data_3QDR # _entry.id 3QDR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3QDR RCSB RCSB063516 WWPDB D_1000063516 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3QDP _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3QDR _pdbx_database_status.recvd_initial_deposition_date 2011-01-19 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _audit_author.name 'Li, C.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Structural Evidence That Colicin A Protein Binds to a Novel Binding Site of TolA Protein in Escherichia coli Periplasm.' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 287 _citation.page_first 19048 _citation.page_last 19057 _citation.year 2012 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22493500 _citation.pdbx_database_id_DOI 10.1074/jbc.M112.342246 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Li, C.' 1 primary 'Zhang, Y.' 2 primary 'Vankemmelbeke, M.' 3 primary 'Hecht, O.' 4 primary 'Aleanizy, F.S.' 5 primary 'Macdonald, C.' 6 primary 'Moore, G.R.' 7 primary 'James, R.' 8 primary 'Penfold, C.N.' 9 # _cell.entry_id 3QDR _cell.length_a 47.497 _cell.length_b 119.624 _cell.length_c 30.147 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3QDR _symmetry.space_group_name_H-M 'P 21 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? # 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 man 'Protein tolA' 13140.814 1 ? ? 'TolA domain III, residues 302-421' ? 2 polymer man Colicin-A 6803.556 1 ? ? 'ColA, residues 53-107' ? 3 non-polymer syn 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 122.143 1 ? ? ? ? 4 water nat water 18.015 26 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no yes ;HHHHHHMSSGKNAPKTGGGAKGNNASPAGSGNTKNNGASGADINNYAGQIKSAIES(MLY)FYDASSYAGKTCTLRIKLA PDGMLLDIKPEGGDPALCQAALAAAKLAKIPKPPSQAVYEVFKNAPLDFKP ; ;HHHHHHMSSGKNAPKTGGGAKGNNASPAGSGNTKNNGASGADINNYAGQIKSAIESKFYDASSYAGKTCTLRIKLAPDGM LLDIKPEGGDPALCQAALAAAKLAKIPKPPSQAVYEVFKNAPLDFKP ; A ? 2 'polypeptide(L)' no no GSKPGDSYNTPWGKVIINAAGQPTMNGTVMTADNSSMVPYGRGFTRVLNSLVNNPVSHHHHHH GSKPGDSYNTPWGKVIINAAGQPTMNGTVMTADNSSMVPYGRGFTRVLNSLVNNPVSHHHHHH B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 HIS n 1 2 HIS n 1 3 HIS n 1 4 HIS n 1 5 HIS n 1 6 HIS n 1 7 MET n 1 8 SER n 1 9 SER n 1 10 GLY n 1 11 LYS n 1 12 ASN n 1 13 ALA n 1 14 PRO n 1 15 LYS n 1 16 THR n 1 17 GLY n 1 18 GLY n 1 19 GLY n 1 20 ALA n 1 21 LYS n 1 22 GLY n 1 23 ASN n 1 24 ASN n 1 25 ALA n 1 26 SER n 1 27 PRO n 1 28 ALA n 1 29 GLY n 1 30 SER n 1 31 GLY n 1 32 ASN n 1 33 THR n 1 34 LYS n 1 35 ASN n 1 36 ASN n 1 37 GLY n 1 38 ALA n 1 39 SER n 1 40 GLY n 1 41 ALA n 1 42 ASP n 1 43 ILE n 1 44 ASN n 1 45 ASN n 1 46 TYR n 1 47 ALA n 1 48 GLY n 1 49 GLN n 1 50 ILE n 1 51 LYS n 1 52 SER n 1 53 ALA n 1 54 ILE n 1 55 GLU n 1 56 SER n 1 57 MLY n 1 58 PHE n 1 59 TYR n 1 60 ASP n 1 61 ALA n 1 62 SER n 1 63 SER n 1 64 TYR n 1 65 ALA n 1 66 GLY n 1 67 LYS n 1 68 THR n 1 69 CYS n 1 70 THR n 1 71 LEU n 1 72 ARG n 1 73 ILE n 1 74 LYS n 1 75 LEU n 1 76 ALA n 1 77 PRO n 1 78 ASP n 1 79 GLY n 1 80 MET n 1 81 LEU n 1 82 LEU n 1 83 ASP n 1 84 ILE n 1 85 LYS n 1 86 PRO n 1 87 GLU n 1 88 GLY n 1 89 GLY n 1 90 ASP n 1 91 PRO n 1 92 ALA n 1 93 LEU n 1 94 CYS n 1 95 GLN n 1 96 ALA n 1 97 ALA n 1 98 LEU n 1 99 ALA n 1 100 ALA n 1 101 ALA n 1 102 LYS n 1 103 LEU n 1 104 ALA n 1 105 LYS n 1 106 ILE n 1 107 PRO n 1 108 LYS n 1 109 PRO n 1 110 PRO n 1 111 SER n 1 112 GLN n 1 113 ALA n 1 114 VAL n 1 115 TYR n 1 116 GLU n 1 117 VAL n 1 118 PHE n 1 119 LYS n 1 120 ASN n 1 121 ALA n 1 122 PRO n 1 123 LEU n 1 124 ASP n 1 125 PHE n 1 126 LYS n 1 127 PRO n 2 1 GLY n 2 2 SER n 2 3 LYS n 2 4 PRO n 2 5 GLY n 2 6 ASP n 2 7 SER n 2 8 TYR n 2 9 ASN n 2 10 THR n 2 11 PRO n 2 12 TRP n 2 13 GLY n 2 14 LYS n 2 15 VAL n 2 16 ILE n 2 17 ILE n 2 18 ASN n 2 19 ALA n 2 20 ALA n 2 21 GLY n 2 22 GLN n 2 23 PRO n 2 24 THR n 2 25 MET n 2 26 ASN n 2 27 GLY n 2 28 THR n 2 29 VAL n 2 30 MET n 2 31 THR n 2 32 ALA n 2 33 ASP n 2 34 ASN n 2 35 SER n 2 36 SER n 2 37 MET n 2 38 VAL n 2 39 PRO n 2 40 TYR n 2 41 GLY n 2 42 ARG n 2 43 GLY n 2 44 PHE n 2 45 THR n 2 46 ARG n 2 47 VAL n 2 48 LEU n 2 49 ASN n 2 50 SER n 2 51 LEU n 2 52 VAL n 2 53 ASN n 2 54 ASN n 2 55 PRO n 2 56 VAL n 2 57 SER n 2 58 HIS n 2 59 HIS n 2 60 HIS n 2 61 HIS n 2 62 HIS n 2 63 HIS n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample ? ? ? ? ? 'tolA, cim, excC, lky, b0739, JW0729' ? K-12 ? ? ? ? 'Escherichia coli' 83333 ? ? ? ? ? ? ? ? 'Escherichia coli' 469008 ? ? ? ? ? ? 'BL21(DE3)' ? ? ? ? ? ? ? plasmid ? ? ? pET21a ? ? 2 1 sample ? ? ? ? ? 'caa, ColA' ? ? ? ? ? ? 'Citrobacter freundii' 546 ? ? ? ? ? ? ? ? 'Escherichia coli' 469008 ? ? ? ? ? ? 'BL21(DE3)' ? ? ? ? ? ? ? plasmid ? ? ? pET21A ? ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP TOLA_ECOLI P19934 1 ;SSGKNAPKTGGGAKGNNASPAGSGNTKNNGASGADINNYAGQIKSAIESKFYDASSYAGKTCTLRIKLAPDGMLLDIKPE GGDPALCQAALAAAKLAKIPKPPSQAVYEVFKNAPLDFKP ; 302 ? 2 UNP CEA_CITFR P04480 2 KPGDSYNTPWGKVIINAAGQPTMNGTVMTADNSSMVPYGRGFTRVLNSLVNNPVS 53 ? # 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 3QDR A 8 ? 127 ? P19934 302 ? 421 ? 302 421 2 2 3QDR B 3 ? 57 ? P04480 53 ? 107 ? 53 107 # 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 3QDR HIS A 1 ? UNP P19934 ? ? 'EXPRESSION TAG' 295 1 1 3QDR HIS A 2 ? UNP P19934 ? ? 'EXPRESSION TAG' 296 2 1 3QDR HIS A 3 ? UNP P19934 ? ? 'EXPRESSION TAG' 297 3 1 3QDR HIS A 4 ? UNP P19934 ? ? 'EXPRESSION TAG' 298 4 1 3QDR HIS A 5 ? UNP P19934 ? ? 'EXPRESSION TAG' 299 5 1 3QDR HIS A 6 ? UNP P19934 ? ? 'EXPRESSION TAG' 300 6 1 3QDR MET A 7 ? UNP P19934 ? ? 'EXPRESSION TAG' 301 7 2 3QDR GLY B 1 ? UNP P04480 ? ? 'EXPRESSION TAG' 51 8 2 3QDR SER B 2 ? UNP P04480 ? ? 'EXPRESSION TAG' 52 9 2 3QDR HIS B 58 ? UNP P04480 ? ? 'EXPRESSION TAG' 108 10 2 3QDR HIS B 59 ? UNP P04480 ? ? 'EXPRESSION TAG' 109 11 2 3QDR HIS B 60 ? UNP P04480 ? ? 'EXPRESSION TAG' 110 12 2 3QDR HIS B 61 ? UNP P04480 ? ? 'EXPRESSION TAG' 111 13 2 3QDR HIS B 62 ? UNP P04480 ? ? 'EXPRESSION TAG' 112 14 2 3QDR HIS B 63 ? UNP P04480 ? ? 'EXPRESSION TAG' 113 15 # 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 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MLY 'L-peptide linking' n N-DIMETHYL-LYSINE ? 'C8 H18 N2 O2' 174.241 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 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TRS non-polymer . 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 'TRIS BUFFER' 'C4 H12 N O3 1' 122.143 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3QDR _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_percent_sol 42.71 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '0.2 M K2HPO4, 2.2 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K' # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 298 ? 1 2 298 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'MARMOSAIC 225 mm CCD' 2009-06-15 ? 2 CCD 'ADSC QUANTUM 315r' 2010-03-12 ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M 'horizontally diffracting monochromator' 'SINGLE WAVELENGTH' x-ray 2 1 M 'channel cut ESRF monochromator' 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.8726 1.0 2 0.9795 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'ESRF BEAMLINE ID23-2' ESRF ID23-2 ? 0.8726 2 SYNCHROTRON 'ESRF BEAMLINE ID14-4' ESRF ID14-4 ? 0.9795 # _reflns.entry_id 3QDR _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 59.8 _reflns.d_resolution_high 2.65 _reflns.number_obs 5238 _reflns.number_all ? _reflns.percent_possible_obs 97.4 _reflns.pdbx_Rmerge_I_obs 0.098 _reflns.pdbx_Rsym_value 0.129 _reflns.pdbx_netI_over_sigmaI 10.5 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.6 _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1,2 # _reflns_shell.d_res_high 2.65 _reflns_shell.d_res_low 2.79 _reflns_shell.percent_possible_all 98.2 _reflns_shell.Rmerge_I_obs 0.344 _reflns_shell.pdbx_Rsym_value 0.454 _reflns_shell.meanI_over_sigI_obs 3.8 _reflns_shell.pdbx_redundancy 3.6 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1,2 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3QDR _refine.ls_number_reflns_obs 4973 _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 59.8 _refine.ls_d_res_high 2.65 _refine.ls_percent_reflns_obs 96.32 _refine.ls_R_factor_obs 0.24518 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.24385 _refine.ls_R_factor_R_free 0.27263 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.5 _refine.ls_number_reflns_R_free 234 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.891 _refine.correlation_coeff_Fo_to_Fc_free 0.857 _refine.B_iso_mean 33.445 _refine.aniso_B[1][1] -1.51 _refine.aniso_B[2][2] 1.16 _refine.aniso_B[3][3] 0.35 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _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 0.928 _refine.pdbx_overall_ESU_R_Free 0.350 _refine.overall_SU_ML 0.272 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 12.681 _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.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1,2 _refine.pdbx_TLS_residual_ADP_flag ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1053 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 26 _refine_hist.number_atoms_total 1087 _refine_hist.d_res_high 2.65 _refine_hist.d_res_low 59.8 # 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 0.014 0.022 ? 1098 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.867 1.989 ? 1495 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 8.362 5.000 ? 144 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 40.683 25.952 ? 42 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 23.886 15.000 ? 170 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 17.891 15.000 ? 3 'X-RAY DIFFRACTION' ? r_chiral_restr 0.134 0.200 ? 165 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.010 0.022 ? 841 '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 0.594 1.500 ? 718 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.140 2.000 ? 1152 'X-RAY DIFFRACTION' ? r_scbond_it 1.529 3.000 ? 380 'X-RAY DIFFRACTION' ? r_scangle_it 2.476 4.500 ? 342 '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 2.650 _refine_ls_shell.d_res_low 2.719 _refine_ls_shell.number_reflns_R_work 363 _refine_ls_shell.R_factor_R_work 0.274 _refine_ls_shell.percent_reflns_obs 98.94 _refine_ls_shell.R_factor_R_free 0.322 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 12 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 3QDR _struct.title 'Structural characterization of the interaction of colicin A, colicin N, and TolB with the TolAIII translocon' _struct.pdbx_descriptor 'Protein tolA, Colicin-A' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3QDR _struct_keywords.pdbx_keywords 'PROTEIN TRANSPORT/TOXIN' _struct_keywords.text 'ColA, TolA, Complex, translocation, ColA binds to TolA, Methylation, PROTEIN TRANSPORT-TOXIN complex' # 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 2 ? C N N 3 ? D N N 4 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ALA A 38 ? SER A 56 ? ALA A 332 SER A 350 1 ? 19 HELX_P HELX_P2 2 ASP A 60 ? ALA A 65 ? ASP A 354 ALA A 359 5 ? 6 HELX_P HELX_P3 3 ASP A 90 ? LYS A 102 ? ASP A 384 LYS A 396 1 ? 13 HELX_P HELX_P4 4 SER A 111 ? LYS A 119 ? SER A 405 LYS A 413 1 ? 9 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf1 disulf ? ? A CYS 69 SG ? ? ? 1_555 A CYS 94 SG ? ? A CYS 363 A CYS 388 1_555 ? ? ? ? ? ? ? 2.904 ? covale1 covale ? ? A SER 56 C ? ? ? 1_555 A MLY 57 N ? ? A SER 350 A MLY 351 1_555 ? ? ? ? ? ? ? 1.330 ? covale2 covale ? ? A MLY 57 C ? ? ? 1_555 A PHE 58 N ? ? A MLY 351 A PHE 352 1_555 ? ? ? ? ? ? ? 1.342 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 4 ? # 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 A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-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 A 1 ALA A 121 ? PHE A 125 ? ALA A 415 PHE A 419 A 2 CYS A 69 ? LEU A 75 ? CYS A 363 LEU A 369 A 3 LEU A 81 ? GLY A 89 ? LEU A 375 GLY A 383 A 4 GLY B 43 ? VAL B 47 ? GLY B 93 VAL B 97 A 5 SER B 36 ? TYR B 40 ? SER B 86 TYR B 90 B 1 TYR B 8 ? THR B 10 ? TYR B 58 THR B 60 B 2 GLY B 13 ? ILE B 16 ? GLY B 63 ILE B 66 B 3 THR B 24 ? MET B 25 ? THR B 74 MET B 75 B 4 THR B 28 ? VAL B 29 ? THR B 78 VAL B 79 # 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 A 1 2 O PHE A 125 ? O PHE A 419 N CYS A 69 ? N CYS A 363 A 2 3 N ARG A 72 ? N ARG A 366 O LYS A 85 ? O LYS A 379 A 3 4 N ILE A 84 ? N ILE A 378 O PHE B 44 ? O PHE B 94 A 4 5 O THR B 45 ? O THR B 95 N VAL B 38 ? N VAL B 88 B 1 2 N TYR B 8 ? N TYR B 58 O VAL B 15 ? O VAL B 65 B 2 3 N ILE B 16 ? N ILE B 66 O THR B 24 ? O THR B 74 B 3 4 N MET B 25 ? N MET B 75 O THR B 28 ? O THR B 78 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _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 5 _struct_site.details 'BINDING SITE FOR RESIDUE TRS A 501' # 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 5 PHE A 58 ? PHE A 352 . ? 1_555 ? 2 AC1 5 TYR A 59 ? TYR A 353 . ? 1_555 ? 3 AC1 5 ASP A 60 ? ASP A 354 . ? 1_555 ? 4 AC1 5 SER A 62 ? SER A 356 . ? 1_555 ? 5 AC1 5 ARG A 72 ? ARG A 366 . ? 4_456 ? # _database_PDB_matrix.entry_id 3QDR _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 # _atom_sites.entry_id 3QDR _atom_sites.fract_transf_matrix[1][1] 0.021054 _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] 0.008360 _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] 0.033171 _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 S # 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 HIS 1 295 ? ? ? A . n A 1 2 HIS 2 296 ? ? ? A . n A 1 3 HIS 3 297 ? ? ? A . n A 1 4 HIS 4 298 ? ? ? A . n A 1 5 HIS 5 299 ? ? ? A . n A 1 6 HIS 6 300 ? ? ? A . n A 1 7 MET 7 301 ? ? ? A . n A 1 8 SER 8 302 ? ? ? A . n A 1 9 SER 9 303 ? ? ? A . n A 1 10 GLY 10 304 ? ? ? A . n A 1 11 LYS 11 305 ? ? ? A . n A 1 12 ASN 12 306 ? ? ? A . n A 1 13 ALA 13 307 ? ? ? A . n A 1 14 PRO 14 308 ? ? ? A . n A 1 15 LYS 15 309 ? ? ? A . n A 1 16 THR 16 310 ? ? ? A . n A 1 17 GLY 17 311 ? ? ? A . n A 1 18 GLY 18 312 ? ? ? A . n A 1 19 GLY 19 313 ? ? ? A . n A 1 20 ALA 20 314 ? ? ? A . n A 1 21 LYS 21 315 ? ? ? A . n A 1 22 GLY 22 316 ? ? ? A . n A 1 23 ASN 23 317 ? ? ? A . n A 1 24 ASN 24 318 ? ? ? A . n A 1 25 ALA 25 319 ? ? ? A . n A 1 26 SER 26 320 ? ? ? A . n A 1 27 PRO 27 321 ? ? ? A . n A 1 28 ALA 28 322 ? ? ? A . n A 1 29 GLY 29 323 ? ? ? A . n A 1 30 SER 30 324 ? ? ? A . n A 1 31 GLY 31 325 ? ? ? A . n A 1 32 ASN 32 326 ? ? ? A . n A 1 33 THR 33 327 ? ? ? A . n A 1 34 LYS 34 328 ? ? ? A . n A 1 35 ASN 35 329 329 ASN ASN A . n A 1 36 ASN 36 330 330 ASN ASN A . n A 1 37 GLY 37 331 331 GLY GLY A . n A 1 38 ALA 38 332 332 ALA ALA A . n A 1 39 SER 39 333 333 SER SER A . n A 1 40 GLY 40 334 334 GLY GLY A . n A 1 41 ALA 41 335 335 ALA ALA A . n A 1 42 ASP 42 336 336 ASP ASP A . n A 1 43 ILE 43 337 337 ILE ILE A . n A 1 44 ASN 44 338 338 ASN ASN A . n A 1 45 ASN 45 339 339 ASN ASN A . n A 1 46 TYR 46 340 340 TYR TYR A . n A 1 47 ALA 47 341 341 ALA ALA A . n A 1 48 GLY 48 342 342 GLY GLY A . n A 1 49 GLN 49 343 343 GLN GLN A . n A 1 50 ILE 50 344 344 ILE ILE A . n A 1 51 LYS 51 345 345 LYS LYS A . n A 1 52 SER 52 346 346 SER SER A . n A 1 53 ALA 53 347 347 ALA ALA A . n A 1 54 ILE 54 348 348 ILE ILE A . n A 1 55 GLU 55 349 349 GLU GLU A . n A 1 56 SER 56 350 350 SER SER A . n A 1 57 MLY 57 351 351 MLY MLY A . n A 1 58 PHE 58 352 352 PHE PHE A . n A 1 59 TYR 59 353 353 TYR TYR A . n A 1 60 ASP 60 354 354 ASP ASP A . n A 1 61 ALA 61 355 355 ALA ALA A . n A 1 62 SER 62 356 356 SER SER A . n A 1 63 SER 63 357 357 SER SER A . n A 1 64 TYR 64 358 358 TYR TYR A . n A 1 65 ALA 65 359 359 ALA ALA A . n A 1 66 GLY 66 360 360 GLY GLY A . n A 1 67 LYS 67 361 361 LYS LYS A . n A 1 68 THR 68 362 362 THR THR A . n A 1 69 CYS 69 363 363 CYS CYS A . n A 1 70 THR 70 364 364 THR THR A . n A 1 71 LEU 71 365 365 LEU LEU A . n A 1 72 ARG 72 366 366 ARG ARG A . n A 1 73 ILE 73 367 367 ILE ILE A . n A 1 74 LYS 74 368 368 LYS LYS A . n A 1 75 LEU 75 369 369 LEU LEU A . n A 1 76 ALA 76 370 370 ALA ALA A . n A 1 77 PRO 77 371 371 PRO PRO A . n A 1 78 ASP 78 372 372 ASP ASP A . n A 1 79 GLY 79 373 373 GLY GLY A . n A 1 80 MET 80 374 374 MET MET A . n A 1 81 LEU 81 375 375 LEU LEU A . n A 1 82 LEU 82 376 376 LEU LEU A . n A 1 83 ASP 83 377 377 ASP ASP A . n A 1 84 ILE 84 378 378 ILE ILE A . n A 1 85 LYS 85 379 379 LYS LYS A . n A 1 86 PRO 86 380 380 PRO PRO A . n A 1 87 GLU 87 381 381 GLU GLU A . n A 1 88 GLY 88 382 382 GLY GLY A . n A 1 89 GLY 89 383 383 GLY GLY A . n A 1 90 ASP 90 384 384 ASP ASP A . n A 1 91 PRO 91 385 385 PRO PRO A . n A 1 92 ALA 92 386 386 ALA ALA A . n A 1 93 LEU 93 387 387 LEU LEU A . n A 1 94 CYS 94 388 388 CYS CYS A . n A 1 95 GLN 95 389 389 GLN GLN A . n A 1 96 ALA 96 390 390 ALA ALA A . n A 1 97 ALA 97 391 391 ALA ALA A . n A 1 98 LEU 98 392 392 LEU LEU A . n A 1 99 ALA 99 393 393 ALA ALA A . n A 1 100 ALA 100 394 394 ALA ALA A . n A 1 101 ALA 101 395 395 ALA ALA A . n A 1 102 LYS 102 396 396 LYS LYS A . n A 1 103 LEU 103 397 397 LEU LEU A . n A 1 104 ALA 104 398 398 ALA ALA A . n A 1 105 LYS 105 399 399 LYS LYS A . n A 1 106 ILE 106 400 400 ILE ILE A . n A 1 107 PRO 107 401 401 PRO PRO A . n A 1 108 LYS 108 402 402 LYS LYS A . n A 1 109 PRO 109 403 403 PRO PRO A . n A 1 110 PRO 110 404 404 PRO PRO A . n A 1 111 SER 111 405 405 SER SER A . n A 1 112 GLN 112 406 406 GLN GLN A . n A 1 113 ALA 113 407 407 ALA ALA A . n A 1 114 VAL 114 408 408 VAL VAL A . n A 1 115 TYR 115 409 409 TYR TYR A . n A 1 116 GLU 116 410 410 GLU GLU A . n A 1 117 VAL 117 411 411 VAL VAL A . n A 1 118 PHE 118 412 412 PHE PHE A . n A 1 119 LYS 119 413 413 LYS LYS A . n A 1 120 ASN 120 414 414 ASN ASN A . n A 1 121 ALA 121 415 415 ALA ALA A . n A 1 122 PRO 122 416 416 PRO PRO A . n A 1 123 LEU 123 417 417 LEU LEU A . n A 1 124 ASP 124 418 418 ASP ASP A . n A 1 125 PHE 125 419 419 PHE PHE A . n A 1 126 LYS 126 420 420 LYS LYS A . n A 1 127 PRO 127 421 421 PRO PRO A . n B 2 1 GLY 1 51 ? ? ? B . n B 2 2 SER 2 52 ? ? ? B . n B 2 3 LYS 3 53 ? ? ? B . n B 2 4 PRO 4 54 ? ? ? B . n B 2 5 GLY 5 55 ? ? ? B . n B 2 6 ASP 6 56 ? ? ? B . n B 2 7 SER 7 57 57 SER SER B . n B 2 8 TYR 8 58 58 TYR TYR B . n B 2 9 ASN 9 59 59 ASN ASN B . n B 2 10 THR 10 60 60 THR THR B . n B 2 11 PRO 11 61 61 PRO PRO B . n B 2 12 TRP 12 62 62 TRP TRP B . n B 2 13 GLY 13 63 63 GLY GLY B . n B 2 14 LYS 14 64 64 LYS LYS B . n B 2 15 VAL 15 65 65 VAL VAL B . n B 2 16 ILE 16 66 66 ILE ILE B . n B 2 17 ILE 17 67 67 ILE ILE B . n B 2 18 ASN 18 68 68 ASN ASN B . n B 2 19 ALA 19 69 69 ALA ALA B . n B 2 20 ALA 20 70 70 ALA ALA B . n B 2 21 GLY 21 71 71 GLY GLY B . n B 2 22 GLN 22 72 72 GLN GLN B . n B 2 23 PRO 23 73 73 PRO PRO B . n B 2 24 THR 24 74 74 THR THR B . n B 2 25 MET 25 75 75 MET MET B . n B 2 26 ASN 26 76 76 ASN ASN B . n B 2 27 GLY 27 77 77 GLY GLY B . n B 2 28 THR 28 78 78 THR THR B . n B 2 29 VAL 29 79 79 VAL VAL B . n B 2 30 MET 30 80 80 MET MET B . n B 2 31 THR 31 81 81 THR THR B . n B 2 32 ALA 32 82 82 ALA ALA B . n B 2 33 ASP 33 83 83 ASP ASP B . n B 2 34 ASN 34 84 84 ASN ASN B . n B 2 35 SER 35 85 85 SER SER B . n B 2 36 SER 36 86 86 SER SER B . n B 2 37 MET 37 87 87 MET MET B . n B 2 38 VAL 38 88 88 VAL VAL B . n B 2 39 PRO 39 89 89 PRO PRO B . n B 2 40 TYR 40 90 90 TYR TYR B . n B 2 41 GLY 41 91 91 GLY GLY B . n B 2 42 ARG 42 92 92 ARG ARG B . n B 2 43 GLY 43 93 93 GLY GLY B . n B 2 44 PHE 44 94 94 PHE PHE B . n B 2 45 THR 45 95 95 THR THR B . n B 2 46 ARG 46 96 96 ARG ARG B . n B 2 47 VAL 47 97 97 VAL VAL B . n B 2 48 LEU 48 98 98 LEU LEU B . n B 2 49 ASN 49 99 99 ASN ASN B . n B 2 50 SER 50 100 100 SER SER B . n B 2 51 LEU 51 101 101 LEU LEU B . n B 2 52 VAL 52 102 102 VAL VAL B . n B 2 53 ASN 53 103 103 ASN ASN B . n B 2 54 ASN 54 104 104 ASN ASN B . n B 2 55 PRO 55 105 105 PRO PRO B . n B 2 56 VAL 56 106 ? ? ? B . n B 2 57 SER 57 107 ? ? ? B . n B 2 58 HIS 58 108 ? ? ? B . n B 2 59 HIS 59 109 ? ? ? B . n B 2 60 HIS 60 110 ? ? ? B . n B 2 61 HIS 61 111 ? ? ? B . n B 2 62 HIS 62 112 ? ? ? B . n B 2 63 HIS 63 113 ? ? ? B . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id MLY _pdbx_struct_mod_residue.label_seq_id 57 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id MLY _pdbx_struct_mod_residue.auth_seq_id 351 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id LYS _pdbx_struct_mod_residue.details N-DIMETHYL-LYSINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # 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)' 1400 ? 1 MORE -6 ? 1 'SSA (A^2)' 7910 ? # _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_ _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 2012-01-25 2 'Structure model' 1 1 2012-05-09 3 'Structure model' 1 2 2012-06-20 # _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 ? # 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' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 16.6852 29.2459 1.5180 0.1569 0.1703 0.2216 0.0124 0.1018 0.0409 1.0773 2.2112 2.3780 0.5718 1.5227 0.7030 -0.0479 0.3592 0.0074 -0.4545 0.0205 -0.5973 -0.1050 0.6009 0.0274 'X-RAY DIFFRACTION' 2 ? refined 1.6200 34.0455 14.6216 0.1039 0.0134 0.0307 -0.0307 0.0257 0.0010 3.0768 1.7503 0.1719 -0.2787 -0.3353 0.0571 0.0726 -0.0226 0.1453 -0.0427 -0.0153 -0.1142 -0.1263 0.0354 -0.0573 'X-RAY DIFFRACTION' 3 ? refined 8.4992 24.9480 17.3670 0.0925 0.0476 0.0415 -0.0088 0.0066 0.0080 0.9844 0.2263 0.9637 0.1300 0.4467 -0.2447 0.0320 -0.1160 0.0803 0.1071 -0.0390 0.0207 -0.0162 -0.0260 0.0070 'X-RAY DIFFRACTION' 4 ? refined 1.4009 18.1856 5.8750 0.0673 0.1234 0.1197 -0.0116 -0.0218 0.0342 0.1273 1.4375 6.2587 -0.2738 -0.6583 2.8565 0.0135 0.1094 -0.0056 -0.0877 -0.0785 0.1436 -0.0968 -0.3429 0.0650 'X-RAY DIFFRACTION' 5 ? refined 3.9797 24.9949 21.6472 0.0850 0.0406 0.0471 -0.0021 0.0240 0.0081 1.1630 0.0589 0.7790 0.2212 0.8881 0.2018 0.0150 0.0144 -0.0729 0.0394 -0.0004 -0.0099 0.1022 0.0142 -0.0147 'X-RAY DIFFRACTION' 6 ? refined 0.9697 24.5869 5.5973 0.0408 0.0278 0.0411 0.0009 -0.0058 -0.0008 3.1970 0.2566 4.7023 -0.8639 -3.8614 1.0459 0.0860 0.0394 0.0796 -0.0467 -0.0204 -0.0015 -0.0918 -0.0380 -0.0656 'X-RAY DIFFRACTION' 7 ? refined 11.0248 23.6675 9.6470 0.0123 0.0316 0.0439 0.0062 -0.0217 -0.0057 1.9107 0.6152 1.1067 -0.3556 -0.1599 -0.6833 -0.0030 -0.0833 0.0592 0.0389 0.0331 -0.0457 -0.0098 0.0224 -0.0300 'X-RAY DIFFRACTION' 8 ? refined 4.6391 7.6222 12.0794 0.1379 0.1533 0.1454 0.0115 0.0065 0.0093 0.0197 0.0276 0.0613 0.0204 -0.0214 -0.0073 -0.0160 -0.0257 -0.0471 -0.0128 0.0000 -0.0623 0.0440 0.0879 0.0160 'X-RAY DIFFRACTION' 9 ? refined 1.7613 8.5367 3.0594 0.1364 0.1429 0.1388 0.0035 0.0043 0.0038 0.0093 0.0332 0.0287 -0.0046 0.0156 -0.0100 0.0001 0.0357 0.0083 -0.0395 -0.0081 -0.0558 0.0159 0.0620 0.0080 'X-RAY DIFFRACTION' 10 ? refined -5.8199 8.7307 8.0715 0.1815 0.1693 0.1510 0.0178 -0.0093 -0.0042 0.1163 0.4060 1.2711 -0.1668 0.2609 -0.6135 0.0464 0.1063 0.0027 -0.1570 -0.0536 0.0338 0.0476 0.0321 0.0072 'X-RAY DIFFRACTION' 11 ? refined -3.2074 13.9686 18.4317 0.1350 0.1336 0.1431 0.0143 -0.0206 -0.0187 0.4533 0.3445 1.4088 0.2811 0.6180 0.4242 -0.0093 0.1147 -0.0348 -0.1192 0.0269 0.0940 0.0405 -0.0718 -0.0176 'X-RAY DIFFRACTION' 12 ? refined 0.2671 15.9701 19.5001 0.0707 0.0971 0.0949 0.0072 0.0049 -0.0150 0.5403 1.6694 2.2344 -0.6971 -0.5091 -0.2353 0.0232 0.1100 -0.1102 -0.1123 -0.0100 0.1328 0.1520 -0.1117 -0.0132 'X-RAY DIFFRACTION' 13 ? refined -6.7434 5.1534 20.6471 0.2580 0.2787 0.2150 0.0194 -0.0132 0.0544 0.2021 0.4959 1.8915 -0.0340 0.0601 -0.7769 -0.0200 -0.2144 -0.1241 0.2149 0.0942 -0.0170 -0.0152 -0.1650 -0.0742 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 A 332 ? ? A 339 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 340 ? ? A 360 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 361 ? ? A 369 ? ? ? ? 'X-RAY DIFFRACTION' 4 4 A 370 ? ? A 375 ? ? ? ? 'X-RAY DIFFRACTION' 5 5 A 376 ? ? A 395 ? ? ? ? 'X-RAY DIFFRACTION' 6 6 A 396 ? ? A 405 ? ? ? ? 'X-RAY DIFFRACTION' 7 7 A 406 ? ? A 421 ? ? ? ? 'X-RAY DIFFRACTION' 8 8 B 60 ? ? B 66 ? ? ? ? 'X-RAY DIFFRACTION' 9 9 B 67 ? ? B 74 ? ? ? ? 'X-RAY DIFFRACTION' 10 10 B 75 ? ? B 83 ? ? ? ? 'X-RAY DIFFRACTION' 11 11 B 84 ? ? B 91 ? ? ? ? 'X-RAY DIFFRACTION' 12 12 B 92 ? ? B 97 ? ? ? ? 'X-RAY DIFFRACTION' 13 13 B 98 ? ? B 104 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 PHASES phasing . ? 2 REFMAC refinement 5.5.0109 ? 3 XDS 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ALA A 415 ? ? -171.52 140.20 2 1 ASN B 68 ? ? 56.44 -129.01 3 1 TYR B 90 ? ? -166.46 110.39 4 1 LEU B 98 ? ? -117.28 -75.52 # 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 HIS 295 ? A HIS 1 2 1 Y 1 A HIS 296 ? A HIS 2 3 1 Y 1 A HIS 297 ? A HIS 3 4 1 Y 1 A HIS 298 ? A HIS 4 5 1 Y 1 A HIS 299 ? A HIS 5 6 1 Y 1 A HIS 300 ? A HIS 6 7 1 Y 1 A MET 301 ? A MET 7 8 1 Y 1 A SER 302 ? A SER 8 9 1 Y 1 A SER 303 ? A SER 9 10 1 Y 1 A GLY 304 ? A GLY 10 11 1 Y 1 A LYS 305 ? A LYS 11 12 1 Y 1 A ASN 306 ? A ASN 12 13 1 Y 1 A ALA 307 ? A ALA 13 14 1 Y 1 A PRO 308 ? A PRO 14 15 1 Y 1 A LYS 309 ? A LYS 15 16 1 Y 1 A THR 310 ? A THR 16 17 1 Y 1 A GLY 311 ? A GLY 17 18 1 Y 1 A GLY 312 ? A GLY 18 19 1 Y 1 A GLY 313 ? A GLY 19 20 1 Y 1 A ALA 314 ? A ALA 20 21 1 Y 1 A LYS 315 ? A LYS 21 22 1 Y 1 A GLY 316 ? A GLY 22 23 1 Y 1 A ASN 317 ? A ASN 23 24 1 Y 1 A ASN 318 ? A ASN 24 25 1 Y 1 A ALA 319 ? A ALA 25 26 1 Y 1 A SER 320 ? A SER 26 27 1 Y 1 A PRO 321 ? A PRO 27 28 1 Y 1 A ALA 322 ? A ALA 28 29 1 Y 1 A GLY 323 ? A GLY 29 30 1 Y 1 A SER 324 ? A SER 30 31 1 Y 1 A GLY 325 ? A GLY 31 32 1 Y 1 A ASN 326 ? A ASN 32 33 1 Y 1 A THR 327 ? A THR 33 34 1 Y 1 A LYS 328 ? A LYS 34 35 1 Y 1 B GLY 51 ? B GLY 1 36 1 Y 1 B SER 52 ? B SER 2 37 1 Y 1 B LYS 53 ? B LYS 3 38 1 Y 1 B PRO 54 ? B PRO 4 39 1 Y 1 B GLY 55 ? B GLY 5 40 1 Y 1 B ASP 56 ? B ASP 6 41 1 Y 1 B VAL 106 ? B VAL 56 42 1 Y 1 B SER 107 ? B SER 57 43 1 Y 1 B HIS 108 ? B HIS 58 44 1 Y 1 B HIS 109 ? B HIS 59 45 1 Y 1 B HIS 110 ? B HIS 60 46 1 Y 1 B HIS 111 ? B HIS 61 47 1 Y 1 B HIS 112 ? B HIS 62 48 1 Y 1 B HIS 113 ? B HIS 63 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL TRS 4 water HOH # 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 C 3 TRS 1 501 501 TRS TRS A . D 4 HOH 1 1 1 HOH HOH A . D 4 HOH 2 2 2 HOH HOH A . D 4 HOH 3 3 3 HOH HOH A . D 4 HOH 4 5 5 HOH HOH A . D 4 HOH 5 6 6 HOH HOH A . D 4 HOH 6 9 9 HOH HOH A . D 4 HOH 7 12 12 HOH HOH A . D 4 HOH 8 13 13 HOH HOH A . D 4 HOH 9 14 14 HOH HOH A . D 4 HOH 10 18 18 HOH HOH A . D 4 HOH 11 19 19 HOH HOH A . D 4 HOH 12 20 20 HOH HOH A . D 4 HOH 13 21 21 HOH HOH A . D 4 HOH 14 23 23 HOH HOH A . D 4 HOH 15 24 24 HOH HOH A . E 4 HOH 1 4 4 HOH HOH B . E 4 HOH 2 7 7 HOH HOH B . E 4 HOH 3 8 8 HOH HOH B . E 4 HOH 4 10 10 HOH HOH B . E 4 HOH 5 11 11 HOH HOH B . E 4 HOH 6 15 15 HOH HOH B . E 4 HOH 7 16 16 HOH HOH B . E 4 HOH 8 17 17 HOH HOH B . E 4 HOH 9 22 22 HOH HOH B . E 4 HOH 10 25 25 HOH HOH B . E 4 HOH 11 26 26 HOH HOH B . #