data_17560 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignment of the stemloop 4 of RSMZ ; _BMRB_accession_number 17560 _BMRB_flat_file_name bmr17560.str _Entry_type original _Submission_date 2011-03-31 _Accession_date 2011-03-31 _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 Aeschbacher Thomas H. . 2 Schubert Mario . . 3 Duss Olivier . . 4 Allain Frederic H.T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 57 "13C chemical shifts" 56 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-03-08 update BMRB 'update entry citation' 2012-01-24 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 17326 '20 nt RNA stem loop' 17559 'Assignment of the stem loop 2 of RsmZ' 17566 '22 nt artificial stemloop TASL1' 17567 '26 nt artificial stemloop TASL2' 17568 '30 nt artificial stemloop TASL2' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _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 'FZL4 (monomer)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label FZL4 $FZL4 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_FZL4 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common FZL4 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; GGGUCAUCAGGACGAUGACC C ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 G 4 U 5 C 6 A 7 U 8 C 9 A 10 G 11 G 12 A 13 C 14 G 15 A 16 U 17 G 18 A 19 C 20 C 21 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 $FZL4 g-proteobacteria 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 $FZL4 'cell free synthesis' . . . . . 'Production method: In vitro transcription using a chemically synthesized DNA template' 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 $FZL4 2 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 $FZL4 2 mM 'natural abundance' D2O 5 % 'natural abundance' H2O 95 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 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 Bruker _Model Avance _Field_strength 900 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _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 temperature 303 . K pH 7.4 . pH pressure 1 . atm 'ionic strength' 0 . M 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS C 13 'methyl protons' ppm 0.00 . indirect . . . 0.251449530 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 TOCSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC' 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 FZL4 _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 5.794 0.005 1 2 1 1 G H8 H 8.124 0.006 1 3 1 1 G C1' C 91.579 0.050 1 4 1 1 G C8 C 139.129 0.050 1 5 2 2 G H1' H 5.918 0.004 1 6 2 2 G H8 H 7.516 0.003 1 7 2 2 G C1' C 92.817 0.050 1 8 2 2 G C8 C 136.839 0.050 1 9 3 3 G H1' H 5.771 0.004 1 10 3 3 G H8 H 7.192 0.003 1 11 3 3 G C1' C 93.290 0.050 1 12 4 4 U H1' H 5.559 0.004 1 13 4 4 U H5 H 5.068 0.003 1 14 4 4 U H6 H 7.713 0.002 1 15 4 4 U C1' C 93.766 0.050 1 16 4 4 U C5 C 102.610 0.050 1 17 4 4 U C6 C 141.696 0.100 1 18 5 5 C H1' H 5.521 0.004 1 19 5 5 C H5 H 5.676 0.005 1 20 5 5 C H6 H 7.802 0.002 1 21 5 5 C C1' C 93.967 0.050 1 22 5 5 C C5 C 98.203 0.050 1 23 5 5 C C6 C 141.386 0.100 1 24 6 6 A H1' H 5.835 0.004 1 25 6 6 A H2 H 7.224 0.005 1 26 6 6 A H8 H 8.046 0.003 1 27 6 6 A C1' C 93.098 0.050 1 28 6 6 A C2 C 153.072 0.050 1 29 6 6 A C8 C 139.749 0.050 1 30 7 7 U H1' H 5.423 0.002 1 31 7 7 U H5 H 4.933 0.003 1 32 7 7 U H6 H 7.597 0.005 1 33 7 7 U C1' C 93.362 0.100 1 34 7 7 U C5 C 102.493 0.050 1 35 7 7 U C6 C 141.565 0.100 1 36 8 8 C H1' H 5.461 0.004 1 37 8 8 C H5 H 5.379 0.006 1 38 8 8 C H6 H 7.561 0.004 1 39 8 8 C C1' C 93.823 0.050 1 40 8 8 C C5 C 97.632 0.050 1 41 8 8 C C6 C 141.058 0.100 1 42 9 9 A H1' H 5.672 0.004 1 43 9 9 A H2 H 7.254 0.002 1 44 9 9 A H8 H 7.923 0.003 1 45 9 9 A C1' C 92.484 0.050 1 46 9 9 A C2 C 154.507 0.050 1 47 9 9 A C8 C 139.655 0.050 1 48 10 10 G H1' H 5.104 0.005 1 49 10 10 G H8 H 7.292 0.006 1 50 10 10 G C1' C 89.976 0.050 1 51 10 10 G C8 C 139.909 0.050 1 52 11 11 G H1' H 5.661 0.006 1 53 11 11 G H8 H 7.854 0.004 1 54 11 11 G C1' C 89.284 0.050 1 55 11 11 G C8 C 140.238 0.050 1 56 12 12 A H1' H 5.829 0.003 1 57 12 12 A H2 H 7.922 0.002 1 58 12 12 A H8 H 8.229 0.003 1 59 12 12 A C1' C 90.619 0.050 1 60 12 12 A C2 C 155.084 0.050 1 61 12 12 A C8 C 141.834 0.050 1 62 13 13 C H1' H 5.859 0.004 1 63 13 13 C H5 H 5.754 0.004 1 64 13 13 C H6 H 7.725 0.003 1 65 13 13 C C1' C 91.890 0.050 1 66 13 13 C C5 C 98.627 0.050 1 67 13 13 C C6 C 143.158 0.100 1 68 14 14 G H1' H 5.393 0.003 1 69 14 14 G H8 H 7.852 0.003 1 70 14 14 G C1' C 91.893 0.050 1 71 14 14 G C8 C 138.097 0.050 1 72 15 15 A H1' H 5.950 0.003 1 73 15 15 A H2 H 7.626 0.003 1 74 15 15 A H8 H 7.835 0.004 1 75 15 15 A C1' C 93.197 0.050 1 76 15 15 A C2 C 153.724 0.050 1 77 15 15 A C8 C 139.895 0.050 1 78 16 16 U H1' H 5.406 0.003 1 79 16 16 U H5 H 4.979 0.004 1 80 16 16 U H6 H 7.445 0.002 1 81 16 16 U C1' C 93.063 0.100 1 82 16 16 U C5 C 103.152 0.050 1 83 16 16 U C6 C 140.727 0.100 1 84 17 17 G H1' H 5.700 0.003 1 85 17 17 G H8 H 7.625 0.003 1 86 17 17 G C1' C 92.392 0.050 1 87 17 17 G C8 C 136.482 0.050 1 88 18 18 A H1' H 5.886 0.003 1 89 18 18 A H2 H 7.700 0.002 1 90 18 18 A H8 H 7.870 0.002 1 91 18 18 A C1' C 92.765 0.050 1 92 18 18 A C2 C 154.103 0.050 1 93 18 18 A C8 C 139.596 0.050 1 94 19 19 C H1' H 5.352 0.004 1 95 19 19 C H5 H 5.159 0.003 1 96 19 19 C H6 H 7.453 0.002 1 97 19 19 C C1' C 93.733 0.050 1 98 19 19 C C5 C 97.193 0.050 1 99 19 19 C C6 C 140.684 0.050 1 100 20 20 C H1' H 5.488 0.006 1 101 20 20 C H5 H 5.407 0.003 1 102 20 20 C H6 H 7.732 0.004 1 103 20 20 C C1' C 94.315 0.050 1 104 20 20 C C5 C 97.637 0.050 1 105 20 20 C C6 C 141.510 0.100 1 106 21 21 C H1' H 5.747 0.005 1 107 21 21 C H3' H 4.165 0.002 1 108 21 21 C H5 H 5.468 0.004 1 109 21 21 C H6 H 7.651 0.005 1 110 21 21 C C1' C 92.825 0.050 1 111 21 21 C C3' C 69.817 0.050 1 112 21 21 C C5 C 98.102 0.050 1 113 21 21 C C6 C 141.876 0.100 1 stop_ save_