data_3O8S # _entry.id 3O8S # _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 3O8S pdb_00003o8s 10.2210/pdb3o8s/pdb RCSB RCSB060808 ? ? WWPDB D_1000060808 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 371505 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3O8S _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-08-03 _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 an ADP-ribose pyrophosphatase (SSU98_1448) from STREPTOCOCCUS SUIS 89-1591 at 2.27 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 3O8S _cell.length_a 64.780 _cell.length_b 64.780 _cell.length_c 108.290 _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 3O8S _symmetry.Int_Tables_number 95 _symmetry.space_group_name_H-M 'P 43 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 'ADP-ribose pyrophosphatase' 23365.881 1 ? ? ? ? 2 non-polymer syn 1,2-ETHANEDIOL 62.068 5 ? ? ? ? 3 non-polymer syn 'ACETATE ION' 59.044 1 ? ? ? ? 4 water nat water 18.015 35 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'NUDIX hydrolase' # _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 ;G(MSE)SQDKWLEWAVRLQALAQTGLAYGKDVYD(MSE)ERFEEIRQIAAE(MSE)LVEPSGQPLEVVKDLFCNETGYQT PKLDTRAAIFQEDKILLVQENDGLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILDKHKNNPAKSAHRVTKV FILCRLLGGEFQPNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASRSEHWETRFD ; _entity_poly.pdbx_seq_one_letter_code_can ;GMSQDKWLEWAVRLQALAQTGLAYGKDVYDMERFEEIRQIAAEMLVEPSGQPLEVVKDLFCNETGYQTPKLDTRAAIFQE DKILLVQENDGLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILDKHKNNPAKSAHRVTKVFILCRLLGGEFQ PNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASRSEHWETRFD ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 371505 # 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 MSE n 1 3 SER n 1 4 GLN n 1 5 ASP n 1 6 LYS n 1 7 TRP n 1 8 LEU n 1 9 GLU n 1 10 TRP n 1 11 ALA n 1 12 VAL n 1 13 ARG n 1 14 LEU n 1 15 GLN n 1 16 ALA n 1 17 LEU n 1 18 ALA n 1 19 GLN n 1 20 THR n 1 21 GLY n 1 22 LEU n 1 23 ALA n 1 24 TYR n 1 25 GLY n 1 26 LYS n 1 27 ASP n 1 28 VAL n 1 29 TYR n 1 30 ASP n 1 31 MSE n 1 32 GLU n 1 33 ARG n 1 34 PHE n 1 35 GLU n 1 36 GLU n 1 37 ILE n 1 38 ARG n 1 39 GLN n 1 40 ILE n 1 41 ALA n 1 42 ALA n 1 43 GLU n 1 44 MSE n 1 45 LEU n 1 46 VAL n 1 47 GLU n 1 48 PRO n 1 49 SER n 1 50 GLY n 1 51 GLN n 1 52 PRO n 1 53 LEU n 1 54 GLU n 1 55 VAL n 1 56 VAL n 1 57 LYS n 1 58 ASP n 1 59 LEU n 1 60 PHE n 1 61 CYS n 1 62 ASN n 1 63 GLU n 1 64 THR n 1 65 GLY n 1 66 TYR n 1 67 GLN n 1 68 THR n 1 69 PRO n 1 70 LYS n 1 71 LEU n 1 72 ASP n 1 73 THR n 1 74 ARG n 1 75 ALA n 1 76 ALA n 1 77 ILE n 1 78 PHE n 1 79 GLN n 1 80 GLU n 1 81 ASP n 1 82 LYS n 1 83 ILE n 1 84 LEU n 1 85 LEU n 1 86 VAL n 1 87 GLN n 1 88 GLU n 1 89 ASN n 1 90 ASP n 1 91 GLY n 1 92 LEU n 1 93 TRP n 1 94 SER n 1 95 LEU n 1 96 PRO n 1 97 GLY n 1 98 GLY n 1 99 TRP n 1 100 CYS n 1 101 ASP n 1 102 VAL n 1 103 ASP n 1 104 GLN n 1 105 SER n 1 106 VAL n 1 107 LYS n 1 108 ASP n 1 109 ASN n 1 110 VAL n 1 111 VAL n 1 112 LYS n 1 113 GLU n 1 114 VAL n 1 115 LYS n 1 116 GLU n 1 117 GLU n 1 118 ALA n 1 119 GLY n 1 120 LEU n 1 121 ASP n 1 122 VAL n 1 123 GLU n 1 124 ALA n 1 125 GLN n 1 126 ARG n 1 127 VAL n 1 128 VAL n 1 129 ALA n 1 130 ILE n 1 131 LEU n 1 132 ASP n 1 133 LYS n 1 134 HIS n 1 135 LYS n 1 136 ASN n 1 137 ASN n 1 138 PRO n 1 139 ALA n 1 140 LYS n 1 141 SER n 1 142 ALA n 1 143 HIS n 1 144 ARG n 1 145 VAL n 1 146 THR n 1 147 LYS n 1 148 VAL n 1 149 PHE n 1 150 ILE n 1 151 LEU n 1 152 CYS n 1 153 ARG n 1 154 LEU n 1 155 LEU n 1 156 GLY n 1 157 GLY n 1 158 GLU n 1 159 PHE n 1 160 GLN n 1 161 PRO n 1 162 ASN n 1 163 SER n 1 164 GLU n 1 165 THR n 1 166 VAL n 1 167 ALA n 1 168 SER n 1 169 GLY n 1 170 PHE n 1 171 PHE n 1 172 SER n 1 173 LEU n 1 174 ASP n 1 175 ASP n 1 176 LEU n 1 177 PRO n 1 178 PRO n 1 179 LEU n 1 180 TYR n 1 181 LEU n 1 182 GLY n 1 183 LYS n 1 184 ASN n 1 185 THR n 1 186 ALA n 1 187 GLU n 1 188 GLN n 1 189 LEU n 1 190 ALA n 1 191 LEU n 1 192 CYS n 1 193 LEU n 1 194 GLU n 1 195 ALA n 1 196 SER n 1 197 ARG n 1 198 SER n 1 199 GLU n 1 200 HIS n 1 201 TRP n 1 202 GLU n 1 203 THR n 1 204 ARG n 1 205 PHE n 1 206 ASP 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 SsuiDRAFT_3457 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 89/1591 _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 'Streptococcus suis' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 286604 _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 B9WTJ0_STRSU _struct_ref.pdbx_db_accession B9WTJ0 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSQDKWLEWAVRLQALAQTGLAYGKDVYDMERFEEIRQIAAEMLVEPSGQPLEVVKDLFCNETGYQTPKLDTRAAIFQED KILLVQENDGLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILDKHKNNPAKSAHRVTKVFILCRLLGGEFQP NSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASRSEHWETRFD ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3O8S _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 206 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession B9WTJ0 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 205 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 205 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3O8S _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 B9WTJ0 _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 ACT non-polymer . 'ACETATE ION' ? 'C2 H3 O2 -1' 59.044 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 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.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 3O8S # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.43 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 49.40 _exptl_crystal.description 'DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-MERGE, COMPLETENESS AND ' _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 4.5 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details ;50.0% ethylene glycol, 5.0% polyethylene glycol 1000, 0.1M sodium acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K ; _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 2007-04-08 # _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 'SINGLE WAVELENGTH' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97885 _diffrn_radiation_wavelength.wt 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 0.97885 _diffrn_source.pdbx_wavelength_list ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3O8S _reflns.d_resolution_high 2.27 _reflns.d_resolution_low 28.970 _reflns.number_obs 10944 _reflns.pdbx_Rmerge_I_obs 0.050 _reflns.pdbx_netI_over_sigmaI 17.090 _reflns.percent_possible_obs 97.700 _reflns.B_iso_Wilson_estimate 52.960 _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 2.270 2.350 7656 ? 1982 0.761 2.3 ? ? ? ? ? 98.900 1 1 2.350 2.440 7533 ? 1945 0.570 2.9 ? ? ? ? ? 99.100 2 1 2.440 2.560 8383 ? 2155 0.400 4.0 ? ? ? ? ? 98.200 3 1 2.560 2.690 7620 ? 1952 0.286 5.7 ? ? ? ? ? 98.200 4 1 2.690 2.860 7840 ? 2010 0.185 8.0 ? ? ? ? ? 98.500 5 1 2.860 3.080 7838 ? 1999 0.110 12.6 ? ? ? ? ? 98.100 6 1 3.080 3.390 7872 ? 2002 0.064 19.9 ? ? ? ? ? 97.800 7 1 3.390 3.870 7621 ? 1931 0.039 29.6 ? ? ? ? ? 97.400 8 1 3.870 4.870 7902 ? 1998 0.026 41.6 ? ? ? ? ? 96.900 9 1 4.870 ? 7765 ? 1961 0.024 45.7 ? ? ? ? ? 94.000 10 1 # _refine.entry_id 3O8S _refine.ls_d_res_high 2.2700 _refine.ls_d_res_low 28.970 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs ? _refine.ls_number_reflns_obs 10920 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1. 1,2-ETHANEDIOL (EDO) AND ACETATE (ACT) FROM THE CRYSTALLIZATION CONDITION ARE MODELED INTO THE STRUCTURE. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. ELECTRON DENSITY FOR RESIDUES 1-66 IN THE N-TERMINAL REGION OF THE PROTEIN IS DISORDERED, AND THIS REGION COULD NOT BE MODELED. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1931 _refine.ls_R_factor_R_work 0.1906 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2179 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 8.7800 _refine.ls_number_reflns_R_free 959 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 61.3391 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -3.4675 _refine.aniso_B[2][2] -3.4675 _refine.aniso_B[3][3] 6.9349 _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 0.9475 _refine.correlation_coeff_Fo_to_Fc_free 0.9375 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.solvent_model_details ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 122.350 _refine.B_iso_min 32.570 _refine.occupancy_max 1.000 _refine.occupancy_min 0.500 _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 ? _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 1046 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 24 _refine_hist.number_atoms_solvent 35 _refine_hist.number_atoms_total 1105 _refine_hist.d_res_high 2.2700 _refine_hist.d_res_low 28.970 # loop_ _refine_ls_restr.pdbx_refine_id _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_restraint_function 'X-RAY DIFFRACTION' t_dihedral_angle_d 499 ? ? 2.000 SINUSOIDAL 'X-RAY DIFFRACTION' t_trig_c_planes 37 ? ? 2.000 HARMONIC 'X-RAY DIFFRACTION' t_gen_planes 149 ? ? 5.000 HARMONIC 'X-RAY DIFFRACTION' t_it 1083 ? ? 20.000 HARMONIC 'X-RAY DIFFRACTION' t_nbd ? ? ? ? ? 'X-RAY DIFFRACTION' t_improper_torsion ? ? ? ? ? 'X-RAY DIFFRACTION' t_pseud_angle ? ? ? ? ? 'X-RAY DIFFRACTION' t_chiral_improper_torsion 136 ? ? 5.000 SEMIHARMONIC 'X-RAY DIFFRACTION' t_sum_occupancies ? ? ? ? ? 'X-RAY DIFFRACTION' t_utility_distance ? ? ? ? ? 'X-RAY DIFFRACTION' t_utility_angle ? ? ? ? ? 'X-RAY DIFFRACTION' t_utility_torsion ? ? ? ? ? 'X-RAY DIFFRACTION' t_ideal_dist_contact 1203 ? ? 4.000 SEMIHARMONIC 'X-RAY DIFFRACTION' t_bond_d 1083 0.010 ? 2.000 HARMONIC 'X-RAY DIFFRACTION' t_angle_deg 1460 1.070 ? 2.000 HARMONIC 'X-RAY DIFFRACTION' t_omega_torsion ? 3.690 ? ? ? 'X-RAY DIFFRACTION' t_other_torsion ? 2.870 ? ? ? # _refine_ls_shell.d_res_high 2.2700 _refine_ls_shell.d_res_low 2.4900 _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.number_reflns_R_work 2394 _refine_ls_shell.R_factor_all 0.1937 _refine_ls_shell.R_factor_R_work 0.1920 _refine_ls_shell.R_factor_R_free 0.2144 _refine_ls_shell.percent_reflns_R_free 7.4200 _refine_ls_shell.number_reflns_R_free 192 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 2586 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3O8S _struct.title 'Crystal structure of an ADP-ribose pyrophosphatase (SSU98_1448) from STREPTOCOCCUS SUIS 89-1591 at 2.27 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, HYDROLASE, NUDIX PROTEIN ; _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.entry_id 3O8S # 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 2 ? E N N 2 ? F N N 2 ? G N N 3 ? H N N 4 ? # _struct_biol.id 1 # 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 105 ? GLY A 119 ? SER A 104 GLY A 118 1 ? 15 HELX_P HELX_P2 2 LYS A 133 ? ASN A 137 ? LYS A 132 ASN A 136 1 ? 5 HELX_P HELX_P3 3 THR A 185 ? SER A 198 ? THR A 184 SER A 197 1 ? 14 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 6 ? # 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 B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 4 5 ? anti-parallel B 5 6 ? 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 TRP A 93 ? SER A 94 ? TRP A 92 SER A 93 A 2 LYS A 82 ? GLN A 87 ? LYS A 81 GLN A 86 A 3 LYS A 70 ? GLN A 79 ? LYS A 69 GLN A 78 A 4 ALA A 167 ? PHE A 171 ? ALA A 166 PHE A 170 B 1 GLY A 97 ? TRP A 99 ? GLY A 96 TRP A 98 B 2 LYS A 70 ? GLN A 79 ? LYS A 69 GLN A 78 B 3 LYS A 82 ? GLN A 87 ? LYS A 81 GLN A 86 B 4 VAL A 145 ? GLY A 157 ? VAL A 144 GLY A 156 B 5 LEU A 120 ? ASP A 132 ? LEU A 119 ASP A 131 B 6 ARG A 204 ? PHE A 205 ? ARG A 203 PHE A 204 # 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 94 ? O SER A 93 N VAL A 86 ? N VAL A 85 A 2 3 O LEU A 84 ? O LEU A 83 N ILE A 77 ? N ILE A 76 B 1 2 O GLY A 98 ? O GLY A 97 N THR A 73 ? N THR A 72 B 2 3 N ILE A 77 ? N ILE A 76 O LEU A 84 ? O LEU A 83 B 4 5 O LYS A 147 ? O LYS A 146 N LEU A 131 ? N LEU A 130 B 5 6 N ILE A 130 ? N ILE A 129 O ARG A 204 ? O ARG A 203 # 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 EDO 206 ? 4 'BINDING SITE FOR RESIDUE EDO A 206' AC2 Software A EDO 207 ? 6 'BINDING SITE FOR RESIDUE EDO A 207' AC3 Software A EDO 208 ? 3 'BINDING SITE FOR RESIDUE EDO A 208' AC4 Software A EDO 209 ? 6 'BINDING SITE FOR RESIDUE EDO A 209' AC5 Software A EDO 210 ? 5 'BINDING SITE FOR RESIDUE EDO A 210' AC6 Software A ACT 211 ? 7 'BINDING SITE FOR RESIDUE ACT A 211' # 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 4 ARG A 197 ? ARG A 196 . ? 1_555 ? 2 AC1 4 SER A 198 ? SER A 197 . ? 1_555 ? 3 AC1 4 GLU A 199 ? GLU A 198 . ? 1_555 ? 4 AC1 4 HIS A 200 ? HIS A 199 . ? 1_555 ? 5 AC2 6 LEU A 84 ? LEU A 83 . ? 1_555 ? 6 AC2 6 ALA A 118 ? ALA A 117 . ? 1_555 ? 7 AC2 6 LEU A 120 ? LEU A 119 . ? 1_555 ? 8 AC2 6 PHE A 159 ? PHE A 158 . ? 1_555 ? 9 AC2 6 SER A 168 ? SER A 167 . ? 1_555 ? 10 AC2 6 EDO D . ? EDO A 208 . ? 1_555 ? 11 AC3 3 GLY A 157 ? GLY A 156 . ? 1_555 ? 12 AC3 3 PHE A 170 ? PHE A 169 . ? 1_555 ? 13 AC3 3 EDO C . ? EDO A 207 . ? 1_555 ? 14 AC4 6 GLN A 79 ? GLN A 78 . ? 3_654 ? 15 AC4 6 LEU A 155 ? LEU A 154 . ? 3_654 ? 16 AC4 6 HIS A 200 ? HIS A 199 . ? 8_665 ? 17 AC4 6 HIS A 200 ? HIS A 199 . ? 1_555 ? 18 AC4 6 HOH H . ? HOH A 218 . ? 1_555 ? 19 AC4 6 HOH H . ? HOH A 226 . ? 8_665 ? 20 AC5 5 ARG A 74 ? ARG A 73 . ? 1_555 ? 21 AC5 5 GLU A 88 ? GLU A 87 . ? 1_555 ? 22 AC5 5 SER A 94 ? SER A 93 . ? 1_555 ? 23 AC5 5 GLU A 117 ? GLU A 116 . ? 1_555 ? 24 AC5 5 LYS A 183 ? LYS A 182 . ? 1_555 ? 25 AC6 7 GLN A 125 ? GLN A 124 . ? 1_555 ? 26 AC6 7 ARG A 126 ? ARG A 125 . ? 1_555 ? 27 AC6 7 LEU A 151 ? LEU A 150 . ? 1_555 ? 28 AC6 7 ARG A 153 ? ARG A 152 . ? 5_656 ? 29 AC6 7 ALA A 195 ? ALA A 194 . ? 1_555 ? 30 AC6 7 SER A 196 ? SER A 195 . ? 1_555 ? 31 AC6 7 SER A 198 ? SER A 197 . ? 1_555 ? # _atom_sites.entry_id 3O8S _atom_sites.fract_transf_matrix[1][1] 0.015437 _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] 0.015437 _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] 0.009234 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 ? ? ? A . n A 1 2 MSE 2 1 ? ? ? A . n A 1 3 SER 3 2 ? ? ? A . n A 1 4 GLN 4 3 ? ? ? A . n A 1 5 ASP 5 4 ? ? ? A . n A 1 6 LYS 6 5 ? ? ? A . n A 1 7 TRP 7 6 ? ? ? A . n A 1 8 LEU 8 7 ? ? ? A . n A 1 9 GLU 9 8 ? ? ? A . n A 1 10 TRP 10 9 ? ? ? A . n A 1 11 ALA 11 10 ? ? ? A . n A 1 12 VAL 12 11 ? ? ? A . n A 1 13 ARG 13 12 ? ? ? A . n A 1 14 LEU 14 13 ? ? ? A . n A 1 15 GLN 15 14 ? ? ? A . n A 1 16 ALA 16 15 ? ? ? A . n A 1 17 LEU 17 16 ? ? ? A . n A 1 18 ALA 18 17 ? ? ? A . n A 1 19 GLN 19 18 ? ? ? A . n A 1 20 THR 20 19 ? ? ? A . n A 1 21 GLY 21 20 ? ? ? A . n A 1 22 LEU 22 21 ? ? ? A . n A 1 23 ALA 23 22 ? ? ? A . n A 1 24 TYR 24 23 ? ? ? A . n A 1 25 GLY 25 24 ? ? ? A . n A 1 26 LYS 26 25 ? ? ? A . n A 1 27 ASP 27 26 ? ? ? A . n A 1 28 VAL 28 27 ? ? ? A . n A 1 29 TYR 29 28 ? ? ? A . n A 1 30 ASP 30 29 ? ? ? A . n A 1 31 MSE 31 30 ? ? ? A . n A 1 32 GLU 32 31 ? ? ? A . n A 1 33 ARG 33 32 ? ? ? A . n A 1 34 PHE 34 33 ? ? ? A . n A 1 35 GLU 35 34 ? ? ? A . n A 1 36 GLU 36 35 ? ? ? A . n A 1 37 ILE 37 36 ? ? ? A . n A 1 38 ARG 38 37 ? ? ? A . n A 1 39 GLN 39 38 ? ? ? A . n A 1 40 ILE 40 39 ? ? ? A . n A 1 41 ALA 41 40 ? ? ? A . n A 1 42 ALA 42 41 ? ? ? A . n A 1 43 GLU 43 42 ? ? ? A . n A 1 44 MSE 44 43 ? ? ? A . n A 1 45 LEU 45 44 ? ? ? A . n A 1 46 VAL 46 45 ? ? ? A . n A 1 47 GLU 47 46 ? ? ? A . n A 1 48 PRO 48 47 ? ? ? A . n A 1 49 SER 49 48 ? ? ? A . n A 1 50 GLY 50 49 ? ? ? A . n A 1 51 GLN 51 50 ? ? ? A . n A 1 52 PRO 52 51 ? ? ? A . n A 1 53 LEU 53 52 ? ? ? A . n A 1 54 GLU 54 53 ? ? ? A . n A 1 55 VAL 55 54 ? ? ? A . n A 1 56 VAL 56 55 ? ? ? A . n A 1 57 LYS 57 56 ? ? ? A . n A 1 58 ASP 58 57 ? ? ? A . n A 1 59 LEU 59 58 ? ? ? A . n A 1 60 PHE 60 59 ? ? ? A . n A 1 61 CYS 61 60 ? ? ? A . n A 1 62 ASN 62 61 ? ? ? A . n A 1 63 GLU 63 62 ? ? ? A . n A 1 64 THR 64 63 ? ? ? A . n A 1 65 GLY 65 64 ? ? ? A . n A 1 66 TYR 66 65 ? ? ? A . n A 1 67 GLN 67 66 ? ? ? A . n A 1 68 THR 68 67 67 THR THR A . n A 1 69 PRO 69 68 68 PRO PRO A . n A 1 70 LYS 70 69 69 LYS LYS A . n A 1 71 LEU 71 70 70 LEU LEU A . n A 1 72 ASP 72 71 71 ASP ASP A . n A 1 73 THR 73 72 72 THR THR A . n A 1 74 ARG 74 73 73 ARG ARG A . n A 1 75 ALA 75 74 74 ALA ALA A . n A 1 76 ALA 76 75 75 ALA ALA A . n A 1 77 ILE 77 76 76 ILE ILE A . n A 1 78 PHE 78 77 77 PHE PHE A . n A 1 79 GLN 79 78 78 GLN GLN A . n A 1 80 GLU 80 79 79 GLU GLU A . n A 1 81 ASP 81 80 80 ASP ASP A . n A 1 82 LYS 82 81 81 LYS LYS A . n A 1 83 ILE 83 82 82 ILE ILE A . n A 1 84 LEU 84 83 83 LEU LEU A . n A 1 85 LEU 85 84 84 LEU LEU A . n A 1 86 VAL 86 85 85 VAL VAL A . n A 1 87 GLN 87 86 86 GLN GLN A . n A 1 88 GLU 88 87 87 GLU GLU A . n A 1 89 ASN 89 88 88 ASN ASN A . n A 1 90 ASP 90 89 89 ASP ASP A . n A 1 91 GLY 91 90 90 GLY GLY A . n A 1 92 LEU 92 91 91 LEU LEU A . n A 1 93 TRP 93 92 92 TRP TRP A . n A 1 94 SER 94 93 93 SER SER A . n A 1 95 LEU 95 94 94 LEU LEU A . n A 1 96 PRO 96 95 95 PRO PRO A . n A 1 97 GLY 97 96 96 GLY GLY A . n A 1 98 GLY 98 97 97 GLY GLY A . n A 1 99 TRP 99 98 98 TRP TRP A . n A 1 100 CYS 100 99 99 CYS CYS A . n A 1 101 ASP 101 100 100 ASP ASP A . n A 1 102 VAL 102 101 101 VAL VAL A . n A 1 103 ASP 103 102 102 ASP ASP A . n A 1 104 GLN 104 103 103 GLN GLN A . n A 1 105 SER 105 104 104 SER SER A . n A 1 106 VAL 106 105 105 VAL VAL A . n A 1 107 LYS 107 106 106 LYS LYS A . n A 1 108 ASP 108 107 107 ASP ASP A . n A 1 109 ASN 109 108 108 ASN ASN A . n A 1 110 VAL 110 109 109 VAL VAL A . n A 1 111 VAL 111 110 110 VAL VAL A . n A 1 112 LYS 112 111 111 LYS LYS A . n A 1 113 GLU 113 112 112 GLU GLU A . n A 1 114 VAL 114 113 113 VAL VAL A . n A 1 115 LYS 115 114 114 LYS LYS A . n A 1 116 GLU 116 115 115 GLU GLU A . n A 1 117 GLU 117 116 116 GLU GLU A . n A 1 118 ALA 118 117 117 ALA ALA A . n A 1 119 GLY 119 118 118 GLY GLY A . n A 1 120 LEU 120 119 119 LEU LEU A . n A 1 121 ASP 121 120 120 ASP ASP A . n A 1 122 VAL 122 121 121 VAL VAL A . n A 1 123 GLU 123 122 122 GLU GLU A . n A 1 124 ALA 124 123 123 ALA ALA A . n A 1 125 GLN 125 124 124 GLN GLN A . n A 1 126 ARG 126 125 125 ARG ARG A . n A 1 127 VAL 127 126 126 VAL VAL A . n A 1 128 VAL 128 127 127 VAL VAL A . n A 1 129 ALA 129 128 128 ALA ALA A . n A 1 130 ILE 130 129 129 ILE ILE A . n A 1 131 LEU 131 130 130 LEU LEU A . n A 1 132 ASP 132 131 131 ASP ASP A . n A 1 133 LYS 133 132 132 LYS LYS A . n A 1 134 HIS 134 133 133 HIS HIS A . n A 1 135 LYS 135 134 134 LYS LYS A . n A 1 136 ASN 136 135 135 ASN ASN A . n A 1 137 ASN 137 136 136 ASN ASN A . n A 1 138 PRO 138 137 137 PRO PRO A . n A 1 139 ALA 139 138 ? ? ? A . n A 1 140 LYS 140 139 ? ? ? A . n A 1 141 SER 141 140 ? ? ? A . n A 1 142 ALA 142 141 ? ? ? A . n A 1 143 HIS 143 142 ? ? ? A . n A 1 144 ARG 144 143 143 ARG ARG A . n A 1 145 VAL 145 144 144 VAL VAL A . n A 1 146 THR 146 145 145 THR THR A . n A 1 147 LYS 147 146 146 LYS LYS A . n A 1 148 VAL 148 147 147 VAL VAL A . n A 1 149 PHE 149 148 148 PHE PHE A . n A 1 150 ILE 150 149 149 ILE ILE A . n A 1 151 LEU 151 150 150 LEU LEU A . n A 1 152 CYS 152 151 151 CYS CYS A . n A 1 153 ARG 153 152 152 ARG ARG A . n A 1 154 LEU 154 153 153 LEU LEU A . n A 1 155 LEU 155 154 154 LEU LEU A . n A 1 156 GLY 156 155 155 GLY GLY A . n A 1 157 GLY 157 156 156 GLY GLY A . n A 1 158 GLU 158 157 157 GLU GLU A . n A 1 159 PHE 159 158 158 PHE PHE A . n A 1 160 GLN 160 159 159 GLN GLN A . n A 1 161 PRO 161 160 160 PRO PRO A . n A 1 162 ASN 162 161 161 ASN ASN A . n A 1 163 SER 163 162 162 SER SER A . n A 1 164 GLU 164 163 163 GLU GLU A . n A 1 165 THR 165 164 164 THR THR A . n A 1 166 VAL 166 165 165 VAL VAL A . n A 1 167 ALA 167 166 166 ALA ALA A . n A 1 168 SER 168 167 167 SER SER A . n A 1 169 GLY 169 168 168 GLY GLY A . n A 1 170 PHE 170 169 169 PHE PHE A . n A 1 171 PHE 171 170 170 PHE PHE A . n A 1 172 SER 172 171 171 SER SER A . n A 1 173 LEU 173 172 172 LEU LEU A . n A 1 174 ASP 174 173 173 ASP ASP A . n A 1 175 ASP 175 174 174 ASP ASP A . n A 1 176 LEU 176 175 175 LEU LEU A . n A 1 177 PRO 177 176 176 PRO PRO A . n A 1 178 PRO 178 177 177 PRO PRO A . n A 1 179 LEU 179 178 178 LEU LEU A . n A 1 180 TYR 180 179 179 TYR TYR A . n A 1 181 LEU 181 180 180 LEU LEU A . n A 1 182 GLY 182 181 181 GLY GLY A . n A 1 183 LYS 183 182 182 LYS LYS A . n A 1 184 ASN 184 183 183 ASN ASN A . n A 1 185 THR 185 184 184 THR THR A . n A 1 186 ALA 186 185 185 ALA ALA A . n A 1 187 GLU 187 186 186 GLU GLU A . n A 1 188 GLN 188 187 187 GLN GLN A . n A 1 189 LEU 189 188 188 LEU LEU A . n A 1 190 ALA 190 189 189 ALA ALA A . n A 1 191 LEU 191 190 190 LEU LEU A . n A 1 192 CYS 192 191 191 CYS CYS A . n A 1 193 LEU 193 192 192 LEU LEU A . n A 1 194 GLU 194 193 193 GLU GLU A . n A 1 195 ALA 195 194 194 ALA ALA A . n A 1 196 SER 196 195 195 SER SER A . n A 1 197 ARG 197 196 196 ARG ARG A . n A 1 198 SER 198 197 197 SER SER A . n A 1 199 GLU 199 198 198 GLU GLU A . n A 1 200 HIS 200 199 199 HIS HIS A . n A 1 201 TRP 201 200 200 TRP TRP A . n A 1 202 GLU 202 201 201 GLU GLU A . n A 1 203 THR 203 202 202 THR THR A . n A 1 204 ARG 204 203 203 ARG ARG A . n A 1 205 PHE 205 204 204 PHE PHE A . n A 1 206 ASP 206 205 205 ASP ASP 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 EDO 1 206 1 EDO EDO A . C 2 EDO 1 207 2 EDO EDO A . D 2 EDO 1 208 3 EDO EDO A . E 2 EDO 1 209 4 EDO EDO A . F 2 EDO 1 210 5 EDO EDO A . G 3 ACT 1 211 6 ACT ACT A . H 4 HOH 1 212 7 HOH HOH A . H 4 HOH 2 213 8 HOH HOH A . H 4 HOH 3 214 9 HOH HOH A . H 4 HOH 4 215 10 HOH HOH A . H 4 HOH 5 216 11 HOH HOH A . H 4 HOH 6 217 12 HOH HOH A . H 4 HOH 7 218 13 HOH HOH A . H 4 HOH 8 219 14 HOH HOH A . H 4 HOH 9 220 15 HOH HOH A . H 4 HOH 10 221 16 HOH HOH A . H 4 HOH 11 222 17 HOH HOH A . H 4 HOH 12 223 18 HOH HOH A . H 4 HOH 13 224 19 HOH HOH A . H 4 HOH 14 225 20 HOH HOH A . H 4 HOH 15 226 21 HOH HOH A . H 4 HOH 16 227 22 HOH HOH A . H 4 HOH 17 228 23 HOH HOH A . H 4 HOH 18 229 24 HOH HOH A . H 4 HOH 19 230 25 HOH HOH A . H 4 HOH 20 231 26 HOH HOH A . H 4 HOH 21 232 27 HOH HOH A . H 4 HOH 22 233 28 HOH HOH A . H 4 HOH 23 234 29 HOH HOH A . H 4 HOH 24 235 30 HOH HOH A . H 4 HOH 25 236 31 HOH HOH A . H 4 HOH 26 237 32 HOH HOH A . H 4 HOH 27 238 33 HOH HOH A . H 4 HOH 28 239 34 HOH HOH A . H 4 HOH 29 240 35 HOH HOH A . H 4 HOH 30 241 36 HOH HOH A . H 4 HOH 31 242 37 HOH HOH A . H 4 HOH 32 243 38 HOH HOH A . H 4 HOH 33 244 39 HOH HOH A . H 4 HOH 34 245 40 HOH HOH A . H 4 HOH 35 246 41 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # 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)' 4080 ? 1 MORE 10 ? 1 'SSA (A^2)' 12790 ? # 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' 8_665 -y+1,-x+1,-z+3/4 0.0000000000 -1.0000000000 0.0000000000 64.7800000000 -1.0000000000 0.0000000000 0.0000000000 64.7800000000 0.0000000000 0.0000000000 -1.0000000000 81.2175000000 # 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_ref_seq_dif 3 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_ref_seq_dif.details' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 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 16.6105 _pdbx_refine_tls.origin_y 36.7788 _pdbx_refine_tls.origin_z 51.9120 _pdbx_refine_tls.T[1][1] -0.2379 _pdbx_refine_tls.T[2][2] 0.1112 _pdbx_refine_tls.T[3][3] -0.1745 _pdbx_refine_tls.T[1][2] 0.0425 _pdbx_refine_tls.T[1][3] 0.0089 _pdbx_refine_tls.T[2][3] 0.0088 _pdbx_refine_tls.L[1][1] 3.1357 _pdbx_refine_tls.L[2][2] 1.0587 _pdbx_refine_tls.L[3][3] 6.8452 _pdbx_refine_tls.L[1][2] 0.0389 _pdbx_refine_tls.L[1][3] -0.5016 _pdbx_refine_tls.L[2][3] -0.4393 _pdbx_refine_tls.S[1][1] -0.0629 _pdbx_refine_tls.S[2][2] 0.0957 _pdbx_refine_tls.S[3][3] -0.0328 _pdbx_refine_tls.S[1][2] -0.4622 _pdbx_refine_tls.S[1][3] 0.0470 _pdbx_refine_tls.S[2][3] 0.2468 _pdbx_refine_tls.S[2][1] -0.0718 _pdbx_refine_tls.S[3][1] -0.1676 _pdbx_refine_tls.S[3][2] -1.0800 # _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 67 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 205 _pdbx_refine_tls_group.selection_details '{ A|* }' _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 MR # 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 BUSTER-TNT 'BUSTER 2.8.0' ? program 'Gerard Bricogne' buster-develop@GlobalPhasing.com refinement http://www.globalphasing.com/buster/ ? ? 2 XSCALE . ? package 'Wolfgang Kabsch' ? 'data processing' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 3 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 4 XDS . ? ? ? ? 'data reduction' ? ? ? 5 XSCALE . ? ? ? ? 'data scaling' ? ? ? 6 Rosetta . ? ? ? ? phasing ? ? ? 7 PHASER . ? ? ? ? phasing ? ? ? 8 BUSTER 2.8.0 ? ? ? ? refinement ? ? ? # _pdbx_entry_details.entry_id 3O8S _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT 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_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 LYS 69 ? CD ? A LYS 70 CD 2 1 Y 1 A LYS 69 ? CE ? A LYS 70 CE 3 1 Y 1 A LYS 69 ? NZ ? A LYS 70 NZ 4 1 Y 1 A LYS 111 ? CG ? A LYS 112 CG 5 1 Y 1 A LYS 111 ? CD ? A LYS 112 CD 6 1 Y 1 A LYS 111 ? CE ? A LYS 112 CE 7 1 Y 1 A LYS 111 ? NZ ? A LYS 112 NZ 8 1 Y 1 A ARG 143 ? CG ? A ARG 144 CG 9 1 Y 1 A ARG 143 ? CD ? A ARG 144 CD 10 1 Y 1 A ARG 143 ? NE ? A ARG 144 NE 11 1 Y 1 A ARG 143 ? CZ ? A ARG 144 CZ 12 1 Y 1 A ARG 143 ? NH1 ? A ARG 144 NH1 13 1 Y 1 A ARG 143 ? NH2 ? A ARG 144 NH2 # 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 MSE 1 ? A MSE 2 3 1 Y 1 A SER 2 ? A SER 3 4 1 Y 1 A GLN 3 ? A GLN 4 5 1 Y 1 A ASP 4 ? A ASP 5 6 1 Y 1 A LYS 5 ? A LYS 6 7 1 Y 1 A TRP 6 ? A TRP 7 8 1 Y 1 A LEU 7 ? A LEU 8 9 1 Y 1 A GLU 8 ? A GLU 9 10 1 Y 1 A TRP 9 ? A TRP 10 11 1 Y 1 A ALA 10 ? A ALA 11 12 1 Y 1 A VAL 11 ? A VAL 12 13 1 Y 1 A ARG 12 ? A ARG 13 14 1 Y 1 A LEU 13 ? A LEU 14 15 1 Y 1 A GLN 14 ? A GLN 15 16 1 Y 1 A ALA 15 ? A ALA 16 17 1 Y 1 A LEU 16 ? A LEU 17 18 1 Y 1 A ALA 17 ? A ALA 18 19 1 Y 1 A GLN 18 ? A GLN 19 20 1 Y 1 A THR 19 ? A THR 20 21 1 Y 1 A GLY 20 ? A GLY 21 22 1 Y 1 A LEU 21 ? A LEU 22 23 1 Y 1 A ALA 22 ? A ALA 23 24 1 Y 1 A TYR 23 ? A TYR 24 25 1 Y 1 A GLY 24 ? A GLY 25 26 1 Y 1 A LYS 25 ? A LYS 26 27 1 Y 1 A ASP 26 ? A ASP 27 28 1 Y 1 A VAL 27 ? A VAL 28 29 1 Y 1 A TYR 28 ? A TYR 29 30 1 Y 1 A ASP 29 ? A ASP 30 31 1 Y 1 A MSE 30 ? A MSE 31 32 1 Y 1 A GLU 31 ? A GLU 32 33 1 Y 1 A ARG 32 ? A ARG 33 34 1 Y 1 A PHE 33 ? A PHE 34 35 1 Y 1 A GLU 34 ? A GLU 35 36 1 Y 1 A GLU 35 ? A GLU 36 37 1 Y 1 A ILE 36 ? A ILE 37 38 1 Y 1 A ARG 37 ? A ARG 38 39 1 Y 1 A GLN 38 ? A GLN 39 40 1 Y 1 A ILE 39 ? A ILE 40 41 1 Y 1 A ALA 40 ? A ALA 41 42 1 Y 1 A ALA 41 ? A ALA 42 43 1 Y 1 A GLU 42 ? A GLU 43 44 1 Y 1 A MSE 43 ? A MSE 44 45 1 Y 1 A LEU 44 ? A LEU 45 46 1 Y 1 A VAL 45 ? A VAL 46 47 1 Y 1 A GLU 46 ? A GLU 47 48 1 Y 1 A PRO 47 ? A PRO 48 49 1 Y 1 A SER 48 ? A SER 49 50 1 Y 1 A GLY 49 ? A GLY 50 51 1 Y 1 A GLN 50 ? A GLN 51 52 1 Y 1 A PRO 51 ? A PRO 52 53 1 Y 1 A LEU 52 ? A LEU 53 54 1 Y 1 A GLU 53 ? A GLU 54 55 1 Y 1 A VAL 54 ? A VAL 55 56 1 Y 1 A VAL 55 ? A VAL 56 57 1 Y 1 A LYS 56 ? A LYS 57 58 1 Y 1 A ASP 57 ? A ASP 58 59 1 Y 1 A LEU 58 ? A LEU 59 60 1 Y 1 A PHE 59 ? A PHE 60 61 1 Y 1 A CYS 60 ? A CYS 61 62 1 Y 1 A ASN 61 ? A ASN 62 63 1 Y 1 A GLU 62 ? A GLU 63 64 1 Y 1 A THR 63 ? A THR 64 65 1 Y 1 A GLY 64 ? A GLY 65 66 1 Y 1 A TYR 65 ? A TYR 66 67 1 Y 1 A GLN 66 ? A GLN 67 68 1 Y 1 A ALA 138 ? A ALA 139 69 1 Y 1 A LYS 139 ? A LYS 140 70 1 Y 1 A SER 140 ? A SER 141 71 1 Y 1 A ALA 141 ? A ALA 142 72 1 Y 1 A HIS 142 ? A HIS 143 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 1,2-ETHANEDIOL EDO 3 'ACETATE ION' ACT 4 water HOH #