data_5N9I # _entry.id 5N9I # _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 5N9I pdb_00005n9i 10.2210/pdb5n9i/pdb WWPDB D_1200003197 ? ? # 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 2024-05-01 # _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' 5 4 'Structure model' 'Refinement description' # 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 7 4 'Structure model' diffrn_radiation_wavelength 8 4 'Structure model' pdbx_initial_refinement_model # 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 5N9I _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 'Colletier, J.P.' 1 ? 'Nasrallah, C.' 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 1' 590.624 4 ? ? 'DIMERIZATION DOMAIN, UNP residues 228-233' ? 2 water nat water 18.015 18 ? ? ? ? # _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 GVVTSE _entity_poly.pdbx_seq_one_letter_code_can GVVTSE _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 VAL n 1 3 VAL n 1 4 THR n 1 5 SER n 1 6 GLU 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 6 _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 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # 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 GLY 1 1 1 GLY GLY A . n A 1 2 VAL 2 2 2 VAL VAL A . n A 1 3 VAL 3 3 3 VAL VAL A . n A 1 4 THR 4 4 4 THR THR A . n A 1 5 SER 5 5 5 SER SER A . n A 1 6 GLU 6 6 6 GLU GLU A . n B 1 1 GLY 1 1 1 GLY GLY B . n B 1 2 VAL 2 2 2 VAL VAL B . n B 1 3 VAL 3 3 3 VAL VAL B . n B 1 4 THR 4 4 4 THR THR B . n B 1 5 SER 5 5 5 SER SER B . n B 1 6 GLU 6 6 6 GLU GLU B . n C 1 1 GLY 1 1 1 GLY GLY C . n C 1 2 VAL 2 2 2 VAL VAL C . n C 1 3 VAL 3 3 3 VAL VAL C . n C 1 4 THR 4 4 4 THR THR C . n C 1 5 SER 5 5 5 SER SER C . n C 1 6 GLU 6 6 6 GLU GLU C . n D 1 1 GLY 1 1 1 GLY GLY D . n D 1 2 VAL 2 2 2 VAL VAL D . n D 1 3 VAL 3 3 3 VAL VAL D . n D 1 4 THR 4 4 4 THR THR D . n D 1 5 SER 5 5 5 SER SER D . n D 1 6 GLU 6 6 6 GLU GLU D . 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 HOH 1 101 11 HOH HOH A . E 2 HOH 2 102 5 HOH HOH A . E 2 HOH 3 103 6 HOH HOH A . E 2 HOH 4 104 15 HOH HOH A . E 2 HOH 5 105 13 HOH HOH A . F 2 HOH 1 101 2 HOH HOH B . F 2 HOH 2 102 18 HOH HOH B . F 2 HOH 3 103 17 HOH HOH B . F 2 HOH 4 104 1 HOH HOH B . F 2 HOH 5 105 12 HOH HOH B . G 2 HOH 1 101 4 HOH HOH C . G 2 HOH 2 102 10 HOH HOH C . G 2 HOH 3 103 14 HOH HOH C . G 2 HOH 4 104 3 HOH HOH C . H 2 HOH 1 101 9 HOH HOH D . H 2 HOH 2 102 8 HOH HOH D . H 2 HOH 3 103 7 HOH HOH D . H 2 HOH 4 104 16 HOH HOH D . # 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 ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.7.0029 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.entry_id 5N9I _cell.length_a 4.800 _cell.length_b 16.910 _cell.length_c 45.450 _cell.angle_alpha 90.05 _cell.angle_beta 90.01 _cell.angle_gamma 90.05 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N9I _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _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 5N9I _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 1.62 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 23.9 _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 ;2.5 M AMONIUM SULFATE, 0.1 M ACID CITRIC PH4 ; _exptl_crystal_grow.pdbx_pH_range 4 # _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 MARRESEARCH _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2012-11-18 # _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 15.748 _reflns.entry_id 5N9I _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.91 _reflns.d_resolution_low 50 _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 1076 _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 3.0 _reflns.percent_possible_obs 96.66 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 2.20 _reflns.pdbx_Rmerge_I_obs 0.1197 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 4.9 _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 0.1623 _reflns.pdbx_Rpim_I_all 0.1088 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.991 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.91 _reflns_shell.d_res_low 1.979 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 3.24 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 122 _reflns_shell.percent_possible_all 100 _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 0.1879 _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 2.2 _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 0.2535 _reflns_shell.pdbx_Rpim_I_all 0.169 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.973 _reflns_shell.pdbx_R_split ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5N9I _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 890 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 45.45 _refine.ls_d_res_high 1.91 _refine.ls_percent_reflns_obs 92.24 _refine.ls_R_factor_obs 0.15705 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.14735 _refine.ls_R_factor_R_free 0.20590 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 15.9 _refine.ls_number_reflns_R_free 168 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.975 _refine.correlation_coeff_Fo_to_Fc_free 0.951 _refine.B_iso_mean 12.675 _refine.aniso_B[1][1] -7.24 _refine.aniso_B[2][2] 24.21 _refine.aniso_B[3][3] -16.97 _refine.aniso_B[1][2] 15.14 _refine.aniso_B[1][3] -15.62 _refine.aniso_B[2][3] -0.38 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT' _refine.pdbx_starting_model 'a canonical beta-sheet' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.066 _refine.pdbx_overall_ESU_R_Free 0.039 _refine.overall_SU_ML 0.111 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 4.112 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id 1 _refine_hist.pdbx_number_atoms_protein 164 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 18 _refine_hist.number_atoms_total 182 _refine_hist.d_res_high 1.91 _refine_hist.d_res_low 45.45 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.018 0.020 ? 160 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.229 2.026 ? 216 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 8.322 5.000 ? 20 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 56.565 30.000 ? 4 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 17.174 15.000 ? 24 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.138 0.200 ? 32 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 112 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.906 _refine_ls_shell.d_res_low 1.956 _refine_ls_shell.number_reflns_R_work 88 _refine_ls_shell.R_factor_R_work 0.208 _refine_ls_shell.percent_reflns_obs 96.08 _refine_ls_shell.R_factor_R_free 0.532 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 10 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.number_reflns_obs ? # _database_PDB_matrix.entry_id 5N9I _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 5N9I _struct.title 'STRUCTURE OF 206-GVVTSE-211, THE STERIC ZIPPER THAT SUPPORTS THE SELF-ASSOCIATION OF P. STUARTII OMP-PST1 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 5N9I _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 2 ? H N N 2 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code E3U904_PROST _struct_ref.pdbx_db_accession E3U904 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GVVTSE _struct_ref.pdbx_align_begin 228 # 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 5N9I A 1 ? 6 ? E3U904 228 ? 233 ? 1 6 2 1 5N9I B 1 ? 6 ? E3U904 228 ? 233 ? 1 6 3 1 5N9I C 1 ? 6 ? E3U904 228 ? 233 ? 1 6 4 1 5N9I D 1 ? 6 ? E3U904 228 ? 233 ? 1 6 # _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)' 500 ? 1 MORE -2 ? 1 'SSA (A^2)' 2930 ? # _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 # _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 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OE2 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 GLU _pdbx_validate_close_contact.auth_seq_id_1 6 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 OXT _pdbx_validate_close_contact.auth_asym_id_2 C _pdbx_validate_close_contact.auth_comp_id_2 GLU _pdbx_validate_close_contact.auth_seq_id_2 6 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.12 # 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 GLU N N N N 1 GLU CA C N S 2 GLU C C N N 3 GLU O O N N 4 GLU CB C N N 5 GLU CG C N N 6 GLU CD C N N 7 GLU OE1 O N N 8 GLU OE2 O N N 9 GLU OXT O N N 10 GLU H H N N 11 GLU H2 H N N 12 GLU HA H N N 13 GLU HB2 H N N 14 GLU HB3 H N N 15 GLU HG2 H N N 16 GLU HG3 H N N 17 GLU HE2 H N N 18 GLU HXT H N N 19 GLY N N N N 20 GLY CA C N N 21 GLY C C N N 22 GLY O O N N 23 GLY OXT O N N 24 GLY H H N N 25 GLY H2 H N N 26 GLY HA2 H N N 27 GLY HA3 H N N 28 GLY HXT H N N 29 HOH O O N N 30 HOH H1 H N N 31 HOH H2 H N N 32 SER N N N N 33 SER CA C N S 34 SER C C N N 35 SER O O N N 36 SER CB C N N 37 SER OG O N N 38 SER OXT O N N 39 SER H H N N 40 SER H2 H N N 41 SER HA H N N 42 SER HB2 H N N 43 SER HB3 H N N 44 SER HG H N N 45 SER HXT H N N 46 THR N N N N 47 THR CA C N S 48 THR C C N N 49 THR O O N N 50 THR CB C N R 51 THR OG1 O N N 52 THR CG2 C N N 53 THR OXT O N N 54 THR H H N N 55 THR H2 H N N 56 THR HA H N N 57 THR HB H N N 58 THR HG1 H N N 59 THR HG21 H N N 60 THR HG22 H N N 61 THR HG23 H N N 62 THR HXT H N N 63 VAL N N N N 64 VAL CA C N S 65 VAL C C N N 66 VAL O O N N 67 VAL CB C N N 68 VAL CG1 C N N 69 VAL CG2 C N N 70 VAL OXT O N N 71 VAL H H N N 72 VAL H2 H N N 73 VAL HA H N N 74 VAL HB H N N 75 VAL HG11 H N N 76 VAL HG12 H N N 77 VAL HG13 H N N 78 VAL HG21 H N N 79 VAL HG22 H N N 80 VAL HG23 H N N 81 VAL HXT H N N 82 # 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 GLU N CA sing N N 1 GLU N H sing N N 2 GLU N H2 sing N N 3 GLU CA C sing N N 4 GLU CA CB sing N N 5 GLU CA HA sing N N 6 GLU C O doub N N 7 GLU C OXT sing N N 8 GLU CB CG sing N N 9 GLU CB HB2 sing N N 10 GLU CB HB3 sing N N 11 GLU CG CD sing N N 12 GLU CG HG2 sing N N 13 GLU CG HG3 sing N N 14 GLU CD OE1 doub N N 15 GLU CD OE2 sing N N 16 GLU OE2 HE2 sing N N 17 GLU OXT HXT sing N N 18 GLY N CA sing N N 19 GLY N H sing N N 20 GLY N H2 sing N N 21 GLY CA C sing N N 22 GLY CA HA2 sing N N 23 GLY CA HA3 sing N N 24 GLY C O doub N N 25 GLY C OXT sing N N 26 GLY OXT HXT sing N N 27 HOH O H1 sing N N 28 HOH O H2 sing N N 29 SER N CA sing N N 30 SER N H sing N N 31 SER N H2 sing N N 32 SER CA C sing N N 33 SER CA CB sing N N 34 SER CA HA sing N N 35 SER C O doub N N 36 SER C OXT sing N N 37 SER CB OG sing N N 38 SER CB HB2 sing N N 39 SER CB HB3 sing N N 40 SER OG HG sing N N 41 SER OXT HXT sing N N 42 THR N CA sing N N 43 THR N H sing N N 44 THR N H2 sing N N 45 THR CA C sing N N 46 THR CA CB sing N N 47 THR CA HA sing N N 48 THR C O doub N N 49 THR C OXT sing N N 50 THR CB OG1 sing N N 51 THR CB CG2 sing N N 52 THR CB HB sing N N 53 THR OG1 HG1 sing N N 54 THR CG2 HG21 sing N N 55 THR CG2 HG22 sing N N 56 THR CG2 HG23 sing N N 57 THR OXT HXT sing N N 58 VAL N CA sing N N 59 VAL N H sing N N 60 VAL N H2 sing N N 61 VAL CA C sing N N 62 VAL CA CB sing N N 63 VAL CA HA sing N N 64 VAL C O doub N N 65 VAL C OXT sing N N 66 VAL CB CG1 sing N N 67 VAL CB CG2 sing N N 68 VAL CB HB sing N N 69 VAL CG1 HG11 sing N N 70 VAL CG1 HG12 sing N N 71 VAL CG1 HG13 sing N N 72 VAL CG2 HG21 sing N N 73 VAL CG2 HG22 sing N N 74 VAL CG2 HG23 sing N N 75 VAL 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 # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type other _pdbx_initial_refinement_model.source_name ? _pdbx_initial_refinement_model.details 'a canonical beta-sheet' # loop_ _pdbx_reflns_twin.domain_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.type _pdbx_reflns_twin.operator _pdbx_reflns_twin.fraction 1 1 1 ? 'H, K, L' 0.298 2 1 1 ? -h,-k,l 0.198 3 1 1 ? h,-k,-l 0.288 4 1 1 ? '-H, K, -L' 0.216 # _atom_sites.entry_id 5N9I _atom_sites.fract_transf_matrix[1][1] 0.208333 _atom_sites.fract_transf_matrix[1][2] 0.000182 _atom_sites.fract_transf_matrix[1][3] 0.000029 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.059137 _atom_sites.fract_transf_matrix[2][3] 0.000046 _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] 0.022002 _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 N O # loop_