data_17559 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignment of the stem loop 2 of RsmZ ; _BMRB_accession_number 17559 _BMRB_flat_file_name bmr17559.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 Schubert Mario . . 2 Aeschbacher Thomas H. . 3 Duss Olivier . . 4 Allain Frederic HT . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 59 "13C chemical shifts" 59 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' 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 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 'FZL2 (monomer)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'FZL2 (monomer)' $FZL2 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_FZL2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common FZL2 _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGGCCAUCAAGGACGAUGGU CC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 G 4 C 5 C 6 A 7 U 8 C 9 A 10 A 11 G 12 G 13 A 14 C 15 G 16 A 17 U 18 G 19 G 20 U 21 C 22 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 $FZL2 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_type _Vector_name _Details $FZL2 'cell free synthesis' . not applicable . 'not applicable' 'not applicable' ; Production method should be: "in vitro transcription" using a chemically synthetized DNA template (cell free synthesis is not really correct) ; 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 $FZL2 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 $FZL2 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 refinement 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 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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_2 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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 'ionic strength' 0 . M pH 7.4 . pH pressure 1 . atm temperature 303 . 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 DSS C 13 'methyl protons' ppm 0.00 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 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-1H NOESY' '2D 1H-1H TOCSY' '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 'FZL2 (monomer)' _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 5.786 0.004 1 2 1 1 G H8 H 8.155 0.005 1 3 1 1 G C1' C 90.739 0.050 1 4 1 1 G C8 C 139.212 0.050 1 5 2 2 G H1' H 5.934 0.003 1 6 2 2 G H8 H 7.657 0.005 1 7 2 2 G C1' C 92.357 0.050 1 8 2 2 G C8 C 137.127 0.050 1 9 3 3 G H1' H 5.808 0.002 1 10 3 3 G H8 H 7.289 0.007 1 11 3 3 G C1' C 93.419 0.050 1 12 3 3 G C8 C 136.822 0.050 1 13 4 4 C H1' H 5.521 0.002 1 14 4 4 C H5 H 5.348 0.002 1 15 4 4 C H6 H 7.672 0.002 1 16 4 4 C C1' C 93.843 0.050 1 17 4 4 C C5 C 97.400 0.050 1 18 4 4 C C6 C 140.546 0.050 1 19 5 5 C H1' H 5.458 0.003 1 20 5 5 C H5 H 5.532 0.002 1 21 5 5 C H6 H 7.728 0.004 1 22 5 5 C C1' C 93.950 0.050 1 23 5 5 C C5 C 98.113 0.050 1 24 5 5 C C6 C 140.954 0.050 1 25 6 6 A H1' H 5.901 0.003 1 26 6 6 A H2 H 7.303 0.002 1 27 6 6 A H8 H 8.062 0.005 1 28 6 6 A C1' C 93.151 0.050 1 29 6 6 A C2 C 153.190 0.050 1 30 6 6 A C8 C 139.736 0.050 1 31 7 7 U H1' H 5.462 0.002 1 32 7 7 U H5 H 4.967 0.004 1 33 7 7 U H6 H 7.633 0.004 1 34 7 7 U C1' C 93.275 0.050 1 35 7 7 U C5 C 102.615 0.050 1 36 7 7 U C6 C 141.523 0.050 1 37 8 8 C H1' H 5.495 0.002 1 38 8 8 C H5 H 5.419 0.003 1 39 8 8 C H6 H 7.624 0.001 1 40 8 8 C C1' C 93.707 0.050 1 41 8 8 C C5 C 97.630 0.050 1 42 8 8 C C6 C 141.180 0.050 1 43 9 9 A H1' H 5.641 0.001 1 44 9 9 A H2 H 6.955 0.001 1 45 9 9 A H8 H 7.855 0.001 1 46 9 9 A C1' C 92.727 0.050 1 47 9 9 A C2 C 153.570 0.050 1 48 9 9 A C8 C 139.728 0.050 1 49 10 10 A H1' H 5.498 0.003 1 50 10 10 A H2 H 7.905 0.001 1 51 10 10 A H8 H 7.794 0.002 1 52 10 10 A C1' C 91.522 0.050 1 53 10 10 A C2 C 155.299 0.050 1 54 10 10 A C8 C 139.954 0.050 1 55 11 11 G H1' H 5.141 0.004 1 56 11 11 G H8 H 7.289 0.002 1 57 11 11 G C1' C 89.516 0.050 1 58 11 11 G C8 C 140.716 0.056 1 59 12 12 G H1' H 5.783 0.002 1 60 12 12 G H8 H 7.931 0.003 1 61 12 12 G C1' C 89.330 0.050 1 62 12 12 G C8 C 140.144 0.050 1 63 13 13 A H1' H 5.871 0.002 1 64 13 13 A H2 H 7.918 0.002 1 65 13 13 A H8 H 8.281 0.003 1 66 13 13 A C1' C 91.532 0.050 1 67 13 13 A C2 C 155.022 0.050 1 68 13 13 A C8 C 141.486 0.023 1 69 14 14 C H1' H 5.852 0.007 1 70 14 14 C H5 H 5.625 0.002 1 71 14 14 C H6 H 7.734 0.003 1 72 14 14 C C1' C 91.912 0.050 1 73 14 14 C C5 C 98.111 0.050 1 74 14 14 C C6 C 142.743 0.050 1 75 15 15 G H1' H 5.667 0.002 1 76 15 15 G H8 H 7.907 0.002 1 77 15 15 G C1' C 92.867 0.050 1 78 15 15 G C8 C 138.109 0.050 1 79 16 16 A H1' H 5.933 0.003 1 80 16 16 A H2 H 7.641 0.001 1 81 16 16 A H8 H 7.813 0.005 1 82 16 16 A C1' C 93.085 0.050 1 83 16 16 A C2 C 153.698 0.050 1 84 16 16 A C8 C 139.743 0.050 1 85 17 17 U H1' H 5.432 0.002 1 86 17 17 U H5 H 4.994 0.002 1 87 17 17 U H6 H 7.467 0.004 1 88 17 17 U C1' C 93.028 0.050 1 89 17 17 U C5 C 103.075 0.050 1 90 17 17 U C6 C 140.817 0.050 1 91 18 18 G H1' H 5.764 0.003 1 92 18 18 G H8 H 7.617 0.003 1 93 18 18 G C1' C 92.463 0.050 1 94 18 18 G C8 C 136.284 0.050 1 95 19 19 G H1' H 5.666 0.002 1 96 19 19 G H8 H 7.214 0.004 1 97 19 19 G C1' C 92.867 0.050 1 98 19 19 G C8 C 135.978 0.050 1 99 20 20 U H1' H 5.485 0.003 1 100 20 20 U H5 H 5.386 0.001 1 101 20 20 U H6 H 7.690 0.002 1 102 20 20 U C1' C 93.764 0.050 1 103 20 20 U C5 C 104.078 0.050 1 104 20 20 U C6 C 140.628 0.050 1 105 21 21 C H1' H 5.636 0.001 1 106 21 21 C H5 H 5.672 0.003 1 107 21 21 C H6 H 7.944 0.003 1 108 21 21 C C1' C 93.947 0.050 1 109 21 21 C C5 C 97.593 0.050 1 110 21 21 C C6 C 142.541 0.050 1 111 22 22 C H1' H 5.752 0.000 1 112 22 22 C H3' H 4.157 0.000 1 113 22 22 C H5 H 5.560 0.004 1 114 22 22 C H6 H 7.656 0.004 1 115 22 22 C C1' C 92.789 0.050 1 116 22 22 C C3' C 69.779 0.050 1 117 22 22 C C5 C 98.176 0.050 1 118 22 22 C C6 C 141.808 0.050 1 stop_ save_