data_17326 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Shin-Dalgarno sequence of the hcnA gene of Pseudomonas fluourescens ; _BMRB_accession_number 17326 _BMRB_flat_file_name bmr17326.str _Entry_type original _Submission_date 2010-11-29 _Accession_date 2010-11-29 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'sequentail chemical shift assignment a 20 nt RNA stem loop containing the Shin-Dalgarno sequence of the hcnA gene of Pseudomonas fluourescens' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schubert Mario . . 2 Allain Frederic H.-T. . 3 Aeschbacher Thomas H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 60 "13C chemical shifts" 54 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-03-12 update BMRB 'update entry citation' 2012-01-24 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 17559 'Assignment of the stem loop 2 of RsmZ' 17560 'Assignment of the stem loop 4 of RsmZ' 17566 '22 nt artificial stemloop TASL1' 17567 '26 nt artificial stemloop TASL2' 17568 '30 nt artificial stemloop TASL3' stop_ save_ ############################# # Citation for this entry # ############################# save_Reference_paper _Saveframe_category entry_citation _Citation_full . _Citation_title 'A procedure to validate and correct the (13)C chemical shift calibration of RNA datasets.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22252483 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Aeschbacher Thomas . . 2 Schubert Mario . . 3 Allain 'Frederic H-T' . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 52 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 179 _Page_last 190 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name RP1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label RP1 $RP1 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_RP1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RP1 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; GGGCUUCACGGAUGAAGCCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 G 4 C 5 U 6 U 7 C 8 A 9 C 10 G 11 G 12 A 13 U 14 G 15 A 16 A 17 G 18 C 19 C 20 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $RP1 'Pseudomonas fluorescens' 294 bacteria . Pseudomonas fluorescens 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 _Details $RP1 'in vitro transcription' . in vitro . . 'the DNA template was synthesized by Microsynth (Switzerland)' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'pH7.4 (in H2O before lyophilization)' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RP1 1.3 mM 'natural abundance' H2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 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 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _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 'no buffer, just pHed' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 . M pH 7.4 . pH pressure 1 . atm temperature 313 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'external sample of sucrose/DSS (Bruker)' 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . 'separate tube (no insert) similar to the experimental sample tube' . 1.000000000 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 HSQC' '2D 1H-1H TOCSY' '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 RP1 _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 5.784 0.009 1 2 1 1 G H8 H 8.090 0.006 1 3 1 1 G C1' C 91.476 0.2 1 4 1 1 G C8 C 138.937 0.2 1 5 2 2 G H1 H 12.902 0.001 1 6 2 2 G H1' H 5.899 0.005 1 7 2 2 G H8 H 7.532 0.003 1 8 2 2 G C1' C 92.822 0.2 1 9 2 2 G C8 C 136.755 0.2 1 10 3 3 G H1 H 13.315 0.015 1 11 3 3 G H1' H 5.769 0.003 1 12 3 3 G H8 H 7.262 0.005 1 13 3 3 G C1' C 92.815 0.2 1 14 3 3 G C8 C 136.031 0.2 1 15 4 4 C H1' H 5.513 0.02 1 16 4 4 C H5 H 5.247 0.004 1 17 4 4 C H6 H 7.551 0.005 1 18 4 4 C C1' C 94.073 0.2 1 19 4 4 C C5 C 97.299 0.2 1 20 4 4 C C6 C 140.940 0.2 1 21 5 5 U H1' H 5.534 0.02 1 22 5 5 U H3 H 14.050 0.003 1 23 5 5 U H5 H 5.433 0.005 1 24 5 5 U H6 H 7.821 0.006 1 25 5 5 U C1' C 94.092 0.2 1 26 5 5 U C5 C 103.623 0.2 1 27 5 5 U C6 C 142.010 0.2 1 28 6 6 U H1' H 5.584 0.003 1 29 6 6 U H3 H 13.779 0.004 1 30 6 6 U H5 H 5.556 0.006 1 31 6 6 U H6 H 7.970 0.006 1 32 6 6 U C1' C 93.633 0.2 1 33 6 6 U C5 C 103.221 0.2 1 34 6 6 U C6 C 142.563 0.2 1 35 7 7 C H1' H 5.460 0.002 1 36 7 7 C H5 H 5.563 0.02 1 37 7 7 C H6 H 7.711 0.005 1 38 7 7 C C1' C 93.720 0.2 1 39 7 7 C C5 C 97.767 0.2 1 40 7 7 C C6 C 141.259 0.2 1 41 8 8 A H1' H 5.800 0.001 1 42 8 8 A H2 H 7.277 0.003 1 43 8 8 A H8 H 7.886 0.001 1 44 8 8 A C1' C 92.040 0.2 1 45 8 8 A C2 C 153.858 0.2 1 46 8 8 A C8 C 139.652 0.2 1 47 9 9 C H1' H 5.062 0.027 1 48 9 9 C H5 H 5.513 0.003 1 49 9 9 C H6 H 7.414 0.003 1 50 9 9 C C1' C 93.077 0.2 1 51 9 9 C C5 C 97.820 0.2 1 52 9 9 C C6 C 141.948 0.2 1 53 10 10 G H1' H 5.391 0.008 1 54 10 10 G H8 H 7.662 0.003 1 55 10 10 G C1' C 89.978 0.2 1 56 10 10 G C8 C 140.940 0.2 1 57 11 11 G H1' H 5.678 0.007 1 58 11 11 G H8 H 7.824 0.004 1 59 11 11 G C1' C 89.846 0.2 1 60 11 11 G C8 C 140.052 0.2 1 61 12 12 A H1' H 5.926 0.007 1 62 12 12 A H2 H 8.012 0.001 1 63 12 12 A H8 H 8.276 0.006 1 64 12 12 A C1' C 89.848 0.2 1 65 12 12 A C2 C 155.027 0.2 1 66 12 12 A C8 C 141.962 0.2 1 67 13 13 U H1' H 5.932 0.005 1 68 13 13 U H5 H 5.660 0.019 1 69 13 13 U H6 H 7.719 0.011 1 70 13 13 U C1' C 90.301 0.2 1 71 13 13 U C5 C 104.791 0.2 1 72 13 13 U C6 C 143.051 0.2 1 73 14 14 G H1 H 11.589 0.02 1 74 14 14 G H1' H 5.723 0.002 1 75 14 14 G H8 H 7.850 0.02 1 76 14 14 G C1' C 92.721 0.2 1 77 14 14 G C8 C 137.639 0.2 1 78 15 15 A H1' H 5.854 0.001 1 79 15 15 A H2 H 7.051 0.002 1 80 15 15 A H8 H 7.736 0.003 1 81 15 15 A C1' C 92.804 0.2 1 82 15 15 A C2 C 152.786 0.2 1 83 15 15 A C8 C 139.578 0.2 1 84 16 16 A H1' H 5.817 0.02 1 85 16 16 A H2 H 7.400 0.001 1 86 16 16 A H8 H 7.602 0.007 1 87 16 16 A C1' C 92.565 0.2 1 88 16 16 A C2 C 153.093 0.2 1 89 16 16 A C8 C 138.925 0.2 1 90 17 17 G H1 H 13.486 0.002 1 91 17 17 G H1' H 5.564 0.002 1 92 17 17 G H8 H 7.125 0.007 1 93 17 17 G C1' C 92.651 0.2 1 94 17 17 G C8 C 135.686 0.2 1 95 18 18 C H1' H 5.487 0.001 1 96 18 18 C H5 H 5.153 0.002 1 97 18 18 C H6 H 7.568 0.007 1 98 18 18 C C1' C 94.089 0.2 1 99 18 18 C C5 C 97.093 0.2 1 100 18 18 C C6 C 141.007 0.2 1 101 19 19 C H1' H 5.479 0.02 1 102 19 19 C H5 H 5.470 0.003 1 103 19 19 C H6 H 7.743 0.002 1 104 19 19 C C1' C 93.982 0.2 1 105 19 19 C C5 C 97.832 0.2 1 106 19 19 C C6 C 141.431 0.2 1 107 20 20 C H1' H 5.747 0.002 1 108 20 20 C H3' H 4.157 0.02 1 109 20 20 C H5 H 5.494 0.003 1 110 20 20 C H6 H 7.661 0.003 1 111 20 20 C C1' C 92.778 0.2 1 112 20 20 C C3' C 69.743 0.2 1 113 20 20 C C5 C 97.859 0.2 1 114 20 20 C C6 C 141.597 0.2 1 stop_ save_