data_27479 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural studies suggest aggregation as one of the modes of action for teixobactin ; _BMRB_accession_number 27479 _BMRB_flat_file_name bmr27479.str _Entry_type original _Submission_date 2018-05-14 _Accession_date 2018-05-14 _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 Oster Carl . . 2 Lewandowski Jozef R. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 57 "13C chemical shifts" 39 "15N chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-01-29 update BMRB 'update entry citation' 2018-09-20 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 27478 'teixobactin in DPC micelles' 27480 'teixobactin:lipid II complex in DPC micelles' stop_ _Original_release_date 2018-05-14 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural studies suggest aggregation as one of the modes of action for teixobactin. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30627403 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Oster Carl . . 2 Walkowiak Grzegorz P. . 3 Hughes Dallas E. . 4 Spoering Amy L. . 5 Peoples Aaron J. . 6 Catherwood Anita C. . 7 Tod Julie A. . 8 Lloyd Adrian J. . 9 Herrmann Torsten . . 10 Lewis Kim . . 11 Dowson Christopher G. . 12 Lewandowski Jozef R. . stop_ _Journal_abbreviation 'Chem. Sci.' _Journal_name_full 'Chemical science' _Journal_volume 9 _Journal_issue 47 _Journal_ISSN 2041-6520 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8850 _Page_last 8859 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'teixobactin in solution' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label teixobactin $teixobactin 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_teixobactin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common teixobactin _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function antibiotic stop_ _Details ; Lactone bond formed between OG1 of 8 D-threonine and C of 11 isoleucine; The residue 10 is: L-allo-Enduracididine; C6 H12 N4 O2. ; ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence ; XISXXISXAXI ; loop_ _Residue_seq_code _Residue_label 1 ZAE 2 ILE 3 SER 4 DGN 5 28J 6 ILE 7 SER 8 DTH 9 ALA 10 XXX 11 ILE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ZAE _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common N-methyl-D-phenylalanine _BMRB_code ZAE _PDB_code ZAE _Standard_residue_derivative . _Molecular_mass 179.216 _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 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CE1 CE1 C . 0 . ? CE2 CE2 C . 0 . ? CZ CZ C . 0 . ? C10 C10 C . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 H . 0 . ? HZ HZ H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H13 H13 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 C10 ? ? SING N H ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 CE1 ? ? SING CD1 HD1 ? ? DOUB CD2 CE2 ? ? SING CD2 HD2 ? ? DOUB CE1 CZ ? ? SING CE1 HE1 ? ? SING CE2 CZ ? ? SING CE2 HE2 ? ? SING CZ HZ ? ? SING C10 H11 ? ? SING C10 H12 ? ? SING C10 H13 ? ? stop_ save_ save_chem_comp_DGN _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-GLUTAMINE _BMRB_code DGN _PDB_code DGN _Standard_residue_derivative . _Molecular_mass 146.144 _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 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? OE1 OE1 O . 0 . ? NE2 NE2 N . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HE21 HE21 H . 0 . ? HE22 HE22 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 C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB CD OE1 ? ? SING CD NE2 ? ? SING NE2 HE21 ? ? SING NE2 HE22 ? ? stop_ save_ save_chem_comp_28J _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-alloisoleucine _BMRB_code 28J _PDB_code 28J _Standard_residue_derivative . _Molecular_mass 131.173 _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 . ? CG2 CG2 C . 0 . ? CG1 CG1 C . 0 . ? CD1 CD1 C . 0 . ? C C C . 0 . ? O O O . 0 . ? H20 H20 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H23 H23 H . 0 . ? H24 H24 H . 0 . ? H25 H25 H . 0 . ? H26 H26 H . 0 . ? H27 H27 H . 0 . ? H28 H28 H . 0 . ? H29 H29 H . 0 . ? H30 H30 H . 0 . ? H2 H2 H . 0 . ? OXT OXT O . 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 CG2 CB ? ? SING CB CG1 ? ? SING CB CA ? ? SING CG1 CD1 ? ? SING CA N ? ? SING CA C ? ? DOUB C O ? ? SING N H20 ? ? SING CA H21 ? ? SING CB H22 ? ? SING CG2 H23 ? ? SING CG2 H24 ? ? SING CG2 H25 ? ? SING CG1 H26 ? ? SING CG1 H27 ? ? SING CD1 H28 ? ? SING CD1 H29 ? ? SING CD1 H30 ? ? SING N H2 ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DTH _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-THREONINE _BMRB_code DTH _PDB_code DTH _Standard_residue_derivative . _Molecular_mass 119.119 _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 . ? CG2 CG2 C . 0 . ? OG1 OG1 O . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB HB H . 0 . ? HG21 HG21 H . 0 . ? HG22 HG22 H . 0 . ? HG23 HG23 H . 0 . ? HG1 HG1 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 HN2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG2 ? ? SING CB OG1 ? ? SING CB HB ? ? SING CG2 HG21 ? ? SING CG2 HG22 ? ? SING CG2 HG23 ? ? SING OG1 HG1 ? ? 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 $teixobactin 'Eleftheria terrae' 1597781 Bacteria . Eleftheria terrae 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 $teixobactin 'purified from the natural source' . Eleftheria terrae . - 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 $teixobactin . mM . 'sodium phosphate' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_3D_HCCH-TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $sample_1 save_ save_3D_HNCACB_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_HNCA_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _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' 0.014 . M pH 6.5 . pH pressure 1 . atm 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-13C HSQC' '3D HCCH-TOCSY' '3D HNCACB' '3D HNCA' 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 teixobactin _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 ZAE H12 H 2.572 0.00 1 2 1 1 ZAE HA H 3.982 0.01 1 3 1 1 ZAE HB2 H 2.978 0.00 1 4 1 1 ZAE HB3 H 3.253 0.00 1 5 1 1 ZAE C10 C 34.758 0.01 1 6 1 1 ZAE CA C 66.007 0.00 1 7 1 1 ZAE CB C 39.435 0.04 1 8 2 2 ILE HA H 4.180 0.00 1 9 2 2 ILE HB H 1.891 0.00 1 10 2 2 ILE HG12 H 1.470 0.00 1 11 2 2 ILE HG13 H 1.198 0.00 1 12 2 2 ILE HG2 H 0.933 0.00 1 13 2 2 ILE HD1 H 0.859 0.00 1 14 2 2 ILE CA C 60.891 0.06 1 15 2 2 ILE CB C 38.458 0.09 1 16 2 2 ILE CG1 C 27.205 0.13 1 17 2 2 ILE CG2 C 17.591 0.03 1 18 2 2 ILE CD1 C 12.646 0.08 1 19 3 3 SER H H 8.389 0.00 1 20 3 3 SER HA H 4.435 0.00 1 21 3 3 SER HB2 H 3.835 0.00 2 22 3 3 SER HB3 H 3.835 0.00 2 23 3 3 SER CA C 58.234 0.03 1 24 3 3 SER CB C 63.952 0.03 1 25 3 3 SER N N 119.929 0.00 1 26 4 4 DGN H H 8.378 0.00 1 27 4 4 DGN HA H 4.379 0.00 1 28 4 4 DGN HB2 H 1.953 0.00 1 29 4 4 DGN HB3 H 2.078 0.00 1 30 4 4 DGN HG2 H 2.320 0.00 1 31 4 4 DGN HG3 H 2.332 0.00 1 32 4 4 DGN HE21 H 6.882 0.00 1 33 4 4 DGN HE22 H 7.557 0.00 1 34 4 4 DGN CA C 55.824 0.25 1 35 4 4 DGN CB C 29.620 0.05 1 36 4 4 DGN CG C 33.848 0.04 1 37 4 4 DGN N N 122.469 0.00 1 38 4 4 DGN NE2 N 112.423 0.01 1 39 5 5 28J H H 8.173 0.00 1 40 5 5 28J HA H 4.306 0.00 1 41 5 5 28J HB H 1.880 0.00 1 42 5 5 28J HG12 H 1.187 0.00 1 43 5 5 28J HG13 H 1.329 0.00 1 44 5 5 28J HG22 H 0.880 0.00 1 45 5 5 28J HD12 H 0.863 0.00 1 46 5 5 28J CA C 60.495 0.04 1 47 5 5 28J CB C 39.273 0.03 1 48 5 5 28J CG1 C 28.272 0.02 1 49 5 5 28J CG2 C 16.743 0.01 1 50 5 5 28J CD1 C 13.391 0.03 1 51 5 5 28J N N 120.555 0.00 1 52 6 6 ILE H H 8.321 0.00 1 53 6 6 ILE HA H 4.190 0.00 1 54 6 6 ILE HB H 1.801 0.00 1 55 6 6 ILE HG12 H 1.155 0.01 1 56 6 6 ILE HG13 H 1.452 0.00 1 57 6 6 ILE HG2 H 0.889 0.00 1 58 6 6 ILE HD1 H 0.868 0.00 1 59 6 6 ILE CA C 60.975 0.04 1 60 6 6 ILE CB C 39.111 0.04 1 61 6 6 ILE CG1 C 27.464 0.01 1 62 6 6 ILE CG2 C 17.158 0.06 1 63 6 6 ILE CD1 C 12.649 0.05 1 64 6 6 ILE N N 123.485 0.00 1 65 7 7 SER H H 8.703 0.00 1 66 7 7 SER HA H 4.475 0.00 1 67 7 7 SER HB2 H 3.913 0.00 1 68 7 7 SER HB3 H 3.958 0.00 1 69 7 7 SER CA C 59.297 0.06 1 70 7 7 SER CB C 63.452 0.06 1 71 7 7 SER N N 121.907 0.00 1 72 8 8 DTH HB H 5.567 0.00 1 73 8 8 DTH HG22 H 1.279 0.00 1 74 8 8 DTH CA C 59.135 0.04 1 75 8 8 DTH CB C 74.768 0.01 1 76 8 8 DTH CG2 C 17.751 0.02 1 77 9 9 ALA H H 8.088 0.00 1 78 9 9 ALA HA H 4.186 0.00 1 79 9 9 ALA HB H 1.462 0.00 1 80 9 9 ALA CA C 55.226 0.02 1 81 9 9 ALA CB C 18.334 0.13 1 82 9 9 ALA N N 125.266 0.00 1 83 10 10 XXX HA H 4.533 0.00 1 84 10 10 XXX HB2 H 2.065 0.00 1 85 10 10 XXX HB3 H 2.143 0.00 1 86 10 10 XXX HG H 4.131 0.00 1 87 10 10 XXX HD1 H 3.438 0.00 1 88 10 10 XXX HD2 H 3.863 0.00 1 89 10 10 XXX CA C 54.626 0.05 1 90 10 10 XXX CB C 38.653 0.05 1 91 10 10 XXX CG C 55.327 0.00 1 92 10 10 XXX CD C 50.670 0.03 1 93 11 11 ILE HA H 3.938 0.00 1 94 11 11 ILE HB H 1.543 0.00 1 95 11 11 ILE HG12 H 0.924 0.00 1 96 11 11 ILE HG13 H 0.719 0.00 1 97 11 11 ILE HG2 H 0.662 0.00 1 98 11 11 ILE HD1 H 0.675 0.00 1 99 11 11 ILE CA C 61.402 0.03 1 100 11 11 ILE CB C 38.484 0.03 1 101 11 11 ILE CG1 C 26.989 0.05 1 102 11 11 ILE CG2 C 17.273 0.02 1 103 11 11 ILE CD1 C 12.818 0.02 1 stop_ save_