data_34388 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The solution NMR structure of cis-dicarba-brevinin-1BYa in sodium dodecyl sulphate micelles ; _BMRB_accession_number 34388 _BMRB_flat_file_name bmr34388.str _Entry_type original _Submission_date 2019-04-02 _Accession_date 2019-04-02 _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 Timmons P. B. . 2 O'Flynn D. P. . 3 Conlon J. M. . 4 Hewage C. M. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 138 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-10-18 original BMRB . stop_ _Original_release_date 2019-10-11 save_ ############################# # Citation for this entry # ############################# save_citation_3 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Insights into conformation and membrane interactions of the acyclic and dicarba-bridged brevinin-1BYa antimicrobial peptides. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 31515575 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Timmons P. B. . 2 O'Flynn D. P. . 3 Conlon J. M. . 4 Hewage C. M. . stop_ _Journal_abbreviation 'Eur. Biophys. J.' _Journal_volume . _Journal_issue . _Journal_ASTM EBJOE8 _Journal_ISSN 0175-7571 _Journal_CSD 0997 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2019 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_citation_1 _Saveframe_category citation _Citation_full . _Citation_title ; Isolation of peptides of the brevinin-1 family with potent candidacidal activity from the skin secretions of the frog Rana boylii. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 14531844 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Conlon J. M. . 2 Sonnevend A. . . 3 Patel M. . . 4 Davidson C. . . 5 Nielsen P. F. . 6 Pal T. . . 7 Rollins-Smith L. A. . stop_ _Journal_abbreviation 'J. Pept. Res.' _Journal_name_full . _Journal_volume 62 _Journal_issue 5 _Journal_CSD 2150 _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 207 _Page_last 213 _Year 2003 _Details . save_ save_citation_2 _Saveframe_category citation _Citation_full . _Citation_title ; Synthesis, conformational analysis and biological properties of a dicarba derivative of the antimicrobial peptide, brevinin-1BYa. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21312033 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hossain M. A. . 2 Guilhaudis L. . . 3 Sonnevend A. . . 4 Attoub S. . . 5 'van Lierop' B. J. . 6 Robinson A. J. . 7 Wade J. D. . 8 Conlon J. M. . stop_ _Journal_abbreviation 'Eur. Biophys. J.' _Journal_name_full . _Journal_volume 40 _Journal_issue 4 _Journal_CSD 0997 _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 555 _Page_last 564 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Brevinin-1BYa _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 2577.240 _Mol_thiol_state 'not present' _Details 'AGL = allylglycine An intramolecular vinylic bond exists between the residues AGL-18 and AGL-24.' ############################## # Polymer residue sequence # ############################## _Residue_count 24 _Mol_residue_sequence ; FLPILASLAAKFGPKLFXLV TKKX ; loop_ _Residue_seq_code _Residue_label 1 PHE 2 LEU 3 PRO 4 ILE 5 LEU 6 ALA 7 SER 8 LEU 9 ALA 10 ALA 11 LYS 12 PHE 13 GLY 14 PRO 15 LYS 16 LEU 17 PHE 18 ABA 19 LEU 20 VAL 21 THR 22 LYS 23 LYS 24 ABA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ABA _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 'ALPHA-AMINOBUTYRIC ACID' _BMRB_code ABA _PDB_code ABA _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 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB3 HB3 H . 0 . ? HB2 HB2 H . 0 . ? HG1 HG1 H . 0 . ? HG3 HG3 H . 0 . ? HG2 HG2 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 C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB3 ? ? SING CB HB2 ? ? SING CG HG1 ? ? SING CG HG3 ? ? SING CG HG2 ? ? 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 'Foothill yellow-legged frog' 160499 Eukaryota Metazoa Rana boylii 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 micelle _Details '1.5 mM NA- dicarba-brevinin-1BYa, 230 mM sodium dodecyl sulfphate, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.5 mM 'natural abundance' 'sodium dodecyl sulfphate' 230 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NAMD _Version . loop_ _Vendor _Address _Electronic_address 'UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name NMRFAM-SPARKY _Version . loop_ _Vendor _Address _Electronic_address NMRFAM . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _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' 0 . 'Not defined' pH 7.0 . 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 -0.083 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 PHE HA H 4.223 0.003 . 2 1 1 PHE HB2 H 3.205 0.000 . 3 1 1 PHE HB3 H 3.205 0.000 . 4 2 2 LEU H H 7.939 0.003 . 5 2 2 LEU HA H 4.653 0.003 . 6 2 2 LEU HB2 H 1.624 0.004 . 7 2 2 LEU HB3 H 1.624 0.004 . 8 2 2 LEU HG H 1.593 0.008 . 9 2 2 LEU HD1 H 0.965 0.005 . 10 2 2 LEU HD2 H 0.965 0.005 . 11 3 3 PRO HA H 4.415 0.008 . 12 3 3 PRO HB2 H 2.050 0.004 . 13 3 3 PRO HB3 H 2.359 0.003 . 14 3 3 PRO HG2 H 2.359 0.000 . 15 3 3 PRO HG3 H 2.359 0.000 . 16 3 3 PRO HD2 H 3.459 0.009 . 17 3 3 PRO HD3 H 3.767 0.006 . 18 4 4 ILE H H 7.539 0.003 . 19 4 4 ILE HA H 4.021 0.003 . 20 4 4 ILE HB H 1.965 0.006 . 21 4 4 ILE HG12 H 1.302 0.003 . 22 4 4 ILE HG13 H 1.606 0.005 . 23 4 4 ILE HG2 H 0.985 0.004 . 24 4 4 ILE HD1 H 0.897 0.001 . 25 5 5 LEU H H 7.547 0.002 . 26 5 5 LEU HA H 4.167 0.006 . 27 5 5 LEU HB3 H 1.738 0.007 . 28 5 5 LEU HG H 1.725 0.001 . 29 5 5 LEU HD1 H 1.002 0.003 . 30 5 5 LEU HD2 H 0.938 0.011 . 31 6 6 ALA H H 7.914 0.002 . 32 6 6 ALA HA H 4.113 0.005 . 33 6 6 ALA HB H 1.518 0.005 . 34 7 7 SER H H 7.809 0.003 . 35 7 7 SER HA H 4.273 0.006 . 36 7 7 SER HB2 H 3.992 0.004 . 37 7 7 SER HB3 H 4.117 0.007 . 38 8 8 LEU H H 8.084 0.003 . 39 8 8 LEU HA H 4.244 0.007 . 40 8 8 LEU HB2 H 1.933 0.003 . 41 8 8 LEU HB3 H 2.054 0.002 . 42 8 8 LEU HG H 1.617 0.002 . 43 8 8 LEU HD1 H 0.958 0.005 . 44 9 9 ALA H H 8.526 0.003 . 45 9 9 ALA HA H 4.015 0.002 . 46 9 9 ALA HB H 1.432 0.003 . 47 10 10 ALA H H 7.877 0.002 . 48 10 10 ALA HA H 4.141 0.006 . 49 10 10 ALA HB H 1.543 0.005 . 50 11 11 LYS H H 7.617 0.002 . 51 11 11 LYS HA H 4.149 0.004 . 52 11 11 LYS HB2 H 1.530 0.004 . 53 11 11 LYS HB3 H 1.719 0.004 . 54 11 11 LYS HG2 H 0.996 0.001 . 55 11 11 LYS HG3 H 1.186 0.010 . 56 12 12 PHE H H 8.426 0.003 . 57 12 12 PHE HA H 4.745 0.001 . 58 12 12 PHE HB2 H 3.005 0.001 . 59 12 12 PHE HB3 H 3.271 0.002 . 60 12 12 PHE HD1 H 7.339 0.003 . 61 12 12 PHE HD2 H 7.339 0.003 . 62 13 13 GLY H H 8.325 0.004 . 63 13 13 GLY HA2 H 4.002 0.008 . 64 13 13 GLY HA3 H 4.364 0.002 . 65 14 14 PRO HA H 4.390 0.004 . 66 14 14 PRO HB2 H 2.136 0.002 . 67 14 14 PRO HB3 H 2.430 0.003 . 68 14 14 PRO HG2 H 2.040 0.013 . 69 14 14 PRO HG3 H 2.040 0.013 . 70 14 14 PRO HD2 H 3.743 0.003 . 71 14 14 PRO HD3 H 3.846 0.004 . 72 15 15 LYS H H 7.816 0.002 . 73 15 15 LYS HA H 4.124 0.005 . 74 15 15 LYS HB2 H 2.005 0.004 . 75 15 15 LYS HB3 H 1.962 0.004 . 76 15 15 LYS HG2 H 1.508 0.001 . 77 15 15 LYS HG3 H 1.602 0.003 . 78 15 15 LYS HD2 H 1.785 0.001 . 79 15 15 LYS HD3 H 1.785 0.001 . 80 15 15 LYS HE2 H 3.025 0.002 . 81 15 15 LYS HE3 H 3.025 0.002 . 82 16 16 LEU H H 7.910 0.013 . 83 16 16 LEU HA H 4.101 0.003 . 84 16 16 LEU HB2 H 1.655 0.027 . 85 16 16 LEU HB3 H 1.722 0.004 . 86 16 16 LEU HG H 1.512 0.003 . 87 17 17 PHE H H 7.866 0.002 . 88 17 17 PHE HA H 4.219 0.004 . 89 17 17 PHE HB2 H 3.180 0.004 . 90 17 17 PHE HB3 H 3.180 0.004 . 91 17 17 PHE HD1 H 7.199 0.002 . 92 17 17 PHE HD2 H 7.199 0.002 . 93 17 17 PHE HE1 H 7.304 0.000 . 94 17 17 PHE HE2 H 7.304 0.000 . 95 18 18 ABA H H 8.016 0.003 . 96 18 18 ABA HA H 3.690 0.004 . 97 18 18 ABA HB2 H 2.837 0.003 . 98 18 18 ABA HB3 H 2.686 0.004 . 99 18 18 ABA HG3 H 5.354 0.002 . 100 19 19 LEU H H 7.632 0.002 . 101 19 19 LEU HA H 4.292 0.003 . 102 19 19 LEU HB2 H 1.574 0.000 . 103 19 19 LEU HB3 H 1.967 0.003 . 104 19 19 LEU HG H 1.837 0.002 . 105 19 19 LEU HD1 H 0.975 0.004 . 106 19 19 LEU HD2 H 0.835 0.003 . 107 20 20 VAL H H 8.708 0.004 . 108 20 20 VAL HA H 3.809 0.002 . 109 20 20 VAL HB H 2.126 0.005 . 110 20 20 VAL HG1 H 1.058 0.002 . 111 20 20 VAL HG2 H 0.979 0.003 . 112 21 21 THR H H 7.625 0.003 . 113 21 21 THR HA H 4.161 0.008 . 114 21 21 THR HB H 4.045 0.008 . 115 22 22 LYS H H 7.736 0.002 . 116 22 22 LYS HA H 4.043 0.004 . 117 22 22 LYS HB2 H 2.079 0.002 . 118 22 22 LYS HB3 H 2.194 0.007 . 119 22 22 LYS HG2 H 1.449 0.001 . 120 22 22 LYS HG3 H 1.449 0.001 . 121 22 22 LYS HD2 H 1.722 0.000 . 122 22 22 LYS HD3 H 1.804 0.003 . 123 22 22 LYS HE2 H 3.077 0.001 . 124 22 22 LYS HE3 H 3.077 0.001 . 125 23 23 LYS H H 8.122 0.002 . 126 23 23 LYS HA H 4.296 0.006 . 127 23 23 LYS HB2 H 1.938 0.000 . 128 23 23 LYS HB3 H 1.952 0.005 . 129 23 23 LYS HG2 H 1.516 0.009 . 130 23 23 LYS HG3 H 1.516 0.009 . 131 23 23 LYS HD3 H 1.730 0.007 . 132 23 23 LYS HE2 H 3.019 0.005 . 133 23 23 LYS HE3 H 3.089 0.006 . 134 24 24 ABA H H 7.402 0.003 . 135 24 24 ABA HA H 4.493 0.002 . 136 24 24 ABA HB2 H 2.507 0.002 . 137 24 24 ABA HB3 H 2.507 0.002 . 138 24 24 ABA HG3 H 5.353 0.002 . stop_ save_