data_3JYB # _entry.id 3JYB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.313 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3JYB RCSB RCSB055312 WWPDB D_1000055312 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3JYB _pdbx_database_status.recvd_initial_deposition_date 2009-09-21 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Jing, X.' 1 'Schubot, F.D.' 2 'Robinson, H.' 3 # _citation.id primary _citation.title 'Crystal structure and oligomeric state of the RetS signaling kinase sensory domain.' _citation.journal_abbrev Proteins _citation.journal_volume 78 _citation.page_first 1631 _citation.page_last 1640 _citation.year 2010 _citation.journal_id_ASTM PSFGEY _citation.country US _citation.journal_id_ISSN 0887-3585 _citation.journal_id_CSD 0867 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20112417 _citation.pdbx_database_id_DOI 10.1002/prot.22679 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Jing, X.' 1 ? primary 'Jaw, J.' 2 ? primary 'Robinson, H.H.' 3 ? primary 'Schubot, F.D.' 4 ? # _cell.entry_id 3JYB _cell.length_a 51.164 _cell.length_b 67.193 _cell.length_c 86.214 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 3JYB _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 'Sensor protein' 17026.943 2 2.7.13.3 ? 'periplasmic domain (UNP 41-185)' ? 2 water nat water 18.015 104 ? ? ? ? # _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 ;ATTPSANQNWRLLRDESAQLRIADVLQRKEQFRPLAKRSFIFPASPQAVWLQVQLPAQKVPSWLWIFAPRVQYLDYYLVQ DGQLVRDQHTGESRPFQERPLPSRSYLFSLPVDGKP(MSE)TLYVR(MSE)TSNHPL(MSE)AWFDQIDEAGLVGLE ; _entity_poly.pdbx_seq_one_letter_code_can ;ATTPSANQNWRLLRDESAQLRIADVLQRKEQFRPLAKRSFIFPASPQAVWLQVQLPAQKVPSWLWIFAPRVQYLDYYLVQ DGQLVRDQHTGESRPFQERPLPSRSYLFSLPVDGKPMTLYVRMTSNHPLMAWFDQIDEAGLVGLE ; _entity_poly.pdbx_strand_id A,B _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 ALA n 1 2 THR n 1 3 THR n 1 4 PRO n 1 5 SER n 1 6 ALA n 1 7 ASN n 1 8 GLN n 1 9 ASN n 1 10 TRP n 1 11 ARG n 1 12 LEU n 1 13 LEU n 1 14 ARG n 1 15 ASP n 1 16 GLU n 1 17 SER n 1 18 ALA n 1 19 GLN n 1 20 LEU n 1 21 ARG n 1 22 ILE n 1 23 ALA n 1 24 ASP n 1 25 VAL n 1 26 LEU n 1 27 GLN n 1 28 ARG n 1 29 LYS n 1 30 GLU n 1 31 GLN n 1 32 PHE n 1 33 ARG n 1 34 PRO n 1 35 LEU n 1 36 ALA n 1 37 LYS n 1 38 ARG n 1 39 SER n 1 40 PHE n 1 41 ILE n 1 42 PHE n 1 43 PRO n 1 44 ALA n 1 45 SER n 1 46 PRO n 1 47 GLN n 1 48 ALA n 1 49 VAL n 1 50 TRP n 1 51 LEU n 1 52 GLN n 1 53 VAL n 1 54 GLN n 1 55 LEU n 1 56 PRO n 1 57 ALA n 1 58 GLN n 1 59 LYS n 1 60 VAL n 1 61 PRO n 1 62 SER n 1 63 TRP n 1 64 LEU n 1 65 TRP n 1 66 ILE n 1 67 PHE n 1 68 ALA n 1 69 PRO n 1 70 ARG n 1 71 VAL n 1 72 GLN n 1 73 TYR n 1 74 LEU n 1 75 ASP n 1 76 TYR n 1 77 TYR n 1 78 LEU n 1 79 VAL n 1 80 GLN n 1 81 ASP n 1 82 GLY n 1 83 GLN n 1 84 LEU n 1 85 VAL n 1 86 ARG n 1 87 ASP n 1 88 GLN n 1 89 HIS n 1 90 THR n 1 91 GLY n 1 92 GLU n 1 93 SER n 1 94 ARG n 1 95 PRO n 1 96 PHE n 1 97 GLN n 1 98 GLU n 1 99 ARG n 1 100 PRO n 1 101 LEU n 1 102 PRO n 1 103 SER n 1 104 ARG n 1 105 SER n 1 106 TYR n 1 107 LEU n 1 108 PHE n 1 109 SER n 1 110 LEU n 1 111 PRO n 1 112 VAL n 1 113 ASP n 1 114 GLY n 1 115 LYS n 1 116 PRO n 1 117 MSE n 1 118 THR n 1 119 LEU n 1 120 TYR n 1 121 VAL n 1 122 ARG n 1 123 MSE n 1 124 THR n 1 125 SER n 1 126 ASN n 1 127 HIS n 1 128 PRO n 1 129 LEU n 1 130 MSE n 1 131 ALA n 1 132 TRP n 1 133 PHE n 1 134 ASP n 1 135 GLN n 1 136 ILE n 1 137 ASP n 1 138 GLU n 1 139 ALA n 1 140 GLY n 1 141 LEU n 1 142 VAL n 1 143 GLY n 1 144 LEU n 1 145 GLU 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 'PA14_64230, PA4856, retS, rets (AMINO ACIDS 41 - 185)' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain UCBPP-PA14 _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 'Pseudomonas aeruginosa' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 208963 _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)codonplus RIL' _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 HisMBPpDEST _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q9HUV7_PSEAE _struct_ref.pdbx_db_accession Q9HUV7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ATTPSANQNWRLLRDESAQLRIADVLQRKEQFRPLAKRSFIFPASPQAVWLQVQLPAQKVPSWLWIFAPRVQYLDYYLVQ DGQLVRDQHTGESRPFQERPLPSRSYLFSLPVDGKPMTLYVRMTSNHPLMAWFDQIDEAGLVGLE ; _struct_ref.pdbx_align_begin 41 _struct_ref.pdbx_db_isoform ? # 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 3JYB A 1 ? 145 ? Q9HUV7 41 ? 185 ? 41 185 2 1 3JYB B 1 ? 145 ? Q9HUV7 41 ? 185 ? 41 185 # 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 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 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 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 3JYB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_percent_sol 43.47 _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 291.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 3.0 _exptl_crystal_grow.pdbx_details '22.5% PEG 3350, 0.1M citric acid, 10% glycerol, pH 3.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2008-11-20 _diffrn_detector.details 'SAGITALLY FOCUSED Si(111)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'SAGITALLY FOCUSED Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97900 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X29A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X29A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97900 # _reflns.entry_id 3JYB _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 30.0 _reflns.d_resolution_high 2.04 _reflns.number_obs 19459 _reflns.number_all 19459 _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.114 _reflns.pdbx_Rsym_value 0.114 _reflns.pdbx_netI_over_sigmaI 26.32 _reflns.B_iso_Wilson_estimate 18.747 _reflns.pdbx_redundancy 13.1 _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 2.04 _reflns_shell.d_res_low 2.11 _reflns_shell.percent_possible_all 100.00 _reflns_shell.Rmerge_I_obs 0.444 _reflns_shell.pdbx_Rsym_value 0.444 _reflns_shell.meanI_over_sigI_obs 4.65 _reflns_shell.pdbx_redundancy 8.9 _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 # _refine.entry_id 3JYB _refine.ls_number_reflns_obs 17870 _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 29.62 _refine.ls_d_res_high 2.04 _refine.ls_percent_reflns_obs 100.00 _refine.ls_R_factor_obs 0.20119 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.19937 _refine.ls_R_factor_R_free 0.23491 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.2 _refine.ls_number_reflns_R_free 975 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.936 _refine.correlation_coeff_Fo_to_Fc_free 0.922 _refine.B_iso_mean 18.747 _refine.aniso_B[1][1] -0.32 _refine.aniso_B[2][2] 0.35 _refine.aniso_B[3][3] -0.03 _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 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _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 0.224 _refine.pdbx_overall_ESU_R_Free 0.179 _refine.overall_SU_ML 0.121 _refine.overall_SU_B 8.563 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _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_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3JYB _refine_analyze.Luzzati_coordinate_error_obs 0.224 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2298 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 104 _refine_hist.number_atoms_total 2402 _refine_hist.d_res_high 2.04 _refine_hist.d_res_low 29.62 # 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 0.007 0.022 ? 2368 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.119 1.956 ? 3224 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.281 5.000 ? 274 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 31.181 22.951 ? 122 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 15.143 15.000 ? 392 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 16.425 15.000 ? 24 'X-RAY DIFFRACTION' ? r_chiral_restr 0.072 0.200 ? 336 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 0.020 ? 1854 'X-RAY DIFFRACTION' ? r_nbd_refined 0.188 0.200 ? 974 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.304 0.200 ? 1559 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.117 0.200 ? 127 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.169 0.200 ? 44 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.128 0.200 ? 8 'X-RAY DIFFRACTION' ? r_mcbond_it 0.513 1.500 ? 1439 'X-RAY DIFFRACTION' ? r_mcangle_it 0.743 2.000 ? 2260 'X-RAY DIFFRACTION' ? r_scbond_it 1.076 3.000 ? 1091 'X-RAY DIFFRACTION' ? r_scangle_it 1.835 4.500 ? 964 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.044 _refine_ls_shell.d_res_low 2.097 _refine_ls_shell.number_reflns_R_work 1208 _refine_ls_shell.R_factor_R_work 0.207 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.275 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 57 _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 3JYB _struct.title 'Crystal Structure of the RetS periplasmic domain' _struct.pdbx_descriptor 'Sensor protein (E.C.2.7.13.3)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3JYB _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text 'BETA BARREL, carbohydrate binding domain, signaling kinase, two component system, RetS, Kinase, Phosphoprotein, Transferase' # 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 2 ? D N N 2 ? # _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 ARG A 21 ? GLN A 27 ? ARG A 61 GLN A 67 1 ? 7 HELX_P HELX_P2 2 ARG A 28 ? PHE A 32 ? ARG A 68 PHE A 72 5 ? 5 HELX_P HELX_P3 3 GLU A 138 ? VAL A 142 ? GLU A 178 VAL A 182 1 ? 5 HELX_P HELX_P4 4 ARG B 21 ? LEU B 26 ? ARG B 61 LEU B 66 1 ? 6 HELX_P HELX_P5 5 GLN B 27 ? PHE B 32 ? GLN B 67 PHE B 72 5 ? 6 HELX_P HELX_P6 6 GLU B 138 ? GLY B 143 ? GLU B 178 GLY B 183 1 ? 6 # _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 covale1 covale both ? A PRO 116 C ? ? ? 1_555 A MSE 117 N ? ? A PRO 156 A MSE 157 1_555 ? ? ? ? ? ? ? 1.328 ? covale2 covale both ? A MSE 117 C ? ? ? 1_555 A THR 118 N ? ? A MSE 157 A THR 158 1_555 ? ? ? ? ? ? ? 1.328 ? covale3 covale both ? A ARG 122 C ? ? ? 1_555 A MSE 123 N ? ? A ARG 162 A MSE 163 1_555 ? ? ? ? ? ? ? 1.329 ? covale4 covale both ? A MSE 123 C ? ? ? 1_555 A THR 124 N ? ? A MSE 163 A THR 164 1_555 ? ? ? ? ? ? ? 1.335 ? covale5 covale both ? A LEU 129 C ? ? ? 1_555 A MSE 130 N ? ? A LEU 169 A MSE 170 1_555 ? ? ? ? ? ? ? 1.330 ? covale6 covale both ? A MSE 130 C ? ? ? 1_555 A ALA 131 N ? ? A MSE 170 A ALA 171 1_555 ? ? ? ? ? ? ? 1.328 ? covale7 covale both ? B PRO 116 C ? ? ? 1_555 B MSE 117 N ? ? B PRO 156 B MSE 157 1_555 ? ? ? ? ? ? ? 1.329 ? covale8 covale both ? B MSE 117 C ? ? ? 1_555 B THR 118 N ? ? B MSE 157 B THR 158 1_555 ? ? ? ? ? ? ? 1.331 ? covale9 covale both ? B ARG 122 C ? ? ? 1_555 B MSE 123 N ? ? B ARG 162 B MSE 163 1_555 ? ? ? ? ? ? ? 1.329 ? covale10 covale both ? B MSE 123 C ? ? ? 1_555 B THR 124 N ? ? B MSE 163 B THR 164 1_555 ? ? ? ? ? ? ? 1.335 ? covale11 covale both ? B LEU 129 C ? ? ? 1_555 B MSE 130 N ? ? B LEU 169 B MSE 170 1_555 ? ? ? ? ? ? ? 1.331 ? covale12 covale both ? B MSE 130 C ? ? ? 1_555 B ALA 131 N ? ? B MSE 170 B ALA 171 1_555 ? ? ? ? ? ? ? 1.329 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 4 ? C ? 6 ? D ? 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 A 5 6 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel C 3 4 ? anti-parallel C 4 5 ? anti-parallel C 5 6 ? anti-parallel D 1 2 ? anti-parallel D 2 3 ? anti-parallel D 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 ARG A 33 ? PRO A 34 ? ARG A 73 PRO A 74 A 2 TRP A 10 ? ASP A 15 ? TRP A 50 ASP A 55 A 3 ALA A 48 ? LEU A 55 ? ALA A 88 LEU A 95 A 4 MSE A 117 ? THR A 124 ? MSE A 157 THR A 164 A 5 TYR A 73 ? GLN A 80 ? TYR A 113 GLN A 120 A 6 GLN A 83 ? THR A 90 ? GLN A 123 THR A 130 B 1 SER A 39 ? PHE A 42 ? SER A 79 PHE A 82 B 2 LEU A 129 ? ASP A 137 ? LEU A 169 ASP A 177 B 3 SER A 62 ? PHE A 67 ? SER A 102 PHE A 107 B 4 TYR A 106 ? LEU A 110 ? TYR A 146 LEU A 150 C 1 ARG B 33 ? PRO B 34 ? ARG B 73 PRO B 74 C 2 TRP B 10 ? ASP B 15 ? TRP B 50 ASP B 55 C 3 ALA B 48 ? LEU B 55 ? ALA B 88 LEU B 95 C 4 MSE B 117 ? THR B 124 ? MSE B 157 THR B 164 C 5 TYR B 73 ? GLN B 80 ? TYR B 113 GLN B 120 C 6 GLN B 83 ? THR B 90 ? GLN B 123 THR B 130 D 1 SER B 39 ? PHE B 42 ? SER B 79 PHE B 82 D 2 LEU B 129 ? ASP B 137 ? LEU B 169 ASP B 177 D 3 SER B 62 ? PHE B 67 ? SER B 102 PHE B 107 D 4 TYR B 106 ? LEU B 110 ? TYR B 146 LEU B 150 # 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 ARG A 33 ? O ARG A 73 N LEU A 12 ? N LEU A 52 A 2 3 N ASP A 15 ? N ASP A 55 O ALA A 48 ? O ALA A 88 A 3 4 N LEU A 55 ? N LEU A 95 O MSE A 117 ? O MSE A 157 A 4 5 O TYR A 120 ? O TYR A 160 N TYR A 77 ? N TYR A 117 A 5 6 N LEU A 78 ? N LEU A 118 O VAL A 85 ? O VAL A 125 B 1 2 N PHE A 42 ? N PHE A 82 O LEU A 129 ? O LEU A 169 B 2 3 O ASP A 134 ? O ASP A 174 N TRP A 65 ? N TRP A 105 B 3 4 N ILE A 66 ? N ILE A 106 O TYR A 106 ? O TYR A 146 C 1 2 O ARG B 33 ? O ARG B 73 N LEU B 12 ? N LEU B 52 C 2 3 N LEU B 13 ? N LEU B 53 O TRP B 50 ? O TRP B 90 C 3 4 N LEU B 55 ? N LEU B 95 O MSE B 117 ? O MSE B 157 C 4 5 O THR B 118 ? O THR B 158 N VAL B 79 ? N VAL B 119 C 5 6 N LEU B 78 ? N LEU B 118 O ARG B 86 ? O ARG B 126 D 1 2 N PHE B 40 ? N PHE B 80 O ALA B 131 ? O ALA B 171 D 2 3 O ASP B 134 ? O ASP B 174 N TRP B 65 ? N TRP B 105 D 3 4 N ILE B 66 ? N ILE B 106 O TYR B 106 ? O TYR B 146 # _database_PDB_matrix.entry_id 3JYB _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 3JYB _atom_sites.fract_transf_matrix[1][1] 0.019545 _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] 0.014883 _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] 0.011599 _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 SE # 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 ALA 1 41 ? ? ? A . n A 1 2 THR 2 42 ? ? ? A . n A 1 3 THR 3 43 ? ? ? A . n A 1 4 PRO 4 44 ? ? ? A . n A 1 5 SER 5 45 ? ? ? A . n A 1 6 ALA 6 46 ? ? ? A . n A 1 7 ASN 7 47 ? ? ? A . n A 1 8 GLN 8 48 48 GLN GLN A . n A 1 9 ASN 9 49 49 ASN ASN A . n A 1 10 TRP 10 50 50 TRP TRP A . n A 1 11 ARG 11 51 51 ARG ARG A . n A 1 12 LEU 12 52 52 LEU LEU A . n A 1 13 LEU 13 53 53 LEU LEU A . n A 1 14 ARG 14 54 54 ARG ARG A . n A 1 15 ASP 15 55 55 ASP ASP A . n A 1 16 GLU 16 56 56 GLU GLU A . n A 1 17 SER 17 57 57 SER SER A . n A 1 18 ALA 18 58 58 ALA ALA A . n A 1 19 GLN 19 59 59 GLN GLN A . n A 1 20 LEU 20 60 60 LEU LEU A . n A 1 21 ARG 21 61 61 ARG ARG A . n A 1 22 ILE 22 62 62 ILE ILE A . n A 1 23 ALA 23 63 63 ALA ALA A . n A 1 24 ASP 24 64 64 ASP ASP A . n A 1 25 VAL 25 65 65 VAL VAL A . n A 1 26 LEU 26 66 66 LEU LEU A . n A 1 27 GLN 27 67 67 GLN GLN A . n A 1 28 ARG 28 68 68 ARG ARG A . n A 1 29 LYS 29 69 69 LYS LYS A . n A 1 30 GLU 30 70 70 GLU GLU A . n A 1 31 GLN 31 71 71 GLN GLN A . n A 1 32 PHE 32 72 72 PHE PHE A . n A 1 33 ARG 33 73 73 ARG ARG A . n A 1 34 PRO 34 74 74 PRO PRO A . n A 1 35 LEU 35 75 75 LEU LEU A . n A 1 36 ALA 36 76 76 ALA ALA A . n A 1 37 LYS 37 77 77 LYS LYS A . n A 1 38 ARG 38 78 78 ARG ARG A . n A 1 39 SER 39 79 79 SER SER A . n A 1 40 PHE 40 80 80 PHE PHE A . n A 1 41 ILE 41 81 81 ILE ILE A . n A 1 42 PHE 42 82 82 PHE PHE A . n A 1 43 PRO 43 83 83 PRO PRO A . n A 1 44 ALA 44 84 84 ALA ALA A . n A 1 45 SER 45 85 85 SER SER A . n A 1 46 PRO 46 86 86 PRO PRO A . n A 1 47 GLN 47 87 87 GLN GLN A . n A 1 48 ALA 48 88 88 ALA ALA A . n A 1 49 VAL 49 89 89 VAL VAL A . n A 1 50 TRP 50 90 90 TRP TRP A . n A 1 51 LEU 51 91 91 LEU LEU A . n A 1 52 GLN 52 92 92 GLN GLN A . n A 1 53 VAL 53 93 93 VAL VAL A . n A 1 54 GLN 54 94 94 GLN GLN A . n A 1 55 LEU 55 95 95 LEU LEU A . n A 1 56 PRO 56 96 96 PRO PRO A . n A 1 57 ALA 57 97 97 ALA ALA A . n A 1 58 GLN 58 98 98 GLN GLN A . n A 1 59 LYS 59 99 99 LYS LYS A . n A 1 60 VAL 60 100 100 VAL VAL A . n A 1 61 PRO 61 101 101 PRO PRO A . n A 1 62 SER 62 102 102 SER SER A . n A 1 63 TRP 63 103 103 TRP TRP A . n A 1 64 LEU 64 104 104 LEU LEU A . n A 1 65 TRP 65 105 105 TRP TRP A . n A 1 66 ILE 66 106 106 ILE ILE A . n A 1 67 PHE 67 107 107 PHE PHE A . n A 1 68 ALA 68 108 108 ALA ALA A . n A 1 69 PRO 69 109 109 PRO PRO A . n A 1 70 ARG 70 110 110 ARG ARG A . n A 1 71 VAL 71 111 111 VAL VAL A . n A 1 72 GLN 72 112 112 GLN GLN A . n A 1 73 TYR 73 113 113 TYR TYR A . n A 1 74 LEU 74 114 114 LEU LEU A . n A 1 75 ASP 75 115 115 ASP ASP A . n A 1 76 TYR 76 116 116 TYR TYR A . n A 1 77 TYR 77 117 117 TYR TYR A . n A 1 78 LEU 78 118 118 LEU LEU A . n A 1 79 VAL 79 119 119 VAL VAL A . n A 1 80 GLN 80 120 120 GLN GLN A . n A 1 81 ASP 81 121 121 ASP ASP A . n A 1 82 GLY 82 122 122 GLY GLY A . n A 1 83 GLN 83 123 123 GLN GLN A . n A 1 84 LEU 84 124 124 LEU LEU A . n A 1 85 VAL 85 125 125 VAL VAL A . n A 1 86 ARG 86 126 126 ARG ARG A . n A 1 87 ASP 87 127 127 ASP ASP A . n A 1 88 GLN 88 128 128 GLN GLN A . n A 1 89 HIS 89 129 129 HIS HIS A . n A 1 90 THR 90 130 130 THR THR A . n A 1 91 GLY 91 131 131 GLY GLY A . n A 1 92 GLU 92 132 132 GLU GLU A . n A 1 93 SER 93 133 133 SER SER A . n A 1 94 ARG 94 134 134 ARG ARG A . n A 1 95 PRO 95 135 135 PRO PRO A . n A 1 96 PHE 96 136 136 PHE PHE A . n A 1 97 GLN 97 137 137 GLN GLN A . n A 1 98 GLU 98 138 138 GLU GLU A . n A 1 99 ARG 99 139 139 ARG ARG A . n A 1 100 PRO 100 140 140 PRO PRO A . n A 1 101 LEU 101 141 141 LEU LEU A . n A 1 102 PRO 102 142 142 PRO PRO A . n A 1 103 SER 103 143 143 SER SER A . n A 1 104 ARG 104 144 144 ARG ARG A . n A 1 105 SER 105 145 145 SER SER A . n A 1 106 TYR 106 146 146 TYR TYR A . n A 1 107 LEU 107 147 147 LEU LEU A . n A 1 108 PHE 108 148 148 PHE PHE A . n A 1 109 SER 109 149 149 SER SER A . n A 1 110 LEU 110 150 150 LEU LEU A . n A 1 111 PRO 111 151 151 PRO PRO A . n A 1 112 VAL 112 152 152 VAL VAL A . n A 1 113 ASP 113 153 153 ASP ASP A . n A 1 114 GLY 114 154 154 GLY GLY A . n A 1 115 LYS 115 155 155 LYS LYS A . n A 1 116 PRO 116 156 156 PRO PRO A . n A 1 117 MSE 117 157 157 MSE MSE A . n A 1 118 THR 118 158 158 THR THR A . n A 1 119 LEU 119 159 159 LEU LEU A . n A 1 120 TYR 120 160 160 TYR TYR A . n A 1 121 VAL 121 161 161 VAL VAL A . n A 1 122 ARG 122 162 162 ARG ARG A . n A 1 123 MSE 123 163 163 MSE MSE A . n A 1 124 THR 124 164 164 THR THR A . n A 1 125 SER 125 165 165 SER SER A . n A 1 126 ASN 126 166 166 ASN ASN A . n A 1 127 HIS 127 167 167 HIS HIS A . n A 1 128 PRO 128 168 168 PRO PRO A . n A 1 129 LEU 129 169 169 LEU LEU A . n A 1 130 MSE 130 170 170 MSE MSE A . n A 1 131 ALA 131 171 171 ALA ALA A . n A 1 132 TRP 132 172 172 TRP TRP A . n A 1 133 PHE 133 173 173 PHE PHE A . n A 1 134 ASP 134 174 174 ASP ASP A . n A 1 135 GLN 135 175 175 GLN GLN A . n A 1 136 ILE 136 176 176 ILE ILE A . n A 1 137 ASP 137 177 177 ASP ASP A . n A 1 138 GLU 138 178 178 GLU GLU A . n A 1 139 ALA 139 179 179 ALA ALA A . n A 1 140 GLY 140 180 180 GLY GLY A . n A 1 141 LEU 141 181 181 LEU LEU A . n A 1 142 VAL 142 182 182 VAL VAL A . n A 1 143 GLY 143 183 183 GLY GLY A . n A 1 144 LEU 144 184 184 LEU LEU A . n A 1 145 GLU 145 185 185 GLU GLU A . n B 1 1 ALA 1 41 ? ? ? B . n B 1 2 THR 2 42 ? ? ? B . n B 1 3 THR 3 43 ? ? ? B . n B 1 4 PRO 4 44 ? ? ? B . n B 1 5 SER 5 45 ? ? ? B . n B 1 6 ALA 6 46 ? ? ? B . n B 1 7 ASN 7 47 ? ? ? B . n B 1 8 GLN 8 48 48 GLN GLN B . n B 1 9 ASN 9 49 49 ASN ASN B . n B 1 10 TRP 10 50 50 TRP TRP B . n B 1 11 ARG 11 51 51 ARG ARG B . n B 1 12 LEU 12 52 52 LEU LEU B . n B 1 13 LEU 13 53 53 LEU LEU B . n B 1 14 ARG 14 54 54 ARG ARG B . n B 1 15 ASP 15 55 55 ASP ASP B . n B 1 16 GLU 16 56 56 GLU GLU B . n B 1 17 SER 17 57 57 SER SER B . n B 1 18 ALA 18 58 58 ALA ALA B . n B 1 19 GLN 19 59 59 GLN GLN B . n B 1 20 LEU 20 60 60 LEU LEU B . n B 1 21 ARG 21 61 61 ARG ARG B . n B 1 22 ILE 22 62 62 ILE ILE B . n B 1 23 ALA 23 63 63 ALA ALA B . n B 1 24 ASP 24 64 64 ASP ASP B . n B 1 25 VAL 25 65 65 VAL VAL B . n B 1 26 LEU 26 66 66 LEU LEU B . n B 1 27 GLN 27 67 67 GLN GLN B . n B 1 28 ARG 28 68 68 ARG ARG B . n B 1 29 LYS 29 69 69 LYS LYS B . n B 1 30 GLU 30 70 70 GLU GLU B . n B 1 31 GLN 31 71 71 GLN GLN B . n B 1 32 PHE 32 72 72 PHE PHE B . n B 1 33 ARG 33 73 73 ARG ARG B . n B 1 34 PRO 34 74 74 PRO PRO B . n B 1 35 LEU 35 75 75 LEU LEU B . n B 1 36 ALA 36 76 76 ALA ALA B . n B 1 37 LYS 37 77 77 LYS LYS B . n B 1 38 ARG 38 78 78 ARG ARG B . n B 1 39 SER 39 79 79 SER SER B . n B 1 40 PHE 40 80 80 PHE PHE B . n B 1 41 ILE 41 81 81 ILE ILE B . n B 1 42 PHE 42 82 82 PHE PHE B . n B 1 43 PRO 43 83 83 PRO PRO B . n B 1 44 ALA 44 84 84 ALA ALA B . n B 1 45 SER 45 85 85 SER SER B . n B 1 46 PRO 46 86 86 PRO PRO B . n B 1 47 GLN 47 87 87 GLN GLN B . n B 1 48 ALA 48 88 88 ALA ALA B . n B 1 49 VAL 49 89 89 VAL VAL B . n B 1 50 TRP 50 90 90 TRP TRP B . n B 1 51 LEU 51 91 91 LEU LEU B . n B 1 52 GLN 52 92 92 GLN GLN B . n B 1 53 VAL 53 93 93 VAL VAL B . n B 1 54 GLN 54 94 94 GLN GLN B . n B 1 55 LEU 55 95 95 LEU LEU B . n B 1 56 PRO 56 96 96 PRO PRO B . n B 1 57 ALA 57 97 97 ALA ALA B . n B 1 58 GLN 58 98 98 GLN GLN B . n B 1 59 LYS 59 99 99 LYS LYS B . n B 1 60 VAL 60 100 100 VAL VAL B . n B 1 61 PRO 61 101 101 PRO PRO B . n B 1 62 SER 62 102 102 SER SER B . n B 1 63 TRP 63 103 103 TRP TRP B . n B 1 64 LEU 64 104 104 LEU LEU B . n B 1 65 TRP 65 105 105 TRP TRP B . n B 1 66 ILE 66 106 106 ILE ILE B . n B 1 67 PHE 67 107 107 PHE PHE B . n B 1 68 ALA 68 108 108 ALA ALA B . n B 1 69 PRO 69 109 109 PRO PRO B . n B 1 70 ARG 70 110 110 ARG ARG B . n B 1 71 VAL 71 111 111 VAL VAL B . n B 1 72 GLN 72 112 112 GLN GLN B . n B 1 73 TYR 73 113 113 TYR TYR B . n B 1 74 LEU 74 114 114 LEU LEU B . n B 1 75 ASP 75 115 115 ASP ASP B . n B 1 76 TYR 76 116 116 TYR TYR B . n B 1 77 TYR 77 117 117 TYR TYR B . n B 1 78 LEU 78 118 118 LEU LEU B . n B 1 79 VAL 79 119 119 VAL VAL B . n B 1 80 GLN 80 120 120 GLN GLN B . n B 1 81 ASP 81 121 121 ASP ASP B . n B 1 82 GLY 82 122 122 GLY GLY B . n B 1 83 GLN 83 123 123 GLN GLN B . n B 1 84 LEU 84 124 124 LEU LEU B . n B 1 85 VAL 85 125 125 VAL VAL B . n B 1 86 ARG 86 126 126 ARG ARG B . n B 1 87 ASP 87 127 127 ASP ASP B . n B 1 88 GLN 88 128 128 GLN GLN B . n B 1 89 HIS 89 129 129 HIS HIS B . n B 1 90 THR 90 130 130 THR THR B . n B 1 91 GLY 91 131 131 GLY GLY B . n B 1 92 GLU 92 132 132 GLU GLU B . n B 1 93 SER 93 133 133 SER SER B . n B 1 94 ARG 94 134 134 ARG ARG B . n B 1 95 PRO 95 135 135 PRO PRO B . n B 1 96 PHE 96 136 136 PHE PHE B . n B 1 97 GLN 97 137 137 GLN GLN B . n B 1 98 GLU 98 138 138 GLU GLU B . n B 1 99 ARG 99 139 139 ARG ARG B . n B 1 100 PRO 100 140 140 PRO PRO B . n B 1 101 LEU 101 141 141 LEU LEU B . n B 1 102 PRO 102 142 142 PRO PRO B . n B 1 103 SER 103 143 143 SER SER B . n B 1 104 ARG 104 144 144 ARG ARG B . n B 1 105 SER 105 145 145 SER SER B . n B 1 106 TYR 106 146 146 TYR TYR B . n B 1 107 LEU 107 147 147 LEU LEU B . n B 1 108 PHE 108 148 148 PHE PHE B . n B 1 109 SER 109 149 149 SER SER B . n B 1 110 LEU 110 150 150 LEU LEU B . n B 1 111 PRO 111 151 151 PRO PRO B . n B 1 112 VAL 112 152 152 VAL VAL B . n B 1 113 ASP 113 153 153 ASP ASP B . n B 1 114 GLY 114 154 154 GLY GLY B . n B 1 115 LYS 115 155 155 LYS LYS B . n B 1 116 PRO 116 156 156 PRO PRO B . n B 1 117 MSE 117 157 157 MSE MSE B . n B 1 118 THR 118 158 158 THR THR B . n B 1 119 LEU 119 159 159 LEU LEU B . n B 1 120 TYR 120 160 160 TYR TYR B . n B 1 121 VAL 121 161 161 VAL VAL B . n B 1 122 ARG 122 162 162 ARG ARG B . n B 1 123 MSE 123 163 163 MSE MSE B . n B 1 124 THR 124 164 164 THR THR B . n B 1 125 SER 125 165 165 SER SER B . n B 1 126 ASN 126 166 166 ASN ASN B . n B 1 127 HIS 127 167 167 HIS HIS B . n B 1 128 PRO 128 168 168 PRO PRO B . n B 1 129 LEU 129 169 169 LEU LEU B . n B 1 130 MSE 130 170 170 MSE MSE B . n B 1 131 ALA 131 171 171 ALA ALA B . n B 1 132 TRP 132 172 172 TRP TRP B . n B 1 133 PHE 133 173 173 PHE PHE B . n B 1 134 ASP 134 174 174 ASP ASP B . n B 1 135 GLN 135 175 175 GLN GLN B . n B 1 136 ILE 136 176 176 ILE ILE B . n B 1 137 ASP 137 177 177 ASP ASP B . n B 1 138 GLU 138 178 178 GLU GLU B . n B 1 139 ALA 139 179 179 ALA ALA B . n B 1 140 GLY 140 180 180 GLY GLY B . n B 1 141 LEU 141 181 181 LEU LEU B . n B 1 142 VAL 142 182 182 VAL VAL B . n B 1 143 GLY 143 183 183 GLY GLY B . n B 1 144 LEU 144 184 184 LEU LEU B . n B 1 145 GLU 145 185 185 GLU GLU B . 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 C 2 HOH 1 1 1 HOH HOH A . C 2 HOH 2 2 2 HOH HOH A . C 2 HOH 3 3 3 HOH HOH A . C 2 HOH 4 5 5 HOH HOH A . C 2 HOH 5 6 6 HOH HOH A . C 2 HOH 6 11 11 HOH HOH A . C 2 HOH 7 12 12 HOH HOH A . C 2 HOH 8 15 15 HOH HOH A . C 2 HOH 9 16 16 HOH HOH A . C 2 HOH 10 17 17 HOH HOH A . C 2 HOH 11 19 19 HOH HOH A . C 2 HOH 12 20 20 HOH HOH A . C 2 HOH 13 21 21 HOH HOH A . C 2 HOH 14 24 24 HOH HOH A . C 2 HOH 15 26 26 HOH HOH A . C 2 HOH 16 27 27 HOH HOH A . C 2 HOH 17 29 29 HOH HOH A . C 2 HOH 18 30 30 HOH HOH A . C 2 HOH 19 31 31 HOH HOH A . C 2 HOH 20 34 34 HOH HOH A . C 2 HOH 21 35 35 HOH HOH A . C 2 HOH 22 36 36 HOH HOH A . C 2 HOH 23 37 37 HOH HOH A . C 2 HOH 24 38 38 HOH HOH A . C 2 HOH 25 40 40 HOH HOH A . C 2 HOH 26 186 42 HOH HOH A . C 2 HOH 27 187 43 HOH HOH A . C 2 HOH 28 188 44 HOH HOH A . C 2 HOH 29 189 47 HOH HOH A . C 2 HOH 30 190 50 HOH HOH A . C 2 HOH 31 191 52 HOH HOH A . C 2 HOH 32 192 53 HOH HOH A . C 2 HOH 33 193 54 HOH HOH A . C 2 HOH 34 194 56 HOH HOH A . C 2 HOH 35 195 57 HOH HOH A . C 2 HOH 36 196 58 HOH HOH A . C 2 HOH 37 197 59 HOH HOH A . C 2 HOH 38 198 63 HOH HOH A . C 2 HOH 39 199 65 HOH HOH A . C 2 HOH 40 200 66 HOH HOH A . C 2 HOH 41 201 72 HOH HOH A . C 2 HOH 42 202 74 HOH HOH A . C 2 HOH 43 203 79 HOH HOH A . C 2 HOH 44 204 80 HOH HOH A . C 2 HOH 45 205 82 HOH HOH A . C 2 HOH 46 206 83 HOH HOH A . C 2 HOH 47 207 86 HOH HOH A . C 2 HOH 48 208 88 HOH HOH A . C 2 HOH 49 209 90 HOH HOH A . C 2 HOH 50 210 91 HOH HOH A . C 2 HOH 51 211 92 HOH HOH A . C 2 HOH 52 212 93 HOH HOH A . C 2 HOH 53 213 95 HOH HOH A . C 2 HOH 54 214 97 HOH HOH A . C 2 HOH 55 215 100 HOH HOH A . C 2 HOH 56 216 101 HOH HOH A . D 2 HOH 1 4 4 HOH HOH B . D 2 HOH 2 7 7 HOH HOH B . D 2 HOH 3 8 8 HOH HOH B . D 2 HOH 4 9 9 HOH HOH B . D 2 HOH 5 10 10 HOH HOH B . D 2 HOH 6 13 13 HOH HOH B . D 2 HOH 7 14 14 HOH HOH B . D 2 HOH 8 18 18 HOH HOH B . D 2 HOH 9 22 22 HOH HOH B . D 2 HOH 10 23 23 HOH HOH B . D 2 HOH 11 25 25 HOH HOH B . D 2 HOH 12 28 28 HOH HOH B . D 2 HOH 13 32 32 HOH HOH B . D 2 HOH 14 33 33 HOH HOH B . D 2 HOH 15 39 39 HOH HOH B . D 2 HOH 16 186 41 HOH HOH B . D 2 HOH 17 187 45 HOH HOH B . D 2 HOH 18 188 46 HOH HOH B . D 2 HOH 19 189 48 HOH HOH B . D 2 HOH 20 190 49 HOH HOH B . D 2 HOH 21 191 51 HOH HOH B . D 2 HOH 22 192 55 HOH HOH B . D 2 HOH 23 193 60 HOH HOH B . D 2 HOH 24 194 61 HOH HOH B . D 2 HOH 25 195 62 HOH HOH B . D 2 HOH 26 196 64 HOH HOH B . D 2 HOH 27 197 67 HOH HOH B . D 2 HOH 28 198 68 HOH HOH B . D 2 HOH 29 199 69 HOH HOH B . D 2 HOH 30 200 70 HOH HOH B . D 2 HOH 31 201 71 HOH HOH B . D 2 HOH 32 202 73 HOH HOH B . D 2 HOH 33 203 75 HOH HOH B . D 2 HOH 34 204 76 HOH HOH B . D 2 HOH 35 205 77 HOH HOH B . D 2 HOH 36 206 78 HOH HOH B . D 2 HOH 37 207 81 HOH HOH B . D 2 HOH 38 208 84 HOH HOH B . D 2 HOH 39 209 85 HOH HOH B . D 2 HOH 40 210 87 HOH HOH B . D 2 HOH 41 211 94 HOH HOH B . D 2 HOH 42 212 96 HOH HOH B . D 2 HOH 43 213 98 HOH HOH B . D 2 HOH 44 214 99 HOH HOH B . D 2 HOH 45 215 102 HOH HOH B . D 2 HOH 46 216 103 HOH HOH B . D 2 HOH 47 217 104 HOH HOH B . D 2 HOH 48 218 105 HOH HOH B . # 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 MSE 117 A MSE 157 ? MET SELENOMETHIONINE 2 A MSE 123 A MSE 163 ? MET SELENOMETHIONINE 3 A MSE 130 A MSE 170 ? MET SELENOMETHIONINE 4 B MSE 117 B MSE 157 ? MET SELENOMETHIONINE 5 B MSE 123 B MSE 163 ? MET SELENOMETHIONINE 6 B MSE 130 B MSE 170 ? MET SELENOMETHIONINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA monomeric 1 2 author_and_software_defined_assembly PISA monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C 2 1 B,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 2010-02-16 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2019-07-24 # _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' Advisory 2 2 'Structure model' 'Refinement description' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Derived calculations' 6 3 '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 3 'Structure model' software 2 3 'Structure model' struct_conn # 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 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 3 'Structure model' '_software.version' 4 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # 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[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 6.9115 48.3983 61.5405 -0.0396 -0.0337 -0.0233 0.0058 -0.0022 0.0047 0.7409 0.8253 1.6439 0.3338 -0.4247 -0.4709 -0.0279 -0.0215 0.0494 -0.0301 0.0205 -0.0166 0.0473 -0.0011 -0.0020 'X-RAY DIFFRACTION' 2 ? refined -6.9121 31.8190 41.8151 -0.0341 -0.0346 -0.0307 0.0023 -0.0068 -0.0020 1.2875 1.6612 0.9893 0.8167 0.6778 0.5637 0.0644 0.0085 -0.0728 -0.0253 -0.1496 -0.0875 0.0162 0.0943 -0.0035 # 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.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 48 A 145 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 B 48 B 145 ? . . . . ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 PHENIX 'model building' . ? 2 PHENIX refinement . ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 REFMAC phasing 5.2.0019 ? 6 HKL-2000 'data collection' . ? 7 # 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 THR A 130 ? ? -144.17 -155.97 2 1 ARG A 134 ? ? -117.46 77.19 3 1 ARG B 134 ? ? -103.75 77.24 4 1 ASP B 153 ? ? -144.20 18.44 5 1 PRO B 156 ? ? -62.09 -175.97 # 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 ALA 41 ? A ALA 1 2 1 Y 1 A THR 42 ? A THR 2 3 1 Y 1 A THR 43 ? A THR 3 4 1 Y 1 A PRO 44 ? A PRO 4 5 1 Y 1 A SER 45 ? A SER 5 6 1 Y 1 A ALA 46 ? A ALA 6 7 1 Y 1 A ASN 47 ? A ASN 7 8 1 Y 1 B ALA 41 ? B ALA 1 9 1 Y 1 B THR 42 ? B THR 2 10 1 Y 1 B THR 43 ? B THR 3 11 1 Y 1 B PRO 44 ? B PRO 4 12 1 Y 1 B SER 45 ? B SER 5 13 1 Y 1 B ALA 46 ? B ALA 6 14 1 Y 1 B ASN 47 ? B ASN 7 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #