data_17573 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR ; _BMRB_accession_number 17573 _BMRB_flat_file_name bmr17573.str _Entry_type original _Submission_date 2011-04-05 _Accession_date 2011-04-05 _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 Denmon Andria P . 2 Wang Jiachen . . 3 Nikonowicz Edward P . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 75 "13C chemical shifts" 38 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-03-08 update BMRB 'update entry citation' 2011-08-02 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 17517 'Pseudouridine ASL_Tyr' 17520 'unmodified ASL_Tyr' 17572 'i6A37 tyrASL' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Conformation effects of base modification on the anticodon stem-loop of Bacillus subtilis tRNA(Tyr).' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21782828 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Denmon Andria P. . 2 Wang Jiachen . . 3 Nikonowicz Edward P. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of molecular biology' _Journal_volume 412 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 285 _Page_last 303 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Anticodon Stem-loop (coi6y)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label coi6y $coi6y 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_coi6y _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common coi6y _Molecular_mass 417.358 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence GGGGACUGUAXAXCCCC loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 G 4 G 5 A 6 C 7 U 8 G 9 U 10 A 11 6IA 12 A 13 PSU 14 C 15 C 16 C 17 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_6IA _Saveframe_category polymer_residue _Mol_type 'RNA linking' _Name_common N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE _BMRB_code . _PDB_code 6IA _Standard_residue_derivative . _Molecular_mass 417.354 _Mol_paramagnetic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Apr 8 15:04:03 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons OP3 OP3 O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 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 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? N6 N6 N . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C12 C12 C . 0 . ? C13 C13 C . 0 . ? C14 C14 C . 0 . ? C15 C15 C . 0 . ? C16 C16 C . 0 . ? HOP3 HOP3 H . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? HO2' HO2' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? HN6 HN6 H . 0 . ? H2 H2 H . 0 . ? H121 H121 H . 0 . ? H122 H122 H . 0 . ? H131 H131 H . 0 . ? H132 H132 H . 0 . ? H14 H14 H . 0 . ? H151 H151 H . 0 . ? H152 H152 H . 0 . ? H153 H153 H . 0 . ? H161 H161 H . 0 . ? H162 H162 H . 0 . ? H163 H163 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 SING OP3 P ? ? SING OP3 HOP3 ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING OP2 HOP2 ? ? 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 C2' O2' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING O2' HO2' ? ? SING C1' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? SING C6 N6 ? ? DOUB C6 N1 ? ? SING N6 C12 ? ? SING N6 HN6 ? ? SING N1 C2 ? ? DOUB C2 N3 ? ? SING C2 H2 ? ? SING N3 C4 ? ? SING C12 C13 ? ? SING C12 H121 ? ? SING C12 H122 ? ? SING C13 C14 ? ? SING C13 H131 ? ? SING C13 H132 ? ? SING C14 C15 ? ? SING C14 C16 ? ? SING C14 H14 ? ? SING C15 H151 ? ? SING C15 H152 ? ? SING C15 H153 ? ? SING C16 H161 ? ? SING C16 H162 ? ? SING C16 H163 ? ? stop_ save_ save_chem_comp_PSU _Saveframe_category polymer_residue _Mol_type 'RNA linking' _Name_common PSEUDOURIDINE-5'-MONOPHOSPHATE _BMRB_code . _PDB_code PSU _Standard_residue_derivative . _Molecular_mass 324.181 _Mol_paramagnetic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Apr 8 11:51:04 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O2 O2 O . 0 . ? O4 O4 O . 0 . ? C1' C1' C . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? C3' C3' C . 0 . ? C4' C4' C . 0 . ? O3' O3' O . 0 . ? O4' O4' O . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? HN1 HN1 H . 0 . ? HN3 HN3 H . 0 . ? H6 H6 H . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? HO2' HO2' H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? HO3' HO3' H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 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 SING N1 C2 ? ? SING N1 C6 ? ? SING N1 HN1 ? ? SING C2 N3 ? ? DOUB C2 O2 ? ? SING N3 C4 ? ? SING N3 HN3 ? ? SING C4 C5 ? ? DOUB C4 O4 ? ? DOUB C5 C6 ? ? SING C5 C1' ? ? SING C6 H6 ? ? SING C1' C2' ? ? SING C1' O4' ? ? SING C1' H1' ? ? SING C2' O2' ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING O2' HO2' ? ? SING C3' C4' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING C4' H4' ? ? SING O3' HO3' ? ? SING C5' O5' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING O5' P ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING OP3 HOP3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $coi6y 'B. subtilis' 1423 Bacteria . Bacillus subtilis stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name _Details $coi6y 'enzymatic semisynthesis' . cell free . n/a n/a 'molecule was made using T7 polymerase and primers' 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 $coi6y 2.0 mM 'natural abundance' 'potassium chloride' 10 mM 'natural abundance' EDTA 0.02 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_Felix _Saveframe_category software _Name FELIX _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'data analysis' processing stop_ _Details . save_ save_InsightII _Saveframe_category software _Name InsightII _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _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_Natural_abundance_2D_1H-13C_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'Natural abundance 2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _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 6.3 . 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 4.17 internal direct . . . 1.0 water H 1 protons ppm 4.17 internal direct . . . 1.0 water N 15 protons ppm 4.17 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 'Natural abundance 2D 1H-13C HSQC' '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 coi6y _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 H1' H 5.69 0.03 1 2 1 1 G H8 H 7.88 0.03 1 3 1 1 G HO2' H 4.40 0.03 1 4 1 1 G C1' C 92.22 0.03 1 5 2 2 G H1' H 5.89 0.03 1 6 2 2 G H8 H 7.58 0.03 1 7 2 2 G HO2' H 4.59 0.03 1 8 2 2 G C1' C 91.57 0.03 1 9 2 2 G C8 C 137.11 0.03 1 10 3 3 G H1' H 5.81 0.03 1 11 3 3 G H3' H 4.53 0.03 1 12 3 3 G H8 H 7.30 0.03 1 13 3 3 G HO2' H 4.59 0.03 1 14 3 3 G C1' C 91.53 0.03 1 15 3 3 G C8 C 136.35 0.03 1 16 4 4 G H1' H 5.75 0.03 1 17 4 4 G H5'' H 4.05 0.03 1 18 4 4 G H8 H 7.21 0.03 1 19 4 4 G HO2' H 4.48 0.03 1 20 4 4 G C8 C 136.50 0.03 1 21 5 5 A H1' H 6.03 0.03 1 22 5 5 A H2 H 7.95 0.03 1 23 5 5 A H3' H 4.43 0.03 1 24 5 5 A H5' H 4.05 0.03 1 25 5 5 A H8 H 7.76 0.03 1 26 5 5 A HO2' H 4.58 0.03 1 27 5 5 A C1' C 92.04 0.03 1 28 5 5 A C2 C 155.49 0.03 1 29 5 5 A C8 C 139.32 0.03 1 30 6 6 C H1' H 5.56 0.03 1 31 6 6 C H5 H 5.21 0.03 1 32 6 6 C H5'' H 4.05 0.03 1 33 6 6 C H6 H 7.44 0.03 1 34 6 6 C HO2' H 4.40 0.03 1 35 6 6 C C1' C 91.74 0.03 1 36 6 6 C C5 C 96.89 0.03 1 37 6 6 C C6 C 141.55 0.03 1 38 7 7 U H1' H 5.74 0.03 1 39 7 7 U H5 H 5.55 0.03 1 40 7 7 U H6 H 7.66 0.03 1 41 7 7 U HO2' H 4.26 0.03 1 42 7 7 U C1' C 92.18 0.03 1 43 7 7 U C5 C 104.16 0.03 1 44 7 7 U C6 C 143.25 0.03 1 45 8 8 G H1' H 5.71 0.03 1 46 8 8 G H8 H 7.88 0.03 1 47 8 8 G C1' C 90.41 0.03 1 48 8 8 G C8 C 140.64 0.03 1 49 9 9 U H1' H 5.73 0.03 1 50 9 9 U H5 H 5.49 0.03 1 51 9 9 U H6 H 7.66 0.03 1 52 9 9 U C1' C 92.18 0.03 1 53 9 9 U C5 C 104.16 0.03 1 54 9 9 U C6 C 143.86 0.03 1 55 10 10 A H1' H 5.87 0.03 1 56 10 10 A H2 H 7.73 0.03 1 57 10 10 A H8 H 8.20 0.03 1 58 10 10 A HO2' H 4.89 0.03 1 59 10 10 A C1' C 90.41 0.03 1 60 10 10 A C2 C 155.45 0.03 1 61 10 10 A C8 C 141.43 0.03 1 62 11 11 6IA C1' C 92.82 0.03 1 63 11 11 6IA C2 C 154.57 0.03 1 64 11 11 6IA C8 C 138.70 0.03 1 65 11 11 6IA H1' H 5.58 0.03 1 66 11 11 6IA H121 H 3.67 0.03 1 67 11 11 6IA H122 H 3.47 0.03 1 68 11 11 6IA H132 H 5.06 0.03 1 69 11 11 6IA H161 H 1.55 0.03 1 70 11 11 6IA H162 H 1.55 0.03 1 71 11 11 6IA H163 H 1.55 0.03 1 72 11 11 6IA H2 H 7.88 0.03 1 73 11 11 6IA H3' H 4.25 0.03 1 74 11 11 6IA H8 H 7.70 0.03 1 75 11 11 6IA HO2' H 4.37 0.03 1 76 12 12 A H1' H 5.45 0.03 1 77 12 12 A H2 H 8.00 0.03 1 78 12 12 A H3' H 4.47 0.03 1 79 12 12 A H8 H 7.69 0.03 1 80 12 12 A HO2' H 4.27 0.03 1 81 12 12 A C1' C 93.28 0.03 1 82 12 12 A C2 C 155.79 0.03 1 83 12 12 A C8 C 139.20 0.03 1 84 13 13 PSU C6 C 140.08 0.03 1 85 13 13 PSU H1' H 4.35 0.03 1 86 13 13 PSU H6 H 6.99 0.03 1 87 13 13 PSU HO2' H 4.14 0.03 1 88 14 14 C H1' H 5.56 0.03 1 89 14 14 C H5 H 5.61 0.03 1 90 14 14 C H6 H 8.01 0.03 1 91 14 14 C HO2' H 4.24 0.03 1 92 14 14 C C5 C 96.49 0.03 1 93 14 14 C C6 C 142.89 0.03 1 94 15 15 C H1' H 5.43 0.03 1 95 15 15 C H3' H 4.26 0.03 1 96 15 15 C H5 H 5.44 0.03 1 97 15 15 C H6 H 7.87 0.03 1 98 15 15 C HO2' H 4.35 0.03 1 99 15 15 C C5 C 96.55 0.03 1 100 15 15 C C6 C 142.23 0.03 1 101 16 16 C H1' H 5.45 0.03 1 102 16 16 C H3' H 4.24 0.03 1 103 16 16 C H5 H 5.45 0.03 1 104 16 16 C H6 H 7.82 0.03 1 105 16 16 C HO2' H 4.39 0.03 1 106 16 16 C C5 C 96.55 0.03 1 107 16 16 C C6 C 142.23 0.03 1 108 17 17 C H1' H 5.66 0.03 1 109 17 17 C H5 H 5.47 0.03 1 110 17 17 C H6 H 7.68 0.03 1 111 17 17 C HO2' H 4.00 0.03 1 112 17 17 C C5 C 97.24 0.03 1 113 17 17 C C6 C 142.27 0.03 1 stop_ save_