data_3O13 # _entry.id 3O13 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3O13 pdb_00003o13 10.2210/pdb3o13/pdb RCSB RCSB060531 ? ? WWPDB D_1000060531 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 417440 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3O13 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-07-20 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of a superantigen-like protein (SAV0433) from Staphylococcus aureus MU50 at 2.05 A resolution' _citation.journal_abbrev 'To be published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # _citation_author.citation_id primary _citation_author.name 'Joint Center for Structural Genomics (JCSG)' _citation_author.ordinal 1 _citation_author.identifier_ORCID ? # _cell.entry_id 3O13 _cell.length_a 50.161 _cell.length_b 90.804 _cell.length_c 109.129 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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 3O13 _symmetry.Int_Tables_number 23 _symmetry.space_group_name_H-M 'I 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _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 'Superantigen-like protein' 22555.809 1 ? ? 'sequence database residues 31-227' ? 2 non-polymer syn 'CHLORIDE ION' 35.453 2 ? ? ? ? 3 non-polymer syn 1,2-ETHANEDIOL 62.068 1 ? ? ? ? 4 water nat water 18.015 108 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Exotoxin 15' # _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 ;GSTLEVRSQATQDLSEYYKGRGFELTNVTGYKYGNKVTFIDNSQQIDVTLTGNEKLTVKDDDEVSNVDVFVVREGSDKSA ITTSIGGITKTNGTQHKDTVQNVNLSVSKSTGQHTTSVTSEYYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIR IT(MSE)KNGGYYTFELNKKLQPHR(MSE)GDTIDSRNIEKIEVNL ; _entity_poly.pdbx_seq_one_letter_code_can ;GSTLEVRSQATQDLSEYYKGRGFELTNVTGYKYGNKVTFIDNSQQIDVTLTGNEKLTVKDDDEVSNVDVFVVREGSDKSA ITTSIGGITKTNGTQHKDTVQNVNLSVSKSTGQHTTSVTSEYYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIR ITMKNGGYYTFELNKKLQPHRMGDTIDSRNIEKIEVNL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 417440 # 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 SER n 1 3 THR n 1 4 LEU n 1 5 GLU n 1 6 VAL n 1 7 ARG n 1 8 SER n 1 9 GLN n 1 10 ALA n 1 11 THR n 1 12 GLN n 1 13 ASP n 1 14 LEU n 1 15 SER n 1 16 GLU n 1 17 TYR n 1 18 TYR n 1 19 LYS n 1 20 GLY n 1 21 ARG n 1 22 GLY n 1 23 PHE n 1 24 GLU n 1 25 LEU n 1 26 THR n 1 27 ASN n 1 28 VAL n 1 29 THR n 1 30 GLY n 1 31 TYR n 1 32 LYS n 1 33 TYR n 1 34 GLY n 1 35 ASN n 1 36 LYS n 1 37 VAL n 1 38 THR n 1 39 PHE n 1 40 ILE n 1 41 ASP n 1 42 ASN n 1 43 SER n 1 44 GLN n 1 45 GLN n 1 46 ILE n 1 47 ASP n 1 48 VAL n 1 49 THR n 1 50 LEU n 1 51 THR n 1 52 GLY n 1 53 ASN n 1 54 GLU n 1 55 LYS n 1 56 LEU n 1 57 THR n 1 58 VAL n 1 59 LYS n 1 60 ASP n 1 61 ASP n 1 62 ASP n 1 63 GLU n 1 64 VAL n 1 65 SER n 1 66 ASN n 1 67 VAL n 1 68 ASP n 1 69 VAL n 1 70 PHE n 1 71 VAL n 1 72 VAL n 1 73 ARG n 1 74 GLU n 1 75 GLY n 1 76 SER n 1 77 ASP n 1 78 LYS n 1 79 SER n 1 80 ALA n 1 81 ILE n 1 82 THR n 1 83 THR n 1 84 SER n 1 85 ILE n 1 86 GLY n 1 87 GLY n 1 88 ILE n 1 89 THR n 1 90 LYS n 1 91 THR n 1 92 ASN n 1 93 GLY n 1 94 THR n 1 95 GLN n 1 96 HIS n 1 97 LYS n 1 98 ASP n 1 99 THR n 1 100 VAL n 1 101 GLN n 1 102 ASN n 1 103 VAL n 1 104 ASN n 1 105 LEU n 1 106 SER n 1 107 VAL n 1 108 SER n 1 109 LYS n 1 110 SER n 1 111 THR n 1 112 GLY n 1 113 GLN n 1 114 HIS n 1 115 THR n 1 116 THR n 1 117 SER n 1 118 VAL n 1 119 THR n 1 120 SER n 1 121 GLU n 1 122 TYR n 1 123 TYR n 1 124 SER n 1 125 ILE n 1 126 TYR n 1 127 LYS n 1 128 GLU n 1 129 GLU n 1 130 ILE n 1 131 SER n 1 132 LEU n 1 133 LYS n 1 134 GLU n 1 135 LEU n 1 136 ASP n 1 137 PHE n 1 138 LYS n 1 139 LEU n 1 140 ARG n 1 141 LYS n 1 142 HIS n 1 143 LEU n 1 144 ILE n 1 145 ASP n 1 146 LYS n 1 147 HIS n 1 148 ASP n 1 149 LEU n 1 150 TYR n 1 151 LYS n 1 152 THR n 1 153 GLU n 1 154 PRO n 1 155 LYS n 1 156 ASP n 1 157 SER n 1 158 LYS n 1 159 ILE n 1 160 ARG n 1 161 ILE n 1 162 THR n 1 163 MSE n 1 164 LYS n 1 165 ASN n 1 166 GLY n 1 167 GLY n 1 168 TYR n 1 169 TYR n 1 170 THR n 1 171 PHE n 1 172 GLU n 1 173 LEU n 1 174 ASN n 1 175 LYS n 1 176 LYS n 1 177 LEU n 1 178 GLN n 1 179 PRO n 1 180 HIS n 1 181 ARG n 1 182 MSE n 1 183 GLY n 1 184 ASP n 1 185 THR n 1 186 ILE n 1 187 ASP n 1 188 SER n 1 189 ARG n 1 190 ASN n 1 191 ILE n 1 192 GLU n 1 193 LYS n 1 194 ILE n 1 195 GLU n 1 196 VAL n 1 197 ASN n 1 198 LEU 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 'set15, SAV0433' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'Mu50 / ATCC 700699' _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 'Staphylococcus aureus subsp. aureus Mu50' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 158878 _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 HK100 _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 SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q99WG9_STAAM _struct_ref.pdbx_db_accession Q99WG9 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;STLEVRSQATQDLSEYYKGRGFELTNVTGYKYGNKVTFIDNSQQIDVTLTGNEKLTVKDDDEVSNVDVFVVREGSDKSAI TTSIGGITKTNGTQHKDTVQNVNLSVSKSTGQHTTSVTSEYYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRI TMKNGGYYTFELNKKLQPHRMGDTIDSRNIEKIEVNL ; _struct_ref.pdbx_align_begin 31 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3O13 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 198 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q99WG9 _struct_ref_seq.db_align_beg 31 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 227 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 31 _struct_ref_seq.pdbx_auth_seq_align_end 227 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3O13 _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q99WG9 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 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.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 3O13 # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.75 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 55.35 _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.pH 7.0 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '1.000000000M NaCitrate, 0.200000000M NaCl, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _exptl_crystal_grow.temp_details ? _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 'MARMOSAIC 325 mm CCD' _diffrn_detector.details 'Flat mirror (vertical focusing)' _diffrn_detector.pdbx_collection_date 2010-06-11 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Single crystal Si(111) bent monochromator (horizontal focusing)' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.91837 1.0 2 0.97941 1.0 3 0.97895 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_wavelength_list 0.91837,0.97941,0.97895 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3O13 _reflns.d_resolution_high 2.05 _reflns.d_resolution_low 29.448 _reflns.number_obs 15922 _reflns.pdbx_Rmerge_I_obs 0.055 _reflns.pdbx_netI_over_sigmaI 11.440 _reflns.percent_possible_obs 98.000 _reflns.B_iso_Wilson_estimate 29.753 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy ? _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 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.050 2.120 5830 ? 2765 0.517 1.9 ? ? ? ? ? 94.400 1 1 2.120 2.210 6780 ? 3175 0.368 2.6 ? ? ? ? ? 98.800 2 1 2.210 2.310 6282 ? 2927 0.291 3.2 ? ? ? ? ? 98.500 3 1 2.310 2.430 6344 ? 2958 0.225 4.0 ? ? ? ? ? 98.700 4 1 2.430 2.580 6356 ? 2955 0.175 5.0 ? ? ? ? ? 99.000 5 1 2.580 2.780 6502 ? 3013 0.123 7.1 ? ? ? ? ? 98.900 6 1 2.780 3.060 6440 ? 2992 0.074 11.0 ? ? ? ? ? 98.700 7 1 3.060 3.500 6378 ? 2948 0.040 18.4 ? ? ? ? ? 98.400 8 1 3.500 4.400 6434 ? 2972 0.025 27.8 ? ? ? ? ? 97.900 9 1 4.400 29.448 6513 ? 2969 0.021 33.2 ? ? ? ? ? 96.800 10 1 # _refine.entry_id 3O13 _refine.ls_d_res_high 2.0500 _refine.ls_d_res_low 29.448 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.1300 _refine.ls_number_reflns_obs 15922 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.CHLORIDE (CL) FROM THE CRYSTALLIZATION SOLUTION AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1931 _refine.ls_R_factor_R_work 0.1908 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2396 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.0000 _refine.ls_number_reflns_R_free 799 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 52.7329 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -2.3000 _refine.aniso_B[2][2] -2.6600 _refine.aniso_B[3][3] 4.9600 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9580 _refine.correlation_coeff_Fo_to_Fc_free 0.9430 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free 0.1650 _refine.overall_SU_ML 0.1380 _refine.overall_SU_B 10.1350 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 118.540 _refine.B_iso_min 26.220 _refine.occupancy_max 1.000 _refine.occupancy_min 0.400 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R 0.175 _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 1489 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 108 _refine_hist.number_atoms_total 1603 _refine_hist.d_res_high 2.0500 _refine_hist.d_res_low 29.448 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 1553 0.015 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 1047 0.004 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2101 1.502 1.960 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 2583 0.944 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 198 6.135 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 76 37.154 25.658 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 299 11.654 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 7 17.266 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 244 0.090 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1717 0.005 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 290 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 944 1.825 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 390 0.480 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1546 3.159 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 609 5.178 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 548 7.290 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.0500 _refine_ls_shell.d_res_low 2.1030 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 95.0000 _refine_ls_shell.number_reflns_R_work 1064 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2930 _refine_ls_shell.R_factor_R_free 0.3660 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 58 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1122 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3O13 _struct.title 'Crystal structure of a superantigen-like protein (SAV0433) from Staphylococcus aureus MU50 at 2.05 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text 'STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-BIOLOGY, TOXIN' _struct_keywords.pdbx_keywords TOXIN _struct_keywords.entry_id 3O13 # 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 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details 'CRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.' # 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 SER A 8 ? LYS A 19 ? SER A 37 LYS A 48 1 ? 12 HELX_P HELX_P2 2 LEU A 132 ? HIS A 147 ? LEU A 161 HIS A 176 1 ? 16 HELX_P HELX_P3 3 GLN A 178 ? MSE A 182 ? GLN A 207 MSE A 211 5 ? 5 # _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 _struct_conn.pdbx_role covale1 covale both ? A THR 162 C ? ? ? 1_555 A MSE 163 N ? ? A THR 191 A MSE 192 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale2 covale both ? A MSE 163 C ? ? ? 1_555 A LYS 164 N ? ? A MSE 192 A LYS 193 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale3 covale both ? A ARG 181 C ? ? ? 1_555 A MSE 182 N ? ? A ARG 210 A MSE 211 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale4 covale both ? A MSE 182 C ? ? ? 1_555 A GLY 183 N ? ? A MSE 211 A GLY 212 1_555 ? ? ? ? ? ? ? 1.338 ? ? # _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 ? 5 ? C ? 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 ? 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 ? parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel C 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 82 ? ILE A 85 ? THR A 111 ILE A 114 A 2 GLN A 44 ? THR A 49 ? GLN A 73 THR A 78 A 3 LYS A 36 ? ASP A 41 ? LYS A 65 ASP A 70 A 4 GLY A 22 ? TYR A 33 ? GLY A 51 TYR A 62 A 5 GLU A 63 ? VAL A 72 ? GLU A 92 VAL A 101 A 6 ILE A 88 ? LYS A 90 ? ILE A 117 LYS A 119 B 1 SER A 117 ? ILE A 125 ? SER A 146 ILE A 154 B 2 GLN A 101 ? LYS A 109 ? GLN A 130 LYS A 138 B 3 ILE A 191 ? ASN A 197 ? ILE A 220 ASN A 226 B 4 LYS A 158 ? MSE A 163 ? LYS A 187 MSE A 192 B 5 TYR A 168 ? GLU A 172 ? TYR A 197 GLU A 201 C 1 GLU A 129 ? SER A 131 ? GLU A 158 SER A 160 C 2 THR A 185 ? ASP A 187 ? THR A 214 ASP A 216 # 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 SER A 84 ? O SER A 113 N THR A 49 ? N THR A 78 A 2 3 O VAL A 48 ? O VAL A 77 N VAL A 37 ? N VAL A 66 A 3 4 O THR A 38 ? O THR A 67 N TYR A 31 ? N TYR A 60 A 4 5 N PHE A 23 ? N PHE A 52 O VAL A 71 ? O VAL A 100 A 5 6 N ASP A 68 ? N ASP A 97 O THR A 89 ? O THR A 118 B 1 2 O ILE A 125 ? O ILE A 154 N GLN A 101 ? N GLN A 130 B 2 3 N SER A 108 ? N SER A 137 O VAL A 196 ? O VAL A 225 B 3 4 O GLU A 195 ? O GLU A 224 N ARG A 160 ? N ARG A 189 B 4 5 N ILE A 159 ? N ILE A 188 O PHE A 171 ? O PHE A 200 C 1 2 N ILE A 130 ? N ILE A 159 O ILE A 186 ? O ILE A 215 # 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 A CL 1 ? 2 'BINDING SITE FOR RESIDUE CL A 1' AC2 Software A CL 2 ? 5 'BINDING SITE FOR RESIDUE CL A 2' AC3 Software A EDO 3 ? 2 'BINDING SITE FOR RESIDUE EDO A 3' # 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 2 ASP A 187 ? ASP A 216 . ? 1_555 ? 2 AC1 2 ASN A 190 ? ASN A 219 . ? 1_555 ? 3 AC2 5 TYR A 169 ? TYR A 198 . ? 1_555 ? 4 AC2 5 THR A 170 ? THR A 199 . ? 1_555 ? 5 AC2 5 ARG A 181 ? ARG A 210 . ? 1_555 ? 6 AC2 5 HOH E . ? HOH A 230 . ? 1_555 ? 7 AC2 5 HOH E . ? HOH A 307 . ? 1_555 ? 8 AC3 2 PRO A 179 ? PRO A 208 . ? 1_555 ? 9 AC3 2 HIS A 180 ? HIS A 209 . ? 1_555 ? # _atom_sites.entry_id 3O13 _atom_sites.fract_transf_matrix[1][1] 0.019936 _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] 0.011013 _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] 0.009163 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C CL 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 0 ? ? ? A . n A 1 2 SER 2 31 ? ? ? A . n A 1 3 THR 3 32 ? ? ? A . n A 1 4 LEU 4 33 ? ? ? A . n A 1 5 GLU 5 34 34 GLU GLU A . n A 1 6 VAL 6 35 35 VAL VAL A . n A 1 7 ARG 7 36 36 ARG ARG A . n A 1 8 SER 8 37 37 SER SER A . n A 1 9 GLN 9 38 38 GLN GLN A . n A 1 10 ALA 10 39 39 ALA ALA A . n A 1 11 THR 11 40 40 THR THR A . n A 1 12 GLN 12 41 41 GLN GLN A . n A 1 13 ASP 13 42 42 ASP ASP A . n A 1 14 LEU 14 43 43 LEU LEU A . n A 1 15 SER 15 44 44 SER SER A . n A 1 16 GLU 16 45 45 GLU GLU A . n A 1 17 TYR 17 46 46 TYR TYR A . n A 1 18 TYR 18 47 47 TYR TYR A . n A 1 19 LYS 19 48 48 LYS LYS A . n A 1 20 GLY 20 49 49 GLY GLY A . n A 1 21 ARG 21 50 50 ARG ARG A . n A 1 22 GLY 22 51 51 GLY GLY A . n A 1 23 PHE 23 52 52 PHE PHE A . n A 1 24 GLU 24 53 53 GLU GLU A . n A 1 25 LEU 25 54 54 LEU LEU A . n A 1 26 THR 26 55 55 THR THR A . n A 1 27 ASN 27 56 56 ASN ASN A . n A 1 28 VAL 28 57 57 VAL VAL A . n A 1 29 THR 29 58 58 THR THR A . n A 1 30 GLY 30 59 59 GLY GLY A . n A 1 31 TYR 31 60 60 TYR TYR A . n A 1 32 LYS 32 61 61 LYS LYS A . n A 1 33 TYR 33 62 62 TYR TYR A . n A 1 34 GLY 34 63 63 GLY GLY A . n A 1 35 ASN 35 64 64 ASN ASN A . n A 1 36 LYS 36 65 65 LYS LYS A . n A 1 37 VAL 37 66 66 VAL VAL A . n A 1 38 THR 38 67 67 THR THR A . n A 1 39 PHE 39 68 68 PHE PHE A . n A 1 40 ILE 40 69 69 ILE ILE A . n A 1 41 ASP 41 70 70 ASP ASP A . n A 1 42 ASN 42 71 71 ASN ASN A . n A 1 43 SER 43 72 72 SER SER A . n A 1 44 GLN 44 73 73 GLN GLN A . n A 1 45 GLN 45 74 74 GLN GLN A . n A 1 46 ILE 46 75 75 ILE ILE A . n A 1 47 ASP 47 76 76 ASP ASP A . n A 1 48 VAL 48 77 77 VAL VAL A . n A 1 49 THR 49 78 78 THR THR A . n A 1 50 LEU 50 79 79 LEU LEU A . n A 1 51 THR 51 80 80 THR THR A . n A 1 52 GLY 52 81 81 GLY GLY A . n A 1 53 ASN 53 82 82 ASN ASN A . n A 1 54 GLU 54 83 83 GLU GLU A . n A 1 55 LYS 55 84 84 LYS LYS A . n A 1 56 LEU 56 85 85 LEU LEU A . n A 1 57 THR 57 86 86 THR THR A . n A 1 58 VAL 58 87 87 VAL VAL A . n A 1 59 LYS 59 88 88 LYS LYS A . n A 1 60 ASP 60 89 89 ASP ASP A . n A 1 61 ASP 61 90 90 ASP ASP A . n A 1 62 ASP 62 91 91 ASP ASP A . n A 1 63 GLU 63 92 92 GLU GLU A . n A 1 64 VAL 64 93 93 VAL VAL A . n A 1 65 SER 65 94 94 SER SER A . n A 1 66 ASN 66 95 95 ASN ASN A . n A 1 67 VAL 67 96 96 VAL VAL A . n A 1 68 ASP 68 97 97 ASP ASP A . n A 1 69 VAL 69 98 98 VAL VAL A . n A 1 70 PHE 70 99 99 PHE PHE A . n A 1 71 VAL 71 100 100 VAL VAL A . n A 1 72 VAL 72 101 101 VAL VAL A . n A 1 73 ARG 73 102 102 ARG ARG A . n A 1 74 GLU 74 103 103 GLU GLU A . n A 1 75 GLY 75 104 104 GLY GLY A . n A 1 76 SER 76 105 105 SER SER A . n A 1 77 ASP 77 106 ? ? ? A . n A 1 78 LYS 78 107 ? ? ? A . n A 1 79 SER 79 108 108 SER SER A . n A 1 80 ALA 80 109 109 ALA ALA A . n A 1 81 ILE 81 110 110 ILE ILE A . n A 1 82 THR 82 111 111 THR THR A . n A 1 83 THR 83 112 112 THR THR A . n A 1 84 SER 84 113 113 SER SER A . n A 1 85 ILE 85 114 114 ILE ILE A . n A 1 86 GLY 86 115 115 GLY GLY A . n A 1 87 GLY 87 116 116 GLY GLY A . n A 1 88 ILE 88 117 117 ILE ILE A . n A 1 89 THR 89 118 118 THR THR A . n A 1 90 LYS 90 119 119 LYS LYS A . n A 1 91 THR 91 120 120 THR THR A . n A 1 92 ASN 92 121 121 ASN ASN A . n A 1 93 GLY 93 122 122 GLY GLY A . n A 1 94 THR 94 123 123 THR THR A . n A 1 95 GLN 95 124 124 GLN GLN A . n A 1 96 HIS 96 125 125 HIS HIS A . n A 1 97 LYS 97 126 126 LYS LYS A . n A 1 98 ASP 98 127 127 ASP ASP A . n A 1 99 THR 99 128 128 THR THR A . n A 1 100 VAL 100 129 129 VAL VAL A . n A 1 101 GLN 101 130 130 GLN GLN A . n A 1 102 ASN 102 131 131 ASN ASN A . n A 1 103 VAL 103 132 132 VAL VAL A . n A 1 104 ASN 104 133 133 ASN ASN A . n A 1 105 LEU 105 134 134 LEU LEU A . n A 1 106 SER 106 135 135 SER SER A . n A 1 107 VAL 107 136 136 VAL VAL A . n A 1 108 SER 108 137 137 SER SER A . n A 1 109 LYS 109 138 138 LYS LYS A . n A 1 110 SER 110 139 139 SER SER A . n A 1 111 THR 111 140 ? ? ? A . n A 1 112 GLY 112 141 ? ? ? A . n A 1 113 GLN 113 142 ? ? ? A . n A 1 114 HIS 114 143 ? ? ? A . n A 1 115 THR 115 144 ? ? ? A . n A 1 116 THR 116 145 145 THR THR A . n A 1 117 SER 117 146 146 SER SER A . n A 1 118 VAL 118 147 147 VAL VAL A . n A 1 119 THR 119 148 148 THR THR A . n A 1 120 SER 120 149 149 SER SER A . n A 1 121 GLU 121 150 150 GLU GLU A . n A 1 122 TYR 122 151 151 TYR TYR A . n A 1 123 TYR 123 152 152 TYR TYR A . n A 1 124 SER 124 153 153 SER SER A . n A 1 125 ILE 125 154 154 ILE ILE A . n A 1 126 TYR 126 155 155 TYR TYR A . n A 1 127 LYS 127 156 156 LYS LYS A . n A 1 128 GLU 128 157 157 GLU GLU A . n A 1 129 GLU 129 158 158 GLU GLU A . n A 1 130 ILE 130 159 159 ILE ILE A . n A 1 131 SER 131 160 160 SER SER A . n A 1 132 LEU 132 161 161 LEU LEU A . n A 1 133 LYS 133 162 162 LYS LYS A . n A 1 134 GLU 134 163 163 GLU GLU A . n A 1 135 LEU 135 164 164 LEU LEU A . n A 1 136 ASP 136 165 165 ASP ASP A . n A 1 137 PHE 137 166 166 PHE PHE A . n A 1 138 LYS 138 167 167 LYS LYS A . n A 1 139 LEU 139 168 168 LEU LEU A . n A 1 140 ARG 140 169 169 ARG ARG A . n A 1 141 LYS 141 170 170 LYS LYS A . n A 1 142 HIS 142 171 171 HIS HIS A . n A 1 143 LEU 143 172 172 LEU LEU A . n A 1 144 ILE 144 173 173 ILE ILE A . n A 1 145 ASP 145 174 174 ASP ASP A . n A 1 146 LYS 146 175 175 LYS LYS A . n A 1 147 HIS 147 176 176 HIS HIS A . n A 1 148 ASP 148 177 177 ASP ASP A . n A 1 149 LEU 149 178 178 LEU LEU A . n A 1 150 TYR 150 179 179 TYR TYR A . n A 1 151 LYS 151 180 180 LYS LYS A . n A 1 152 THR 152 181 181 THR THR A . n A 1 153 GLU 153 182 182 GLU GLU A . n A 1 154 PRO 154 183 183 PRO PRO A . n A 1 155 LYS 155 184 184 LYS LYS A . n A 1 156 ASP 156 185 185 ASP ASP A . n A 1 157 SER 157 186 186 SER SER A . n A 1 158 LYS 158 187 187 LYS LYS A . n A 1 159 ILE 159 188 188 ILE ILE A . n A 1 160 ARG 160 189 189 ARG ARG A . n A 1 161 ILE 161 190 190 ILE ILE A . n A 1 162 THR 162 191 191 THR THR A . n A 1 163 MSE 163 192 192 MSE MSE A . n A 1 164 LYS 164 193 193 LYS LYS A . n A 1 165 ASN 165 194 194 ASN ASN A . n A 1 166 GLY 166 195 195 GLY GLY A . n A 1 167 GLY 167 196 196 GLY GLY A . n A 1 168 TYR 168 197 197 TYR TYR A . n A 1 169 TYR 169 198 198 TYR TYR A . n A 1 170 THR 170 199 199 THR THR A . n A 1 171 PHE 171 200 200 PHE PHE A . n A 1 172 GLU 172 201 201 GLU GLU A . n A 1 173 LEU 173 202 202 LEU LEU A . n A 1 174 ASN 174 203 203 ASN ASN A . n A 1 175 LYS 175 204 204 LYS LYS A . n A 1 176 LYS 176 205 205 LYS LYS A . n A 1 177 LEU 177 206 206 LEU LEU A . n A 1 178 GLN 178 207 207 GLN GLN A . n A 1 179 PRO 179 208 208 PRO PRO A . n A 1 180 HIS 180 209 209 HIS HIS A . n A 1 181 ARG 181 210 210 ARG ARG A . n A 1 182 MSE 182 211 211 MSE MSE A . n A 1 183 GLY 183 212 212 GLY GLY A . n A 1 184 ASP 184 213 213 ASP ASP A . n A 1 185 THR 185 214 214 THR THR A . n A 1 186 ILE 186 215 215 ILE ILE A . n A 1 187 ASP 187 216 216 ASP ASP A . n A 1 188 SER 188 217 217 SER SER A . n A 1 189 ARG 189 218 218 ARG ARG A . n A 1 190 ASN 190 219 219 ASN ASN A . n A 1 191 ILE 191 220 220 ILE ILE A . n A 1 192 GLU 192 221 221 GLU GLU A . n A 1 193 LYS 193 222 222 LYS LYS A . n A 1 194 ILE 194 223 223 ILE ILE A . n A 1 195 GLU 195 224 224 GLU GLU A . n A 1 196 VAL 196 225 225 VAL VAL A . n A 1 197 ASN 197 226 226 ASN ASN A . n A 1 198 LEU 198 227 227 LEU LEU A . n # _pdbx_SG_project.project_name PSI:Biology _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # 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 CL 1 1 1 CL CL A . C 2 CL 1 2 2 CL CL A . D 3 EDO 1 3 3 EDO EDO A . E 4 HOH 1 4 4 HOH HOH A . E 4 HOH 2 5 5 HOH HOH A . E 4 HOH 3 6 6 HOH HOH A . E 4 HOH 4 7 7 HOH HOH A . E 4 HOH 5 8 8 HOH HOH A . E 4 HOH 6 9 9 HOH HOH A . E 4 HOH 7 10 10 HOH HOH A . E 4 HOH 8 11 11 HOH HOH A . E 4 HOH 9 12 12 HOH HOH A . E 4 HOH 10 13 13 HOH HOH A . E 4 HOH 11 14 14 HOH HOH A . E 4 HOH 12 15 15 HOH HOH A . E 4 HOH 13 16 16 HOH HOH A . E 4 HOH 14 17 17 HOH HOH A . E 4 HOH 15 18 18 HOH HOH A . E 4 HOH 16 19 19 HOH HOH A . E 4 HOH 17 20 20 HOH HOH A . E 4 HOH 18 21 21 HOH HOH A . E 4 HOH 19 22 22 HOH HOH A . E 4 HOH 20 23 23 HOH HOH A . E 4 HOH 21 24 24 HOH HOH A . E 4 HOH 22 25 25 HOH HOH A . E 4 HOH 23 26 26 HOH HOH A . E 4 HOH 24 27 27 HOH HOH A . E 4 HOH 25 28 28 HOH HOH A . E 4 HOH 26 29 29 HOH HOH A . E 4 HOH 27 228 30 HOH HOH A . E 4 HOH 28 229 31 HOH HOH A . E 4 HOH 29 230 32 HOH HOH A . E 4 HOH 30 231 33 HOH HOH A . E 4 HOH 31 232 34 HOH HOH A . E 4 HOH 32 233 35 HOH HOH A . E 4 HOH 33 234 36 HOH HOH A . E 4 HOH 34 235 37 HOH HOH A . E 4 HOH 35 236 38 HOH HOH A . E 4 HOH 36 237 39 HOH HOH A . E 4 HOH 37 238 40 HOH HOH A . E 4 HOH 38 239 41 HOH HOH A . E 4 HOH 39 240 42 HOH HOH A . E 4 HOH 40 241 43 HOH HOH A . E 4 HOH 41 242 44 HOH HOH A . E 4 HOH 42 243 45 HOH HOH A . E 4 HOH 43 244 46 HOH HOH A . E 4 HOH 44 245 47 HOH HOH A . E 4 HOH 45 246 48 HOH HOH A . E 4 HOH 46 247 49 HOH HOH A . E 4 HOH 47 248 50 HOH HOH A . E 4 HOH 48 249 51 HOH HOH A . E 4 HOH 49 250 52 HOH HOH A . E 4 HOH 50 251 53 HOH HOH A . E 4 HOH 51 252 54 HOH HOH A . E 4 HOH 52 253 55 HOH HOH A . E 4 HOH 53 254 56 HOH HOH A . E 4 HOH 54 255 57 HOH HOH A . E 4 HOH 55 256 58 HOH HOH A . E 4 HOH 56 257 59 HOH HOH A . E 4 HOH 57 258 60 HOH HOH A . E 4 HOH 58 259 61 HOH HOH A . E 4 HOH 59 260 62 HOH HOH A . E 4 HOH 60 261 63 HOH HOH A . E 4 HOH 61 262 64 HOH HOH A . E 4 HOH 62 263 65 HOH HOH A . E 4 HOH 63 264 66 HOH HOH A . E 4 HOH 64 265 67 HOH HOH A . E 4 HOH 65 266 68 HOH HOH A . E 4 HOH 66 267 69 HOH HOH A . E 4 HOH 67 268 70 HOH HOH A . E 4 HOH 68 269 71 HOH HOH A . E 4 HOH 69 270 72 HOH HOH A . E 4 HOH 70 271 73 HOH HOH A . E 4 HOH 71 272 74 HOH HOH A . E 4 HOH 72 273 75 HOH HOH A . E 4 HOH 73 274 76 HOH HOH A . E 4 HOH 74 275 77 HOH HOH A . E 4 HOH 75 276 78 HOH HOH A . E 4 HOH 76 277 79 HOH HOH A . E 4 HOH 77 278 80 HOH HOH A . E 4 HOH 78 279 81 HOH HOH A . E 4 HOH 79 280 82 HOH HOH A . E 4 HOH 80 281 83 HOH HOH A . E 4 HOH 81 282 84 HOH HOH A . E 4 HOH 82 283 85 HOH HOH A . E 4 HOH 83 284 86 HOH HOH A . E 4 HOH 84 285 87 HOH HOH A . E 4 HOH 85 286 88 HOH HOH A . E 4 HOH 86 287 89 HOH HOH A . E 4 HOH 87 288 90 HOH HOH A . E 4 HOH 88 289 91 HOH HOH A . E 4 HOH 89 290 92 HOH HOH A . E 4 HOH 90 291 93 HOH HOH A . E 4 HOH 91 292 94 HOH HOH A . E 4 HOH 92 293 95 HOH HOH A . E 4 HOH 93 294 96 HOH HOH A . E 4 HOH 94 295 97 HOH HOH A . E 4 HOH 95 296 98 HOH HOH A . E 4 HOH 96 297 99 HOH HOH A . E 4 HOH 97 298 100 HOH HOH A . E 4 HOH 98 299 101 HOH HOH A . E 4 HOH 99 300 102 HOH HOH A . E 4 HOH 100 301 103 HOH HOH A . E 4 HOH 101 302 104 HOH HOH A . E 4 HOH 102 303 105 HOH HOH A . E 4 HOH 103 304 106 HOH HOH A . E 4 HOH 104 305 107 HOH HOH A . E 4 HOH 105 306 108 HOH HOH A . E 4 HOH 106 307 109 HOH HOH A . E 4 HOH 107 308 110 HOH HOH A . E 4 HOH 108 309 111 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 MSE 163 A MSE 192 ? MET SELENOMETHIONINE 2 A MSE 182 A MSE 211 ? MET 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 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,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 8 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 2010-08-25 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2011-07-20 4 'Structure model' 1 3 2023-02-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Structure summary' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' # 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 4 'Structure model' database_2 2 4 'Structure model' struct_conn 3 4 'Structure model' struct_ref_seq_dif 4 4 'Structure model' struct_site # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_struct_ref_seq_dif.details' 5 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _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 12.7154 _pdbx_refine_tls.origin_y 25.5663 _pdbx_refine_tls.origin_z 37.8181 _pdbx_refine_tls.T[1][1] 0.1676 _pdbx_refine_tls.T[2][2] 0.1658 _pdbx_refine_tls.T[3][3] 0.0278 _pdbx_refine_tls.T[1][2] -0.0263 _pdbx_refine_tls.T[1][3] 0.0073 _pdbx_refine_tls.T[2][3] -0.0163 _pdbx_refine_tls.L[1][1] 4.2904 _pdbx_refine_tls.L[2][2] 3.8748 _pdbx_refine_tls.L[3][3] 0.8066 _pdbx_refine_tls.L[1][2] 1.3732 _pdbx_refine_tls.L[1][3] -0.0561 _pdbx_refine_tls.L[2][3] 0.1136 _pdbx_refine_tls.S[1][1] 0.0909 _pdbx_refine_tls.S[2][2] -0.0662 _pdbx_refine_tls.S[3][3] -0.0248 _pdbx_refine_tls.S[1][2] -0.2971 _pdbx_refine_tls.S[1][3] -0.2886 _pdbx_refine_tls.S[2][3] -0.0056 _pdbx_refine_tls.S[2][1] 0.2800 _pdbx_refine_tls.S[3][1] 0.0788 _pdbx_refine_tls.S[3][2] 0.0734 # _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 A _pdbx_refine_tls_group.beg_auth_seq_id 34 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 227 _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 ? # _phasing.method MAD # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 2 REFMAC 5.5.0110 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 3 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 4 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 XDS . ? ? ? ? 'data reduction' ? ? ? 6 SHELXD . ? ? ? ? phasing ? ? ? 7 autoSHARP . ? ? ? ? phasing ? ? ? # _pdbx_entry_details.entry_id 3O13 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THIS CONSTRUCT (RESIDUES 31-227) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # 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 ASN A 71 ? ? 60.50 -119.58 2 1 LYS A 84 ? ? -107.65 70.02 3 1 ASP A 90 ? ? -114.24 -166.16 4 1 LYS A 184 ? ? 55.83 -123.54 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A GLU 45 ? CG ? A GLU 16 CG 2 1 Y 1 A GLU 45 ? CD ? A GLU 16 CD 3 1 Y 1 A GLU 45 ? OE1 ? A GLU 16 OE1 4 1 Y 1 A GLU 45 ? OE2 ? A GLU 16 OE2 5 1 Y 1 A LYS 88 ? CG ? A LYS 59 CG 6 1 Y 1 A LYS 88 ? CD ? A LYS 59 CD 7 1 Y 1 A LYS 88 ? CE ? A LYS 59 CE 8 1 Y 1 A LYS 88 ? NZ ? A LYS 59 NZ 9 1 Y 1 A LYS 184 ? CD ? A LYS 155 CD 10 1 Y 1 A LYS 184 ? CE ? A LYS 155 CE 11 1 Y 1 A LYS 184 ? NZ ? A LYS 155 NZ # 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 GLY 0 ? A GLY 1 2 1 Y 1 A SER 31 ? A SER 2 3 1 Y 1 A THR 32 ? A THR 3 4 1 Y 1 A LEU 33 ? A LEU 4 5 1 Y 1 A ASP 106 ? A ASP 77 6 1 Y 1 A LYS 107 ? A LYS 78 7 1 Y 1 A THR 140 ? A THR 111 8 1 Y 1 A GLY 141 ? A GLY 112 9 1 Y 1 A GLN 142 ? A GLN 113 10 1 Y 1 A HIS 143 ? A HIS 114 11 1 Y 1 A THR 144 ? A THR 115 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CHLORIDE ION' CL 3 1,2-ETHANEDIOL EDO 4 water HOH #