data_30424 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; LyeTxI-b, a synthetic peptide derived from Lycosa erythrognatha spider venom, shows potent antibiotic activity, in vitro and in vivo ; _BMRB_accession_number 30424 _BMRB_flat_file_name bmr30424.str _Entry_type original _Submission_date 2018-03-01 _Accession_date 2018-03-01 _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 'de Lima' M. E. . 2 'dos Reis' P. V. . 3 Resende J. M. . 4 Verly R. M. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 141 "13C chemical shifts" 75 "15N chemical shifts" 29 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-05-06 update BMRB 'update entry citation' 2018-05-24 original author 'original release' stop_ _Original_release_date 2018-05-14 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; LyeTxI-b, a Synthetic Peptide Derived From Lycosa erythrognatha Spider Venom, Shows Potent Antibiotic Activity in Vitro and in Vivo ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29681894 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Reis Pablo . . 2 Boff Daiane . . 3 Verly Rodrigo M. . 4 Melo-Braga Marcella N. . 5 Cortes Maria E. . 6 Santos Daniel M. . 7 Pimenta Adriano . . 8 Amaral Flavio A. . 9 Resende Jarbas M. . 10 'de Lima' Maria E. . stop_ _Journal_abbreviation 'Front. Microbiol.' _Journal_name_full 'Frontiers in microbiology' _Journal_volume 9 _Journal_issue . _Journal_ISSN 1664-302X _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 667 _Page_last 667 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Peptide LyeTxI-b' _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 2725.407 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 26 _Mol_residue_sequence ; XIWLTALKFLGKNLGKLAKQ QLAKLX ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 0 ACE 2 1 ILE 3 2 TRP 4 3 LEU 5 4 THR 6 5 ALA 7 6 LEU 8 7 LYS 9 8 PHE 10 9 LEU 11 10 GLY 12 11 LYS 13 12 ASN 14 13 LEU 15 14 GLY 16 15 LYS 17 16 LEU 18 17 ALA 19 18 LYS 20 19 GLN 21 20 GLN 22 21 LEU 23 22 ALA 24 23 LYS 25 24 LEU 26 25 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _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 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? stop_ save_ save_chem_comp_ACE _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'ACETYL GROUP' _BMRB_code ACE _PDB_code ACE _Standard_residue_derivative . _Molecular_mass 44.053 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? CH3 CH3 C . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 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 DOUB C O ? ? SING C CH3 ? ? SING C H ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? 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 Spider 332789 Eukaryota Metazoa Lycosa erythrognatha 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 '2 mM LyeTxI-b, 20 mM phosphate buffer, 1 mM DSS, TFE-d2/H2O (60:40%, v/v)' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2 mM 'natural abundance' 'phosphate buffer' 20 mM 'natural abundance' DSS 1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_software_4 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_5 _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_6 _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance III 600' _Field_strength 600.043 _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_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_HMQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HMQC' _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 7.0 . pH pressure 1 . atm temperature 293 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details '(DSS) SODIUM 2,2-DIMETHYL- 2-SILAPENTANE-5-SULFONATE' 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 0.0 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' '2D 1H-13C HSQC' '2D 1H-15N HMQC' 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 2 ILE H H 7.665 . . 2 1 2 ILE HA H 3.954 . . 3 1 2 ILE HB H 1.985 . . 4 1 2 ILE CB C 38.438 . . 5 1 2 ILE CD1 C 22.513 . . 6 1 2 ILE N N 125.438 . . 7 2 3 TRP H H 7.284 . . 8 2 3 TRP HA H 4.528 . . 9 2 3 TRP HB2 H 3.343 . . 10 2 3 TRP HB3 H 3.451 . . 11 2 3 TRP HD1 H 7.213 . . 12 2 3 TRP HE1 H 9.814 . . 13 2 3 TRP HE3 H 7.559 . . 14 2 3 TRP HZ2 H 7.507 . . 15 2 3 TRP CA C 58.401 . . 16 2 3 TRP CB C 27.947 . . 17 2 3 TRP CD1 C 124.284 . . 18 2 3 TRP CE3 C 118.315 . . 19 2 3 TRP CZ2 C 112.654 . . 20 2 3 TRP N N 118.594 . . 21 2 3 TRP NE1 N 127.714 . . 22 3 4 LEU H H 7.017 . . 23 3 4 LEU HA H 4.079 . . 24 3 4 LEU HB2 H 1.188 . . 25 3 4 LEU HB3 H 1.470 . . 26 3 4 LEU HG H 1.179 . . 27 3 4 LEU HD1 H 0.871 . . 28 3 4 LEU HD1 H 0.823 . . 29 3 4 LEU HD1 H 0.871 . . 30 3 4 LEU HD2 H 0.822 . . 31 3 4 LEU CA C 57.603 . . 32 3 4 LEU CB C 41.645 . . 33 3 4 LEU CG C 26.929 . . 34 3 4 LEU CD1 C 23.771 . . 35 3 4 LEU CD2 C 23.126 . . 36 3 4 LEU N N 120.817 . . 37 4 5 THR H H 7.611 . . 38 4 5 THR HA H 4.247 . . 39 4 5 THR HB H 3.900 . . 40 4 5 THR HG1 H 1.309 . . 41 4 5 THR HG2 H 1.224 . . 42 4 5 THR CA C 69.003 . . 43 4 5 THR CB C 66.333 . . 44 4 5 THR CG2 C 21.392 . . 45 4 5 THR N N 113.394 . . 46 5 6 ALA H H 7.822 . . 47 5 6 ALA HA H 4.225 . . 48 5 6 ALA HB H 1.599 . . 49 5 6 ALA CA C 55.379 . . 50 5 6 ALA CB C 17.577 . . 51 5 6 ALA N N 123.363 . . 52 6 7 LEU H H 7.955 . . 53 6 7 LEU HA H 4.226 . . 54 6 7 LEU HB2 H 1.715 . . 55 6 7 LEU HB3 H 1.963 . . 56 6 7 LEU HD1 H 1.052 . . 57 6 7 LEU HD2 H 0.985 . . 58 6 7 LEU CA C 58.180 . . 59 6 7 LEU CB C 41.893 . . 60 6 7 LEU CD1 C 24.427 . . 61 6 7 LEU CD2 C 22.879 . . 62 6 7 LEU N N 117.522 . . 63 7 8 LYS H H 8.137 . . 64 7 8 LYS HA H 4.110 . . 65 7 8 LYS HB2 H 1.970 . . 66 7 8 LYS HB3 H 2.028 . . 67 7 8 LYS HG3 H 1.438 . . 68 7 8 LYS HD2 H 1.601 . . 69 7 8 LYS HD3 H 1.727 . . 70 7 8 LYS HE3 H 2.972 . . 71 7 8 LYS CA C 59.662 . . 72 7 8 LYS CB C 32.269 . . 73 7 8 LYS CG C 27.421 . . 74 7 8 LYS CD C 29.659 . . 75 7 8 LYS N N 119.830 . . 76 8 9 PHE H H 8.280 . . 77 8 9 PHE HA H 4.314 . . 78 8 9 PHE HB2 H 3.280 . . 79 8 9 PHE HB3 H 3.344 . . 80 8 9 PHE HD1 H 7.293 . . 81 8 9 PHE HE1 H 7.360 . . 82 8 9 PHE CA C 61.381 . . 83 8 9 PHE CB C 39.192 . . 84 8 9 PHE CD1 C 129.528 . . 85 8 9 PHE CE1 C 129.500 . . 86 8 9 PHE N N 120.108 . . 87 9 10 LEU H H 8.778 . . 88 9 10 LEU HA H 4.314 . . 89 9 10 LEU HB2 H 1.816 . . 90 9 10 LEU HB3 H 1.977 . . 91 9 10 LEU HD1 H 1.010 . . 92 9 10 LEU CB C 41.967 . . 93 9 10 LEU CG C 27.186 . . 94 9 10 LEU CD1 C 24.822 . . 95 9 10 LEU CD2 C 23.154 . . 96 9 10 LEU N N 122.195 . . 97 10 11 GLY H H 8.591 . . 98 10 11 GLY HA2 H 3.832 . . 99 10 11 GLY HA3 H 3.988 . . 100 10 11 GLY CA C 47.318 . . 101 10 11 GLY N N 105.794 . . 102 11 12 LYS H H 8.281 . . 103 11 12 LYS HA H 4.207 . . 104 11 12 LYS HB3 H 2.053 . . 105 11 12 LYS HG2 H 1.680 . . 106 11 12 LYS HG3 H 1.662 . . 107 11 12 LYS HD3 H 2.014 . . 108 11 12 LYS HE3 H 3.045 . . 109 11 12 LYS CA C 58.588 . . 110 11 12 LYS CB C 32.398 . . 111 11 12 LYS CG C 26.144 . . 112 11 12 LYS CD C 25.128 . . 113 11 12 LYS N N 121.480 . . 114 12 13 ASN H H 7.930 . . 115 12 13 ASN HA H 4.476 . . 116 12 13 ASN HB2 H 2.582 . . 117 12 13 ASN HB3 H 2.760 . . 118 12 13 ASN HD21 H 6.737 . . 119 12 13 ASN HD22 H 5.638 . . 120 12 13 ASN CA C 56.799 . . 121 12 13 ASN CB C 39.139 . . 122 12 13 ASN N N 117.834 . . 123 12 13 ASN ND2 N 111.405 . . 124 13 14 LEU H H 8.752 . . 125 13 14 LEU HA H 4.216 . . 126 13 14 LEU HB2 H 1.602 . . 127 13 14 LEU HB3 H 1.888 . . 128 13 14 LEU HD1 H 0.949 . . 129 13 14 LEU HD2 H 0.913 . . 130 13 14 LEU CA C 58.543 . . 131 13 14 LEU CB C 42.611 . . 132 13 14 LEU CG C 27.093 . . 133 13 14 LEU N N 121.285 . . 134 14 15 GLY H H 8.228 . . 135 14 15 GLY HA2 H 3.878 . . 136 14 15 GLY HA3 H 3.983 . . 137 14 15 GLY CA C 47.018 . . 138 14 15 GLY N N 105.421 . . 139 15 16 LYS H H 7.710 . . 140 15 16 LYS HA H 4.132 . . 141 15 16 LYS HB2 H 1.998 . . 142 15 16 LYS HB3 H 2.093 . . 143 15 16 LYS HD3 H 2.063 . . 144 15 16 LYS HE3 H 2.975 . . 145 15 16 LYS CA C 58.885 . . 146 15 16 LYS CB C 32.281 . . 147 15 16 LYS CD C 27.925 . . 148 15 16 LYS N N 120.867 . . 149 16 17 LEU H H 7.901 . . 150 16 17 LEU HA H 4.166 . . 151 16 17 LEU HB2 H 1.769 . . 152 16 17 LEU HB3 H 1.929 . . 153 16 17 LEU HG H 1.667 . . 154 16 17 LEU HD1 H 0.969 . . 155 16 17 LEU HD2 H 0.932 . . 156 16 17 LEU CA C 57.720 . . 157 16 17 LEU CB C 41.677 . . 158 16 17 LEU CG C 26.987 . . 159 16 17 LEU CD1 C 23.558 . . 160 16 17 LEU N N 120.582 . . 161 17 18 ALA H H 8.496 . . 162 17 18 ALA HA H 4.129 . . 163 17 18 ALA HB H 1.550 . . 164 17 18 ALA HB H 1.616 . . 165 17 18 ALA CA C 55.501 . . 166 17 18 ALA CB C 17.966 . . 167 17 18 ALA N N 121.991 . . 168 18 19 LYS H H 8.063 . . 169 18 19 LYS HA H 4.006 . . 170 18 19 LYS HB2 H 1.981 . . 171 18 19 LYS HB3 H 2.021 . . 172 18 19 LYS HG3 H 1.484 . . 173 18 19 LYS HD3 H 1.748 . . 174 18 19 LYS HE3 H 2.981 . . 175 18 19 LYS CA C 60.239 . . 176 18 19 LYS CB C 32.331 . . 177 18 19 LYS CG C 25.121 . . 178 18 19 LYS N N 116.803 . . 179 19 20 GLN H H 7.970 . . 180 19 20 GLN HA H 4.109 . . 181 19 20 GLN HB2 H 2.247 . . 182 19 20 GLN HB3 H 2.344 . . 183 19 20 GLN HG2 H 2.449 . . 184 19 20 GLN HG3 H 2.649 . . 185 19 20 GLN HE21 H 7.212 . . 186 19 20 GLN HE22 H 6.595 . . 187 19 20 GLN CA C 58.566 . . 188 19 20 GLN CB C 28.614 . . 189 19 20 GLN CG C 34.249 . . 190 19 20 GLN N N 117.288 . . 191 19 20 GLN NE2 N 108.733 . . 192 20 21 GLN H H 8.096 . . 193 20 21 GLN HA H 4.169 . . 194 20 21 GLN HB2 H 2.222 . . 195 20 21 GLN HB3 H 2.299 . . 196 20 21 GLN HG3 H 2.496 . . 197 20 21 GLN HE21 H 6.992 . . 198 20 21 GLN HE22 H 6.621 . . 199 20 21 GLN CA C 58.571 . . 200 20 21 GLN CB C 28.593 . . 201 20 21 GLN CG C 33.821 . . 202 20 21 GLN N N 118.054 . . 203 20 21 GLN NE2 N 108.984 . . 204 21 22 LEU H H 8.300 . . 205 21 22 LEU HA H 4.158 . . 206 21 22 LEU HB2 H 1.627 . . 207 21 22 LEU HB3 H 1.897 . . 208 21 22 LEU HD1 H 0.933 . . 209 21 22 LEU CA C 58.344 . . 210 21 22 LEU CB C 41.727 . . 211 21 22 LEU CD1 C 0.946 . . 212 21 22 LEU N N 119.639 . . 213 22 23 ALA H H 8.024 . . 214 22 23 ALA HA H 4.149 . . 215 22 23 ALA HB H 1.550 . . 216 22 23 ALA CA C 57.074 . . 217 22 23 ALA CB C 17.634 . . 218 22 23 ALA N N 120.497 . . 219 23 24 LYS H H 7.652 . . 220 23 24 LYS HA H 4.203 . . 221 23 24 LYS HB3 H 2.005 . . 222 23 24 LYS HG3 H 1.544 . . 223 23 24 LYS HD2 H 1.685 . . 224 23 24 LYS HD3 H 1.762 . . 225 23 24 LYS HE3 H 3.033 . . 226 23 24 LYS CA C 57.831 . . 227 23 24 LYS CB C 32.674 . . 228 23 24 LYS CG C 25.550 . . 229 23 24 LYS CD C 29.158 . . 230 23 24 LYS CE C 42.335 . . 231 23 24 LYS N N 116.067 . . 232 24 25 LEU H H 7.801 . . 233 24 25 LEU HA H 4.257 . . 234 24 25 LEU HB2 H 1.911 . . 235 24 25 LEU HB3 H 1.658 . . 236 24 25 LEU HG H 1.756 . . 237 24 25 LEU HD1 H 0.939 . . 238 24 25 LEU HD2 H 0.909 . . 239 24 25 LEU CA C 55.916 . . 240 24 25 LEU CB C 42.115 . . 241 24 25 LEU CG C 28.396 . . 242 24 25 LEU N N 119.865 . . 243 25 26 NH2 N N 103.733 . . 244 25 26 NH2 HN1 H 7.241 . . 245 25 26 NH2 HN2 H 6.784 . . stop_ save_