data_9S7O # _entry.id 9S7O # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.416 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 9S7O pdb_00009s7o 10.2210/pdb9s7o/pdb WWPDB D_1292147851 ? ? EMDB EMD-54645 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2026-08-26 ? 2 'EM metadata' 1 0 2026-08-26 ? # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 2 'EM metadata' repository 'Initial release' ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9S7O _pdbx_database_status.recvd_initial_deposition_date 2025-08-05 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 1 in water' _pdbx_database_related.db_id EMD-54645 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email meytal.landau@cssb-hamburg.de _pdbx_contact_author.name_first Meytal _pdbx_contact_author.name_last Landau _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-1743-3430 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Ragonis-Bachar, P.' 1 ? 'Strati, F.' 2 ? 'Gustavsson, E.' 3 ? 'Khokhlov, A.' 4 ? 'Barnea, E.' 5 ? 'Rayan, B.' 6 ? 'Upchr, A.' 7 ? 'Landau, M.' 8 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Amyloidogenic Nature and Structural Polymorphism of Antimicrobial, Virulent and Defense Peptides' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ragonis-Bachar, P.' 1 ? primary 'Strati, F.' 2 ? primary 'Gustavsson, E.' 3 ? primary 'Khokhlov, A.' 4 ? primary 'Barnea, E.' 5 ? primary 'Rayan, B.' 6 ? primary 'Upchr, A.' 7 ? primary 'Landau, M.' 8 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description Brevinin-1OKc _entity.formula_weight 2274.832 _entity.pdbx_number_of_molecules 6 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'FFGSIIGALAKGLPSLISLIKK(NH2)' _entity_poly.pdbx_seq_one_letter_code_can FFGSIIGALAKGLPSLISLIKKX _entity_poly.pdbx_strand_id A,B,C,D,E,F _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 PHE n 1 2 PHE n 1 3 GLY n 1 4 SER n 1 5 ILE n 1 6 ILE n 1 7 GLY n 1 8 ALA n 1 9 LEU n 1 10 ALA n 1 11 LYS n 1 12 GLY n 1 13 LEU n 1 14 PRO n 1 15 SER n 1 16 LEU n 1 17 ILE n 1 18 SER n 1 19 LEU n 1 20 ILE n 1 21 LYS n 1 22 LYS n 1 23 NH2 n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 23 _pdbx_entity_src_syn.organism_scientific 'Nidirana okinavana' _pdbx_entity_src_syn.organism_common_name 'Kampira Falls frog' _pdbx_entity_src_syn.ncbi_taxonomy_id 156870 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 PHE 1 1 1 PHE PHE A . n A 1 2 PHE 2 2 2 PHE PHE A . n A 1 3 GLY 3 3 3 GLY GLY A . n A 1 4 SER 4 4 4 SER SER A . n A 1 5 ILE 5 5 5 ILE ILE A . n A 1 6 ILE 6 6 6 ILE ILE A . n A 1 7 GLY 7 7 7 GLY GLY A . n A 1 8 ALA 8 8 8 ALA ALA A . n A 1 9 LEU 9 9 9 LEU LEU A . n A 1 10 ALA 10 10 10 ALA ALA A . n A 1 11 LYS 11 11 11 LYS LYS A . n A 1 12 GLY 12 12 12 GLY GLY A . n A 1 13 LEU 13 13 13 LEU LEU A . n A 1 14 PRO 14 14 14 PRO PRO A . n A 1 15 SER 15 15 15 SER SER A . n A 1 16 LEU 16 16 16 LEU LEU A . n A 1 17 ILE 17 17 17 ILE ILE A . n A 1 18 SER 18 18 18 SER SER A . n A 1 19 LEU 19 19 19 LEU LEU A . n A 1 20 ILE 20 20 20 ILE ILE A . n A 1 21 LYS 21 21 ? ? ? A . n A 1 22 LYS 22 22 ? ? ? A . n A 1 23 NH2 23 23 ? ? ? A . n B 1 1 PHE 1 1 1 PHE PHE B . n B 1 2 PHE 2 2 2 PHE PHE B . n B 1 3 GLY 3 3 3 GLY GLY B . n B 1 4 SER 4 4 4 SER SER B . n B 1 5 ILE 5 5 5 ILE ILE B . n B 1 6 ILE 6 6 6 ILE ILE B . n B 1 7 GLY 7 7 7 GLY GLY B . n B 1 8 ALA 8 8 8 ALA ALA B . n B 1 9 LEU 9 9 9 LEU LEU B . n B 1 10 ALA 10 10 10 ALA ALA B . n B 1 11 LYS 11 11 11 LYS LYS B . n B 1 12 GLY 12 12 12 GLY GLY B . n B 1 13 LEU 13 13 13 LEU LEU B . n B 1 14 PRO 14 14 14 PRO PRO B . n B 1 15 SER 15 15 15 SER SER B . n B 1 16 LEU 16 16 16 LEU LEU B . n B 1 17 ILE 17 17 17 ILE ILE B . n B 1 18 SER 18 18 18 SER SER B . n B 1 19 LEU 19 19 19 LEU LEU B . n B 1 20 ILE 20 20 20 ILE ILE B . n B 1 21 LYS 21 21 ? ? ? B . n B 1 22 LYS 22 22 ? ? ? B . n B 1 23 NH2 23 23 ? ? ? B . n C 1 1 PHE 1 1 1 PHE PHE C . n C 1 2 PHE 2 2 2 PHE PHE C . n C 1 3 GLY 3 3 3 GLY GLY C . n C 1 4 SER 4 4 4 SER SER C . n C 1 5 ILE 5 5 5 ILE ILE C . n C 1 6 ILE 6 6 6 ILE ILE C . n C 1 7 GLY 7 7 7 GLY GLY C . n C 1 8 ALA 8 8 8 ALA ALA C . n C 1 9 LEU 9 9 9 LEU LEU C . n C 1 10 ALA 10 10 10 ALA ALA C . n C 1 11 LYS 11 11 11 LYS LYS C . n C 1 12 GLY 12 12 12 GLY GLY C . n C 1 13 LEU 13 13 13 LEU LEU C . n C 1 14 PRO 14 14 14 PRO PRO C . n C 1 15 SER 15 15 15 SER SER C . n C 1 16 LEU 16 16 16 LEU LEU C . n C 1 17 ILE 17 17 17 ILE ILE C . n C 1 18 SER 18 18 18 SER SER C . n C 1 19 LEU 19 19 19 LEU LEU C . n C 1 20 ILE 20 20 20 ILE ILE C . n C 1 21 LYS 21 21 ? ? ? C . n C 1 22 LYS 22 22 ? ? ? C . n C 1 23 NH2 23 23 ? ? ? C . n D 1 1 PHE 1 1 1 PHE PHE D . n D 1 2 PHE 2 2 2 PHE PHE D . n D 1 3 GLY 3 3 3 GLY GLY D . n D 1 4 SER 4 4 4 SER SER D . n D 1 5 ILE 5 5 5 ILE ILE D . n D 1 6 ILE 6 6 6 ILE ILE D . n D 1 7 GLY 7 7 7 GLY GLY D . n D 1 8 ALA 8 8 8 ALA ALA D . n D 1 9 LEU 9 9 9 LEU LEU D . n D 1 10 ALA 10 10 10 ALA ALA D . n D 1 11 LYS 11 11 11 LYS LYS D . n D 1 12 GLY 12 12 12 GLY GLY D . n D 1 13 LEU 13 13 13 LEU LEU D . n D 1 14 PRO 14 14 14 PRO PRO D . n D 1 15 SER 15 15 15 SER SER D . n D 1 16 LEU 16 16 16 LEU LEU D . n D 1 17 ILE 17 17 17 ILE ILE D . n D 1 18 SER 18 18 18 SER SER D . n D 1 19 LEU 19 19 19 LEU LEU D . n D 1 20 ILE 20 20 20 ILE ILE D . n D 1 21 LYS 21 21 ? ? ? D . n D 1 22 LYS 22 22 ? ? ? D . n D 1 23 NH2 23 23 ? ? ? D . n E 1 1 PHE 1 1 1 PHE PHE E . n E 1 2 PHE 2 2 2 PHE PHE E . n E 1 3 GLY 3 3 3 GLY GLY E . n E 1 4 SER 4 4 4 SER SER E . n E 1 5 ILE 5 5 5 ILE ILE E . n E 1 6 ILE 6 6 6 ILE ILE E . n E 1 7 GLY 7 7 7 GLY GLY E . n E 1 8 ALA 8 8 8 ALA ALA E . n E 1 9 LEU 9 9 9 LEU LEU E . n E 1 10 ALA 10 10 10 ALA ALA E . n E 1 11 LYS 11 11 11 LYS LYS E . n E 1 12 GLY 12 12 12 GLY GLY E . n E 1 13 LEU 13 13 13 LEU LEU E . n E 1 14 PRO 14 14 14 PRO PRO E . n E 1 15 SER 15 15 15 SER SER E . n E 1 16 LEU 16 16 16 LEU LEU E . n E 1 17 ILE 17 17 17 ILE ILE E . n E 1 18 SER 18 18 18 SER SER E . n E 1 19 LEU 19 19 19 LEU LEU E . n E 1 20 ILE 20 20 20 ILE ILE E . n E 1 21 LYS 21 21 ? ? ? E . n E 1 22 LYS 22 22 ? ? ? E . n E 1 23 NH2 23 23 ? ? ? E . n F 1 1 PHE 1 1 1 PHE PHE F . n F 1 2 PHE 2 2 2 PHE PHE F . n F 1 3 GLY 3 3 3 GLY GLY F . n F 1 4 SER 4 4 4 SER SER F . n F 1 5 ILE 5 5 5 ILE ILE F . n F 1 6 ILE 6 6 6 ILE ILE F . n F 1 7 GLY 7 7 7 GLY GLY F . n F 1 8 ALA 8 8 8 ALA ALA F . n F 1 9 LEU 9 9 9 LEU LEU F . n F 1 10 ALA 10 10 10 ALA ALA F . n F 1 11 LYS 11 11 11 LYS LYS F . n F 1 12 GLY 12 12 12 GLY GLY F . n F 1 13 LEU 13 13 13 LEU LEU F . n F 1 14 PRO 14 14 14 PRO PRO F . n F 1 15 SER 15 15 15 SER SER F . n F 1 16 LEU 16 16 16 LEU LEU F . n F 1 17 ILE 17 17 17 ILE ILE F . n F 1 18 SER 18 18 18 SER SER F . n F 1 19 LEU 19 19 19 LEU LEU F . n F 1 20 ILE 20 20 20 ILE ILE F . n F 1 21 LYS 21 21 ? ? ? F . n F 1 22 LYS 22 22 ? ? ? F . n F 1 23 NH2 23 23 ? ? ? F . n # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 9S7O _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9S7O _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9S7O _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 63.699 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.656 _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9S7O _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 3.30 _refine.ls_d_res_low 83.30 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 15162 _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 100.00 _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.63366 _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.63366 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'PARAMETERS FOR MASK CACLULATION' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.814 _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B 42.726 _refine.overall_SU_ML 0.657 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id 1 _refine_hist.details ? _refine_hist.d_res_high . _refine_hist.d_res_low . _refine_hist.number_atoms_solvent ? _refine_hist.number_atoms_total 1430 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein ? _refine_hist.pdbx_number_atoms_nucleic_acid ? _refine_hist.pdbx_number_atoms_ligand ? _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_Zscore _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.007 0.012 1450 ? r_bond_refined_d ? ? ? 'ELECTRON MICROSCOPY' ? 0.000 0.015 1590 ? r_bond_other_d ? ? ? 'ELECTRON MICROSCOPY' ? 1.342 1.728 1950 ? r_angle_refined_deg ? ? ? 'ELECTRON MICROSCOPY' ? 0.422 1.672 3660 ? r_angle_other_deg ? ? ? 'ELECTRON MICROSCOPY' ? 9.683 5.000 190 ? r_dihedral_angle_1_deg ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_dihedral_angle_2_deg ? ? ? 'ELECTRON MICROSCOPY' ? 14.042 10.000 250 ? r_dihedral_angle_3_deg ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_dihedral_angle_4_deg ? ? ? 'ELECTRON MICROSCOPY' ? 0.048 0.200 250 ? r_chiral_restr ? ? ? 'ELECTRON MICROSCOPY' ? 0.007 0.020 1520 ? r_gen_planes_refined ? ? ? 'ELECTRON MICROSCOPY' ? 0.001 0.020 280 ? r_gen_planes_other ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_refined ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_other ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_refined ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_other ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_refined ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_other ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_refined ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_other ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_refined ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_other ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_refined ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_other ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_other ? ? ? 'ELECTRON MICROSCOPY' ? 5.636 5.464 790 ? r_mcbond_it ? ? ? 'ELECTRON MICROSCOPY' ? 5.636 5.464 790 ? r_mcbond_other ? ? ? 'ELECTRON MICROSCOPY' ? 9.636 9.661 970 ? r_mcangle_it ? ? ? 'ELECTRON MICROSCOPY' ? 9.632 9.674 971 ? r_mcangle_other ? ? ? 'ELECTRON MICROSCOPY' ? 4.739 7.126 660 ? r_scbond_it ? ? ? 'ELECTRON MICROSCOPY' ? 4.736 7.138 661 ? r_scbond_other ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_scangle_it ? ? ? 'ELECTRON MICROSCOPY' ? 9.044 12.954 981 ? r_scangle_other ? ? ? 'ELECTRON MICROSCOPY' ? 15.280 68.00 3657 ? r_long_range_B_refined ? ? ? 'ELECTRON MICROSCOPY' ? 15.278 68.01 3658 ? r_long_range_B_other ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_rigid_bond_restr ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_free ? ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_bonded ? ? ? # _refine_ls_shell.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_ls_shell.d_res_high 3.300 _refine_ls_shell.d_res_low 3.386 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 0 _refine_ls_shell.number_reflns_R_work 1131 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.856 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_R_complete ? _refine_ls_shell.correlation_coeff_Fo_to_Fc ? _refine_ls_shell.correlation_coeff_Fo_to_Fc_free ? _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work ? _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? _refine_ls_shell.R_factor_R_free 0.000 # _struct.entry_id 9S7O _struct.title 'Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 1 in water' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9S7O _struct_keywords.text 'Amyloid, Antimicrobial, ANTIMICROBIAL PROTEIN' _struct_keywords.pdbx_keywords 'ANTIMICROBIAL PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 1 ? F N N 1 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code BR1C_NIDOK _struct_ref.pdbx_db_accession C0HL10 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code FFGSIIGALAKGLPSLISLIKK _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 9S7O A 1 ? 22 ? C0HL10 1 ? 22 ? 1 22 2 1 9S7O B 1 ? 22 ? C0HL10 1 ? 22 ? 1 22 3 1 9S7O C 1 ? 22 ? C0HL10 1 ? 22 ? 1 22 4 1 9S7O D 1 ? 22 ? C0HL10 1 ? 22 ? 1 22 5 1 9S7O E 1 ? 22 ? C0HL10 1 ? 22 ? 1 22 6 1 9S7O F 1 ? 22 ? C0HL10 1 ? 22 ? 1 22 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 9S7O NH2 A 23 ? UNP C0HL10 ? ? amidation 23 1 2 9S7O NH2 B 23 ? UNP C0HL10 ? ? amidation 23 2 3 9S7O NH2 C 23 ? UNP C0HL10 ? ? amidation 23 3 4 9S7O NH2 D 23 ? UNP C0HL10 ? ? amidation 23 4 5 9S7O NH2 E 23 ? UNP C0HL10 ? ? amidation 23 5 6 9S7O NH2 F 23 ? UNP C0HL10 ? ? amidation 23 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 3 ? AA3 ? 3 ? AA4 ? 3 ? AA5 ? 3 ? AA6 ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? parallel AA1 2 3 ? parallel AA2 1 2 ? parallel AA2 2 3 ? parallel AA3 1 2 ? parallel AA3 2 3 ? parallel AA4 1 2 ? parallel AA4 2 3 ? parallel AA5 1 2 ? parallel AA5 2 3 ? parallel AA6 1 2 ? parallel AA6 2 3 ? parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 ILE C 5 ? GLY C 12 ? ILE C 5 GLY C 12 AA1 2 ILE A 5 ? GLY A 12 ? ILE A 5 GLY A 12 AA1 3 ILE E 5 ? ILE E 6 ? ILE E 5 ILE E 6 AA2 1 ILE C 5 ? GLY C 12 ? ILE C 5 GLY C 12 AA2 2 ILE A 5 ? GLY A 12 ? ILE A 5 GLY A 12 AA2 3 LEU E 9 ? GLY E 12 ? LEU E 9 GLY E 12 AA3 1 SER C 15 ? LEU C 19 ? SER C 15 LEU C 19 AA3 2 SER A 15 ? LEU A 19 ? SER A 15 LEU A 19 AA3 3 SER E 15 ? LEU E 19 ? SER E 15 LEU E 19 AA4 1 ILE D 5 ? ILE D 6 ? ILE D 5 ILE D 6 AA4 2 ILE B 5 ? ILE B 6 ? ILE B 5 ILE B 6 AA4 3 ILE F 5 ? ILE F 6 ? ILE F 5 ILE F 6 AA5 1 LEU D 9 ? GLY D 12 ? LEU D 9 GLY D 12 AA5 2 LEU B 9 ? GLY B 12 ? LEU B 9 GLY B 12 AA5 3 LEU F 9 ? GLY F 12 ? LEU F 9 GLY F 12 AA6 1 SER D 15 ? SER D 18 ? SER D 15 SER D 18 AA6 2 SER B 15 ? LEU B 19 ? SER B 15 LEU B 19 AA6 3 SER F 15 ? LEU F 19 ? SER F 15 LEU F 19 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 O ILE C 5 ? O ILE C 5 N ILE A 6 ? N ILE A 6 AA1 2 3 N ILE A 5 ? N ILE A 5 O ILE E 6 ? O ILE E 6 AA2 1 2 O ILE C 5 ? O ILE C 5 N ILE A 6 ? N ILE A 6 AA2 2 3 N ALA A 8 ? N ALA A 8 O LEU E 9 ? O LEU E 9 AA3 1 2 O LEU C 16 ? O LEU C 16 N SER A 15 ? N SER A 15 AA3 2 3 N LEU A 16 ? N LEU A 16 O SER E 15 ? O SER E 15 AA4 1 2 O ILE D 5 ? O ILE D 5 N ILE B 6 ? N ILE B 6 AA4 2 3 N ILE B 5 ? N ILE B 5 O ILE F 6 ? O ILE F 6 AA5 1 2 O GLY D 12 ? O GLY D 12 N LYS B 11 ? N LYS B 11 AA5 2 3 N GLY B 12 ? N GLY B 12 O LYS F 11 ? O LYS F 11 AA6 1 2 O LEU D 16 ? O LEU D 16 N SER B 15 ? N SER B 15 AA6 2 3 N LEU B 16 ? N LEU B 16 O SER F 15 ? O SER F 15 # _pdbx_entry_details.entry_id 9S7O _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification N # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9S7O _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol 'FLEXIBLE FIT' # _em_3d_fitting_list.id 1 _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.pdb_entry_id . _em_3d_fitting_list.pdb_chain_id . _em_3d_fitting_list.pdb_chain_residue_range . _em_3d_fitting_list.details 'De novo generated in Coot' _em_3d_fitting_list.chain_id ? _em_3d_fitting_list.chain_residue_range ? _em_3d_fitting_list.source_name Other _em_3d_fitting_list.type other _em_3d_fitting_list.accession_code ? _em_3d_fitting_list.initial_refinement_model_id ? # _em_3d_reconstruction.entry_id 9S7O _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 3.3 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 349067 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type HELICAL # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ddH2O _em_buffer.pH 7 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source NATURAL _em_entity_assembly.type COMPLEX _em_entity_assembly.name Brevinin-1OKc _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9S7O _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'TFS KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER' _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 500 _em_imaging.nominal_defocus_max 2000 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen NITROGEN _em_imaging.objective_aperture ? _em_imaging.microscope_serial_number ? _em_imaging.microscope_version ? # _em_sample_support.id 1 _em_sample_support.film_material ? _em_sample_support.method ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 300 _em_sample_support.grid_type 'Quantifoil R2/1' _em_sample_support.details ? _em_sample_support.specimen_id 1 _em_sample_support.citation_id ? # _em_vitrification.entry_id 9S7O _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE-PROPANE _em_vitrification.humidity 95 _em_vitrification.temp ? _em_vitrification.chamber_temperature 298 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9S7O _em_experiment.id 1 _em_experiment.reconstruction_method HELICAL _em_experiment.aggregation_state FILAMENT _em_experiment.entity_assembly_id 1 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A LYS 21 ? A LYS 21 2 1 Y 1 A LYS 22 ? A LYS 22 3 1 Y 1 A NH2 23 ? A NH2 23 4 1 Y 1 B LYS 21 ? B LYS 21 5 1 Y 1 B LYS 22 ? B LYS 22 6 1 Y 1 B NH2 23 ? B NH2 23 7 1 Y 1 C LYS 21 ? C LYS 21 8 1 Y 1 C LYS 22 ? C LYS 22 9 1 Y 1 C NH2 23 ? C NH2 23 10 1 Y 1 D LYS 21 ? D LYS 21 11 1 Y 1 D LYS 22 ? D LYS 22 12 1 Y 1 D NH2 23 ? D NH2 23 13 1 Y 1 E LYS 21 ? E LYS 21 14 1 Y 1 E LYS 22 ? E LYS 22 15 1 Y 1 E NH2 23 ? E NH2 23 16 1 Y 1 F LYS 21 ? F LYS 21 17 1 Y 1 F LYS 22 ? F LYS 22 18 1 Y 1 F NH2 23 ? F NH2 23 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 GLY N N N N 14 GLY CA C N N 15 GLY C C N N 16 GLY O O N N 17 GLY OXT O N N 18 GLY H H N N 19 GLY H2 H N N 20 GLY HA2 H N N 21 GLY HA3 H N N 22 GLY HXT H N N 23 ILE N N N N 24 ILE CA C N S 25 ILE C C N N 26 ILE O O N N 27 ILE CB C N S 28 ILE CG1 C N N 29 ILE CG2 C N N 30 ILE CD1 C N N 31 ILE OXT O N N 32 ILE H H N N 33 ILE H2 H N N 34 ILE HA H N N 35 ILE HB H N N 36 ILE HG12 H N N 37 ILE HG13 H N N 38 ILE HG21 H N N 39 ILE HG22 H N N 40 ILE HG23 H N N 41 ILE HD11 H N N 42 ILE HD12 H N N 43 ILE HD13 H N N 44 ILE HXT H N N 45 LEU N N N N 46 LEU CA C N S 47 LEU C C N N 48 LEU O O N N 49 LEU CB C N N 50 LEU CG C N N 51 LEU CD1 C N N 52 LEU CD2 C N N 53 LEU OXT O N N 54 LEU H H N N 55 LEU H2 H N N 56 LEU HA H N N 57 LEU HB2 H N N 58 LEU HB3 H N N 59 LEU HG H N N 60 LEU HD11 H N N 61 LEU HD12 H N N 62 LEU HD13 H N N 63 LEU HD21 H N N 64 LEU HD22 H N N 65 LEU HD23 H N N 66 LEU HXT H N N 67 LYS N N N N 68 LYS CA C N S 69 LYS C C N N 70 LYS O O N N 71 LYS CB C N N 72 LYS CG C N N 73 LYS CD C N N 74 LYS CE C N N 75 LYS NZ N N N 76 LYS OXT O N N 77 LYS H H N N 78 LYS H2 H N N 79 LYS HA H N N 80 LYS HB2 H N N 81 LYS HB3 H N N 82 LYS HG2 H N N 83 LYS HG3 H N N 84 LYS HD2 H N N 85 LYS HD3 H N N 86 LYS HE2 H N N 87 LYS HE3 H N N 88 LYS HZ1 H N N 89 LYS HZ2 H N N 90 LYS HZ3 H N N 91 LYS HXT H N N 92 NH2 N N N N 93 NH2 HN1 H N N 94 NH2 HN2 H N N 95 PHE N N N N 96 PHE CA C N S 97 PHE C C N N 98 PHE O O N N 99 PHE CB C N N 100 PHE CG C Y N 101 PHE CD1 C Y N 102 PHE CD2 C Y N 103 PHE CE1 C Y N 104 PHE CE2 C Y N 105 PHE CZ C Y N 106 PHE OXT O N N 107 PHE H H N N 108 PHE H2 H N N 109 PHE HA H N N 110 PHE HB2 H N N 111 PHE HB3 H N N 112 PHE HD1 H N N 113 PHE HD2 H N N 114 PHE HE1 H N N 115 PHE HE2 H N N 116 PHE HZ H N N 117 PHE HXT H N N 118 PRO N N N N 119 PRO CA C N S 120 PRO C C N N 121 PRO O O N N 122 PRO CB C N N 123 PRO CG C N N 124 PRO CD C N N 125 PRO OXT O N N 126 PRO H H N N 127 PRO HA H N N 128 PRO HB2 H N N 129 PRO HB3 H N N 130 PRO HG2 H N N 131 PRO HG3 H N N 132 PRO HD2 H N N 133 PRO HD3 H N N 134 PRO HXT H N N 135 SER N N N N 136 SER CA C N S 137 SER C C N N 138 SER O O N N 139 SER CB C N N 140 SER OG O N N 141 SER OXT O N N 142 SER H H N N 143 SER H2 H N N 144 SER HA H N N 145 SER HB2 H N N 146 SER HB3 H N N 147 SER HG H N N 148 SER HXT H N N 149 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 GLY N CA sing N N 13 GLY N H sing N N 14 GLY N H2 sing N N 15 GLY CA C sing N N 16 GLY CA HA2 sing N N 17 GLY CA HA3 sing N N 18 GLY C O doub N N 19 GLY C OXT sing N N 20 GLY OXT HXT sing N N 21 ILE N CA sing N N 22 ILE N H sing N N 23 ILE N H2 sing N N 24 ILE CA C sing N N 25 ILE CA CB sing N N 26 ILE CA HA sing N N 27 ILE C O doub N N 28 ILE C OXT sing N N 29 ILE CB CG1 sing N N 30 ILE CB CG2 sing N N 31 ILE CB HB sing N N 32 ILE CG1 CD1 sing N N 33 ILE CG1 HG12 sing N N 34 ILE CG1 HG13 sing N N 35 ILE CG2 HG21 sing N N 36 ILE CG2 HG22 sing N N 37 ILE CG2 HG23 sing N N 38 ILE CD1 HD11 sing N N 39 ILE CD1 HD12 sing N N 40 ILE CD1 HD13 sing N N 41 ILE OXT HXT sing N N 42 LEU N CA sing N N 43 LEU N H sing N N 44 LEU N H2 sing N N 45 LEU CA C sing N N 46 LEU CA CB sing N N 47 LEU CA HA sing N N 48 LEU C O doub N N 49 LEU C OXT sing N N 50 LEU CB CG sing N N 51 LEU CB HB2 sing N N 52 LEU CB HB3 sing N N 53 LEU CG CD1 sing N N 54 LEU CG CD2 sing N N 55 LEU CG HG sing N N 56 LEU CD1 HD11 sing N N 57 LEU CD1 HD12 sing N N 58 LEU CD1 HD13 sing N N 59 LEU CD2 HD21 sing N N 60 LEU CD2 HD22 sing N N 61 LEU CD2 HD23 sing N N 62 LEU OXT HXT sing N N 63 LYS N CA sing N N 64 LYS N H sing N N 65 LYS N H2 sing N N 66 LYS CA C sing N N 67 LYS CA CB sing N N 68 LYS CA HA sing N N 69 LYS C O doub N N 70 LYS C OXT sing N N 71 LYS CB CG sing N N 72 LYS CB HB2 sing N N 73 LYS CB HB3 sing N N 74 LYS CG CD sing N N 75 LYS CG HG2 sing N N 76 LYS CG HG3 sing N N 77 LYS CD CE sing N N 78 LYS CD HD2 sing N N 79 LYS CD HD3 sing N N 80 LYS CE NZ sing N N 81 LYS CE HE2 sing N N 82 LYS CE HE3 sing N N 83 LYS NZ HZ1 sing N N 84 LYS NZ HZ2 sing N N 85 LYS NZ HZ3 sing N N 86 LYS OXT HXT sing N N 87 NH2 N HN1 sing N N 88 NH2 N HN2 sing N N 89 PHE N CA sing N N 90 PHE N H sing N N 91 PHE N H2 sing N N 92 PHE CA C sing N N 93 PHE CA CB sing N N 94 PHE CA HA sing N N 95 PHE C O doub N N 96 PHE C OXT sing N N 97 PHE CB CG sing N N 98 PHE CB HB2 sing N N 99 PHE CB HB3 sing N N 100 PHE CG CD1 doub Y N 101 PHE CG CD2 sing Y N 102 PHE CD1 CE1 sing Y N 103 PHE CD1 HD1 sing N N 104 PHE CD2 CE2 doub Y N 105 PHE CD2 HD2 sing N N 106 PHE CE1 CZ doub Y N 107 PHE CE1 HE1 sing N N 108 PHE CE2 CZ sing Y N 109 PHE CE2 HE2 sing N N 110 PHE CZ HZ sing N N 111 PHE OXT HXT sing N N 112 PRO N CA sing N N 113 PRO N CD sing N N 114 PRO N H sing N N 115 PRO CA C sing N N 116 PRO CA CB sing N N 117 PRO CA HA sing N N 118 PRO C O doub N N 119 PRO C OXT sing N N 120 PRO CB CG sing N N 121 PRO CB HB2 sing N N 122 PRO CB HB3 sing N N 123 PRO CG CD sing N N 124 PRO CG HG2 sing N N 125 PRO CG HG3 sing N N 126 PRO CD HD2 sing N N 127 PRO CD HD3 sing N N 128 PRO OXT HXT sing N N 129 SER N CA sing N N 130 SER N H sing N N 131 SER N H2 sing N N 132 SER CA C sing N N 133 SER CA CB sing N N 134 SER CA HA sing N N 135 SER C O doub N N 136 SER C OXT sing N N 137 SER CB OG sing N N 138 SER CB HB2 sing N N 139 SER CB HB3 sing N N 140 SER OG HG sing N N 141 SER OXT HXT sing N N 142 # _em_admin.current_status REL _em_admin.deposition_date 2025-08-05 _em_admin.deposition_site PDBE _em_admin.entry_id 9S7O _em_admin.last_update 2026-08-26 _em_admin.map_release_date 2026-08-26 _em_admin.title 'Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 1 in water' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.units ? _em_entity_assembly_molwt.value ? # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 156870 _em_entity_assembly_naturalsource.organism 'Nidirana okinavana' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.details ? _em_helical_entity.axial_symmetry C1 _em_helical_entity.angular_rotation_per_subunit 179.24 _em_helical_entity.axial_rise_per_subunit 2.39 # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 50 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 BIOQUANTUM (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # _em_particle_selection.details ? _em_particle_selection.id 1 _em_particle_selection.image_processing_id 1 _em_particle_selection.method ? _em_particle_selection.num_particles_selected 1569255 _em_particle_selection.reference_model ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version _em_software.reference_DOI 'PARTICLE SELECTION' ? 1 1 ? ? crYOLO ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 EPU ? ? MASKING ? 3 ? ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? CTFFIND 4.1 ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? ? 'MODEL FITTING' ? 7 ? 1 ? Coot 0.9.8.92 ? OTHER ? 8 ? ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 9 1 ? ? RELION 5 ? 'FINAL EULER ASSIGNMENT' ? 10 1 ? ? RELION 5 ? CLASSIFICATION ? 11 1 ? ? RELION 5 ? RECONSTRUCTION ? 12 1 ? ? RELION 5 ? 'MODEL REFINEMENT' ? 13 ? 1 ? Servalcat ? ? # _em_specimen.concentration ? _em_specimen.details 'This sample was fibrillated in ddH2O' _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'European Research Council (ERC)' 'European Union' 101087140 1 'Israel Science Foundation' Israel 2111/20 2 'Volkswagen Foundation' Germany '76251-4659/2022 (ZN 4042)' 3 'German Research Foundation (DFG)' Germany 152/772-1 4 'German Research Foundation (DFG)' Germany 152/774-1 5 'German Research Foundation (DFG)' Germany 152/775-1 6 'German Research Foundation (DFG)' Germany 152/776-1 7 'German Research Foundation (DFG)' Germany '152/777-1 FUGG' 8 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.type other _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.accession_code ? # _atom_sites.entry_id 9S7O _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O # loop_ #