data_25741 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of octyl-tridecaptin A1 in DPC micelles containing Gram-negative lipid II ; _BMRB_accession_number 25741 _BMRB_flat_file_name bmr25741.str _Entry_type original _Submission_date 2016-09-22 _Accession_date 2016-09-22 _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 Cochrane Stephen A. . 2 Findlay Brandon . . 3 Bakhtiary Alireza . . 4 Rodriguez-Lopez Eva M. . 5 Vederas John C. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 73 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-10-11 update BMRB 'update entry citation' 2016-09-22 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25737 'octyl-tridecaptin A1 in DPC micelles' stop_ _Original_release_date 2016-09-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Antimicrobial lipopeptide tridecaptin A1 selectively binds to Gram-negative lipid II. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27688760 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cochrane Stephen A. . 2 Findlay Brandon . . 3 Bakhtiary Alireza . . 4 Acedo Jeella Z. . 5 Rodriguez-Lopez Eva M. . 6 Mercier Pascal . . 7 Vederas John C. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_name_full 'Proceedings of the National Academy of Sciences of the United States of America' _Journal_volume 113 _Journal_issue 41 _Journal_ISSN 1091-6490 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11561 _Page_last 11566 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'octyl-tridecaptin A1 in DPC micelles containing Gram-negative lipid II' _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 1867.077 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence ; XXGXXSXXFEVXA ; loop_ _Residue_seq_code _Residue_label 1 DVA 2 4FO 3 GLY 4 DSN 5 DTR 6 SER 7 DAB 8 4FO 9 PHE 10 GLU 11 VAL 12 28J 13 ALA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DVA _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-VALINE _BMRB_code DVA _PDB_code DVA _Standard_residue_derivative . _Molecular_mass 117.146 _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 . ? CG1 CG1 C . 0 . ? CG2 CG2 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 . ? HB HB H . 0 . ? HG11 HG11 H . 0 . ? HG12 HG12 H . 0 . ? HG13 HG13 H . 0 . ? HG21 HG21 H . 0 . ? HG22 HG22 H . 0 . ? HG23 HG23 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 CG1 ? ? SING CB CG2 ? ? SING CB HB ? ? SING CG1 HG11 ? ? SING CG1 HG12 ? ? SING CG1 HG13 ? ? SING CG2 HG21 ? ? SING CG2 HG22 ? ? SING CG2 HG23 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_4FO _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common '(2R)-2,4-diaminobutanoic acid' _BMRB_code 4FO _PDB_code 4FO _Standard_residue_derivative . _Molecular_mass 118.134 _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 . ? NZ NZ N . 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 . ? HG3 HG3 H . 0 . ? HG2 HG2 H . 0 . ? HZ3 HZ3 H . 0 . ? HZ2 HZ2 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 CG NZ ? ? SING CG CB ? ? SING N CA ? ? SING CA CB ? ? SING CA C ? ? DOUB C O ? ? SING C OXT ? ? SING N H ? ? SING N H1 ? ? SING CA HA ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG HG3 ? ? SING CG HG2 ? ? SING NZ HZ3 ? ? SING NZ HZ2 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DSN _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-SERINE _BMRB_code DSN _PDB_code DSN _Standard_residue_derivative . _Molecular_mass 105.093 _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 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? OG OG O . 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 . ? HG HG 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 OG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING OG HG ? ? stop_ save_ save_chem_comp_DTR _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-TRYPTOPHAN _BMRB_code DTR _PDB_code DTR _Standard_residue_derivative . _Molecular_mass 204.225 _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 . ? CD1 CD1 C . 0 . ? NE1 NE1 N . 0 . ? CE2 CE2 C . 0 . ? CZ2 CZ2 C . 0 . ? CH2 CH2 C . 0 . ? CZ3 CZ3 C . 0 . ? CE3 CE3 C . 0 . ? CD2 CD2 C . 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 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HE1 HE1 H . 0 . ? HZ2 HZ2 H . 0 . ? HH2 HH2 H . 0 . ? HZ3 HZ3 H . 0 . ? HE3 HE3 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 CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 NE1 ? ? SING CD1 HD1 ? ? SING NE1 CE2 ? ? SING NE1 HE1 ? ? DOUB CE2 CZ2 ? ? SING CE2 CD2 ? ? SING CZ2 CH2 ? ? SING CZ2 HZ2 ? ? DOUB CH2 CZ3 ? ? SING CH2 HH2 ? ? SING CZ3 CE3 ? ? SING CZ3 HZ3 ? ? DOUB CE3 CD2 ? ? SING CE3 HE3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DAB _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common '2,4-DIAMINOBUTYRIC ACID' _BMRB_code DAB _PDB_code DAB _Standard_residue_derivative . _Molecular_mass 118.134 _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 . ? ND ND N . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 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 C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG ND ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING ND HD1 ? ? SING ND HD2 ? ? SING OXT HXT ? ? 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_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity 'Paenibacillus terrae' 159743 Bacteria . Paenibacillus 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 $entity 'chemical synthesis' . Paenibacillus terrae . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'containing Gram-negative lipid II' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity . mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 mM 'natural abundance' DPC 180 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'G??ntert P.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Varian_600_MHz _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _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 pH 6 . 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 DPC H 1 'methylene protons' ppm 1.52 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_chem_shift_list_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 $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 DVA H1 H 7.7087 0.0000 1 2 1 1 DVA HA H 4.2928 0.0000 1 3 1 1 DVA HB H 2.0951 0.0000 1 4 1 1 DVA HG11 H 0.8998 0.0000 2 5 1 1 DVA HG12 H 0.8998 0.0000 2 6 1 1 DVA HG13 H 0.8998 0.0000 2 7 1 1 DVA HG21 H 0.8998 0.0000 2 8 1 1 DVA HG22 H 0.8998 0.0000 2 9 1 1 DVA HG23 H 0.8998 0.0000 2 10 2 2 4FO H H 8.5923 0.0000 1 11 2 2 4FO HA H 4.9228 0.0000 1 12 2 2 4FO HB2 H 2.1503 0.0000 2 13 2 2 4FO HB3 H 1.9929 0.0000 2 14 2 2 4FO HG2 H 2.9270 0.0000 2 15 2 2 4FO HG3 H 2.9308 0.0000 2 16 3 3 GLY H H 8.4556 0.0000 1 17 3 3 GLY HA2 H 4.0653 0.0000 2 18 3 3 GLY HA3 H 3.8393 0.0000 2 19 4 4 DSN H H 8.1429 0.0000 1 20 4 4 DSN HA H 4.8482 0.0000 1 21 4 4 DSN HB2 H 3.6434 0.0000 2 22 4 4 DSN HB3 H 3.6434 0.0000 2 23 5 5 DTR H H 8.4851 0.0000 1 24 5 5 DTR HA H 4.7587 0.0000 1 25 5 5 DTR HB2 H 3.1545 0.0000 2 26 5 5 DTR HB3 H 3.1544 0.0000 2 27 5 5 DTR HD1 H 7.2498 0.0000 1 28 5 5 DTR HE1 H 10.5248 0.0000 1 29 5 5 DTR HE3 H 7.5014 0.0000 1 30 5 5 DTR HH2 H 7.0243 0.0000 1 31 5 5 DTR HZ2 H 7.4141 0.0000 1 32 5 5 DTR HZ3 H 6.9472 0.0000 1 33 6 6 SER H H 8.6218 0.0000 1 34 6 6 SER HA H 3.9938 0.0000 1 35 6 6 SER HB2 H 3.7382 0.0000 2 36 6 6 SER HB3 H 3.4960 0.0000 2 37 7 7 DAB H H 8.5442 0.0000 1 38 7 7 DAB HA H 4.3247 0.0000 1 39 7 7 DAB HB2 H 2.1534 0.0000 2 40 7 7 DAB HB3 H 1.9753 0.0000 2 41 7 7 DAB HG2 H 3.0104 0.0000 2 42 7 7 DAB HG3 H 3.0127 0.0000 2 43 8 8 4FO H H 7.9073 0.0000 1 44 8 8 4FO HA H 4.4886 0.0000 1 45 8 8 4FO HB2 H 2.0442 0.0000 2 46 8 8 4FO HB3 H 1.8089 0.0000 2 47 8 8 4FO HG2 H 2.8130 0.0000 2 48 8 8 4FO HG3 H 2.8158 0.0000 2 49 9 9 PHE H H 8.6407 0.0000 1 50 9 9 PHE HA H 4.8875 0.0000 1 51 9 9 PHE HB2 H 3.0756 0.0000 2 52 9 9 PHE HB3 H 2.9114 0.0000 2 53 9 9 PHE HD1 H 7.2824 0.0000 3 54 9 9 PHE HD2 H 7.2148 0.0000 3 55 9 9 PHE HE1 H 7.1436 0.0000 3 56 9 9 PHE HE2 H 7.1430 0.0000 3 57 10 10 GLU H H 8.3927 0.0000 1 58 10 10 GLU HA H 4.5399 0.0000 1 59 10 10 GLU HB2 H 1.9621 0.0000 2 60 10 10 GLU HB3 H 1.8339 0.0000 2 61 10 10 GLU HG2 H 2.1960 0.0000 2 62 10 10 GLU HG3 H 2.1713 0.0000 2 63 11 11 VAL H H 8.2296 0.0000 1 64 11 11 VAL HA H 4.5548 0.0000 1 65 11 11 VAL HB H 1.9607 0.0000 1 66 11 11 VAL HG1 H 0.9180 0.0000 2 67 11 11 VAL HG2 H 0.9194 0.0000 2 68 12 12 28J H20 H 8.1460 0.0000 1 69 12 12 28J H21 H 4.1142 0.0000 1 70 12 12 28J H26 H 1.3133 0.0000 2 71 13 13 ALA H H 7.9346 0.0000 1 72 13 13 ALA HA H 4.1132 0.0000 1 73 13 13 ALA HB H 1.3091 0.0000 1 stop_ save_