 8.794 . . 17 29 3 U H1' H 5.569 . . 18 29 3 U H2' H 4.565 . . 19 29 3 U H3 H 14.09 . . 20 29 3 U H3' H 4.463 . . 21 29 3 U H4' H 4.452 . . 22 29 3 U H5 H 5.458 . . 23 29 3 U H6 H 7.961 . . 24 30 4 C H1' H 5.535 . . 25 30 4 C H2' H 4.316 . . 26 30 4 C H3' H 4.434 . . 27 30 4 C H4' H 4.315 . . 28 30 4 C H5 H 5.662 . . 29 30 4 C H6 H 7.891 . . 30 30 4 C H41 H 7.024 . . 31 30 4 C H42 H 8.415 . . 32 31 5 C H1' H 5.392 . . 33 31 5 C H2' H 4.493 . . 34 31 5 C H3' H 4.479 . . 35 31 5 C H4' H 4.367 . . 36 31 5 C H5 H 6.475 . . 37 31 5 C H6 H 7.531 . . 38 31 5 C H41 H 6.980 . . 39 31 5 C H42 H 8.314 . . 40 32 6 C H1' H 5.645 . . 41 32 6 C H2' H 4.362 . . 42 32 6 C H3' H 4.505 . . 43 32 6 C H4' H 4.443 . . 44 32 6 C H5 H 5.697 . . 45 32 6 C H6 H 7.772 . . 46 33 7 U H1' H 5.616 . . 47 33 7 U H2' H 4.155 . . 48 33 7 U H3' H 4.579 . . 49 33 7 U H4' H 4.347 . . 50 33 7 U H5 H 5.594 . . 51 33 7 U H6 H 7.635 . . 52 34 8 CM0 H1' H 5.433 . . 53 34 8 CM0 H2' H 4.645 . . 54 34 8 CM0 H3' H 4.662 . . 55 34 8 CM0 H4' H 4.226 . . 56 34 8 CM0 H5' H 4.185 . . 57 34 8 CM0 H5'' H 4.035 . . 58 34 8 CM0 H6 H 7.318 . . 59 34 8 CM0 H7 H 4.235 . . 60 34 8 CM0 H8 H 4.235 . . 61 35 9 A H1' H 5.872 . . 62 35 9 A H2 H 7.842 . . 63 35 9 A H2' H 4.545 . . 64 35 9 A H3' H 4.381 . . 65 35 9 A H4' H 4.236 . . 66 35 9 A H8 H 8.173 . . 67 36 10 C H1' H 5.603 . . 68 36 10 C H2' H 4.425 . . 69 36 10 C H3' H 4.507 . . 70 36 10 C H4' H 4.572 . . 71 36 10 C H5 H 5.638 . . 72 36 10 C H6 H 7.524 . . 73 37 11 A H1' H 5.833 . . 74 37 11 A H2 H 7.745 . . 75 37 11 A H2' H 4.557 . . 76 37 11 A H3' H 4.516 . . 77 37 11 A H4' H 4.419 . . 78 37 11 A H5' H 4.396 . . 79 37 11 A H5'' H 4.222 . . 80 37 11 A H8 H 8.091 . . 81 38 12 A H1' H 5.832 . . 82 38 12 A H2 H 8.015 . . 83 38 12 A H2' H 4.553 . . 84 38 12 A H3' H 4.469 . . 85 38 12 A H4' H 4.453 . . 86 38 12 A H8 H 7.773 . . 87 39 13 G H1 H 12.65 . . 88 39 13 G H1' H 5.135 . . 89 39 13 G H2' H 4.479 . . 90 39 13 G H3' H 4.651 . . 91 39 13 G H4' H 4.332 . . 92 39 13 G H5' H 4.025 . . 93 39 13 G H5'' H 3.998 . . 94 39 13 G H8 H 6.936 . . 95 39 13 G H21 H 6.214 . . 96 39 13 G H22 H 8.318 . . 97 40 14 G H1 H 12.40 . . 98 40 14 G H1' H 5.737 . . 99 40 14 G H2' H 4.535 . . 100 40 14 G H3' H 4.369 . . 101 40 14 G H8 H 7.162 . . 102 40 14 G H21 H 5.953 . . 103 40 14 G H22 H 8.035 . . 104 41 15 A H1' H 5.951 . . 105 41 15 A H2 H 7.514 . . 106 41 15 A H2' H 4.485 . . 107 41 15 A H3' H 4.461 . . 108 41 15 A H8 H 7.683 . . 109 41 15 A H61 H 7.946 . . 110 41 15 A H62 H 6.654 . . 111 42 16 G H1 H 13.19 . . 112 42 16 G H1' H 5.535 . . 113 42 16 G H2' H 4.459 . . 114 42 16 G H3' H 4.297 . . 115 42 16 G H5' H 3.992 . . 116 42 16 G H5'' H 3.975 . . 117 42 16 G H8 H 6.995 . . 118 42 16 G H21 H 6.153 . . 119 42 16 G H22 H 8.604 . . 120 43 17 G H1 H 13.44 . . 121 43 17 G H1' H 5.846 . . 122 43 17 G H2' H 4.022 . . 123 43 17 G H3' H 4.185 . . 124 43 17 G H8 H 7.241 . . stop_ save_