data_3QDP # _entry.id 3QDP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3QDP RCSB RCSB063514 WWPDB D_1000063514 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3QDR _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3QDP _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 3QDP _cell.length_a 70.283 _cell.length_b 70.283 _cell.length_c 53.820 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 3QDP _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _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' 13180.879 1 ? ? 'TolA domain III, residues 302-421' ? 2 non-polymer syn 'NITRATE ION' 62.005 2 ? ? ? ? 3 water nat water 18.015 43 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;HHHHHHMSSGKNAPKTGGGAKGNNASPAGSGNTKNNGASGADINNYAGQI(MLY)SAIES(MLZ)FYDASSYAGKTCTLR IKLAPDGMLLDIKPEGGDPALCQAALAAAKLAKIPKPPSQAVYEVF(MLY)NAPLDFKP ; _entity_poly.pdbx_seq_one_letter_code_can ;HHHHHHMSSGKNAPKTGGGAKGNNASPAGSGNTKNNGASGADINNYAGQIKSAIESKFYDASSYAGKTCTLRIKLAPDGM LLDIKPEGGDPALCQAALAAAKLAKIPKPPSQAVYEVFKNAPLDFKP ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 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 MLY n 1 52 SER n 1 53 ALA n 1 54 ILE n 1 55 GLU n 1 56 SER n 1 57 MLZ 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 MLY 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 # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _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 'tolA, cim, excC, lky, b0739, JW0729' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain K-12 _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 'Escherichia coli' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 83333 _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 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 'BL21(DE3)' _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 plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET21A _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TOLA_ECOLI _struct_ref.pdbx_db_accession P19934 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;SSGKNAPKTGGGAKGNNASPAGSGNTKNNGASGADINNYAGQIKSAIESKFYDASSYAGKTCTLRIKLAPDGMLLDIKPE GGDPALCQAALAAAKLAKIPKPPSQAVYEVFKNAPLDFKP ; _struct_ref.pdbx_align_begin 302 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3QDP _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 8 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 127 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q8FJT1 _struct_ref_seq.db_align_beg 302 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 421 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 302 _struct_ref_seq.pdbx_auth_seq_align_end 421 # 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 3QDP HIS A 1 ? UNP Q8FJT1 ? ? 'EXPRESSION TAG' 295 1 1 3QDP HIS A 2 ? UNP Q8FJT1 ? ? 'EXPRESSION TAG' 296 2 1 3QDP HIS A 3 ? UNP Q8FJT1 ? ? 'EXPRESSION TAG' 297 3 1 3QDP HIS A 4 ? UNP Q8FJT1 ? ? 'EXPRESSION TAG' 298 4 1 3QDP HIS A 5 ? UNP Q8FJT1 ? ? 'EXPRESSION TAG' 299 5 1 3QDP HIS A 6 ? UNP Q8FJT1 ? ? 'EXPRESSION TAG' 300 6 1 3QDP MET A 7 ? UNP Q8FJT1 ? ? 'EXPRESSION TAG' 301 7 # 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 MLZ 'L-peptide linking' n N-METHYL-LYSINE ? 'C7 H16 N2 O2' 160.214 NO3 non-polymer . 'NITRATE ION' ? 'N O3 -1' 62.005 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 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 3QDP _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.91 _exptl_crystal.density_percent_sol 57.75 _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 5.28 _exptl_crystal_grow.pdbx_details '0.2 M NaNO3, 2.2 M ammonium sulphate, pH 5.28, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 298 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'PILATUS 6M' _diffrn_detector.pdbx_collection_date 2010-10-29 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si 111 CHANNEL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97919 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97919 # _reflns.entry_id 3QDP _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 40.32 _reflns.d_resolution_high 2.15 _reflns.number_obs 8641 _reflns.number_all 8641 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs 0.056 _reflns.pdbx_Rsym_value 0.059 _reflns.pdbx_netI_over_sigmaI 25.7 _reflns.B_iso_Wilson_estimate 38.6 _reflns.pdbx_redundancy 9.7 _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 # _reflns_shell.d_res_high 2.15 _reflns_shell.d_res_low 2.27 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.433 _reflns_shell.pdbx_Rsym_value 0.456 _reflns_shell.meanI_over_sigI_obs 5 _reflns_shell.pdbx_redundancy 9.9 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1234 _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 # _refine.entry_id 3QDP _refine.ls_number_reflns_obs 8209 _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 40.32 _refine.ls_d_res_high 2.15 _refine.ls_percent_reflns_obs 99.83 _refine.ls_R_factor_obs 0.19374 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.19211 _refine.ls_R_factor_R_free 0.22520 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 407 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.960 _refine.correlation_coeff_Fo_to_Fc_free 0.951 _refine.B_iso_mean 20.249 _refine.aniso_B[1][1] -0.64 _refine.aniso_B[2][2] -0.64 _refine.aniso_B[3][3] 0.95 _refine.aniso_B[1][2] -0.32 _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 '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_Free 0.148 _refine.overall_SU_ML 0.122 _refine.overall_SU_B 10.676 _refine.overall_SU_R_Cruickshank_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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 LAST _refine_hist.pdbx_number_atoms_protein 659 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 43 _refine_hist.number_atoms_total 710 _refine_hist.d_res_high 2.15 _refine_hist.d_res_low 40.32 # 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 0.029 0.022 ? 712 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.371 2.040 ? 973 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 7.091 5.000 ? 98 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 37.748 26.400 ? 25 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 17.785 15.000 ? 110 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 24.421 15.000 ? 1 'X-RAY DIFFRACTION' ? r_chiral_restr 0.162 0.200 ? 107 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.012 0.022 ? 550 '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 1.234 1.500 ? 466 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 2.014 2.000 ? 741 'X-RAY DIFFRACTION' ? r_scbond_it 3.498 3.000 ? 246 'X-RAY DIFFRACTION' ? r_scangle_it 5.473 4.500 ? 226 '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_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.150 _refine_ls_shell.d_res_low 2.206 _refine_ls_shell.number_reflns_R_work 577 _refine_ls_shell.R_factor_R_work 0.300 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.469 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 41 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3QDP _struct.title 'Structural characterization of the interaction of colicin A, colicin N, and TolB with TolAIII translocon' _struct.pdbx_descriptor 'Protein tolA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3QDP _struct_keywords.pdbx_keywords 'PROTEIN TRANSPORT' _struct_keywords.text 'TolA, Translocation, colicin, TolB, ColA, ColN, methylation, PROTEIN TRANSPORT' # 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 2 ? D N N 3 ? # _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 ASP A 42 ? SER A 56 ? ASP A 336 SER A 350 1 ? 15 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 ? MLY A 119 ? SER A 405 MLY 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 ? ? ? ? ? ? ? 2.252 ? covale1 covale ? ? A ILE 50 C ? ? ? 1_555 A MLY 51 N ? ? A ILE 344 A MLY 345 1_555 ? ? ? ? ? ? ? 1.331 ? covale2 covale ? ? A MLY 51 C ? ? ? 1_555 A SER 52 N ? ? A MLY 345 A SER 346 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? A SER 56 C ? ? ? 1_555 A MLZ 57 N ? ? A SER 350 A MLZ 351 1_555 ? ? ? ? ? ? ? 1.340 ? covale4 covale ? ? A MLZ 57 C ? ? ? 1_555 A PHE 58 N ? ? A MLZ 351 A PHE 352 1_555 ? ? ? ? ? ? ? 1.340 ? covale5 covale ? ? A PHE 118 C ? ? ? 1_555 A MLY 119 N ? ? A PHE 412 A MLY 413 1_555 ? ? ? ? ? ? ? 1.344 ? covale6 covale ? ? A MLY 119 C ? ? ? 1_555 A ASN 120 N ? ? A MLY 413 A ASN 414 1_555 ? ? ? ? ? ? ? 1.306 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 3 _struct_sheet.details ? # 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 # 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 LEU A 81 ? GLY A 89 ? LEU A 375 GLY A 383 A 2 CYS A 69 ? LEU A 75 ? CYS A 363 LEU A 369 A 3 ALA A 121 ? PHE A 125 ? ALA A 415 PHE A 419 # 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 LYS A 85 ? O LYS A 379 N ARG A 72 ? N ARG A 366 A 2 3 N CYS A 69 ? N CYS A 363 O PHE A 125 ? O PHE A 419 # 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 ? ? ? ? 6 'BINDING SITE FOR RESIDUE NO3 A 501' AC2 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE NO3 A 502' # 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 6 HOH D . ? HOH A 13 . ? 1_555 ? 2 AC1 6 HOH D . ? HOH A 38 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 43 . ? 1_555 ? 4 AC1 6 ARG A 72 ? ARG A 366 . ? 6_555 ? 5 AC1 6 MLY A 119 ? MLY A 413 . ? 1_555 ? 6 AC1 6 PRO A 122 ? PRO A 416 . ? 6_555 ? 7 AC2 6 MLY A 51 ? MLY A 345 . ? 1_555 ? 8 AC2 6 PHE A 58 ? PHE A 352 . ? 2_565 ? 9 AC2 6 TYR A 59 ? TYR A 353 . ? 2_565 ? 10 AC2 6 ASP A 60 ? ASP A 354 . ? 2_565 ? 11 AC2 6 LEU A 123 ? LEU A 417 . ? 1_555 ? 12 AC2 6 ASP A 124 ? ASP A 418 . ? 1_555 ? # _database_PDB_matrix.entry_id 3QDP _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 3QDP _atom_sites.fract_transf_matrix[1][1] 0.014228 _atom_sites.fract_transf_matrix[1][2] 0.008215 _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] 0.016429 _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] 0.018580 _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 ? ? ? A . n A 1 36 ASN 36 330 ? ? ? A . n A 1 37 GLY 37 331 ? ? ? A . n A 1 38 ALA 38 332 ? ? ? A . n A 1 39 SER 39 333 ? ? ? 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 MLY 51 345 345 MLY MLY 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 MLZ 57 351 351 MLZ MLZ 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 MLY 119 413 413 MLY MLY 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 # 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 B 2 NO3 1 501 501 NO3 NO3 A . C 2 NO3 1 502 502 NO3 NO3 A . D 3 HOH 1 1 1 HOH HOH A . D 3 HOH 2 2 2 HOH HOH A . D 3 HOH 3 3 3 HOH HOH A . D 3 HOH 4 4 4 HOH HOH A . D 3 HOH 5 5 5 HOH HOH A . D 3 HOH 6 6 6 HOH HOH A . D 3 HOH 7 7 7 HOH HOH A . D 3 HOH 8 8 8 HOH HOH A . D 3 HOH 9 9 9 HOH HOH A . D 3 HOH 10 10 10 HOH HOH A . D 3 HOH 11 11 11 HOH HOH A . D 3 HOH 12 12 12 HOH HOH A . D 3 HOH 13 13 13 HOH HOH A . D 3 HOH 14 14 14 HOH HOH A . D 3 HOH 15 15 15 HOH HOH A . D 3 HOH 16 16 16 HOH HOH A . D 3 HOH 17 17 17 HOH HOH A . D 3 HOH 18 18 18 HOH HOH A . D 3 HOH 19 19 19 HOH HOH A . D 3 HOH 20 20 20 HOH HOH A . D 3 HOH 21 21 21 HOH HOH A . D 3 HOH 22 22 22 HOH HOH A . D 3 HOH 23 23 23 HOH HOH A . D 3 HOH 24 24 24 HOH HOH A . D 3 HOH 25 25 25 HOH HOH A . D 3 HOH 26 26 26 HOH HOH A . D 3 HOH 27 27 27 HOH HOH A . D 3 HOH 28 28 28 HOH HOH A . D 3 HOH 29 29 29 HOH HOH A . D 3 HOH 30 30 30 HOH HOH A . D 3 HOH 31 31 31 HOH HOH A . D 3 HOH 32 32 32 HOH HOH A . D 3 HOH 33 33 33 HOH HOH A . D 3 HOH 34 34 34 HOH HOH A . D 3 HOH 35 35 35 HOH HOH A . D 3 HOH 36 36 36 HOH HOH A . D 3 HOH 37 37 37 HOH HOH A . D 3 HOH 38 38 38 HOH HOH A . D 3 HOH 39 39 39 HOH HOH A . D 3 HOH 40 40 40 HOH HOH A . D 3 HOH 41 41 41 HOH HOH A . D 3 HOH 42 42 42 HOH HOH A . D 3 HOH 43 43 43 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MLY 51 A MLY 345 ? LYS N-DIMETHYL-LYSINE 2 A MLZ 57 A MLZ 351 ? LYS N-METHYL-LYSINE 3 A MLY 119 A MLY 413 ? LYS 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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _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 # _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 -27.0362 30.5266 5.7116 0.2484 0.1333 0.3010 0.0286 -0.0887 -0.0242 4.0413 0.7518 8.1981 -0.7184 -4.7875 1.8837 0.0933 0.0506 0.6173 -0.0724 -0.0555 0.2298 -0.6435 -0.2248 -0.0379 'X-RAY DIFFRACTION' 2 ? refined -31.0536 20.7003 -1.2332 0.1377 0.1377 0.1458 0.0063 0.0046 0.0123 3.7521 3.8469 6.5337 1.0397 2.1412 3.8267 0.0046 -0.0225 0.0650 -0.0532 -0.0485 0.2574 0.0120 -0.2232 0.0439 'X-RAY DIFFRACTION' 3 ? refined -29.3857 12.6764 2.2610 0.2447 0.2116 0.2036 0.0100 -0.0118 0.0057 1.8075 0.4754 1.6166 0.6875 1.2377 0.2668 0.2164 -0.4188 -0.1960 0.2787 -0.1369 -0.1185 0.0813 -0.0666 -0.0795 'X-RAY DIFFRACTION' 4 ? refined -19.0128 17.2466 -0.1737 0.2670 0.2898 0.2727 0.0076 -0.0111 -0.0188 1.7675 4.0677 2.1802 1.1005 -0.7817 -1.5720 -0.0460 -0.0737 -0.1459 -0.0869 -0.0369 -0.1206 0.1895 0.0306 0.0829 'X-RAY DIFFRACTION' 5 ? refined -26.6771 8.5784 -0.0249 0.2843 0.2622 0.3265 -0.0194 -0.0533 0.0311 0.6570 1.7750 4.7045 0.6226 -1.2206 -2.6063 -0.0866 -0.2359 -0.3227 0.0491 -0.0982 -0.1631 0.3982 0.2602 0.1848 'X-RAY DIFFRACTION' 6 ? refined -20.9169 26.7815 -1.0042 0.1227 0.1429 0.1273 0.0314 -0.0016 -0.0118 2.4750 2.5747 3.4709 2.4197 2.3372 2.3107 -0.1169 0.2108 -0.0252 -0.2348 0.0992 0.0596 -0.0132 -0.0160 0.0177 'X-RAY DIFFRACTION' 7 ? refined -24.0601 18.6602 6.0261 0.1906 0.1372 0.1643 0.0333 0.0016 -0.0035 8.5415 4.0956 2.8367 4.1879 1.8341 0.6805 0.2061 -0.3948 0.0707 0.1917 -0.1565 0.1658 0.0890 -0.1452 -0.0496 # 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 334 ? ? A 341 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 342 ? ? A 351 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 352 ? ? A 369 ? ? ? ? 'X-RAY DIFFRACTION' 4 4 A 370 ? ? A 384 ? ? ? ? 'X-RAY DIFFRACTION' 5 5 A 385 ? ? A 395 ? ? ? ? 'X-RAY DIFFRACTION' 6 6 A 396 ? ? A 412 ? ? ? ? 'X-RAY DIFFRACTION' 7 7 A 413 ? ? A 421 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.5.0109 ? 1 XDS 'data reduction' . ? 2 SCALA 'data scaling' . ? 3 # 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 ASP A 384 ? ? -38.30 123.83 2 1 ALA A 415 ? ? 177.71 148.26 # 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 A ASN 329 ? A ASN 35 36 1 Y 1 A ASN 330 ? A ASN 36 37 1 Y 1 A GLY 331 ? A GLY 37 38 1 Y 1 A ALA 332 ? A ALA 38 39 1 Y 1 A SER 333 ? A SER 39 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'NITRATE ION' NO3 3 water HOH #