data_18974 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Modified Helix 69 ; _BMRB_accession_number 18974 _BMRB_flat_file_name bmr18974.str _Entry_type original _Submission_date 2013-01-25 _Accession_date 2013-01-25 _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 JIANG JUN . . 2 ADURI RAVIPRASAD . . 3 CHOW CHRISTINE S. . 4 SANTALUCIA JOHN . Jr. stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 155 "13C chemical shifts" 46 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-17 update BMRB 'update entry citation' 2014-01-02 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24371282 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Jiang Jun . . 2 Aduri Raviprasad . . 3 Chow Christine S. . 4 Santalucia John . Jr. stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name HELIX_69 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label HELIX_69 $HELIX_69 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_HELIX_69 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common HELIX_69 _Molecular_mass 6077.715 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence GGCCGXAACXAXAACGGUC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 C 4 4 C 5 5 G 6 6 PSU 7 7 A 8 8 A 9 9 C 10 10 PSU 11 11 A 12 12 PSU 13 13 A 14 14 A 15 15 C 16 16 G 17 17 G 18 18 U 19 19 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_PSU _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common PSEUDOURIDINE-5'-MONOPHOSPHATE _BMRB_code PSU _PDB_code PSU _Standard_residue_derivative . _Molecular_mass 324.181 _Mol_paramagnetic no _Details . 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 $HELIX_69 Enterobacteria 562 Bacteria . Escherichia coli 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 $HELIX_69 'chemical synthesis' . . . . . 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 $HELIX_69 1.0 mM 'natural abundance' 'Potassium Phosphate' 10 mM 'natural abundance' 'Potassium Chloride' 50 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HELIX_69 1.0 mM 'natural abundance' 'Potassium Phosphate' 10 mM 'natural abundance' 'Potassium Chloride' 50 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Mercury _Field_strength 400 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_NATURAL_ABUNDANCE_HMQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C NATURAL ABUNDANCE HMQC' _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_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_3D_1H-1H-1H_TOCSY-NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-1H-1H TOCSY-NOESY' _Sample_label $sample_1 save_ save_2D_1H-31P_HETCOR_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $sample_1 save_ save_1D_31P_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 31P' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 70 . mM pH 7.3 . pH pressure 1 . atm temperature 310.2 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 70 . mM pH 7.3 . pH pressure 1 . atm temperature 283.2 . 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 TSP H 1 'methyl protons' ppm 0 internal 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-13C NATURAL ABUNDANCE HMQC' '2D 1H-1H NOESY' '2D DQF-COSY' '3D 1H-1H-1H TOCSY-NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name HELIX_69 _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 C1' C 90.134 0.000 1 2 1 1 G C8 C 136.210 0.000 1 3 1 1 G H1' H 5.794 0.002 1 4 1 1 G H2' H 4.814 0.002 1 5 1 1 G H3' H 4.613 0.003 1 6 1 1 G H4' H 4.406 0.002 1 7 1 1 G H5'' H 3.966 0.001 2 8 1 1 G H5' H 4.077 0.002 2 9 1 1 G H8 H 8.084 0.001 1 10 2 2 G C1' C 90.579 0.000 1 11 2 2 G C8 C 134.499 0.000 1 12 2 2 G H1 H 11.843 0.006 1 13 2 2 G H1' H 5.936 0.001 1 14 2 2 G H2' H 4.729 0.001 1 15 2 2 G H3' H 4.602 0.001 1 16 2 2 G H4' H 4.573 0.003 1 17 2 2 G H5'' H 4.228 0.001 2 18 2 2 G H5' H 4.607 0.002 2 19 2 2 G H8 H 7.581 0.002 1 20 3 3 C C1' C 91.180 0.000 1 21 3 3 C C5 C 94.861 0.000 1 22 3 3 C C6 C 137.978 0.000 1 23 3 3 C H1' H 5.585 0.003 1 24 3 3 C H2' H 4.344 0.001 1 25 3 3 C H3' H 4.562 0.002 1 26 3 3 C H4' H 4.469 0.002 1 27 3 3 C H41 H 8.532 0.003 1 28 3 3 C H42 H 7.061 0.005 1 29 3 3 C H5 H 5.510 0.002 1 30 3 3 C H5'' H 4.156 0.003 2 31 3 3 C H5' H 4.588 0.000 2 32 3 3 C H6 H 7.799 0.002 1 33 4 4 C C1' C 91.309 0.000 1 34 4 4 C C5 C 95.575 0.000 1 35 4 4 C C6 C 138.068 0.000 1 36 4 4 C H1' H 5.572 0.001 1 37 4 4 C H2' H 4.607 0.002 1 38 4 4 C H3' H 4.565 0.002 1 39 4 4 C H4' H 4.459 0.002 1 40 4 4 C H41 H 8.450 0.005 1 41 4 4 C H42 H 6.893 0.001 1 42 4 4 C H5 H 5.553 0.001 1 43 4 4 C H5'' H 4.142 0.002 2 44 4 4 C H5' H 4.553 0.002 2 45 4 4 C H6 H 7.759 0.002 1 46 5 5 G C1' C 90.192 0.000 1 47 5 5 G C8 C 133.765 0.000 1 48 5 5 G H1 H 12.872 0.006 1 49 5 5 G H1' H 5.759 0.002 1 50 5 5 G H2' H 4.666 0.002 1 51 5 5 G H3' H 4.600 0.003 1 52 5 5 G H4' H 4.583 0.003 1 53 5 5 G H5'' H 4.137 0.002 2 54 5 5 G H5' H 4.511 0.001 2 55 5 5 G H8 H 7.580 0.003 1 56 6 6 PSU C6 C 136.976 0.000 1 57 6 6 PSU H1 H 10.253 0.002 1 58 6 6 PSU H1' H 4.673 0.002 1 59 6 6 PSU H2' H 4.490 0.003 1 60 6 6 PSU H3 H 13.167 0.003 1 61 6 6 PSU H3' H 4.437 0.002 1 62 6 6 PSU H4' H 4.253 0.003 1 63 6 6 PSU H5'' H 4.062 0.002 2 64 6 6 PSU H5' H 4.444 0.001 2 65 6 6 PSU H6 H 6.977 0.005 1 66 7 7 A C1' C 90.005 0.000 1 67 7 7 A C2 C 151.754 0.000 1 68 7 7 A C8 C 137.285 0.000 1 69 7 7 A H1' H 5.776 0.001 1 70 7 7 A H2 H 7.527 0.002 1 71 7 7 A H2' H 4.569 0.001 1 72 7 7 A H3' H 4.670 0.000 1 73 7 7 A H4' H 4.549 0.002 1 74 7 7 A H5'' H 4.184 0.000 2 75 7 7 A H8 H 8.064 0.002 1 76 8 8 A C1' C 89.592 0.000 1 77 8 8 A C2 C 152.237 0.000 1 78 8 8 A C8 C 137.291 0.000 1 79 8 8 A H1' H 5.657 0.001 1 80 8 8 A H2 H 7.875 0.001 1 81 8 8 A H2' H 4.391 0.001 1 82 8 8 A H3' H 4.516 0.002 1 83 8 8 A H4' H 4.402 0.002 1 84 8 8 A H5'' H 4.106 0.000 2 85 8 8 A H5' H 4.447 0.001 2 86 8 8 A H8 H 7.892 0.001 1 87 9 9 C C1' C 89.682 0.000 1 88 9 9 C C5 C 95.160 0.000 1 89 9 9 C C6 C 139.998 0.000 1 90 9 9 C H1' H 5.588 0.001 1 91 9 9 C H2' H 4.320 0.003 1 92 9 9 C H3' H 4.421 0.001 1 93 9 9 C H4' H 4.275 0.001 1 94 9 9 C H5 H 5.501 0.002 1 95 9 9 C H5'' H 4.039 0.000 2 96 9 9 C H5' H 4.293 0.001 2 97 9 9 C H6 H 7.445 0.001 1 98 10 10 PSU C6 C 139.933 0.000 1 99 10 10 PSU H1' H 4.672 0.002 1 100 10 10 PSU H2' H 4.311 0.003 1 101 10 10 PSU H3' H 4.402 0.001 1 102 10 10 PSU H4' H 4.185 0.004 1 103 10 10 PSU H5'' H 3.955 0.001 2 104 10 10 PSU H5' H 4.132 0.000 2 105 10 10 PSU H6 H 7.535 0.002 1 106 11 11 A C1' C 88.759 0.000 1 107 11 11 A C2 C 152.653 0.000 1 108 11 11 A C8 C 138.526 0.000 1 109 11 11 A H1' H 6.019 0.001 1 110 11 11 A H2 H 8.083 0.002 1 111 11 11 A H2' H 4.822 0.002 1 112 11 11 A H3' H 4.507 0.001 1 113 11 11 A H4' H 4.390 0.002 1 114 11 11 A H5'' H 4.146 0.002 2 115 11 11 A H5' H 4.326 0.002 2 116 11 11 A H8 H 8.216 0.002 1 117 12 12 PSU C6 C 138.759 0.000 1 118 12 12 PSU H1' H 4.624 0.001 1 119 12 12 PSU H2' H 4.281 0.002 1 120 12 12 PSU H3' H 4.540 0.001 1 121 12 12 PSU H4' H 4.293 0.003 1 122 12 12 PSU H5'' H 4.156 0.000 2 123 12 12 PSU H5' H 4.375 0.000 2 124 13 13 A C1' C 88.798 0.000 1 125 13 13 A C2 C 152.234 0.000 1 126 13 13 A C8 C 138.553 0.000 1 127 13 13 A H1' H 5.929 0.002 1 128 13 13 A H2 H 8.042 0.002 1 129 13 13 A H2' H 4.827 0.001 1 130 13 13 A H3' H 4.679 0.001 1 131 13 13 A H4' H 4.423 0.000 1 132 13 13 A H5'' H 4.152 0.001 2 133 13 13 A H5' H 4.384 0.001 2 134 13 13 A H8 H 8.239 0.001 1 135 14 14 A C1' C 90.276 0.000 1 136 14 14 A C2 C 150.849 0.000 1 137 14 14 A C8 C 137.273 0.000 1 138 14 14 A H1' H 5.649 0.001 1 139 14 14 A H2 H 7.693 0.002 1 140 14 14 A H2' H 4.625 0.002 1 141 14 14 A H3' H 4.546 0.001 1 142 14 14 A H4' H 4.533 0.002 1 143 14 14 A H5'' H 4.235 0.002 2 144 14 14 A H5' H 4.450 0.000 2 145 14 14 A H8 H 8.060 0.002 1 146 15 15 C C1' C 91.128 0.000 1 147 15 15 C C5 C 94.799 0.000 1 148 15 15 C C6 C 137.871 0.000 1 149 15 15 C H1' H 5.449 0.001 1 150 15 15 C H2' H 4.457 0.001 1 151 15 15 C H3' H 4.442 0.002 1 152 15 15 C H4' H 4.516 0.001 1 153 15 15 C H41 H 8.237 0.002 1 154 15 15 C H42 H 6.801 0.002 1 155 15 15 C H5 H 5.123 0.001 1 156 15 15 C H5'' H 4.119 0.001 2 157 15 15 C H5' H 4.443 0.000 2 158 15 15 C H6 H 7.378 0.002 1 159 16 16 G C1' C 90.070 0.000 1 160 16 16 G C8 C 133.629 0.000 1 161 16 16 G H1 H 12.489 0.005 1 162 16 16 G H1' H 5.765 0.003 1 163 16 16 G H2' H 4.708 0.003 1 164 16 16 G H3' H 4.601 0.001 1 165 16 16 G H4' H 4.497 0.001 1 166 16 16 G H5'' H 4.137 0.001 2 167 16 16 G H5' H 4.515 0.000 2 168 16 16 G H8 H 7.569 0.001 1 169 17 17 G C1' C 90.470 0.000 1 170 17 17 G C8 C 133.292 0.000 1 171 17 17 G H1 H 13.533 0.004 1 172 17 17 G H1' H 5.759 0.002 1 173 17 17 G H2' H 4.657 0.001 1 174 17 17 G H3' H 4.397 0.001 1 175 17 17 G H4' H 4.498 0.003 1 176 17 17 G H5'' H 4.107 0.001 2 177 17 17 G H5' H 4.521 0.000 2 178 17 17 G H8 H 7.236 0.001 1 179 18 18 U C1' C 91.438 0.000 1 180 18 18 U C5 C 101.387 0.000 1 181 18 18 U C6 C 137.982 0.000 1 182 18 18 U H1' H 5.569 0.002 1 183 18 18 U H2' H 4.173 0.002 1 184 18 18 U H3 H 12.403 0.005 1 185 18 18 U H3' H 4.546 0.001 1 186 18 18 U H4' H 4.433 0.000 1 187 18 18 U H5 H 5.442 0.002 1 188 18 18 U H5'' H 4.095 0.001 2 189 18 18 U H5' H 4.556 0.001 2 190 18 18 U H6 H 7.783 0.002 1 191 19 19 C C1' C 89.986 0.000 1 192 19 19 C C5 C 95.381 0.000 1 193 19 19 C C6 C 140.384 0.000 1 194 19 19 C H1' H 5.939 0.001 1 195 19 19 C H2' H 4.051 0.004 1 196 19 19 C H3' H 4.280 0.001 1 197 19 19 C H4' H 4.182 0.000 1 198 19 19 C H5 H 5.720 0.002 1 199 19 19 C H5'' H 4.080 0.001 2 200 19 19 C H5' H 4.560 0.000 2 201 19 19 C H6 H 7.855 0.003 1 stop_ save_