data_36017 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of a new lasso peptide sphaericin ; _BMRB_accession_number 36017 _BMRB_flat_file_name bmr36017.str _Entry_type original _Submission_date 2016-09-06 _Accession_date 2016-06-08 _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 Inoue Y. . . 4 Suzuki M. . . 5 Dohra H. . . 6 Suzuki T. . . 7 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" 126 "13C chemical shifts" 89 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-06-12 original BMRB . stop_ _Original_release_date 2017-06-08 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Sphaericin, a Lasso Peptide from the Rare Actinomycete Planomonospora sphaerica ; _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 Kodani S. . . 2 Inoue Y. . . 3 Suzuki M. . . 4 Dohra H. . . 5 Suzuki T. . . 6 Hemmi H. . . 7 Ohnishi-Kameyama M. . . stop_ _Journal_abbreviation 'Eur. J. Org. Chem.' _Journal_volume 2017 _Journal_issue 8 _Journal_ISSN 1434-193X _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1177 _Page_last 1183 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Uncharacterized protein' _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 entity_1 _Molecular_mass 2175.509 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence ; GLPIGWWIERPSGWYFPI ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 LEU 3 3 PRO 4 4 ILE 5 5 GLY 6 6 TRP 7 7 TRP 8 8 ILE 9 9 GLU 10 10 ARG 11 11 PRO 12 12 SER 13 13 GLY 14 14 TRP 15 15 TYR 16 16 PHE 17 17 PRO 18 18 ILE 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 'Planomonospora sphaerica' 161355 Bacteria . Planomonospora sphaerica 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 '10 mg/mL NA-C,H peptide, DMSO' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 10 mg/mL NA-C,H DMSO-d6 100 % 'natural abundance' 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 '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' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 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-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_1 save_ save_2D_1H-13C_HMBC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMBC' _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_TOCSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 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-1H TOCSY' '2D DQF-COSY' '2D 1H-1H NOESY' '2D 1H-13C HMBC' 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 7.82 . 1 2 1 1 GLY HA2 H 4.43 . 2 3 1 1 GLY HA3 H 3.16 . 2 4 1 1 GLY CA C 42.4 . 1 5 2 2 LEU H H 8.93 . 1 6 2 2 LEU HA H 5.12 . 1 7 2 2 LEU HB2 H 2.75 . 1 8 2 2 LEU HB3 H 2.75 . 1 9 2 2 LEU HG H 1.43 . 1 10 2 2 LEU HD1 H 1.04 . 2 11 2 2 LEU HD2 H 1.20 . 2 12 2 2 LEU CA C 48.7 . 1 13 2 2 LEU CB C 40.3 . 1 14 2 2 LEU CG C 24.6 . 1 15 2 2 LEU CD1 C 21.8 . 2 16 2 2 LEU CD2 C 23.7 . 2 17 3 3 PRO HA H 4.68 . 1 18 3 3 PRO HB2 H 2.21 . 2 19 3 3 PRO HB3 H 2.01 . 2 20 3 3 PRO HG2 H 2.07 . 2 21 3 3 PRO HG3 H 1.86 . 2 22 3 3 PRO HD2 H 3.73 . 1 23 3 3 PRO HD3 H 3.73 . 1 24 3 3 PRO CA C 60.5 . 1 25 3 3 PRO CB C 29.2 . 1 26 3 3 PRO CG C 24.5 . 1 27 3 3 PRO CD C 46.8 . 1 28 4 4 ILE H H 6.64 . 1 29 4 4 ILE HA H 4.25 . 1 30 4 4 ILE HB H 1.59 . 1 31 4 4 ILE HG12 H 0.87 . 2 32 4 4 ILE HG13 H 0.84 . 2 33 4 4 ILE HG2 H 0.84 . 1 34 4 4 ILE HD1 H 0.74 . 1 35 4 4 ILE CA C 54.6 . 1 36 4 4 ILE CB C 39.2 . 1 37 4 4 ILE CG1 C 22.7 . 1 38 4 4 ILE CG2 C 15.7 . 1 39 4 4 ILE CD1 C 11.4 . 1 40 5 5 GLY H H 7.28 . 1 41 5 5 GLY HA2 H 1.48 . 2 42 5 5 GLY HA3 H 3.39 . 2 43 5 5 GLY CA C 40.5 . 1 44 6 6 TRP H H 6.78 . 1 45 6 6 TRP HA H 4.63 . 1 46 6 6 TRP HB2 H 2.91 . 2 47 6 6 TRP HB3 H 2.65 . 2 48 6 6 TRP HD1 H 6.76 . 1 49 6 6 TRP HE1 H 10.93 . 1 50 6 6 TRP HE3 H 7.34 . 1 51 6 6 TRP HZ2 H 7.34 . 1 52 6 6 TRP HZ3 H 6.97 . 1 53 6 6 TRP HH2 H 7.07 . 1 54 6 6 TRP CA C 53.4 . 1 55 6 6 TRP CB C 29.4 . 1 56 6 6 TRP CD1 C 122.9 . 1 57 6 6 TRP CD2 C 127.7 . 1 58 6 6 TRP CE2 C 135.6 . 1 59 6 6 TRP CE3 C 118.7 . 1 60 6 6 TRP CZ2 C 110.9 . 1 61 6 6 TRP CZ3 C 118.1 . 1 62 6 6 TRP CH2 C 119.9 . 1 63 7 7 TRP H H 7.75 . 1 64 7 7 TRP HA H 5.18 . 1 65 7 7 TRP HB2 H 2.97 . 2 66 7 7 TRP HB3 H 2.31 . 2 67 7 7 TRP HD1 H 7.32 . 1 68 7 7 TRP HE1 H 10.73 . 1 69 7 7 TRP HE3 H 7.78 . 1 70 7 7 TRP HZ2 H 7.34 . 1 71 7 7 TRP HZ3 H 7.01 . 1 72 7 7 TRP HH2 H 7.09 . 1 73 7 7 TRP CA C 50.7 . 1 74 7 7 TRP CB C 30.5 . 1 75 7 7 TRP CD1 C 122.1 . 1 76 7 7 TRP CD2 C 127.0 . 1 77 7 7 TRP CE2 C 136.3 . 1 78 7 7 TRP CE3 C 117.7 . 1 79 7 7 TRP CZ2 C 111.6 . 1 80 7 7 TRP CZ3 C 118.6 . 1 81 7 7 TRP CH2 C 121.3 . 1 82 8 8 ILE H H 8.41 . 1 83 8 8 ILE HA H 3.98 . 1 84 8 8 ILE HB H 1.41 . 1 85 8 8 ILE HG12 H 1.41 . 2 86 8 8 ILE HG13 H 1.34 . 2 87 8 8 ILE HG2 H 0.55 . 1 88 8 8 ILE HD1 H 0.61 . 1 89 8 8 ILE CA C 59.3 . 1 90 8 8 ILE CB C 36.1 . 1 91 8 8 ILE CG1 C 24.3 . 1 92 8 8 ILE CG2 C 15.5 . 1 93 8 8 ILE CD1 C 11.7 . 1 94 9 9 GLU H H 7.56 . 1 95 9 9 GLU HA H 4.62 . 1 96 9 9 GLU HB2 H 1.70 . 2 97 9 9 GLU HB3 H 1.54 . 2 98 9 9 GLU HG2 H 1.81 . 2 99 9 9 GLU HG3 H 1.71 . 2 100 9 9 GLU CA C 49.2 . 1 101 9 9 GLU CB C 27.8 . 1 102 9 9 GLU CG C 30.4 . 1 103 10 10 ARG H H 7.93 . 1 104 10 10 ARG HA H 4.22 . 1 105 10 10 ARG HB2 H 1.48 . 2 106 10 10 ARG HB3 H 1.35 . 2 107 10 10 ARG HG2 H 1.42 . 2 108 10 10 ARG HG3 H 1.28 . 2 109 10 10 ARG HD2 H 3.00 . 1 110 10 10 ARG HD3 H 3.00 . 1 111 10 10 ARG HE H 7.45 . 1 112 10 10 ARG CA C 49.5 . 1 113 10 10 ARG CB C 28.1 . 1 114 10 10 ARG CG C 25.0 . 1 115 10 10 ARG CD C 40.5 . 1 116 10 10 ARG CZ C 156.5 . 1 117 11 11 PRO HA H 4.27 . 1 118 11 11 PRO HB2 H 2.08 . 2 119 11 11 PRO HB3 H 1.98 . 2 120 11 11 PRO HG2 H 1.78 . 1 121 11 11 PRO HG3 H 1.78 . 1 122 11 11 PRO HD2 H 3.31 . 1 123 11 11 PRO HD3 H 3.31 . 1 124 11 11 PRO CA C 60.7 . 1 125 11 11 PRO CB C 31.6 . 1 126 11 11 PRO CG C 21.6 . 1 127 11 11 PRO CD C 46.1 . 1 128 12 12 SER H H 6.59 . 1 129 12 12 SER HA H 4.18 . 1 130 12 12 SER HB2 H 3.53 . 2 131 12 12 SER HB3 H 3.46 . 2 132 12 12 SER HG H 4.62 . 1 133 12 12 SER CA C 54.4 . 1 134 12 12 SER CB C 61.6 . 1 135 13 13 GLY H H 8.84 . 1 136 13 13 GLY HA2 H 3.98 . 2 137 13 13 GLY HA3 H 2.91 . 2 138 13 13 GLY CA C 41.5 . 1 139 14 14 TRP H H 9.15 . 1 140 14 14 TRP HA H 5.54 . 1 141 14 14 TRP HB2 H 2.61 . 2 142 14 14 TRP HB3 H 2.10 . 2 143 14 14 TRP HD1 H 6.53 . 1 144 14 14 TRP HE1 H 10.49 . 1 145 14 14 TRP HE3 H 7.21 . 1 146 14 14 TRP HZ2 H 7.10 . 1 147 14 14 TRP HZ3 H 6.77 . 1 148 14 14 TRP HH2 H 6.86 . 1 149 14 14 TRP CA C 53.7 . 1 150 14 14 TRP CB C 30.3 . 1 151 14 14 TRP CG C 110.8 . 1 152 14 14 TRP CD1 C 122.8 . 1 153 14 14 TRP CD2 C 127.7 . 1 154 14 14 TRP CE2 C 136.1 . 1 155 14 14 TRP CE3 C 119.2 . 1 156 14 14 TRP CZ2 C 110.4 . 1 157 14 14 TRP CZ3 C 118.6 . 1 158 14 14 TRP CH2 C 120.9 . 1 159 15 15 TYR H H 9.24 . 1 160 15 15 TYR HA H 4.86 . 1 161 15 15 TYR HB2 H 3.26 . 2 162 15 15 TYR HB3 H 3.12 . 2 163 15 15 TYR HD1 H 6.91 . 3 164 15 15 TYR HD2 H 6.91 . 3 165 15 15 TYR HE1 H 6.76 . 3 166 15 15 TYR HE2 H 6.76 . 3 167 15 15 TYR HH H 9.07 . 1 168 15 15 TYR CA C 53.3 . 1 169 15 15 TYR CB C 36.4 . 1 170 15 15 TYR CG C 129.4 . 1 171 15 15 TYR CD1 C 131.4 . 3 172 15 15 TYR CD2 C 131.4 . 3 173 15 15 TYR CE1 C 115.1 . 3 174 15 15 TYR CE2 C 115.1 . 3 175 15 15 TYR CZ C 155.6 . 1 176 16 16 PHE H H 9.22 . 1 177 16 16 PHE HA H 4.40 . 1 178 16 16 PHE HB2 H 2.87 . 2 179 16 16 PHE HB3 H 2.49 . 2 180 16 16 PHE HD1 H 6.72 . 3 181 16 16 PHE HD2 H 6.72 . 3 182 16 16 PHE HE1 H 6.88 . 3 183 16 16 PHE HE2 H 6.88 . 3 184 16 16 PHE HZ H 6.77 . 1 185 16 16 PHE CA C 51.8 . 1 186 16 16 PHE CB C 36.5 . 1 187 16 16 PHE CG C 136.3 . 1 188 16 16 PHE CD1 C 129.4 . 3 189 16 16 PHE CD2 C 129.4 . 3 190 16 16 PHE CE1 C 128.1 . 3 191 16 16 PHE CE2 C 128.1 . 3 192 16 16 PHE CZ C 125.2 . 1 193 17 17 PRO HA H 4.41 . 1 194 17 17 PRO HB2 H 1.49 . 2 195 17 17 PRO HB3 H 1.41 . 2 196 17 17 PRO HG2 H 1.26 . 2 197 17 17 PRO HG3 H 0.68 . 2 198 17 17 PRO HD2 H 3.29 . 2 199 17 17 PRO HD3 H 2.54 . 2 200 17 17 PRO CA C 58.9 . 1 201 17 17 PRO CB C 28.4 . 1 202 17 17 PRO CG C 23.5 . 1 203 17 17 PRO CD C 46.9 . 1 204 18 18 ILE H H 8.02 . 1 205 18 18 ILE HA H 4.13 . 1 206 18 18 ILE HB H 1.79 . 1 207 18 18 ILE HG12 H 1.21 . 2 208 18 18 ILE HG13 H 1.20 . 2 209 18 18 ILE HG2 H 0.87 . 1 210 18 18 ILE HD1 H 0.84 . 1 211 18 18 ILE CA C 56.3 . 1 212 18 18 ILE CB C 36.4 . 1 213 18 18 ILE CG1 C 24.6 . 1 214 18 18 ILE CG2 C 15.5 . 1 215 18 18 ILE CD1 C 11.4 . 1 stop_ save_