data_5N9H # _entry.id 5N9H # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 5N9H pdb_00005n9h 10.2210/pdb5n9h/pdb WWPDB D_1200003194 ? ? # 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 1 'Structure model' 1 0 2018-02-21 2 'Structure model' 1 1 2018-03-07 3 'Structure model' 1 2 2018-03-14 4 'Structure model' 1 3 2024-05-08 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' citation 4 4 'Structure model' chem_comp_atom 5 4 'Structure model' chem_comp_bond 6 4 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_abbrev' 2 2 'Structure model' '_citation.pdbx_database_id_PubMed' 3 2 'Structure model' '_citation.title' 4 2 'Structure model' '_citation_author.name' 5 3 'Structure model' '_citation.journal_volume' 6 3 'Structure model' '_citation.page_first' 7 3 'Structure model' '_citation.page_last' 8 4 'Structure model' '_database_2.pdbx_DOI' 9 4 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5N9H _pdbx_database_status.recvd_initial_deposition_date 2017-02-24 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Nasrallah, C.' 1 ? 'Colletier, J.P.' 2 ? # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Proc. Natl. Acad. Sci. U.S.A.' _citation.journal_id_ASTM PNASA6 _citation.journal_id_CSD 0040 _citation.journal_id_ISSN 1091-6490 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 115 _citation.language ? _citation.page_first E2220 _citation.page_last E2228 _citation.title 'Porin self-association enables cell-to-cell contact in' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1073/pnas.1714582115 _citation.pdbx_database_id_PubMed 29476011 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'El-Khatib, M.' 1 ? primary 'Nasrallah, C.' 2 ? primary 'Lopes, J.' 3 ? primary 'Tran, Q.T.' 4 ? primary 'Tetreau, G.' 5 ? primary 'Basbous, H.' 6 ? primary 'Fenel, D.' 7 ? primary 'Gallet, B.' 8 ? primary 'Lethier, M.' 9 ? primary 'Bolla, J.M.' 10 ? primary 'Pages, J.M.' 11 ? primary 'Vivaudou, M.' 12 ? primary 'Weik, M.' 13 ? primary 'Winterhalter, M.' 14 ? primary 'Colletier, J.P.' 15 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn Porin 465.501 4 ? ? 'DIMERIZATION DOMAIN, UNP residues 305-308' ? 2 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 3 water nat water 18.015 8 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code LGNY _entity_poly.pdbx_seq_one_letter_code_can LGNY _entity_poly.pdbx_strand_id A,B,C,M _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LEU n 1 2 GLY n 1 3 ASN n 1 4 TYR 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 4 _pdbx_entity_src_syn.organism_scientific 'Providencia stuartii' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 588 _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 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # 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 LEU 1 255 255 LEU LEU A . n A 1 2 GLY 2 256 256 GLY GLY A . n A 1 3 ASN 3 257 257 ASN ASN A . n A 1 4 TYR 4 258 258 TYR TYR A . n B 1 1 LEU 1 255 255 LEU LEU B . n B 1 2 GLY 2 256 256 GLY GLY B . n B 1 3 ASN 3 257 257 ASN ASN B . n B 1 4 TYR 4 258 258 TYR TYR B . n C 1 1 LEU 1 255 255 LEU LEU C . n C 1 2 GLY 2 256 256 GLY GLY C . n C 1 3 ASN 3 257 257 ASN ASN C . n C 1 4 TYR 4 258 258 TYR TYR C . n D 1 1 LEU 1 255 255 LEU LEU M . n D 1 2 GLY 2 256 256 GLY GLY M . n D 1 3 ASN 3 257 257 ASN ASN M . n D 1 4 TYR 4 258 258 TYR TYR M . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 SO4 1 301 1259 SO4 SO4 A . F 2 SO4 1 301 1259 SO4 SO4 B . G 3 HOH 1 2001 2001 HOH HOH A . G 3 HOH 2 2002 2003 HOH HOH A . G 3 HOH 3 2003 2002 HOH HOH A . H 3 HOH 1 2001 2001 HOH HOH B . H 3 HOH 2 2002 2003 HOH HOH B . H 3 HOH 3 2003 2002 HOH HOH B . I 3 HOH 1 2001 2001 HOH HOH C . J 3 HOH 1 2001 2001 HOH HOH M . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 2 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXD ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXE ? ? ? . 4 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 5 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXL ? ? ? . 6 # _cell.angle_alpha 90.01 _cell.angle_alpha_esd ? _cell.angle_beta 90.01 _cell.angle_beta_esd ? _cell.angle_gamma 90.01 _cell.angle_gamma_esd ? _cell.entry_id 5N9H _cell.details ? _cell.formula_units_Z ? _cell.length_a 4.784 _cell.length_a_esd ? _cell.length_b 11.546 _cell.length_b_esd ? _cell.length_c 47.044 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _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 ? # _symmetry.entry_id 5N9H _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 5N9H _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.45 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 15.4 _exptl_crystal.description Needles _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 4 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;3.2 M AMMONIUM SULFATE; 0.1 M BUFFER ACID CITRIC PH4 ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2012-05-31 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.873 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'ESRF BEAMLINE ID23-2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.873 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ID23-2 _diffrn_source.pdbx_synchrotron_site ESRF # _reflns.B_iso_Wilson_estimate 1.68 _reflns.entry_id 5N9H _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 0.997 _reflns.d_resolution_low 47.04 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 4934 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I 5.5 _reflns.percent_possible_obs 89.7 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 2.17 _reflns.pdbx_Rmerge_I_obs 0.04 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 14.81 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.00 _reflns_shell.d_res_low 1.06 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 5.47 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 87.4 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.15 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 2.12 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] 0.1048 _refine.aniso_B[1][2] 0.3781 _refine.aniso_B[1][3] -0.0048 _refine.aniso_B[2][2] -0.4220 _refine.aniso_B[2][3] 0.3629 _refine.aniso_B[3][3] -0.2565 _refine.B_iso_max ? _refine.B_iso_mean 2.6 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _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 5N9H _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 0.997 _refine.ls_d_res_low 23.522 _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 4918 _refine.ls_number_reflns_R_free 246 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 89.39 _refine.ls_percent_reflns_R_free 5.0 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.0818 _refine.ls_R_factor_R_free 0.0959 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.0811 _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 ? _refine.solvent_model_param_bsol 0.000 _refine.solvent_model_param_ksol 0.000 _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 2.03 _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 NONE _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _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 8.97 _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 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.14 _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 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 132 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 10 _refine_hist.number_atoms_solvent 8 _refine_hist.number_atoms_total 150 _refine_hist.d_res_high 0.997 _refine_hist.d_res_low 23.522 # 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_restraint_function 'X-RAY DIFFRACTION' ? 0.013 ? 148 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.929 ? 200 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 11.338 ? 44 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.113 ? 16 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.007 ? 24 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _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 _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _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_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 0.9972 1.2564 . . 121 2306 87.00 . . . 0.1167 . 0.0971 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.2564 23.5285 . . 125 2366 91.00 . . . 0.0831 . 0.0716 . . . . . . . . . . # _database_PDB_matrix.entry_id 5N9H _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 5N9H _struct.title 'STRUCTURE OF 283-LGNY-286, THE STERIC ZIPPER THAT SUPPORTS THE SELF-ASSOCIATION OF P. STUARTII OMP-PST2 INTO DIMERS OF TRIMERS' _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 5N9H _struct_keywords.text 'STERIC-ZIPPER, PORIN, MICRO-CRYSTAL, SELF-ASSOCIATION, cell adhesion' _struct_keywords.pdbx_keywords 'CELL ADHESION' # 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 2 ? F N N 2 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 3 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A0A0L6X8Y0_PROST _struct_ref.pdbx_db_accession A0A0L6X8Y0 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code LGNY _struct_ref.pdbx_align_begin 305 # 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 5N9H A 1 ? 4 ? A0A0L6X8Y0 305 ? 308 ? 255 258 2 1 5N9H B 1 ? 4 ? A0A0L6X8Y0 305 ? 308 ? 255 258 3 1 5N9H C 1 ? 4 ? A0A0L6X8Y0 305 ? 308 ? 255 258 4 1 5N9H M 1 ? 4 ? A0A0L6X8Y0 305 ? 308 ? 255 258 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 430 ? 1 MORE -15 ? 1 'SSA (A^2)' 2700 ? # _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,G,H,I,J # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _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] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SO4 301 ? 10 'binding site for residue SO4 A 301' AC2 Software B SO4 301 ? 10 'binding site for residue SO4 B 301' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 10 LEU A 1 ? LEU A 255 . ? 1_555 ? 2 AC1 10 LEU A 1 ? LEU A 255 . ? 1_655 ? 3 AC1 10 ASN A 3 ? ASN A 257 . ? 1_555 ? 4 AC1 10 HOH G . ? HOH A 2001 . ? 1_455 ? 5 AC1 10 HOH G . ? HOH A 2001 . ? 1_555 ? 6 AC1 10 HOH G . ? HOH A 2002 . ? 1_655 ? 7 AC1 10 HOH G . ? HOH A 2002 . ? 1_555 ? 8 AC1 10 LEU C 1 ? LEU C 255 . ? 1_554 ? 9 AC1 10 LEU C 1 ? LEU C 255 . ? 1_454 ? 10 AC1 10 ASN C 3 ? ASN C 257 . ? 1_454 ? 11 AC2 10 LEU B 1 ? LEU B 255 . ? 1_455 ? 12 AC2 10 LEU B 1 ? LEU B 255 . ? 1_555 ? 13 AC2 10 ASN B 3 ? ASN B 257 . ? 1_555 ? 14 AC2 10 HOH H . ? HOH B 2001 . ? 1_455 ? 15 AC2 10 HOH H . ? HOH B 2001 . ? 1_555 ? 16 AC2 10 HOH H . ? HOH B 2002 . ? 1_555 ? 17 AC2 10 HOH H . ? HOH B 2002 . ? 1_455 ? 18 AC2 10 LEU D 1 ? LEU M 255 . ? 1_455 ? 19 AC2 10 LEU D 1 ? LEU M 255 . ? 1_555 ? 20 AC2 10 ASN D 3 ? ASN M 257 . ? 1_555 ? # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 2003 ? ? 1_555 O C HOH 2001 ? ? 1_464 1.95 2 1 O B HOH 2003 ? ? 1_555 O M HOH 2001 ? ? 1_545 2.17 # 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 ASN N N N N 1 ASN CA C N S 2 ASN C C N N 3 ASN O O N N 4 ASN CB C N N 5 ASN CG C N N 6 ASN OD1 O N N 7 ASN ND2 N N N 8 ASN OXT O N N 9 ASN H H N N 10 ASN H2 H N N 11 ASN HA H N N 12 ASN HB2 H N N 13 ASN HB3 H N N 14 ASN HD21 H N N 15 ASN HD22 H N N 16 ASN HXT H N N 17 GLY N N N N 18 GLY CA C N N 19 GLY C C N N 20 GLY O O N N 21 GLY OXT O N N 22 GLY H H N N 23 GLY H2 H N N 24 GLY HA2 H N N 25 GLY HA3 H N N 26 GLY HXT H N N 27 HOH O O N N 28 HOH H1 H N N 29 HOH H2 H N N 30 LEU N N N N 31 LEU CA C N S 32 LEU C C N N 33 LEU O O N N 34 LEU CB C N N 35 LEU CG C N N 36 LEU CD1 C N N 37 LEU CD2 C N N 38 LEU OXT O N N 39 LEU H H N N 40 LEU H2 H N N 41 LEU HA H N N 42 LEU HB2 H N N 43 LEU HB3 H N N 44 LEU HG H N N 45 LEU HD11 H N N 46 LEU HD12 H N N 47 LEU HD13 H N N 48 LEU HD21 H N N 49 LEU HD22 H N N 50 LEU HD23 H N N 51 LEU HXT H N N 52 SO4 S S N N 53 SO4 O1 O N N 54 SO4 O2 O N N 55 SO4 O3 O N N 56 SO4 O4 O N N 57 TYR N N N N 58 TYR CA C N S 59 TYR C C N N 60 TYR O O N N 61 TYR CB C N N 62 TYR CG C Y N 63 TYR CD1 C Y N 64 TYR CD2 C Y N 65 TYR CE1 C Y N 66 TYR CE2 C Y N 67 TYR CZ C Y N 68 TYR OH O N N 69 TYR OXT O N N 70 TYR H H N N 71 TYR H2 H N N 72 TYR HA H N N 73 TYR HB2 H N N 74 TYR HB3 H N N 75 TYR HD1 H N N 76 TYR HD2 H N N 77 TYR HE1 H N N 78 TYR HE2 H N N 79 TYR HH H N N 80 TYR HXT H N N 81 # 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 ASN N CA sing N N 1 ASN N H sing N N 2 ASN N H2 sing N N 3 ASN CA C sing N N 4 ASN CA CB sing N N 5 ASN CA HA sing N N 6 ASN C O doub N N 7 ASN C OXT sing N N 8 ASN CB CG sing N N 9 ASN CB HB2 sing N N 10 ASN CB HB3 sing N N 11 ASN CG OD1 doub N N 12 ASN CG ND2 sing N N 13 ASN ND2 HD21 sing N N 14 ASN ND2 HD22 sing N N 15 ASN OXT HXT sing N N 16 GLY N CA sing N N 17 GLY N H sing N N 18 GLY N H2 sing N N 19 GLY CA C sing N N 20 GLY CA HA2 sing N N 21 GLY CA HA3 sing N N 22 GLY C O doub N N 23 GLY C OXT sing N N 24 GLY OXT HXT sing N N 25 HOH O H1 sing N N 26 HOH O H2 sing N N 27 LEU N CA sing N N 28 LEU N H sing N N 29 LEU N H2 sing N N 30 LEU CA C sing N N 31 LEU CA CB sing N N 32 LEU CA HA sing N N 33 LEU C O doub N N 34 LEU C OXT sing N N 35 LEU CB CG sing N N 36 LEU CB HB2 sing N N 37 LEU CB HB3 sing N N 38 LEU CG CD1 sing N N 39 LEU CG CD2 sing N N 40 LEU CG HG sing N N 41 LEU CD1 HD11 sing N N 42 LEU CD1 HD12 sing N N 43 LEU CD1 HD13 sing N N 44 LEU CD2 HD21 sing N N 45 LEU CD2 HD22 sing N N 46 LEU CD2 HD23 sing N N 47 LEU OXT HXT sing N N 48 SO4 S O1 doub N N 49 SO4 S O2 doub N N 50 SO4 S O3 sing N N 51 SO4 S O4 sing N N 52 TYR N CA sing N N 53 TYR N H sing N N 54 TYR N H2 sing N N 55 TYR CA C sing N N 56 TYR CA CB sing N N 57 TYR CA HA sing N N 58 TYR C O doub N N 59 TYR C OXT sing N N 60 TYR CB CG sing N N 61 TYR CB HB2 sing N N 62 TYR CB HB3 sing N N 63 TYR CG CD1 doub Y N 64 TYR CG CD2 sing Y N 65 TYR CD1 CE1 sing Y N 66 TYR CD1 HD1 sing N N 67 TYR CD2 CE2 doub Y N 68 TYR CD2 HD2 sing N N 69 TYR CE1 CZ doub Y N 70 TYR CE1 HE1 sing N N 71 TYR CE2 CZ sing Y N 72 TYR CE2 HE2 sing N N 73 TYR CZ OH sing N N 74 TYR OH HH sing N N 75 TYR OXT HXT sing N N 76 # _pdbx_audit_support.funding_organization 'French National Research Agency' _pdbx_audit_support.country France _pdbx_audit_support.grant_number ANR-15-CE18-0005-02 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 5N9H _atom_sites.fract_transf_matrix[1][1] 0.209030 _atom_sites.fract_transf_matrix[1][2] 0.000036 _atom_sites.fract_transf_matrix[1][3] 0.000036 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.086610 _atom_sites.fract_transf_matrix[2][3] 0.000015 _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] 0.021257 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O S # loop_