data_25297 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution-state NMR structure of the lasso peptide streptomonomicin ; _BMRB_accession_number 25297 _BMRB_flat_file_name bmr25297.str _Entry_type original _Submission_date 2014-10-24 _Accession_date 2014-10-24 _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 Tietz Jonathan I. . 2 Zhu Lingyang . . 3 Mitchell Douglas A. . 4 Metelev Mikhail . . 5 Melby Joel O. . 6 Blair Patricia M. . 7 Livnat Itamar . . 8 Severinov Konstantin . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 122 "13C chemical shifts" 21 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-08-25 update BMRB 'update entry citation' 2015-01-16 original author 'original release' stop_ _Original_release_date 2015-08-25 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure, bioactivity, and resistance mechanism of streptomonomicin, an unusual lasso Peptide from an understudied halophilic actinomycete ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25601074 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Metelev Mikhail . . 2 Tietz Jonathan I. . 3 Melby Joel O. . 4 Zhu Lingyang . . 5 Blair Patricia M. . 6 Livnat Itamar . . 7 Severinov Konstantin . . 8 Mitchell Douglas A. . stop_ _Journal_abbreviation 'Chem. Biol.' _Journal_volume 22 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 241 _Page_last 250 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'lasso peptide streptomonomicin' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 2252.586 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; SLGSSPYNDILGYPALIVIY P ; loop_ _Residue_seq_code _Residue_label 1 SER 2 LEU 3 GLY 4 SER 5 SER 6 PRO 7 TYR 8 ASN 9 ASP 10 ILE 11 LEU 12 GLY 13 TYR 14 PRO 15 ALA 16 LEU 17 ILE 18 VAL 19 ILE 20 TYR 21 PRO stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-25 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 2MW3 "Solution Nmr Structure Of The Lasso Peptide Streptomonomicin" 100.00 21 100.00 100.00 6.21e-04 GB KIH99826 "Streptomonomicin precursor peptide protein [Streptomonospora alba]" 100.00 41 100.00 100.00 2.42e-04 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $entity 'high GC Gram+' 183763 Bacteria . Streptomonospora alba 'YIM 90003' 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 $entity 'purified from the natural source' . Streptomonospora alba 'YIM 90003' . 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 $entity 4 mM 'natural abundance' methanol 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.36 loop_ _Vendor _Address _Electronic_address Brunger . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.115 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 8.2 loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version 3.2A loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_MestReNova _Saveframe_category software _Name MestReNova _Version 8.1.1 loop_ _Vendor _Address _Electronic_address Mestrelab . . stop_ loop_ _Task 'chemical shift assignment' processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model VNMRS _Field_strength 750 _Details '5mm triple resonance (1H-13C-15N) triaxial gradient probe' save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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-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_ save_2D_1H-13C_HMBC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMBC' _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 temperature 273 . 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 methanol C 13 'methyl carbon' ppm 47.8 internal indirect . . . 0.251449530 methanol H 1 'methyl protons' ppm 3.30 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 DQF-COSY' '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' '2D 1H-13C HMBC' 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 entity _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 SER HA H 4.138 0.001 1 2 1 1 SER HB2 H 3.839 0.002 2 3 1 1 SER HB3 H 4.262 0.002 2 4 1 1 SER CA C 56.2 . 1 5 2 2 LEU H H 8.056 0.001 1 6 2 2 LEU HA H 3.737 0.002 1 7 2 2 LEU HB2 H 1.75 . 2 8 2 2 LEU HB3 H 2.25 0.001 2 9 2 2 LEU HG H 1.733 0.002 1 10 2 2 LEU HD1 H 1.056 0.031 2 11 2 2 LEU HD2 H 0.877 0.002 2 12 2 2 LEU CA C 54.6 . 1 13 3 3 GLY H H 8.323 0.003 1 14 3 3 GLY HA2 H 3.357 0.006 2 15 3 3 GLY HA3 H 4.709 0.007 2 16 3 3 GLY CA C 41.6 . 1 17 4 4 SER H H 7.675 0.005 1 18 4 4 SER HA H 4.558 0.002 1 19 4 4 SER HB2 H 3.694 0.006 2 20 4 4 SER HB3 H 3.974 0.001 2 21 4 4 SER CA C 54.5 . 1 22 5 5 SER H H 8.171 0.004 1 23 5 5 SER HA H 4.558 0.002 1 24 5 5 SER HB2 H 3.967 0.004 2 25 5 5 SER HB3 H 4.04 0.005 2 26 5 5 SER CA C 55.2 . 1 27 6 6 PRO HA H 4.369 0.001 1 28 6 6 PRO HB2 H 1.757 0.007 2 29 6 6 PRO HB3 H 1.987 0 2 30 6 6 PRO HG2 H 1.65 0.009 2 31 6 6 PRO HG3 H 1.858 0.004 2 32 6 6 PRO HD2 H 3.669 0.003 2 33 6 6 PRO HD3 H 3.737 0.005 2 34 6 6 PRO CA C 60.6 . 1 35 7 7 TYR H H 7.656 0.002 1 36 7 7 TYR HA H 4.533 0.004 1 37 7 7 TYR HB2 H 2.666 0.003 2 38 7 7 TYR HB3 H 2.955 0.003 2 39 7 7 TYR HD1 H 6.928 0.002 . 40 7 7 TYR HD2 H 6.928 0.002 . 41 7 7 TYR HE1 H 6.928 0.002 . 42 7 7 TYR HE2 H 6.634 0.004 . 43 7 7 TYR CA C 53.4 . 1 44 8 8 ASN H H 8.524 0.006 1 45 8 8 ASN HA H 5.049 0.002 1 46 8 8 ASN HB2 H 2.502 0.001 2 47 8 8 ASN HB3 H 2.728 0.004 2 48 8 8 ASN HD21 H 6.309 0.001 2 49 8 8 ASN HD22 H 7.136 0.001 2 50 8 8 ASN CA C 50 . 1 51 9 9 ASP H H 8.888 0.001 1 52 9 9 ASP HA H 4.844 . 1 53 9 9 ASP HB2 H 2.992 0.001 2 54 9 9 ASP HB3 H 3.667 0.004 2 55 9 9 ASP CA C 48.5 . 1 56 10 10 ILE H H 8.23 0.004 1 57 10 10 ILE HA H 4.051 0.002 1 58 10 10 ILE HB H 1.994 0.002 1 59 10 10 ILE HG12 H 1.436 0.002 2 60 10 10 ILE HG13 H 1.587 0.002 2 61 10 10 ILE HG2 H 1.05 0 1 62 10 10 ILE HD1 H 0.98 0 1 63 10 10 ILE CA C 60.3 . 1 64 11 11 LEU H H 7.283 0.002 1 65 11 11 LEU HA H 4.522 0.001 1 66 11 11 LEU HB2 H 1.801 0.002 2 67 11 11 LEU HB3 H 1.935 0.003 2 68 11 11 LEU HG H 1.735 0.004 1 69 11 11 LEU HD1 H 1.041 0.004 2 70 11 11 LEU HD2 H 0.94 0.002 2 71 11 11 LEU CA C 51.8 . 1 72 12 12 GLY H H 8.394 0.003 1 73 12 12 GLY HA2 H 3.473 0.006 2 74 12 12 GLY HA3 H 4.075 0.001 2 75 12 12 GLY CA C 42.3 . 1 76 13 13 TYR H H 6.984 0.008 1 77 13 13 TYR HA H 4.833 . 1 78 13 13 TYR HB2 H 2.449 0.001 2 79 13 13 TYR HB3 H 3.222 0.001 2 80 13 13 TYR HD1 H 6.999 0.002 . 81 13 13 TYR HD2 H 6.999 0.002 . 82 13 13 TYR HE1 H 6.703 0.001 . 83 13 13 TYR HE2 H 6.703 0.001 . 84 13 13 TYR CA C 52.9 . 1 85 14 14 PRO HA H 4.312 0.001 1 86 14 14 PRO HB2 H 1.868 0.003 2 87 14 14 PRO HB3 H 2.646 0.001 2 88 14 14 PRO HG2 H 1.969 0 2 89 14 14 PRO HG3 H 1.969 0 2 90 14 14 PRO HD2 H 3.577 0.001 2 91 14 14 PRO HD3 H 3.779 0.001 2 92 14 14 PRO CA C 62 . 1 93 15 15 ALA H H 8.566 0.001 1 94 15 15 ALA HA H 4.197 0.004 1 95 15 15 ALA HB H 1.357 0.005 1 96 15 15 ALA CA C 49.8 . 1 97 16 16 LEU H H 8.202 0.007 1 98 16 16 LEU HA H 4.559 0.005 1 99 16 16 LEU HB2 H 1.596 0.008 2 100 16 16 LEU HB3 H 1.826 0.008 2 101 16 16 LEU HG H 1.726 0.003 1 102 16 16 LEU HD1 H 1.015 0.008 2 103 16 16 LEU HD2 H 0.926 0.007 2 104 16 16 LEU CA C 52.4 . 1 105 17 17 ILE H H 7.656 0.005 1 106 17 17 ILE HA H 4.236 0.013 1 107 17 17 ILE HB H 1.898 0 1 108 17 17 ILE HG12 H 1.171 0.005 2 109 17 17 ILE HG13 H 1.592 0.005 2 110 17 17 ILE HG2 H 0.915 0.006 1 111 17 17 ILE HD1 H 0.91 . 1 112 17 17 ILE CA C 57.9 . 1 113 18 18 VAL H H 8.329 0.006 1 114 18 18 VAL HA H 4.191 0.001 1 115 18 18 VAL HB H 2.012 0.002 1 116 18 18 VAL HG1 H 0.912 0.001 2 117 18 18 VAL HG2 H 0.809 0.002 2 118 18 18 VAL CA C 58.7 . 1 119 19 19 ILE H H 8.058 . 1 120 19 19 ILE HA H 4.25 . 1 121 19 19 ILE HB H 1.447 . 1 122 19 19 ILE HG12 H 1.109 . 2 123 19 19 ILE HG13 H 1.445 0.002 2 124 19 19 ILE HG2 H 0.91 . 1 125 19 19 ILE HD1 H 0.829 . 1 126 19 19 ILE CA C 57.8 . 1 127 20 20 TYR H H 8.154 0.023 1 128 20 20 TYR HA H 4.77 . 1 129 20 20 TYR HB2 H 2.82 0.003 2 130 20 20 TYR HB3 H 3.053 0 2 131 20 20 TYR HD1 H 7.086 0.002 . 132 20 20 TYR HD2 H 7.086 0.002 . 133 20 20 TYR HE1 H 6.672 0.002 . 134 20 20 TYR HE2 H 6.672 0.002 . 135 20 20 TYR CA C 52.8 . 1 136 21 21 PRO HA H 4.385 0.001 1 137 21 21 PRO HB2 H 2.002 0.008 2 138 21 21 PRO HB3 H 2.19 0.003 2 139 21 21 PRO HG2 H 1.96 . 2 140 21 21 PRO HG3 H 1.96 . 2 141 21 21 PRO HD2 H 3.418 . 2 142 21 21 PRO HD3 H 3.745 . 2 143 21 21 PRO CA C 59.1 . 1 stop_ save_