data_34059 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Spatial structure of antimicrobial peptide arenicin-1 mutant V8R ; _BMRB_accession_number 34059 _BMRB_flat_file_name bmr34059.str _Entry_type original _Submission_date 2016-11-02 _Accession_date 2016-11-02 _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 Myshkin M. Y. . 2 Shenkarev Z. O. . 3 Panteleev P. V. . 4 Ovchinnikova T. V. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 146 "13C chemical shifts" 79 "15N chemical shifts" 29 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-07-21 original BMRB . stop_ _Original_release_date 2017-07-17 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Dimerization of the antimicrobial peptide arenicin plays a key role in the cytotoxicity but not in the antibacterial activity. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27940358 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Panteleev P. V. . 2 Myshkin M. Y. . 3 Shenkarev Z. O. . 4 Ovchinnikova T. V. . stop_ _Journal_abbreviation 'Biochem. Biophys. Res. Commun.' _Journal_volume 482 _Journal_issue 4 _Journal_ASTM BBRCA9 _Journal_ISSN 1090-2104 _Journal_CSD 0146 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1320 _Page_last 1326 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Arenicin-1 _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 2824.409 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; RWCVYAYRRVRGVLVRYRRC W ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 TRP 3 CYS 4 VAL 5 TYR 6 ALA 7 TYR 8 ARG 9 ARG 10 VAL 11 ARG 12 GLY 13 VAL 14 LEU 15 VAL 16 ARG 17 TYR 18 ARG 19 ARG 20 CYS 21 TRP 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 Lugworm 6344 Eukaryota Metazoa Arenicola marina 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 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1.8 mM [U-99% 15N] arenicin-1 V8R, 95% H2O/5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.8 mM '[U-99% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CARA _Version . loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CYANA _Version 3.97 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_3 _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_4 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceI _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_aliphatic_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_1 save_ save_3D_HNHA_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNHA' _Sample_label $sample_1 save_ save_3D_HNHB_8 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNHB' _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 4.5 . 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 . 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 water H 1 protons ppm 4.85 internal direct . . . 1 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-15N HSQC' '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '3D 1H-15N NOESY' '3D HNHA' '3D HNHB' 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 ARG HA H 4.021 0.000 1 2 1 1 ARG HB2 H 1.605 0.000 2 3 1 1 ARG HB3 H 1.605 0.000 2 4 1 1 ARG HG2 H 1.382 0.000 2 5 1 1 ARG HG3 H 1.321 0.000 2 6 1 1 ARG HD2 H 2.925 0.000 2 7 1 1 ARG HD3 H 2.925 0.000 2 8 1 1 ARG HE H 7.035 0.000 1 9 1 1 ARG CA C 52.759 0.000 1 10 1 1 ARG CB C 28.156 0.000 1 11 1 1 ARG CG C 24.254 0.000 1 12 1 1 ARG CD C 40.551 0.000 1 13 1 1 ARG NE N 84.058 0.000 1 14 2 2 TRP H H 8.737 0.000 1 15 2 2 TRP HA H 4.579 0.000 1 16 2 2 TRP HB2 H 2.558 0.000 1 17 2 2 TRP HB3 H 2.324 0.000 1 18 2 2 TRP HD1 H 6.737 0.000 1 19 2 2 TRP HE1 H 9.823 0.000 1 20 2 2 TRP HE3 H 7.366 0.000 1 21 2 2 TRP HZ2 H 7.238 0.000 1 22 2 2 TRP HZ3 H 7.013 0.000 1 23 2 2 TRP HH2 H 6.953 0.000 1 24 2 2 TRP CB C 28.076 0.000 1 25 2 2 TRP CD1 C 125.000 0.000 1 26 2 2 TRP CE3 C 118.811 0.000 1 27 2 2 TRP CZ2 C 112.144 0.000 1 28 2 2 TRP CZ3 C 122.184 0.000 1 29 2 2 TRP CH2 C 119.581 0.000 1 30 2 2 TRP N N 126.560 0.000 1 31 2 2 TRP NE1 N 128.918 0.000 1 32 3 3 CYS H H 7.788 0.000 1 33 3 3 CYS HA H 5.410 0.000 1 34 3 3 CYS HB2 H 2.555 0.000 1 35 3 3 CYS HB3 H 2.196 0.000 1 36 3 3 CYS CA C 52.329 0.000 1 37 3 3 CYS CB C 46.125 0.000 1 38 3 3 CYS N N 118.675 0.000 1 39 4 4 VAL H H 8.799 0.000 1 40 4 4 VAL HA H 4.266 0.000 1 41 4 4 VAL HB H 2.083 0.000 1 42 4 4 VAL HG1 H 0.854 0.000 2 43 4 4 VAL HG2 H 0.825 0.000 2 44 4 4 VAL CA C 56.581 0.000 1 45 4 4 VAL CB C 33.093 0.000 1 46 4 4 VAL CG1 C 18.687 0.000 1 47 4 4 VAL CG2 C 16.355 0.000 1 48 4 4 VAL N N 116.615 0.000 1 49 5 5 TYR H H 8.284 0.000 1 50 5 5 TYR HA H 4.874 0.000 1 51 5 5 TYR HB2 H 2.573 0.000 1 52 5 5 TYR HB3 H 2.364 0.000 1 53 5 5 TYR HD1 H 6.763 0.000 1 54 5 5 TYR HD2 H 6.763 0.000 1 55 5 5 TYR HE1 H 6.566 0.000 1 56 5 5 TYR HE2 H 6.566 0.000 1 57 5 5 TYR CA C 55.189 0.000 1 58 5 5 TYR CB C 36.706 0.000 1 59 5 5 TYR CD1 C 130.312 0.000 1 60 5 5 TYR CE1 C 115.730 0.000 1 61 5 5 TYR N N 119.671 0.000 1 62 6 6 ALA H H 8.610 0.000 1 63 6 6 ALA HA H 4.349 0.000 1 64 6 6 ALA HB H 0.841 0.000 1 65 6 6 ALA CA C 47.461 0.000 1 66 6 6 ALA CB C 19.337 0.000 1 67 6 6 ALA N N 126.743 0.000 1 68 7 7 TYR H H 8.341 0.000 1 69 7 7 TYR HA H 5.555 0.000 1 70 7 7 TYR HB2 H 2.620 0.000 2 71 7 7 TYR HB3 H 2.620 0.000 2 72 7 7 TYR HD1 H 6.797 0.000 1 73 7 7 TYR HD2 H 6.797 0.000 1 74 7 7 TYR HE1 H 6.637 0.000 1 75 7 7 TYR HE2 H 6.637 0.000 1 76 7 7 TYR CA C 54.337 0.000 1 77 7 7 TYR CB C 39.337 0.000 1 78 7 7 TYR CD1 C 130.763 0.000 1 79 7 7 TYR CE1 C 115.544 0.000 1 80 7 7 TYR N N 114.859 0.000 1 81 8 8 ARG H H 9.154 0.000 1 82 8 8 ARG HA H 4.711 0.000 1 83 8 8 ARG HB2 H 1.667 0.000 2 84 8 8 ARG HB3 H 1.667 0.000 2 85 8 8 ARG HG2 H 1.306 0.000 2 86 8 8 ARG HG3 H 1.187 0.000 2 87 8 8 ARG HD2 H 2.443 0.000 2 88 8 8 ARG HD3 H 2.612 0.000 2 89 8 8 ARG HE H 6.450 0.000 1 90 8 8 ARG CB C 30.493 0.000 1 91 8 8 ARG CG C 23.235 0.000 1 92 8 8 ARG CD C 40.372 0.000 1 93 8 8 ARG N N 120.421 0.000 1 94 8 8 ARG NE N 83.093 0.000 1 95 9 9 ARG H H 8.720 0.000 1 96 9 9 ARG HA H 4.860 0.000 1 97 9 9 ARG HB2 H 1.540 0.000 1 98 9 9 ARG HB3 H 1.454 0.000 1 99 9 9 ARG HG2 H 1.279 0.000 1 100 9 9 ARG HG3 H 1.189 0.000 1 101 9 9 ARG HD2 H 2.904 0.000 2 102 9 9 ARG HD3 H 2.904 0.000 2 103 9 9 ARG HE H 7.191 0.000 1 104 9 9 ARG CA C 52.614 0.000 1 105 9 9 ARG CB C 28.260 0.000 1 106 9 9 ARG CG C 25.123 0.000 1 107 9 9 ARG CD C 40.314 0.000 1 108 9 9 ARG N N 122.709 0.000 1 109 9 9 ARG NE N 83.500 0.000 1 110 10 10 VAL H H 9.097 0.000 1 111 10 10 VAL HA H 4.018 0.000 1 112 10 10 VAL HB H 1.818 0.000 1 113 10 10 VAL HG1 H 0.820 0.000 2 114 10 10 VAL HG2 H 0.711 0.000 2 115 10 10 VAL CA C 59.294 0.000 1 116 10 10 VAL CB C 31.180 0.000 1 117 10 10 VAL CG1 C 23.625 0.000 1 118 10 10 VAL CG2 C 17.815 0.000 1 119 10 10 VAL N N 127.396 0.000 1 120 11 11 ARG H H 9.459 0.000 1 121 11 11 ARG HA H 3.719 0.000 1 122 11 11 ARG HB2 H 1.892 0.000 2 123 11 11 ARG HB3 H 1.740 0.000 2 124 11 11 ARG HG2 H 1.494 0.000 2 125 11 11 ARG HG3 H 1.494 0.000 2 126 11 11 ARG HD2 H 3.103 0.000 2 127 11 11 ARG HD3 H 3.103 0.000 2 128 11 11 ARG HE H 7.104 0.000 1 129 11 11 ARG CA C 54.485 0.000 1 130 11 11 ARG CB C 25.179 0.000 1 131 11 11 ARG CG C 25.223 0.000 1 132 11 11 ARG CD C 40.626 0.000 1 133 11 11 ARG N N 128.020 0.000 1 134 11 11 ARG NE N 84.290 0.000 1 135 12 12 GLY H H 8.359 0.000 1 136 12 12 GLY HA2 H 4.100 0.000 1 137 12 12 GLY HA3 H 3.419 0.000 1 138 12 12 GLY CA C 42.599 0.000 1 139 12 12 GLY N N 102.673 0.000 1 140 13 13 VAL H H 7.690 0.000 1 141 13 13 VAL HA H 4.126 0.000 1 142 13 13 VAL HB H 1.957 0.000 1 143 13 13 VAL HG1 H 0.783 0.000 2 144 13 13 VAL HG2 H 0.790 0.000 2 145 13 13 VAL CA C 58.369 0.000 1 146 13 13 VAL CB C 31.527 0.000 1 147 13 13 VAL CG1 C 18.418 0.000 1 148 13 13 VAL CG2 C 17.933 0.000 1 149 13 13 VAL N N 122.001 0.000 1 150 14 14 LEU H H 8.536 0.000 1 151 14 14 LEU HA H 4.462 0.000 1 152 14 14 LEU HB2 H 1.381 0.000 2 153 14 14 LEU HB3 H 1.381 0.000 2 154 14 14 LEU HD1 H 0.558 0.000 2 155 14 14 LEU HD2 H 0.604 0.000 2 156 14 14 LEU CA C 52.465 0.000 1 157 14 14 LEU CB C 39.639 0.000 1 158 14 14 LEU CD1 C 21.393 0.000 1 159 14 14 LEU CD2 C 21.761 0.000 1 160 14 14 LEU N N 126.674 0.000 1 161 15 15 VAL H H 9.328 0.000 1 162 15 15 VAL HA H 4.308 0.000 1 163 15 15 VAL HB H 1.964 0.000 1 164 15 15 VAL HG1 H 0.827 0.000 2 165 15 15 VAL HG2 H 0.841 0.000 2 166 15 15 VAL CA C 58.646 0.000 1 167 15 15 VAL CB C 32.021 0.000 1 168 15 15 VAL CG1 C 18.434 0.000 1 169 15 15 VAL CG2 C 18.203 0.000 1 170 15 15 VAL N N 126.823 0.000 1 171 16 16 ARG H H 8.471 0.000 1 172 16 16 ARG HA H 4.496 0.000 1 173 16 16 ARG HB2 H 1.572 0.000 2 174 16 16 ARG HB3 H 1.354 0.000 2 175 16 16 ARG HG2 H 1.107 0.000 2 176 16 16 ARG HG3 H 0.856 0.000 2 177 16 16 ARG HD2 H 2.638 0.000 2 178 16 16 ARG HD3 H 2.427 0.000 2 179 16 16 ARG HE H 6.541 0.000 1 180 16 16 ARG CA C 52.277 0.000 1 181 16 16 ARG CB C 29.311 0.000 1 182 16 16 ARG CG C 24.505 0.000 1 183 16 16 ARG CD C 40.638 0.000 1 184 16 16 ARG N N 127.395 0.000 1 185 16 16 ARG NE N 83.749 0.000 1 186 17 17 TYR H H 9.207 0.000 1 187 17 17 TYR HA H 4.801 0.000 1 188 17 17 TYR HB2 H 2.847 0.000 1 189 17 17 TYR HB3 H 2.732 0.000 1 190 17 17 TYR HD1 H 6.786 0.000 1 191 17 17 TYR HD2 H 6.786 0.000 1 192 17 17 TYR HE1 H 6.318 0.000 1 193 17 17 TYR HE2 H 6.318 0.000 1 194 17 17 TYR CA C 53.092 0.000 1 195 17 17 TYR CB C 38.179 0.000 1 196 17 17 TYR CD1 C 131.507 0.000 1 197 17 17 TYR CE1 C 115.119 0.000 1 198 17 17 TYR N N 125.764 0.000 1 199 18 18 ARG H H 8.476 0.000 1 200 18 18 ARG HA H 4.342 0.000 1 201 18 18 ARG HB2 H 1.519 0.000 1 202 18 18 ARG HB3 H 1.278 0.000 1 203 18 18 ARG HG2 H 1.093 0.000 2 204 18 18 ARG HG3 H 0.870 0.000 2 205 18 18 ARG HD2 H 2.659 0.000 2 206 18 18 ARG HD3 H 2.742 0.000 2 207 18 18 ARG HE H 6.760 0.000 1 208 18 18 ARG CA C 52.051 0.000 1 209 18 18 ARG CB C 29.491 0.000 1 210 18 18 ARG CG C 24.635 0.000 1 211 18 18 ARG CD C 40.773 0.000 1 212 18 18 ARG N N 121.385 0.000 1 213 18 18 ARG NE N 84.136 0.000 1 214 19 19 ARG H H 8.674 0.000 1 215 19 19 ARG HA H 4.387 0.000 1 216 19 19 ARG HB2 H 1.280 0.000 2 217 19 19 ARG HB3 H 1.504 0.000 2 218 19 19 ARG HG2 H 1.375 0.000 2 219 19 19 ARG HG3 H 1.179 0.000 2 220 19 19 ARG HD2 H 2.942 0.000 2 221 19 19 ARG HD3 H 2.832 0.000 2 222 19 19 ARG HE H 6.764 0.000 1 223 19 19 ARG CA C 52.247 0.000 1 224 19 19 ARG CB C 30.044 0.000 1 225 19 19 ARG CG C 24.521 0.000 1 226 19 19 ARG CD C 40.645 0.000 1 227 19 19 ARG N N 128.635 0.000 1 228 19 19 ARG NE N 83.934 0.000 1 229 20 20 CYS H H 8.359 0.000 1 230 20 20 CYS HA H 5.658 0.000 1 231 20 20 CYS HB2 H 2.774 0.000 1 232 20 20 CYS HB3 H 2.634 0.000 1 233 20 20 CYS CA C 52.365 0.000 1 234 20 20 CYS CB C 45.441 0.000 1 235 20 20 CYS N N 122.126 0.000 1 236 21 21 TRP H H 8.929 0.000 1 237 21 21 TRP HA H 4.403 0.000 1 238 21 21 TRP HB2 H 3.164 0.000 1 239 21 21 TRP HB3 H 2.973 0.000 1 240 21 21 TRP HD1 H 7.019 0.000 1 241 21 21 TRP HE1 H 9.717 0.000 1 242 21 21 TRP HE3 H 7.181 0.000 1 243 21 21 TRP HZ2 H 7.137 0.000 1 244 21 21 TRP HZ3 H 6.936 0.000 1 245 21 21 TRP HH2 H 6.773 0.000 1 246 21 21 TRP CA C 56.807 0.000 1 247 21 21 TRP CB C 28.339 0.000 1 248 21 21 TRP CD1 C 124.787 0.000 1 249 21 21 TRP CE3 C 119.448 0.000 1 250 21 21 TRP CZ2 C 111.825 0.000 1 251 21 21 TRP CZ3 C 121.467 0.000 1 252 21 21 TRP CH2 C 119.422 0.000 1 253 21 21 TRP N N 129.318 0.000 1 254 21 21 TRP NE1 N 128.396 0.000 1 stop_ save_