data_36158 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Nukacin ISK-1 in inactive state ; _BMRB_accession_number 36158 _BMRB_flat_file_name bmr36158.str _Entry_type original _Submission_date 2018-01-19 _Accession_date 2018-02-27 _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 Kohda D. . . 2 Fujinami D. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 155 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-06-05 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 36157 'Nukacin ISK-1 in active state' stop_ _Original_release_date 2019-01-27 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30272026 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Fujinami Daisuke . . 2 Mahin Abdullah-Al A. . 3 Elsayed 'Khaled M' M. . 4 Islam 'Mohammad R' R. . 5 Nagao Jun-Ichi I. . 6 Roy Urmi . . 7 Momin Sabrina . . 8 Zendo Takeshi . . 9 Kohda Daisuke . . 10 Sonomoto Kenji . . stop_ _Journal_abbreviation 'Commun. Biol.' _Journal_name_full 'Communications Biology' _Journal_volume 1 _Journal_issue . _Journal_ISSN 2399-3642 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 150 _Page_last 150 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Lantibiotic nukacin' _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 'Lantibiotic nukacin' _Molecular_mass 2970.535 _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; KKKSGVIPXVXHDCHMNXFQ FVFXCCS ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 LYS 2 2 LYS 3 3 LYS 4 4 SER 5 5 GLY 6 6 VAL 7 7 ILE 8 8 PRO 9 9 DBB 10 10 VAL 11 11 DAL 12 12 HIS 13 13 ASP 14 14 CYS 15 15 HIS 16 16 MET 17 17 ASN 18 18 DAL 19 19 PHE 20 20 GLN 21 21 PHE 22 22 VAL 23 23 PHE 24 24 DBU 25 25 CYS 26 26 CYS 27 27 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DAL _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-ALANINE _BMRB_code DAL _PDB_code DAL _Standard_residue_derivative . _Molecular_mass 89.093 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB HB1 ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DBB _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common 'D-ALPHA-AMINOBUTYRIC ACID' _BMRB_code DBB _PDB_code DBB _Standard_residue_derivative . _Molecular_mass 103.120 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG1 HG1 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING CA C ? ? SING CA CB ? ? DOUB C O ? ? SING CB CG ? ? SING C OXT ? ? SING N H ? ? SING N H1 ? ? SING CA HA ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG HG1 ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DBU _Saveframe_category polymer_residue _Mol_type 'PEPTIDE LINKING' _Name_common '(2Z)-2-AMINOBUT-2-ENOIC ACID' _BMRB_code DBU _PDB_code DBU _Standard_residue_derivative . _Molecular_mass 101.104 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HB HB H . 0 . ? HG1 HG1 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N H2 ? ? DOUB CA CB ? ? SING CA C ? ? SING CB CG ? ? SING CB HB ? ? SING CG HG1 ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ 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 'Staphylococcus warneri' 1292 Bacteria . Staphylococcus warneri 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 '1.1 mM nukacin ISK-1, 10 mM sodium phosphate, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.1 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert P.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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_ ####################### # 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 . mM pH 6.0 . pH pressure 1 . atm temperature 283 . 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 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 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-1H TOCSY' '2D 1H-1H NOESY' 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 LYS HA H 3.778 0.010 . 2 1 1 LYS HB2 H 1.663 0.006 . 3 1 1 LYS HB3 H 1.663 0.006 . 4 1 1 LYS HG2 H 1.231 0.000 . 5 1 1 LYS HG3 H 1.231 0.000 . 6 1 1 LYS HD2 H 1.478 0.000 . 7 1 1 LYS HD3 H 1.478 0.000 . 8 1 1 LYS HE2 H 2.779 0.000 . 9 1 1 LYS HE3 H 2.779 0.000 . 10 2 2 LYS H H 8.592 0.002 . 11 2 2 LYS HA H 4.087 0.000 . 12 2 2 LYS HB2 H 1.536 0.000 . 13 2 2 LYS HB3 H 1.536 0.000 . 14 2 2 LYS HG2 H 1.199 0.000 . 15 2 2 LYS HG3 H 1.199 0.000 . 16 2 2 LYS HD2 H 2.334 0.000 . 17 2 2 LYS HD3 H 2.334 0.000 . 18 2 2 LYS HE2 H 2.739 0.000 . 19 2 2 LYS HE3 H 2.739 0.000 . 20 3 3 LYS H H 8.465 0.000 . 21 3 3 LYS HA H 4.092 0.006 . 22 3 3 LYS HB2 H 1.559 0.010 . 23 3 3 LYS HB3 H 1.559 0.010 . 24 3 3 LYS HG2 H 1.227 0.005 . 25 3 3 LYS HG3 H 1.227 0.005 . 26 3 3 LYS HD2 H 2.334 0.000 . 27 3 3 LYS HD3 H 2.334 0.000 . 28 3 3 LYS HE2 H 2.748 0.000 . 29 3 3 LYS HE3 H 2.748 0.000 . 30 4 4 SER H H 8.274 0.000 . 31 4 4 SER HA H 4.180 0.006 . 32 4 4 SER HB2 H 3.597 0.005 . 33 4 4 SER HB3 H 3.597 0.005 . 34 5 5 GLY H H 8.268 0.001 . 35 5 5 GLY HA2 H 3.685 0.000 . 36 5 5 GLY HA3 H 3.594 0.000 . 37 6 6 VAL H H 7.522 0.001 . 38 6 6 VAL HA H 3.594 0.009 . 39 6 6 VAL HB H 0.939 0.017 . 40 6 6 VAL HG1 H 0.262 0.010 . 41 6 6 VAL HG2 H 0.178 0.012 . 42 7 7 ILE H H 7.758 0.002 . 43 7 7 ILE HA H 4.441 0.010 . 44 7 7 ILE HB H 1.614 0.014 . 45 7 7 ILE HG12 H 0.790 0.011 . 46 7 7 ILE HG13 H 0.790 0.011 . 47 7 7 ILE HG2 H 0.709 0.008 . 48 7 7 ILE HD1 H 0.617 0.000 . 49 8 8 PRO HA H 4.110 0.010 . 50 8 8 PRO HB2 H 2.086 0.003 . 51 8 8 PRO HB3 H 1.967 0.011 . 52 8 8 PRO HG2 H 1.769 0.024 . 53 8 8 PRO HG3 H 1.769 0.024 . 54 8 8 PRO HD2 H 3.819 0.013 . 55 8 8 PRO HD3 H 3.553 0.017 . 56 9 9 DBB H H 6.928 0.001 . 57 9 9 DBB HA H 4.349 0.013 . 58 9 9 DBB HB2 H 3.356 0.012 . 59 9 9 DBB HG1 H 1.032 0.021 . 60 10 10 VAL H H 7.509 0.001 . 61 10 10 VAL HA H 4.113 0.010 . 62 10 10 VAL HB H 2.095 0.011 . 63 10 10 VAL HG1 H 0.867 0.010 . 64 10 10 VAL HG2 H 0.755 0.011 . 65 11 11 DAL H H 8.935 0.003 . 66 11 11 DAL HA H 4.456 0.013 . 67 11 11 DAL HB1 H 2.875 0.015 . 68 11 11 DAL HB2 H 2.442 0.021 . 69 12 12 HIS H H 8.505 0.006 . 70 12 12 HIS HA H 4.214 0.006 . 71 12 12 HIS HB2 H 2.945 0.002 . 72 12 12 HIS HB3 H 2.945 0.002 . 73 12 12 HIS HD2 H 6.984 0.008 . 74 13 13 ASP H H 8.964 0.004 . 75 13 13 ASP HA H 4.059 0.014 . 76 13 13 ASP HB2 H 2.848 0.003 . 77 13 13 ASP HB3 H 2.412 0.034 . 78 14 14 CYS H H 8.118 0.001 . 79 14 14 CYS HA H 3.939 0.010 . 80 14 14 CYS HB2 H 2.555 0.009 . 81 14 14 CYS HB3 H 2.555 0.009 . 82 15 15 HIS H H 8.479 0.002 . 83 15 15 HIS HA H 4.063 0.010 . 84 15 15 HIS HB2 H 3.025 0.006 . 85 15 15 HIS HB3 H 3.025 0.006 . 86 15 15 HIS HD2 H 7.104 0.002 . 87 16 16 MET H H 7.030 0.004 . 88 16 16 MET HA H 4.539 0.013 . 89 16 16 MET HB2 H 1.564 0.010 . 90 16 16 MET HB3 H 1.564 0.010 . 91 16 16 MET HG2 H 2.221 0.009 . 92 16 16 MET HG3 H 2.008 0.004 . 93 17 17 ASN H H 8.312 0.001 . 94 17 17 ASN HA H 3.933 0.010 . 95 17 17 ASN HB2 H 2.316 0.014 . 96 17 17 ASN HB3 H 2.171 0.026 . 97 17 17 ASN HD21 H 7.309 0.000 . 98 17 17 ASN HD22 H 6.759 0.002 . 99 18 18 DAL H H 7.422 0.003 . 100 18 18 DAL HA H 3.863 0.012 . 101 18 18 DAL HB1 H 3.166 0.016 . 102 18 18 DAL HB2 H 2.084 0.015 . 103 19 19 PHE H H 8.147 0.001 . 104 19 19 PHE HA H 4.373 0.013 . 105 19 19 PHE HB2 H 3.047 0.011 . 106 19 19 PHE HB3 H 2.793 0.003 . 107 19 19 PHE HD1 H 6.932 0.006 . 108 19 19 PHE HD2 H 6.932 0.006 . 109 19 19 PHE HE1 H 7.114 0.005 . 110 19 19 PHE HE2 H 7.114 0.005 . 111 19 19 PHE HZ H 7.053 0.002 . 112 20 20 GLN H H 7.343 0.002 . 113 20 20 GLN HA H 4.347 0.005 . 114 20 20 GLN HB2 H 1.627 0.000 . 115 20 20 GLN HB3 H 1.627 0.000 . 116 20 20 GLN HG2 H 1.985 0.015 . 117 20 20 GLN HG3 H 1.985 0.015 . 118 21 21 PHE H H 8.467 0.002 . 119 21 21 PHE HA H 4.819 0.016 . 120 21 21 PHE HB2 H 2.268 0.012 . 121 21 21 PHE HB3 H 2.442 0.009 . 122 21 21 PHE HD1 H 6.585 0.008 . 123 21 21 PHE HD2 H 6.585 0.008 . 124 21 21 PHE HE1 H 6.938 0.009 . 125 21 21 PHE HE2 H 6.938 0.009 . 126 21 21 PHE HZ H 6.734 0.012 . 127 22 22 VAL H H 8.704 0.004 . 128 22 22 VAL HA H 3.844 0.010 . 129 22 22 VAL HB H 1.646 0.016 . 130 22 22 VAL HG1 H 0.603 0.013 . 131 22 22 VAL HG2 H 0.558 0.029 . 132 23 23 PHE H H 9.350 0.001 . 133 23 23 PHE HA H 4.277 0.007 . 134 23 23 PHE HB2 H 3.215 0.006 . 135 23 23 PHE HB3 H 2.847 0.012 . 136 23 23 PHE HD1 H 7.071 0.006 . 137 23 23 PHE HD2 H 7.071 0.006 . 138 23 23 PHE HE1 H 7.168 0.000 . 139 23 23 PHE HE2 H 7.168 0.000 . 140 23 23 PHE HZ H 7.098 0.000 . 141 24 24 DBU H H 9.347 0.002 . 142 24 24 DBU HB H 6.757 0.011 . 143 24 24 DBU HG1 H 1.490 0.006 . 144 25 25 CYS H H 7.785 0.006 . 145 25 25 CYS HA H 5.008 0.015 . 146 25 25 CYS HB2 H 3.263 0.017 . 147 25 25 CYS HB3 H 2.541 0.014 . 148 26 26 CYS H H 8.724 0.006 . 149 26 26 CYS HA H 3.817 0.003 . 150 26 26 CYS HB2 H 3.072 0.020 . 151 26 26 CYS HB3 H 2.985 0.013 . 152 27 27 SER H H 8.396 0.000 . 153 27 27 SER HA H 4.297 0.000 . 154 27 27 SER HB2 H 3.721 0.000 . 155 27 27 SER HB3 H 3.721 0.000 . stop_ save_