data_3WIT # _entry.id 3WIT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3WIT RCSB RCSB096388 WWPDB D_1000096388 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3WIT _pdbx_database_status.recvd_initial_deposition_date 2013-09-25 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _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.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Uchida, K.' 1 'Leiman, P.G.' 2 'Arisaka, F.' 3 'Kanamaru, S.' 4 # _citation.id primary _citation.title 'Structure and properties of the C-terminal beta-helical domain of VgrG protein from Escherichia coli O157' _citation.journal_abbrev J.Biochem. _citation.journal_volume 155 _citation.page_first 173 _citation.page_last 182 _citation.year 2014 _citation.journal_id_ASTM ? _citation.country JP _citation.journal_id_ISSN 0021-924X _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24307403 _citation.pdbx_database_id_DOI 10.1093/jb/mvt109 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Uchida, K.' 1 primary 'Leiman, P.G.' 2 primary 'Arisaka, F.' 3 primary 'Kanamaru, S.' 4 # _cell.entry_id 3WIT _cell.length_a 49.417 _cell.length_b 49.417 _cell.length_c 199.143 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _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 3WIT _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _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 'Putative Vgr protein' 8618.481 1 ? ? 'UNP residues 561-633' ? 2 water nat water 18.015 13 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Uncharacterized protein' # _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 ;GTIAGSVHVDAVNNGGEGNGIQAYTAIKEI(MSE)LAVEESKIALTPDGIQLQVGESTVIRLSKDGITIVGGSVFINGLE HHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;GTIAGSVHVDAVNNGGEGNGIQAYTAIKEIMLAVEESKIALTPDGIQLQVGESTVIRLSKDGITIVGGSVFINGLEHHHH HH ; _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 GLY n 1 2 THR n 1 3 ILE n 1 4 ALA n 1 5 GLY n 1 6 SER n 1 7 VAL n 1 8 HIS n 1 9 VAL n 1 10 ASP n 1 11 ALA n 1 12 VAL n 1 13 ASN n 1 14 ASN n 1 15 GLY n 1 16 GLY n 1 17 GLU n 1 18 GLY n 1 19 ASN n 1 20 GLY n 1 21 ILE n 1 22 GLN n 1 23 ALA n 1 24 TYR n 1 25 THR n 1 26 ALA n 1 27 ILE n 1 28 LYS n 1 29 GLU n 1 30 ILE n 1 31 MSE n 1 32 LEU n 1 33 ALA n 1 34 VAL n 1 35 GLU n 1 36 GLU n 1 37 SER n 1 38 LYS n 1 39 ILE n 1 40 ALA n 1 41 LEU n 1 42 THR n 1 43 PRO n 1 44 ASP n 1 45 GLY n 1 46 ILE n 1 47 GLN n 1 48 LEU n 1 49 GLN n 1 50 VAL n 1 51 GLY n 1 52 GLU n 1 53 SER n 1 54 THR n 1 55 VAL n 1 56 ILE n 1 57 ARG n 1 58 LEU n 1 59 SER n 1 60 LYS n 1 61 ASP n 1 62 GLY n 1 63 ILE n 1 64 THR n 1 65 ILE n 1 66 VAL n 1 67 GLY n 1 68 GLY n 1 69 SER n 1 70 VAL n 1 71 PHE n 1 72 ILE n 1 73 ASN n 1 74 GLY n 1 75 LEU n 1 76 GLU n 1 77 HIS n 1 78 HIS n 1 79 HIS n 1 80 HIS n 1 81 HIS n 1 82 HIS 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 'ECs0607, VgrG1, Z0707' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'O157:H7 EDL933' _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 83334 _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 562 _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 'B384(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 pET29a _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q8XBY5_ECO57 _struct_ref.pdbx_db_accession Q8XBY5 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GTIAGSVHVDAVNNGGEGNGIQAYTAIKEIMLAVEESKIALTPDGIQLQVGESTVIRLSKDGITIVGGSVFIN _struct_ref.pdbx_align_begin 561 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3WIT _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 73 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q8XBY5 _struct_ref_seq.db_align_beg 561 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 633 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 561 _struct_ref_seq.pdbx_auth_seq_align_end 633 # 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 3WIT GLY A 74 ? UNP Q8XBY5 ? ? 'EXPRESSION TAG' 634 1 1 3WIT LEU A 75 ? UNP Q8XBY5 ? ? 'EXPRESSION TAG' 635 2 1 3WIT GLU A 76 ? UNP Q8XBY5 ? ? 'EXPRESSION TAG' 636 3 1 3WIT HIS A 77 ? UNP Q8XBY5 ? ? 'EXPRESSION TAG' 637 4 1 3WIT HIS A 78 ? UNP Q8XBY5 ? ? 'EXPRESSION TAG' 638 5 1 3WIT HIS A 79 ? UNP Q8XBY5 ? ? 'EXPRESSION TAG' 639 6 1 3WIT HIS A 80 ? UNP Q8XBY5 ? ? 'EXPRESSION TAG' 640 7 1 3WIT HIS A 81 ? UNP Q8XBY5 ? ? 'EXPRESSION TAG' 641 8 1 3WIT HIS A 82 ? UNP Q8XBY5 ? ? 'EXPRESSION TAG' 642 9 # 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 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 3WIT _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.71 _exptl_crystal.density_percent_sol 54.69 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.pdbx_details '35%(v/v) ethanol, 100mM Tris pH8.5, 50mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _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 PIXEL _diffrn_detector.type 'DECTRIS PILATUS 2M-F' _diffrn_detector.pdbx_collection_date 2013-02-09 _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 0.97890 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-1A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-1A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97890 # _reflns.entry_id 3WIT _reflns.observed_criterion_sigma_I 3.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 41.84 _reflns.d_resolution_high 1.95 _reflns.number_obs 7223 _reflns.number_all 7237 _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.036 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 43.1 _reflns.B_iso_Wilson_estimate 32.450 _reflns.pdbx_redundancy 18.3 _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 1.95 _reflns_shell.d_res_low 2.05 _reflns_shell.percent_possible_all 99.7 _reflns_shell.Rmerge_I_obs 0.347 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 7.5 _reflns_shell.pdbx_redundancy 15.2 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1026 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3WIT _refine.ls_number_reflns_obs 7023 _refine.ls_number_reflns_all 7228 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.08 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 33.191 _refine.ls_d_res_high 1.95 _refine.ls_percent_reflns_obs 97.18 _refine.ls_R_factor_obs 0.1978 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1961 _refine.ls_R_factor_R_free 0.2330 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.64 _refine.ls_number_reflns_R_free 326 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 46.9 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.15 _refine.pdbx_overall_phase_error 26.20 _refine.overall_SU_B ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 477 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 13 _refine_hist.number_atoms_total 490 _refine_hist.d_res_high 1.95 _refine_hist.d_res_low 33.191 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.012 ? ? 483 ? 'X-RAY DIFFRACTION' f_angle_d 1.654 ? ? 651 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 17.841 ? ? 170 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.120 ? ? 81 ? 'X-RAY DIFFRACTION' f_plane_restr 0.006 ? ? 81 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.95 _refine_ls_shell.d_res_low 2.4547 _refine_ls_shell.number_reflns_R_work 3213 _refine_ls_shell.R_factor_R_work 0.1826 _refine_ls_shell.percent_reflns_obs 95.00 _refine_ls_shell.R_factor_R_free 0.2452 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 151 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 3213 _refine_ls_shell.redundancy_reflns_obs ? # _struct.entry_id 3WIT _struct.title 'Crystal structure of the C-terminal region of VgrG1 from E. coli O157 EDL933' _struct.pdbx_descriptor 'Putative Vgr protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3WIT _struct_keywords.pdbx_keywords 'STRUCTURAL PROTEIN' _struct_keywords.text 'Triple-stranded beta-helix, All beta proteins, Type 6 secretion system component, STRUCTURAL PROTEIN' # 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 ? # _struct_biol.id 1 _struct_biol.details ? # 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 ? ? A ILE 30 C ? ? ? 1_555 A MSE 31 N ? ? A ILE 590 A MSE 591 1_555 ? ? ? ? ? ? ? 1.331 ? covale2 covale ? ? A MSE 31 C ? ? ? 1_555 A LEU 32 N ? ? A MSE 591 A LEU 592 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 ? 2 ? # 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 # 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 THR A 2 ? VAL A 7 ? THR A 562 VAL A 567 A 2 GLU A 29 ? VAL A 34 ? GLU A 589 VAL A 594 A 3 SER A 37 ? THR A 42 ? SER A 597 THR A 602 A 4 GLY A 45 ? VAL A 50 ? GLY A 605 VAL A 610 A 5 THR A 54 ? SER A 59 ? THR A 614 SER A 619 A 6 GLY A 62 ? VAL A 66 ? GLY A 622 VAL A 626 B 1 PHE A 71 ? ILE A 72 ? PHE A 631 ILE A 632 B 2 LEU A 75 ? GLU A 76 ? LEU A 635 GLU A 636 # 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 N VAL A 7 ? N VAL A 567 O GLU A 29 ? O GLU A 589 A 2 3 N LEU A 32 ? N LEU A 592 O ILE A 39 ? O ILE A 599 A 3 4 N LYS A 38 ? N LYS A 598 O GLN A 49 ? O GLN A 609 A 4 5 N ILE A 46 ? N ILE A 606 O LEU A 58 ? O LEU A 618 A 5 6 N ARG A 57 ? N ARG A 617 O THR A 64 ? O THR A 624 B 1 2 N ILE A 72 ? N ILE A 632 O LEU A 75 ? O LEU A 635 # _database_PDB_matrix.entry_id 3WIT _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 3WIT _atom_sites.fract_transf_matrix[1][1] 0.020236 _atom_sites.fract_transf_matrix[1][2] 0.011683 _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] 0.023366 _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] 0.005022 _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 GLY 1 561 561 GLY GLY A . n A 1 2 THR 2 562 562 THR THR A . n A 1 3 ILE 3 563 563 ILE ILE A . n A 1 4 ALA 4 564 564 ALA ALA A . n A 1 5 GLY 5 565 565 GLY GLY A . n A 1 6 SER 6 566 566 SER SER A . n A 1 7 VAL 7 567 567 VAL VAL A . n A 1 8 HIS 8 568 568 HIS HIS A . n A 1 9 VAL 9 569 569 VAL VAL A . n A 1 10 ASP 10 570 ? ? ? A . n A 1 11 ALA 11 571 ? ? ? A . n A 1 12 VAL 12 572 ? ? ? A . n A 1 13 ASN 13 573 ? ? ? A . n A 1 14 ASN 14 574 ? ? ? A . n A 1 15 GLY 15 575 ? ? ? A . n A 1 16 GLY 16 576 ? ? ? A . n A 1 17 GLU 17 577 ? ? ? A . n A 1 18 GLY 18 578 ? ? ? A . n A 1 19 ASN 19 579 ? ? ? A . n A 1 20 GLY 20 580 ? ? ? A . n A 1 21 ILE 21 581 ? ? ? A . n A 1 22 GLN 22 582 ? ? ? A . n A 1 23 ALA 23 583 ? ? ? A . n A 1 24 TYR 24 584 ? ? ? A . n A 1 25 THR 25 585 ? ? ? A . n A 1 26 ALA 26 586 ? ? ? A . n A 1 27 ILE 27 587 587 ILE ILE A . n A 1 28 LYS 28 588 588 LYS LYS A . n A 1 29 GLU 29 589 589 GLU GLU A . n A 1 30 ILE 30 590 590 ILE ILE A . n A 1 31 MSE 31 591 591 MSE MSE A . n A 1 32 LEU 32 592 592 LEU LEU A . n A 1 33 ALA 33 593 593 ALA ALA A . n A 1 34 VAL 34 594 594 VAL VAL A . n A 1 35 GLU 35 595 595 GLU GLU A . n A 1 36 GLU 36 596 596 GLU GLU A . n A 1 37 SER 37 597 597 SER SER A . n A 1 38 LYS 38 598 598 LYS LYS A . n A 1 39 ILE 39 599 599 ILE ILE A . n A 1 40 ALA 40 600 600 ALA ALA A . n A 1 41 LEU 41 601 601 LEU LEU A . n A 1 42 THR 42 602 602 THR THR A . n A 1 43 PRO 43 603 603 PRO PRO A . n A 1 44 ASP 44 604 604 ASP ASP A . n A 1 45 GLY 45 605 605 GLY GLY A . n A 1 46 ILE 46 606 606 ILE ILE A . n A 1 47 GLN 47 607 607 GLN GLN A . n A 1 48 LEU 48 608 608 LEU LEU A . n A 1 49 GLN 49 609 609 GLN GLN A . n A 1 50 VAL 50 610 610 VAL VAL A . n A 1 51 GLY 51 611 611 GLY GLY A . n A 1 52 GLU 52 612 612 GLU GLU A . n A 1 53 SER 53 613 613 SER SER A . n A 1 54 THR 54 614 614 THR THR A . n A 1 55 VAL 55 615 615 VAL VAL A . n A 1 56 ILE 56 616 616 ILE ILE A . n A 1 57 ARG 57 617 617 ARG ARG A . n A 1 58 LEU 58 618 618 LEU LEU A . n A 1 59 SER 59 619 619 SER SER A . n A 1 60 LYS 60 620 620 LYS LYS A . n A 1 61 ASP 61 621 621 ASP ASP A . n A 1 62 GLY 62 622 622 GLY GLY A . n A 1 63 ILE 63 623 623 ILE ILE A . n A 1 64 THR 64 624 624 THR THR A . n A 1 65 ILE 65 625 625 ILE ILE A . n A 1 66 VAL 66 626 626 VAL VAL A . n A 1 67 GLY 67 627 627 GLY GLY A . n A 1 68 GLY 68 628 628 GLY GLY A . n A 1 69 SER 69 629 629 SER SER A . n A 1 70 VAL 70 630 630 VAL VAL A . n A 1 71 PHE 71 631 631 PHE PHE A . n A 1 72 ILE 72 632 632 ILE ILE A . n A 1 73 ASN 73 633 633 ASN ASN A . n A 1 74 GLY 74 634 634 GLY GLY A . n A 1 75 LEU 75 635 635 LEU LEU A . n A 1 76 GLU 76 636 636 GLU GLU A . n A 1 77 HIS 77 637 637 HIS HIS A . n A 1 78 HIS 78 638 638 HIS HIS A . n A 1 79 HIS 79 639 639 HIS HIS A . n A 1 80 HIS 80 640 640 HIS HIS A . n A 1 81 HIS 81 641 641 HIS HIS A . n A 1 82 HIS 82 642 ? ? ? 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 HOH 1 701 1 HOH HOH A . B 2 HOH 2 702 2 HOH HOH A . B 2 HOH 3 703 3 HOH HOH A . B 2 HOH 4 704 4 HOH HOH A . B 2 HOH 5 705 5 HOH HOH A . B 2 HOH 6 706 6 HOH HOH A . B 2 HOH 7 707 7 HOH HOH A . B 2 HOH 8 708 8 HOH HOH A . B 2 HOH 9 709 9 HOH HOH A . B 2 HOH 10 710 10 HOH HOH A . B 2 HOH 11 711 11 HOH HOH A . B 2 HOH 12 712 12 HOH HOH A . B 2 HOH 13 713 13 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id MSE _pdbx_struct_mod_residue.label_seq_id 31 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id MSE _pdbx_struct_mod_residue.auth_seq_id 591 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id MET _pdbx_struct_mod_residue.details SELENOMETHIONINE # _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B # 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)' 6670 ? 1 MORE -53 ? 1 'SSA (A^2)' 9440 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5000000000 -0.8660254038 0.0000000000 49.4170000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5000000000 0.8660254038 0.0000000000 24.7085000000 -0.8660254038 -0.5000000000 0.0000000000 42.7963773788 0.0000000000 0.0000000000 1.0000000000 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 2013-12-18 2 'Structure model' 1 1 2014-02-19 3 'Structure model' 1 2 2014-03-26 4 'Structure model' 1 3 2017-11-22 # _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' 3 4 'Structure model' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 4 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 4 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_software.name' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 20.2795 _pdbx_refine_tls.origin_y 20.1684 _pdbx_refine_tls.origin_z 85.2587 _pdbx_refine_tls.T[1][1] 0.2357 _pdbx_refine_tls.T[2][2] 0.2017 _pdbx_refine_tls.T[3][3] 0.3322 _pdbx_refine_tls.T[1][2] 0.0423 _pdbx_refine_tls.T[1][3] 0.0047 _pdbx_refine_tls.T[2][3] -0.0265 _pdbx_refine_tls.L[1][1] 2.5830 _pdbx_refine_tls.L[2][2] 1.6787 _pdbx_refine_tls.L[3][3] 6.5166 _pdbx_refine_tls.L[1][2] 0.0288 _pdbx_refine_tls.L[1][3] -0.8271 _pdbx_refine_tls.L[2][3] -0.3416 _pdbx_refine_tls.S[1][1] -0.0490 _pdbx_refine_tls.S[1][2] -0.0250 _pdbx_refine_tls.S[1][3] 0.2240 _pdbx_refine_tls.S[2][1] 0.0661 _pdbx_refine_tls.S[2][2] 0.0194 _pdbx_refine_tls.S[2][3] 0.1568 _pdbx_refine_tls.S[3][1] -0.5238 _pdbx_refine_tls.S[3][2] -0.1961 _pdbx_refine_tls.S[3][3] -0.0058 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _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 all # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SERGUI 'data collection' . ? 1 PHENIX 'model building' . ? 2 PHENIX refinement '(phenix.refine: 1.8_1069)' ? 3 XDS 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 PHENIX phasing . ? 6 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id GLU _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 595 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi 41.46 _pdbx_validate_torsion.psi -118.12 # 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 ASP 570 ? A ASP 10 2 1 Y 1 A ALA 571 ? A ALA 11 3 1 Y 1 A VAL 572 ? A VAL 12 4 1 Y 1 A ASN 573 ? A ASN 13 5 1 Y 1 A ASN 574 ? A ASN 14 6 1 Y 1 A GLY 575 ? A GLY 15 7 1 Y 1 A GLY 576 ? A GLY 16 8 1 Y 1 A GLU 577 ? A GLU 17 9 1 Y 1 A GLY 578 ? A GLY 18 10 1 Y 1 A ASN 579 ? A ASN 19 11 1 Y 1 A GLY 580 ? A GLY 20 12 1 Y 1 A ILE 581 ? A ILE 21 13 1 Y 1 A GLN 582 ? A GLN 22 14 1 Y 1 A ALA 583 ? A ALA 23 15 1 Y 1 A TYR 584 ? A TYR 24 16 1 Y 1 A THR 585 ? A THR 25 17 1 Y 1 A ALA 586 ? A ALA 26 18 1 Y 1 A HIS 642 ? A HIS 82 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #