data_34272 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of temporin B KKG6A in SDS micelles ; _BMRB_accession_number 34272 _BMRB_flat_file_name bmr34272.str _Entry_type original _Submission_date 2018-05-12 _Accession_date 2018-05-12 _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 Manzo G. . . 2 Mason J. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 spectral_peak_list 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 85 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-06-18 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 34273 'NMR structure of temporin B L1FK' 34274 'NMR structure of temporin B' stop_ _Original_release_date 2018-06-06 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity ; _Citation_status 'in preparation' _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 Manzo G. . . 2 Ferguson P. M. . 3 Gustilo V. B. . 4 Ali H. . . 5 Bui T. T. . 6 Drake A. F. . 7 Atkinson R. A. . 8 Batoni G. . . 9 Lorenz C. D. . 10 Phoenix D. A. . 11 Mason J. A. . stop_ _Journal_abbreviation bioRxiv _Journal_volume 312215 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name temporinB_KKG6A _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 temporinB_KKG6A _Molecular_mass 1666.163 _Mol_thiol_state 'not present' _Details ; TemporinB_KKG6A is an analogue of the antimicrobial peptide temporinB from Rana temporaria, obtained by further optimization of an analogue obtained through alanine scanning of the original peptide sequence. ; ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence ; KKLLPIVANLLKSLL ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 LYS 3 LEU 4 LEU 5 PRO 6 ILE 7 VAL 8 ALA 9 ASN 10 LEU 11 LEU 12 LYS 13 SER 14 LEU 15 LEU 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 . 32630 . . . . 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 _Details $entity_1 'chemical synthesis' . . . . . 'The original peptide sequence is from Rana temporaria' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle _Details ; 100 mM U-98% 2H deuterated sodium dodecyl sulphate, 2 mM temporinB_KKG6A, 0.05 % w/w 2H 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'deuterated sodium dodecyl sulphate' 100 mM 'U-98% 2H' $entity_1 2 mM 'natural abundance' '3-(trimethylsilyl)propionic-2,2,3,3-d4 acid' 0.05 '% w/w' 2H stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name DYNAMO _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio and Kuszewski' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CARA _Version 1.9.1.2 loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' 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_ save_software_4 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _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' 'no salts' . 'Not defined' pH 7.00 . pH 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 TSP 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 4.078 0.020 . 2 1 1 LYS HB2 H 2.025 0.020 . 3 1 1 LYS HB3 H 2.025 0.020 . 4 1 1 LYS HG2 H 1.534 0.020 . 5 1 1 LYS HG3 H 1.534 0.020 . 6 1 1 LYS HD2 H 1.740 0.020 . 7 1 1 LYS HD3 H 1.740 0.020 . 8 1 1 LYS HE2 H 3.033 0.020 . 9 1 1 LYS HE3 H 3.033 0.020 . 10 2 2 LYS H H 8.403 0.020 . 11 2 2 LYS HA H 4.445 0.020 . 12 2 2 LYS HB2 H 1.850 0.020 . 13 2 2 LYS HB3 H 1.850 0.020 . 14 2 2 LYS HG2 H 1.486 0.020 . 15 2 2 LYS HG3 H 1.486 0.020 . 16 2 2 LYS HD2 H 1.731 0.020 . 17 2 2 LYS HD3 H 1.731 0.020 . 18 2 2 LYS HE2 H 3.004 0.020 . 19 2 2 LYS HE3 H 3.004 0.020 . 20 3 3 LEU H H 8.129 0.020 . 21 3 3 LEU HA H 4.297 0.020 . 22 3 3 LEU HB2 H 1.788 0.020 . 23 3 3 LEU HB3 H 1.788 0.020 . 24 3 3 LEU HG H 1.659 0.020 . 25 4 4 LEU H H 8.267 0.020 . 26 4 4 LEU HA H 4.281 0.020 . 27 4 4 LEU HB2 H 1.746 0.020 . 28 4 4 LEU HB3 H 1.746 0.020 . 29 4 4 LEU HG H 1.596 0.020 . 30 4 4 LEU HD1 H 0.953 0.020 . 31 4 4 LEU HD2 H 0.896 0.020 . 32 5 5 PRO HA H 4.314 0.020 . 33 5 5 PRO HB2 H 2.312 0.020 . 34 5 5 PRO HB3 H 2.054 0.020 . 35 5 5 PRO HG2 H 1.932 0.020 . 36 5 5 PRO HG3 H 1.862 0.020 . 37 5 5 PRO HD2 H 3.608 0.020 . 38 5 5 PRO HD3 H 3.608 0.020 . 39 6 6 ILE H H 7.436 0.020 . 40 6 6 ILE HA H 3.903 0.020 . 41 6 6 ILE HB H 2.127 0.020 . 42 6 6 ILE HG12 H 1.728 0.020 . 43 6 6 ILE HG13 H 1.236 0.020 . 44 6 6 ILE HG2 H 0.922 0.020 . 45 7 7 VAL H H 7.844 0.020 . 46 7 7 VAL HA H 3.579 0.020 . 47 7 7 VAL HB H 2.260 0.020 . 48 7 7 VAL HG1 H 1.047 0.020 . 49 7 7 VAL HG2 H 0.966 0.020 . 50 8 8 ALA H H 8.263 0.020 . 51 8 8 ALA HA H 4.042 0.020 . 52 8 8 ALA HB H 1.451 0.020 . 53 9 9 ASN H H 7.866 0.020 . 54 9 9 ASN HA H 4.551 0.020 . 55 9 9 ASN HB2 H 2.854 0.020 . 56 9 9 ASN HB3 H 2.913 0.020 . 57 10 10 LEU H H 8.337 0.020 . 58 10 10 LEU HA H 4.084 0.020 . 59 10 10 LEU HB2 H 1.930 0.020 . 60 10 10 LEU HB3 H 1.930 0.020 . 61 10 10 LEU HG H 1.528 0.020 . 62 11 11 LEU H H 7.795 0.020 . 63 11 11 LEU HA H 4.186 0.020 . 64 11 11 LEU HB2 H 1.869 0.020 . 65 11 11 LEU HB3 H 1.869 0.020 . 66 11 11 LEU HG H 1.620 0.020 . 67 12 12 LYS H H 8.391 0.020 . 68 12 12 LYS HA H 3.868 0.020 . 69 12 12 LYS HB2 H 1.959 0.020 . 70 12 12 LYS HB3 H 1.852 0.020 . 71 12 12 LYS HG2 H 1.541 0.020 . 72 12 12 LYS HG3 H 1.439 0.020 . 73 12 12 LYS HD2 H 1.662 0.020 . 74 12 12 LYS HD3 H 1.662 0.020 . 75 12 12 LYS HE2 H 2.950 0.020 . 76 12 12 LYS HE3 H 2.950 0.020 . 77 13 13 SER H H 7.722 0.020 . 78 13 13 SER HA H 4.233 0.020 . 79 13 13 SER HB2 H 3.996 0.020 . 80 13 13 SER HB3 H 3.996 0.020 . 81 14 14 LEU H H 7.745 0.020 . 82 14 14 LEU HA H 4.202 0.020 . 83 14 14 LEU HB2 H 1.774 0.020 . 84 14 14 LEU HB3 H 1.774 0.020 . 85 14 14 LEU HG H 1.594 0.020 . stop_ save_ save_spectral_peak_list_1 _Saveframe_category spectral_peak_list _Details . _Experiment_label '2D 1H-1H NOESY' _Number_of_spectral_dimensions 2 loop_ _Expt_dimension_ID _Atom_type _Spectral_region 1 H HN 2 H HN stop_ _Sample_label $sample_1 _Sample_conditions_label $sample_conditions_1 _Text_data_format "NMR-STAR v3" _Text_data ; >>save_spectral_peak_list_1 >> _Spectral_peak_list.Sf_category spectral_peak_list >> _Spectral_peak_list.Sf_framecode spectral_peak_list_1 >> _Spectral_peak_list.Entry_ID 34272 >> _Spectral_peak_list.ID 1 >> _Spectral_peak_list.Sample_ID 1 >> _Spectral_peak_list.Sample_label $sample_1 >> _Spectral_peak_list.Sample_condition_list_ID 1 >> _Spectral_peak_list.Sample_condition_list_label $sample_conditions_1 >> _Spectral_peak_list.Experiment_ID 2 >> _Spectral_peak_list.Experiment_name '2D 1H-1H NOESY' >> _Spectral_peak_list.Experiment_class . >> _Spectral_peak_list.Experiment_type . >> _Spectral_peak_list.Number_of_spectral_dimensions 2 >> _Spectral_peak_list.Chemical_shift_list . >> _Spectral_peak_list.Assigned_chem_shift_list_ID 1 >> _Spectral_peak_list.Assigned_chem_shift_list_label $assigned_chemical_shifts_1 >> _Spectral_peak_list.Details . >> _Spectral_peak_list.Text_data_format text >> _Spectral_peak_list.Text_data >>; >>VARS INDEX GROUP RESID_I RESNAME_I ATOMNAME_I SEGNAME_I RESID_J RESNAME_J ATOMNAME_J SEGNAME_J D_LO D_HI FC W S >>FORMAT %4d %3d %5d %6s %6s %4s %5d %6s %6s %4s %9.3f %9.3f %.2f %.2f %.2f >> >> 1 1 9 ASN HA A 13 SER HN A 0.000 5.000 100.0 1.0 1.0 >> 2 1 9 ASN HA A 10 LEU HN A 0.000 5.000 100.0 1.0 1.0 >> 3 1 2 LYS HA A 4 LEU HN A 0.000 2.700 100.0 1.0 1.0 >> 4 1 5 PRO HA A 6 ILE HN A 0.000 5.000 100.0 1.0 1.0 >> 5 1 3 LEU HA A 7 VAL HN A 0.000 5.000 100.0 1.0 1.0 >> 6 1 1 LYS HA A 2 LYS HN A 0.000 2.700 100.0 1.0 1.0 >> 7 1 8 ALA HA A 9 ASN HN A 0.000 5.000 100.0 1.0 1.0 >> 8 1 8 ALA HA A 11 LEU HN A 0.000 3.300 100.0 1.0 1.0 >> 9 1 6 ILE HA A 10 LEU HN A 0.000 5.000 100.0 1.0 1.0 >> 10 1 6 ILE HA A 7 VAL HN A 0.000 5.000 100.0 1.0 1.0 >> 11 1 7 VAL HA A 10 LEU HN A 0.000 5.000 100.0 1.0 1.0 >> 12 1 7 VAL HA A 8 ALA HN A 0.000 3.300 100.0 1.0 1.0 >> 13 1 9 ASN HB1 A 10 LEU HN A 0.000 3.300 100.0 1.0 1.0 >> 13 2 9 ASN HB2 A 10 LEU HN A 0.000 3.300 100.0 1.0 1.0 >> 14 1 5 PRO HB1 A 6 ILE HN A 0.000 5.000 100.0 1.0 1.0 >> 14 2 5 PRO HB2 A 6 ILE HN A 0.000 5.000 100.0 1.0 1.0 >> 15 1 7 VAL HB A 8 ALA HN A 0.000 2.700 100.0 1.0 1.0 >> 16 1 6 ILE HB A 7 VAL HN A 0.000 3.300 100.0 1.0 1.0 >> 17 1 8 ALA HB1 A 9 ASN HN A 0.000 3.300 100.0 1.0 1.0 >> 17 1 8 ALA HB2 A 9 ASN HN A 0.000 3.300 100.0 1.0 1.0 >> 17 1 8 ALA HB3 A 9 ASN HN A 0.000 3.300 100.0 1.0 1.0 >> 18 1 10 LEU HN A 9 ASN HN A 0.000 3.300 100.0 1.0 1.0 >> 19 1 8 ALA HN A 7 VAL HN A 0.000 2.700 100.0 1.0 1.0 >> 20 1 12 LYS HN A 13 SER HN A 0.000 3.300 100.0 1.0 1.0 >> 21 1 6 ILE HN A 7 VAL HN A 0.000 3.300 100.0 1.0 1.0 >>; >> >> loop_ >> _Spectral_dim.ID >> _Spectral_dim.Axis_code >> _Spectral_dim.Spectrometer_frequency >> _Spectral_dim.Atom_type >> _Spectral_dim.Atom_isotope_number >> _Spectral_dim.Spectral_region >> _Spectral_dim.Magnetization_linkage_ID >> _Spectral_dim.Under_sampling_type >> _Spectral_dim.Sweep_width >> _Spectral_dim.Sweep_width_units >> _Spectral_dim.Value_first_point >> _Spectral_dim.Absolute_peak_positions >> _Spectral_dim.Acquisition >> _Spectral_dim.Center_frequency_offset >> _Spectral_dim.Encoding_code >> _Spectral_dim.Encoded_reduced_dimension_ID >> _Spectral_dim.Entry_ID >> _Spectral_dim.Spectral_peak_list_ID >> >> 1 . . H 1 HN . 'not observed' 8012.821 Hz . . . 4.773 . . 34272 1 >> 2 . . H 1 HN . 'not observed' 8012.821 Hz . . . 4.773 . . 34272 1 >> >> stop_ >> >>save_ >> ; save_