data_36083 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of a new lasso peptide subterisin ; _BMRB_accession_number 36083 _BMRB_flat_file_name bmr36083.str _Entry_type original _Submission_date 2017-05-12 _Accession_date 2018-04-23 _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 Hemmi H. . . 2 Kodani S. . . 3 Kuroha M. . . 4 Ohnishi-Kameyama M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 98 "13C chemical shifts" 57 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-04-30 original BMRB . stop_ _Original_release_date 2018-04-23 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Isolation and structure determination of a new lasso peptide subterisin from Sphingomonas subterranea ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kuroha M. . . 2 Hemmi H. . . 3 Ohnishi-Kameyama M. . . 4 Kodani S. . . stop_ _Journal_abbreviation 'Tetrahedron Lett.' _Journal_volume 58 _Journal_issue . _Journal_ASTM TELEAY _Journal_ISSN 0040-4039 _Journal_CSD 0024 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3429 _Page_last 3432 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'uncharacterized protein subterisin' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'uncharacterized protein subterisin' _Molecular_mass 1723.947 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence ; GPPGDRIEFGVLAQLPG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 PRO 3 3 PRO 4 4 GLY 5 5 ASP 6 6 ARG 7 7 ILE 8 8 GLU 9 9 PHE 10 10 GLY 11 11 VAL 12 12 LEU 13 13 ALA 14 14 GLN 15 15 LEU 16 16 PRO 17 17 GLY 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 $entity_1 'Novosphingobium subterraneum' 48936 Bacteria . Novosphingobium subterraneum 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_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '16 mg/mL NA-C,N,H subterisin, DMSO' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 16 mg/mL 'natural abundance' DMSO-d6 100 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_software_3 _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_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 800 _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-13C_HMBC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMBC' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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_1 save_ save_2D_1H-1H_COSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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 . 'Not defined' pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 DMSO-d6 C 13 'methyl carbons' ppm 39.5 internal direct . . . 1 DMSO-d6 H 1 'methyl protons' ppm 2.49 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-13C HSQC' '2D 1H-13C HMBC' '2D 1H-15N HSQC' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-1H COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 GLY H H 7.84 . 1 2 1 1 GLY HA2 H 3.82 . 2 3 1 1 GLY HA3 H 4.04 . 2 4 1 1 GLY CA C 41.8 . 1 5 2 2 PRO HA H 4.55 . 1 6 2 2 PRO HB2 H 1.72 . 2 7 2 2 PRO HB3 H 2.24 . 2 8 2 2 PRO HG2 H 1.78 . 1 9 2 2 PRO HG3 H 1.78 . 1 10 2 2 PRO HD2 H 3.42 . 2 11 2 2 PRO HD3 H 3.49 . 2 12 2 2 PRO CA C 58.5 . 1 13 2 2 PRO CB C 27.4 . 1 14 2 2 PRO CG C 24.6 . 1 15 2 2 PRO CD C 46.4 . 1 16 3 3 PRO HA H 4.09 . 1 17 3 3 PRO HB2 H 1.71 . 2 18 3 3 PRO HB3 H 2.11 . 2 19 3 3 PRO HG2 H 1.92 . 2 20 3 3 PRO HG3 H 2.01 . 2 21 3 3 PRO HD2 H 3.38 . 2 22 3 3 PRO HD3 H 3.70 . 2 23 3 3 PRO CA C 61.1 . 1 24 3 3 PRO CB C 29.3 . 1 25 3 3 PRO CG C 25.4 . 1 26 3 3 PRO CD C 46.8 . 1 27 4 4 GLY H H 6.87 . 1 28 4 4 GLY HA2 H 3.65 . 1 29 4 4 GLY HA3 H 3.65 . 1 30 4 4 GLY CA C 43.5 . 1 31 5 5 ASP H H 8.26 . 1 32 5 5 ASP HA H 4.80 . 1 33 5 5 ASP HB2 H 2.43 . 2 34 5 5 ASP HB3 H 2.78 . 2 35 5 5 ASP CA C 49.8 . 1 36 5 5 ASP CB C 37.0 . 1 37 6 6 ARG H H 7.65 . 1 38 6 6 ARG HA H 4.43 . 1 39 6 6 ARG HB2 H 1.47 . 2 40 6 6 ARG HB3 H 1.76 . 2 41 6 6 ARG HG2 H 1.37 . 2 42 6 6 ARG HG3 H 1.46 . 2 43 6 6 ARG HD2 H 3.09 . 1 44 6 6 ARG HD3 H 3.09 . 1 45 6 6 ARG HE H 7.53 . 1 46 6 6 ARG CA C 50.9 . 1 47 6 6 ARG CB C 27.4 . 1 48 6 6 ARG CG C 25.2 . 1 49 6 6 ARG CD C 40.0 . 1 50 7 7 ILE H H 7.14 . 1 51 7 7 ILE HA H 4.85 . 1 52 7 7 ILE HB H 1.45 . 1 53 7 7 ILE HG12 H 0.93 . 2 54 7 7 ILE HG13 H 1.26 . 2 55 7 7 ILE HG2 H 0.69 . 1 56 7 7 ILE HD1 H 0.65 . 1 57 7 7 ILE CA C 55.9 . 1 58 7 7 ILE CB C 38.3 . 1 59 7 7 ILE CG1 C 24.5 . 1 60 7 7 ILE CG2 C 14.9 . 1 61 7 7 ILE CD1 C 10.6 . 1 62 8 8 GLU H H 8.66 . 1 63 8 8 GLU HA H 4.30 . 1 64 8 8 GLU HB2 H 1.62 . 2 65 8 8 GLU HB3 H 1.76 . 2 66 8 8 GLU HG2 H 1.99 . 2 67 8 8 GLU HG3 H 2.18 . 2 68 8 8 GLU CA C 50.9 . 1 69 8 8 GLU CB C 28.3 . 1 70 8 8 GLU CG C 31.5 . 1 71 9 9 PHE H H 9.02 . 1 72 9 9 PHE HA H 3.78 . 1 73 9 9 PHE HB2 H 2.92 . 2 74 9 9 PHE HB3 H 3.27 . 2 75 9 9 PHE HD1 H 7.14 . 1 76 9 9 PHE HD2 H 7.14 . 1 77 9 9 PHE HE1 H 7.25 . 1 78 9 9 PHE HE2 H 7.25 . 1 79 9 9 PHE HZ H 7.18 . 1 80 9 9 PHE CA C 56.3 . 1 81 9 9 PHE CB C 34.7 . 1 82 9 9 PHE CG C 139.1 . 1 83 9 9 PHE CD1 C 129.4 . 1 84 9 9 PHE CD2 C 129.4 . 1 85 9 9 PHE CE1 C 128.4 . 1 86 9 9 PHE CE2 C 128.4 . 1 87 9 9 PHE CZ C 126.4 . 1 88 10 10 GLY H H 7.32 . 1 89 10 10 GLY HA2 H 3.34 . 2 90 10 10 GLY HA3 H 3.92 . 2 91 10 10 GLY CA C 43.1 . 1 92 11 11 VAL H H 7.55 . 1 93 11 11 VAL HA H 4.54 . 1 94 11 11 VAL HB H 2.29 . 1 95 11 11 VAL HG1 H 0.94 . 2 96 11 11 VAL HG2 H 0.88 . 2 97 11 11 VAL CA C 55.7 . 1 98 11 11 VAL CB C 31.5 . 1 99 11 11 VAL CG1 C 23.5 . 2 100 11 11 VAL CG2 C 21.0 . 2 101 12 12 LEU H H 8.06 . 1 102 12 12 LEU HA H 4.61 . 1 103 12 12 LEU HB2 H 1.52 . 2 104 12 12 LEU HB3 H 1.76 . 2 105 12 12 LEU HG H 1.76 . 1 106 12 12 LEU HD1 H 0.92 . 2 107 12 12 LEU HD2 H 0.86 . 2 108 12 12 LEU CA C 52.6 . 1 109 12 12 LEU CB C 39.6 . 1 110 12 12 LEU CG C 24.2 . 1 111 12 12 LEU CD1 C 23.5 . 2 112 12 12 LEU CD2 C 21.0 . 2 113 13 13 ALA H H 7.39 . 1 114 13 13 ALA HA H 4.38 . 1 115 13 13 ALA HB H 0.92 . 1 116 13 13 ALA CA C 48.3 . 1 117 13 13 ALA CB C 21.0 . 1 118 14 14 GLN H H 8.10 . 1 119 14 14 GLN HA H 4.18 . 1 120 14 14 GLN HB2 H 1.56 . 2 121 14 14 GLN HB3 H 1.89 . 2 122 14 14 GLN HG2 H 2.00 . 2 123 14 14 GLN HG3 H 2.16 . 2 124 14 14 GLN HE21 H 7.06 . 2 125 14 14 GLN HE22 H 6.75 . 2 126 14 14 GLN CA C 52.6 . 1 127 14 14 GLN CB C 28.1 . 1 128 14 14 GLN CG C 31.6 . 1 129 15 15 LEU H H 7.99 . 1 130 15 15 LEU HA H 4.39 . 1 131 15 15 LEU HB2 H 1.39 . 2 132 15 15 LEU HB3 H 1.51 . 2 133 15 15 LEU HG H 1.63 . 1 134 15 15 LEU HD1 H 0.92 . 2 135 15 15 LEU HD2 H 0.89 . 2 136 15 15 LEU CA C 49.7 . 1 137 15 15 LEU CB C 39.9 . 1 138 15 15 LEU CG C 24.3 . 1 139 15 15 LEU CD1 C 22.0 . 2 140 15 15 LEU CD2 C 23.1 . 2 141 16 16 PRO HA H 4.29 . 1 142 16 16 PRO HB2 H 1.83 . 2 143 16 16 PRO HB3 H 1.96 . 2 144 16 16 PRO HG2 H 1.83 . 2 145 16 16 PRO HG3 H 1.95 . 2 146 16 16 PRO HD2 H 3.52 . 2 147 16 16 PRO HD3 H 3.65 . 2 148 16 16 PRO CA C 59.4 . 1 149 16 16 PRO CB C 29.2 . 1 150 16 16 PRO CG C 24.6 . 1 151 16 16 PRO CD C 46.8 . 1 152 17 17 GLY H H 8.11 . 1 153 17 17 GLY HA2 H 3.62 . 2 154 17 17 GLY HA3 H 3.77 . 2 155 17 17 GLY CA C 40.8 . 1 stop_ save_