data_3WYZ # _entry.id 3WYZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3WYZ RCSB RCSB096969 WWPDB D_1000096969 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3WZ0 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3WYZ _pdbx_database_status.recvd_initial_deposition_date 2014-09-11 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Suematsu, K.' 1 'Ueda, T.' 2 'Nakashima, T.' 3 'Kakuta, Y.' 4 'Kimura, M.' 5 # _citation.id primary _citation.title 'On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis.' _citation.journal_abbrev Biosci.Biotechnol.Biochem. _citation.journal_volume 79 _citation.page_first 952 _citation.page_last 959 _citation.year 2015 _citation.journal_id_ASTM BBBIEJ _citation.country JA _citation.journal_id_ISSN 0916-8451 _citation.journal_id_CSD 2094 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25704799 _citation.pdbx_database_id_DOI 10.1080/09168451.2014.1003130 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Suematsu, K.' 1 primary 'Ueda, T.' 2 primary 'Nakashima, T.' 3 primary 'Kakuta, Y.' 4 primary 'Kimura, M.' 5 # _cell.entry_id 3WYZ _cell.length_a 40.610 _cell.length_b 58.725 _cell.length_c 43.280 _cell.angle_alpha 90.00 _cell.angle_beta 109.67 _cell.angle_gamma 90.00 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3WYZ _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _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 'Ribonuclease P protein component 3' 25306.330 1 3.1.26.5 ? ? ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 water nat water 18.015 39 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'RNase P component 3, Rpp30' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;MSEEEVSFSRDYFVEMDVRDEEAHELASDWFDEVVFTKKLVLEDPPDWGSLKEELKELRGKYGKVALLLVTRKPSLIREV KSRNLKALLYVQGGDMRINRMAIESGVDALISPWFGRKDPGFDHTLAGMAARRGVAIGFSLSPLLNANPYGRAQILRFMM KTWQLVKKYRVPRFITSSAESRWEVRGPRDLMSLGINIGMEIPEARASLNFYPRTIVWKL ; _entity_poly.pdbx_seq_one_letter_code_can ;MSEEEVSFSRDYFVEMDVRDEEAHELASDWFDEVVFTKKLVLEDPPDWGSLKEELKELRGKYGKVALLLVTRKPSLIREV KSRNLKALLYVQGGDMRINRMAIESGVDALISPWFGRKDPGFDHTLAGMAARRGVAIGFSLSPLLNANPYGRAQILRFMM KTWQLVKKYRVPRFITSSAESRWEVRGPRDLMSLGINIGMEIPEARASLNFYPRTIVWKL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 SER n 1 3 GLU n 1 4 GLU n 1 5 GLU n 1 6 VAL n 1 7 SER n 1 8 PHE n 1 9 SER n 1 10 ARG n 1 11 ASP n 1 12 TYR n 1 13 PHE n 1 14 VAL n 1 15 GLU n 1 16 MET n 1 17 ASP n 1 18 VAL n 1 19 ARG n 1 20 ASP n 1 21 GLU n 1 22 GLU n 1 23 ALA n 1 24 HIS n 1 25 GLU n 1 26 LEU n 1 27 ALA n 1 28 SER n 1 29 ASP n 1 30 TRP n 1 31 PHE n 1 32 ASP n 1 33 GLU n 1 34 VAL n 1 35 VAL n 1 36 PHE n 1 37 THR n 1 38 LYS n 1 39 LYS n 1 40 LEU n 1 41 VAL n 1 42 LEU n 1 43 GLU n 1 44 ASP n 1 45 PRO n 1 46 PRO n 1 47 ASP n 1 48 TRP n 1 49 GLY n 1 50 SER n 1 51 LEU n 1 52 LYS n 1 53 GLU n 1 54 GLU n 1 55 LEU n 1 56 LYS n 1 57 GLU n 1 58 LEU n 1 59 ARG n 1 60 GLY n 1 61 LYS n 1 62 TYR n 1 63 GLY n 1 64 LYS n 1 65 VAL n 1 66 ALA n 1 67 LEU n 1 68 LEU n 1 69 LEU n 1 70 VAL n 1 71 THR n 1 72 ARG n 1 73 LYS n 1 74 PRO n 1 75 SER n 1 76 LEU n 1 77 ILE n 1 78 ARG n 1 79 GLU n 1 80 VAL n 1 81 LYS n 1 82 SER n 1 83 ARG n 1 84 ASN n 1 85 LEU n 1 86 LYS n 1 87 ALA n 1 88 LEU n 1 89 LEU n 1 90 TYR n 1 91 VAL n 1 92 GLN n 1 93 GLY n 1 94 GLY n 1 95 ASP n 1 96 MET n 1 97 ARG n 1 98 ILE n 1 99 ASN n 1 100 ARG n 1 101 MET n 1 102 ALA n 1 103 ILE n 1 104 GLU n 1 105 SER n 1 106 GLY n 1 107 VAL n 1 108 ASP n 1 109 ALA n 1 110 LEU n 1 111 ILE n 1 112 SER n 1 113 PRO n 1 114 TRP n 1 115 PHE n 1 116 GLY n 1 117 ARG n 1 118 LYS n 1 119 ASP n 1 120 PRO n 1 121 GLY n 1 122 PHE n 1 123 ASP n 1 124 HIS n 1 125 THR n 1 126 LEU n 1 127 ALA n 1 128 GLY n 1 129 MET n 1 130 ALA n 1 131 ALA n 1 132 ARG n 1 133 ARG n 1 134 GLY n 1 135 VAL n 1 136 ALA n 1 137 ILE n 1 138 GLY n 1 139 PHE n 1 140 SER n 1 141 LEU n 1 142 SER n 1 143 PRO n 1 144 LEU n 1 145 LEU n 1 146 ASN n 1 147 ALA n 1 148 ASN n 1 149 PRO n 1 150 TYR n 1 151 GLY n 1 152 ARG n 1 153 ALA n 1 154 GLN n 1 155 ILE n 1 156 LEU n 1 157 ARG n 1 158 PHE n 1 159 MET n 1 160 MET n 1 161 LYS n 1 162 THR n 1 163 TRP n 1 164 GLN n 1 165 LEU n 1 166 VAL n 1 167 LYS n 1 168 LYS n 1 169 TYR n 1 170 ARG n 1 171 VAL n 1 172 PRO n 1 173 ARG n 1 174 PHE n 1 175 ILE n 1 176 THR n 1 177 SER n 1 178 SER n 1 179 ALA n 1 180 GLU n 1 181 SER n 1 182 ARG n 1 183 TRP n 1 184 GLU n 1 185 VAL n 1 186 ARG n 1 187 GLY n 1 188 PRO n 1 189 ARG n 1 190 ASP n 1 191 LEU n 1 192 MET n 1 193 SER n 1 194 LEU n 1 195 GLY n 1 196 ILE n 1 197 ASN n 1 198 ILE n 1 199 GLY n 1 200 MET n 1 201 GLU n 1 202 ILE n 1 203 PRO n 1 204 GLU n 1 205 ALA n 1 206 ARG n 1 207 ALA n 1 208 SER n 1 209 LEU n 1 210 ASN n 1 211 PHE n 1 212 TYR n 1 213 PRO n 1 214 ARG n 1 215 THR n 1 216 ILE n 1 217 VAL n 1 218 TRP n 1 219 LYS n 1 220 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 'rnp3, TK1450' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _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 'Thermococcus kodakarensis KOD1' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 69014 _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 ? _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 ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code RNP3_THEKO _struct_ref.pdbx_db_accession Q5JH47 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSEEEVSFSRDYFVEMDVRDEEAHELASDWFDEVVFTKKLVLEDPPDWGSLKEELKELRGKYGKVALLLVTRKPSLIREV KSRNLKALLYVQGGDMRINRMAIESGVDALISPWFGRKDPGFDHTLAGMAARRGVAIGFSLSPLLNANPYGRAQILRFMM KTWQLVKKYRVPRFITSSAESRWEVRGPRDLMSLGINIGMEIPEARASLNFYPRTIVWKL ; _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 3WYZ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 220 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q5JH47 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 220 _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 220 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3WYZ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.92 _exptl_crystal.density_percent_sol 35.95 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method Purification _exptl_crystal_grow.temp 283 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_details '50mM Tris-HCl (pH 7.5), 200mM NaCl, 10mM MgCl2, Purification, temperature 283K' _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 'RAYONIX MX300HE' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL44XU' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL44XU _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9 # _reflns.entry_id 3WYZ _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 50.0 _reflns.d_resolution_high 2.2 _reflns.number_obs 9422 _reflns.number_all 9422 _reflns.percent_possible_obs 96.8 _reflns.pdbx_Rmerge_I_obs 0.141 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 18.4 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.2 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.2 _reflns_shell.d_res_low 2.3 _reflns_shell.percent_possible_all 93.5 _reflns_shell.Rmerge_I_obs 0.917 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.7 _reflns_shell.pdbx_redundancy 3.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3WYZ _refine.ls_number_reflns_obs 8799 _refine.ls_number_reflns_all 8799 _refine.pdbx_ls_sigma_I 0.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 33.48 _refine.ls_d_res_high 2.21 _refine.ls_percent_reflns_obs 94.63 _refine.ls_R_factor_obs 0.22191 _refine.ls_R_factor_all 0.22191 _refine.ls_R_factor_R_work 0.21901 _refine.ls_R_factor_R_free 0.28136 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 431 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.953 _refine.correlation_coeff_Fo_to_Fc_free 0.925 _refine.B_iso_mean 56.060 _refine.aniso_B[1][1] -0.01 _refine.aniso_B[2][2] -0.04 _refine.aniso_B[3][3] 0.02 _refine.aniso_B[1][2] -0.00 _refine.aniso_B[1][3] 0.04 _refine.aniso_B[2][3] -0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.510 _refine.pdbx_overall_ESU_R_Free 0.288 _refine.overall_SU_ML 0.262 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 10.894 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1717 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 39 _refine_hist.number_atoms_total 1762 _refine_hist.d_res_high 2.21 _refine_hist.d_res_low 33.48 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.005 0.019 ? 1775 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.001 0.020 ? 1747 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 0.939 1.972 ? 2394 ? 'X-RAY DIFFRACTION' r_angle_other_deg 0.686 3.000 ? 4012 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 5.043 5.000 ? 215 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 30.083 22.099 ? 81 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 14.138 15.000 ? 326 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 13.973 15.000 ? 20 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.050 0.200 ? 255 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.004 0.021 ? 1960 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.001 0.020 ? 420 ? 'X-RAY DIFFRACTION' r_mcbond_it 1.971 5.355 ? 851 ? 'X-RAY DIFFRACTION' r_mcbond_other 1.971 5.354 ? 850 ? 'X-RAY DIFFRACTION' r_mcangle_it 3.268 8.024 ? 1063 ? 'X-RAY DIFFRACTION' r_mcangle_other 3.267 8.025 ? 1064 ? 'X-RAY DIFFRACTION' r_scbond_it 2.222 5.802 ? 924 ? 'X-RAY DIFFRACTION' r_scbond_other 2.222 5.802 ? 924 ? 'X-RAY DIFFRACTION' r_scangle_other 3.700 8.554 ? 1330 ? 'X-RAY DIFFRACTION' r_long_range_B_refined 7.223 50.702 ? 7366 ? 'X-RAY DIFFRACTION' r_long_range_B_other 7.223 50.698 ? 7365 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.206 _refine_ls_shell.d_res_low 2.263 _refine_ls_shell.number_reflns_R_work 580 _refine_ls_shell.R_factor_R_work 0.332 _refine_ls_shell.percent_reflns_obs 83.45 _refine_ls_shell.R_factor_R_free 0.235 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 25 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # _struct.entry_id 3WYZ _struct.title 'On archaeal homologs of the human RNase P protein Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis' _struct.pdbx_descriptor 'Ribonuclease P protein component 3 (E.C.3.1.26.5)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3WYZ _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'TIM barrel-like structure, pre-tRNA cleavage, RNA binding, HYDROLASE' # 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 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASP A 20 ? PHE A 31 ? ASP A 20 PHE A 31 1 ? 12 HELX_P HELX_P2 2 ASP A 47 ? GLY A 63 ? ASP A 47 GLY A 63 1 ? 17 HELX_P HELX_P3 3 LYS A 73 ? ASN A 84 ? LYS A 73 ASN A 84 1 ? 12 HELX_P HELX_P4 4 ASP A 95 ? SER A 105 ? ASP A 95 SER A 105 1 ? 11 HELX_P HELX_P5 5 ASP A 123 ? GLY A 134 ? ASP A 123 GLY A 134 1 ? 12 HELX_P HELX_P6 6 LEU A 141 ? ASN A 146 ? LEU A 141 ASN A 146 1 ? 6 HELX_P HELX_P7 7 ASN A 148 ? TYR A 169 ? ASN A 148 TYR A 169 1 ? 22 HELX_P HELX_P8 8 SER A 181 ? VAL A 185 ? SER A 181 VAL A 185 5 ? 5 HELX_P HELX_P9 9 GLY A 187 ? GLY A 199 ? GLY A 187 GLY A 199 1 ? 13 HELX_P HELX_P10 10 GLU A 201 ? ASN A 210 ? GLU A 201 ASN A 210 1 ? 10 HELX_P HELX_P11 11 ASN A 210 ? TRP A 218 ? ASN A 210 TRP A 218 1 ? 9 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GLU 43 A . ? GLU 43 A ASP 44 A ? ASP 44 A 1 3.75 2 PRO 46 A . ? PRO 46 A ASP 47 A ? ASP 47 A 1 9.11 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 7 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? parallel A 2 3 ? parallel A 3 4 ? parallel A 4 5 ? parallel A 5 6 ? parallel A 6 7 ? 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 VAL A 14 ? VAL A 18 ? VAL A 14 VAL A 18 A 2 GLU A 33 ? VAL A 41 ? GLU A 33 VAL A 41 A 3 VAL A 65 ? VAL A 70 ? VAL A 65 VAL A 70 A 4 LEU A 88 ? GLN A 92 ? LEU A 88 GLN A 92 A 5 ALA A 109 ? ILE A 111 ? ALA A 109 ILE A 111 A 6 ALA A 136 ? SER A 140 ? ALA A 136 SER A 140 A 7 ARG A 173 ? THR A 176 ? ARG A 173 THR A 176 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N VAL A 18 ? N VAL A 18 O THR A 37 ? O THR A 37 A 2 3 N LEU A 40 ? N LEU A 40 O LEU A 68 ? O LEU A 68 A 3 4 N LEU A 67 ? N LEU A 67 O LEU A 88 ? O LEU A 88 A 4 5 N VAL A 91 ? N VAL A 91 O ILE A 111 ? O ILE A 111 A 5 6 N LEU A 110 ? N LEU A 110 O GLY A 138 ? O GLY A 138 A 6 7 N PHE A 139 ? N PHE A 139 O PHE A 174 ? O PHE A 174 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _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 8 _struct_site.details 'BINDING SITE FOR RESIDUE GOL A 301' # 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 8 ARG A 19 ? ARG A 19 . ? 1_555 ? 2 AC1 8 GLN A 92 ? GLN A 92 . ? 1_555 ? 3 AC1 8 ILE A 111 ? ILE A 111 . ? 1_555 ? 4 AC1 8 SER A 112 ? SER A 112 . ? 1_555 ? 5 AC1 8 SER A 140 ? SER A 140 . ? 1_555 ? 6 AC1 8 SER A 142 ? SER A 142 . ? 1_555 ? 7 AC1 8 SER A 178 ? SER A 178 . ? 1_555 ? 8 AC1 8 HOH C . ? HOH A 402 . ? 1_555 ? # _database_PDB_matrix.entry_id 3WYZ _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3WYZ _atom_sites.fract_transf_matrix[1][1] 0.024624 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.008803 _atom_sites.fract_transf_matrix[2][1] -0.000000 _atom_sites.fract_transf_matrix[2][2] 0.017029 _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] 0.024537 _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 MET 1 1 ? ? ? A . n A 1 2 SER 2 2 ? ? ? A . n A 1 3 GLU 3 3 ? ? ? A . n A 1 4 GLU 4 4 ? ? ? A . n A 1 5 GLU 5 5 ? ? ? A . n A 1 6 VAL 6 6 ? ? ? A . n A 1 7 SER 7 7 ? ? ? A . n A 1 8 PHE 8 8 8 PHE PHE A . n A 1 9 SER 9 9 9 SER SER A . n A 1 10 ARG 10 10 10 ARG ARG A . n A 1 11 ASP 11 11 11 ASP ASP A . n A 1 12 TYR 12 12 12 TYR TYR A . n A 1 13 PHE 13 13 13 PHE PHE A . n A 1 14 VAL 14 14 14 VAL VAL A . n A 1 15 GLU 15 15 15 GLU GLU A . n A 1 16 MET 16 16 16 MET MET A . n A 1 17 ASP 17 17 17 ASP ASP A . n A 1 18 VAL 18 18 18 VAL VAL A . n A 1 19 ARG 19 19 19 ARG ARG A . n A 1 20 ASP 20 20 20 ASP ASP A . n A 1 21 GLU 21 21 21 GLU GLU A . n A 1 22 GLU 22 22 22 GLU GLU A . n A 1 23 ALA 23 23 23 ALA ALA A . n A 1 24 HIS 24 24 24 HIS HIS A . n A 1 25 GLU 25 25 25 GLU GLU A . n A 1 26 LEU 26 26 26 LEU LEU A . n A 1 27 ALA 27 27 27 ALA ALA A . n A 1 28 SER 28 28 28 SER SER A . n A 1 29 ASP 29 29 29 ASP ASP A . n A 1 30 TRP 30 30 30 TRP TRP A . n A 1 31 PHE 31 31 31 PHE PHE A . n A 1 32 ASP 32 32 32 ASP ASP A . n A 1 33 GLU 33 33 33 GLU GLU A . n A 1 34 VAL 34 34 34 VAL VAL A . n A 1 35 VAL 35 35 35 VAL VAL A . n A 1 36 PHE 36 36 36 PHE PHE A . n A 1 37 THR 37 37 37 THR THR A . n A 1 38 LYS 38 38 38 LYS LYS A . n A 1 39 LYS 39 39 39 LYS LYS A . n A 1 40 LEU 40 40 40 LEU LEU A . n A 1 41 VAL 41 41 41 VAL VAL A . n A 1 42 LEU 42 42 42 LEU LEU A . n A 1 43 GLU 43 43 43 GLU GLU A . n A 1 44 ASP 44 44 44 ASP ASP A . n A 1 45 PRO 45 45 45 PRO PRO A . n A 1 46 PRO 46 46 46 PRO PRO A . n A 1 47 ASP 47 47 47 ASP ASP A . n A 1 48 TRP 48 48 48 TRP TRP A . n A 1 49 GLY 49 49 49 GLY GLY A . n A 1 50 SER 50 50 50 SER SER A . n A 1 51 LEU 51 51 51 LEU LEU A . n A 1 52 LYS 52 52 52 LYS LYS A . n A 1 53 GLU 53 53 53 GLU GLU A . n A 1 54 GLU 54 54 54 GLU GLU A . n A 1 55 LEU 55 55 55 LEU LEU A . n A 1 56 LYS 56 56 56 LYS LYS A . n A 1 57 GLU 57 57 57 GLU GLU A . n A 1 58 LEU 58 58 58 LEU LEU A . n A 1 59 ARG 59 59 59 ARG ARG A . n A 1 60 GLY 60 60 60 GLY GLY A . n A 1 61 LYS 61 61 61 LYS LYS A . n A 1 62 TYR 62 62 62 TYR TYR A . n A 1 63 GLY 63 63 63 GLY GLY A . n A 1 64 LYS 64 64 64 LYS LYS A . n A 1 65 VAL 65 65 65 VAL VAL A . n A 1 66 ALA 66 66 66 ALA ALA A . n A 1 67 LEU 67 67 67 LEU LEU A . n A 1 68 LEU 68 68 68 LEU LEU A . n A 1 69 LEU 69 69 69 LEU LEU A . n A 1 70 VAL 70 70 70 VAL VAL A . n A 1 71 THR 71 71 71 THR THR A . n A 1 72 ARG 72 72 72 ARG ARG A . n A 1 73 LYS 73 73 73 LYS LYS A . n A 1 74 PRO 74 74 74 PRO PRO A . n A 1 75 SER 75 75 75 SER SER A . n A 1 76 LEU 76 76 76 LEU LEU A . n A 1 77 ILE 77 77 77 ILE ILE A . n A 1 78 ARG 78 78 78 ARG ARG A . n A 1 79 GLU 79 79 79 GLU GLU A . n A 1 80 VAL 80 80 80 VAL VAL A . n A 1 81 LYS 81 81 81 LYS LYS A . n A 1 82 SER 82 82 82 SER SER A . n A 1 83 ARG 83 83 83 ARG ARG A . n A 1 84 ASN 84 84 84 ASN ASN A . n A 1 85 LEU 85 85 85 LEU LEU A . n A 1 86 LYS 86 86 86 LYS LYS A . n A 1 87 ALA 87 87 87 ALA ALA A . n A 1 88 LEU 88 88 88 LEU LEU A . n A 1 89 LEU 89 89 89 LEU LEU A . n A 1 90 TYR 90 90 90 TYR TYR A . n A 1 91 VAL 91 91 91 VAL VAL A . n A 1 92 GLN 92 92 92 GLN GLN A . n A 1 93 GLY 93 93 93 GLY GLY A . n A 1 94 GLY 94 94 94 GLY GLY A . n A 1 95 ASP 95 95 95 ASP ASP A . n A 1 96 MET 96 96 96 MET MET A . n A 1 97 ARG 97 97 97 ARG ARG A . n A 1 98 ILE 98 98 98 ILE ILE A . n A 1 99 ASN 99 99 99 ASN ASN A . n A 1 100 ARG 100 100 100 ARG ARG A . n A 1 101 MET 101 101 101 MET MET A . n A 1 102 ALA 102 102 102 ALA ALA A . n A 1 103 ILE 103 103 103 ILE ILE A . n A 1 104 GLU 104 104 104 GLU GLU A . n A 1 105 SER 105 105 105 SER SER A . n A 1 106 GLY 106 106 106 GLY GLY A . n A 1 107 VAL 107 107 107 VAL VAL A . n A 1 108 ASP 108 108 108 ASP ASP A . n A 1 109 ALA 109 109 109 ALA ALA A . n A 1 110 LEU 110 110 110 LEU LEU A . n A 1 111 ILE 111 111 111 ILE ILE A . n A 1 112 SER 112 112 112 SER SER A . n A 1 113 PRO 113 113 113 PRO PRO A . n A 1 114 TRP 114 114 114 TRP TRP A . n A 1 115 PHE 115 115 115 PHE PHE A . n A 1 116 GLY 116 116 116 GLY GLY A . n A 1 117 ARG 117 117 117 ARG ARG A . n A 1 118 LYS 118 118 118 LYS LYS A . n A 1 119 ASP 119 119 119 ASP ASP A . n A 1 120 PRO 120 120 120 PRO PRO A . n A 1 121 GLY 121 121 121 GLY GLY A . n A 1 122 PHE 122 122 122 PHE PHE A . n A 1 123 ASP 123 123 123 ASP ASP A . n A 1 124 HIS 124 124 124 HIS HIS A . n A 1 125 THR 125 125 125 THR THR A . n A 1 126 LEU 126 126 126 LEU LEU A . n A 1 127 ALA 127 127 127 ALA ALA A . n A 1 128 GLY 128 128 128 GLY GLY A . n A 1 129 MET 129 129 129 MET MET A . n A 1 130 ALA 130 130 130 ALA ALA A . n A 1 131 ALA 131 131 131 ALA ALA A . n A 1 132 ARG 132 132 132 ARG ARG A . n A 1 133 ARG 133 133 133 ARG ARG A . n A 1 134 GLY 134 134 134 GLY GLY A . n A 1 135 VAL 135 135 135 VAL VAL A . n A 1 136 ALA 136 136 136 ALA ALA A . n A 1 137 ILE 137 137 137 ILE ILE A . n A 1 138 GLY 138 138 138 GLY GLY A . n A 1 139 PHE 139 139 139 PHE PHE A . n A 1 140 SER 140 140 140 SER SER A . n A 1 141 LEU 141 141 141 LEU LEU A . n A 1 142 SER 142 142 142 SER SER A . n A 1 143 PRO 143 143 143 PRO PRO A . n A 1 144 LEU 144 144 144 LEU LEU A . n A 1 145 LEU 145 145 145 LEU LEU A . n A 1 146 ASN 146 146 146 ASN ASN A . n A 1 147 ALA 147 147 147 ALA ALA A . n A 1 148 ASN 148 148 148 ASN ASN A . n A 1 149 PRO 149 149 149 PRO PRO A . n A 1 150 TYR 150 150 150 TYR TYR A . n A 1 151 GLY 151 151 151 GLY GLY A . n A 1 152 ARG 152 152 152 ARG ARG A . n A 1 153 ALA 153 153 153 ALA ALA A . n A 1 154 GLN 154 154 154 GLN GLN A . n A 1 155 ILE 155 155 155 ILE ILE A . n A 1 156 LEU 156 156 156 LEU LEU A . n A 1 157 ARG 157 157 157 ARG ARG A . n A 1 158 PHE 158 158 158 PHE PHE A . n A 1 159 MET 159 159 159 MET MET A . n A 1 160 MET 160 160 160 MET MET A . n A 1 161 LYS 161 161 161 LYS LYS A . n A 1 162 THR 162 162 162 THR THR A . n A 1 163 TRP 163 163 163 TRP TRP A . n A 1 164 GLN 164 164 164 GLN GLN A . n A 1 165 LEU 165 165 165 LEU LEU A . n A 1 166 VAL 166 166 166 VAL VAL A . n A 1 167 LYS 167 167 167 LYS LYS A . n A 1 168 LYS 168 168 168 LYS LYS A . n A 1 169 TYR 169 169 169 TYR TYR A . n A 1 170 ARG 170 170 170 ARG ARG A . n A 1 171 VAL 171 171 171 VAL VAL A . n A 1 172 PRO 172 172 172 PRO PRO A . n A 1 173 ARG 173 173 173 ARG ARG A . n A 1 174 PHE 174 174 174 PHE PHE A . n A 1 175 ILE 175 175 175 ILE ILE A . n A 1 176 THR 176 176 176 THR THR A . n A 1 177 SER 177 177 177 SER SER A . n A 1 178 SER 178 178 178 SER SER A . n A 1 179 ALA 179 179 179 ALA ALA A . n A 1 180 GLU 180 180 180 GLU GLU A . n A 1 181 SER 181 181 181 SER SER A . n A 1 182 ARG 182 182 182 ARG ARG A . n A 1 183 TRP 183 183 183 TRP TRP A . n A 1 184 GLU 184 184 184 GLU GLU A . n A 1 185 VAL 185 185 185 VAL VAL A . n A 1 186 ARG 186 186 186 ARG ARG A . n A 1 187 GLY 187 187 187 GLY GLY A . n A 1 188 PRO 188 188 188 PRO PRO A . n A 1 189 ARG 189 189 189 ARG ARG A . n A 1 190 ASP 190 190 190 ASP ASP A . n A 1 191 LEU 191 191 191 LEU LEU A . n A 1 192 MET 192 192 192 MET MET A . n A 1 193 SER 193 193 193 SER SER A . n A 1 194 LEU 194 194 194 LEU LEU A . n A 1 195 GLY 195 195 195 GLY GLY A . n A 1 196 ILE 196 196 196 ILE ILE A . n A 1 197 ASN 197 197 197 ASN ASN A . n A 1 198 ILE 198 198 198 ILE ILE A . n A 1 199 GLY 199 199 199 GLY GLY A . n A 1 200 MET 200 200 200 MET MET A . n A 1 201 GLU 201 201 201 GLU GLU A . n A 1 202 ILE 202 202 202 ILE ILE A . n A 1 203 PRO 203 203 203 PRO PRO A . n A 1 204 GLU 204 204 204 GLU GLU A . n A 1 205 ALA 205 205 205 ALA ALA A . n A 1 206 ARG 206 206 206 ARG ARG A . n A 1 207 ALA 207 207 207 ALA ALA A . n A 1 208 SER 208 208 208 SER SER A . n A 1 209 LEU 209 209 209 LEU LEU A . n A 1 210 ASN 210 210 210 ASN ASN A . n A 1 211 PHE 211 211 211 PHE PHE A . n A 1 212 TYR 212 212 212 TYR TYR A . n A 1 213 PRO 213 213 213 PRO PRO A . n A 1 214 ARG 214 214 214 ARG ARG A . n A 1 215 THR 215 215 215 THR THR A . n A 1 216 ILE 216 216 216 ILE ILE A . n A 1 217 VAL 217 217 217 VAL VAL A . n A 1 218 TRP 218 218 218 TRP TRP A . n A 1 219 LYS 219 219 219 LYS LYS A . n A 1 220 LEU 220 220 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 GOL 1 301 1 GOL GOL A . C 3 HOH 1 401 19 HOH HOH A . C 3 HOH 2 402 20 HOH HOH A . C 3 HOH 3 403 31 HOH HOH A . C 3 HOH 4 404 37 HOH HOH A . C 3 HOH 5 405 39 HOH HOH A . C 3 HOH 6 406 40 HOH HOH A . C 3 HOH 7 407 43 HOH HOH A . C 3 HOH 8 408 48 HOH HOH A . C 3 HOH 9 409 50 HOH HOH A . C 3 HOH 10 410 51 HOH HOH A . C 3 HOH 11 411 53 HOH HOH A . C 3 HOH 12 412 54 HOH HOH A . C 3 HOH 13 413 55 HOH HOH A . C 3 HOH 14 414 56 HOH HOH A . C 3 HOH 15 415 59 HOH HOH A . C 3 HOH 16 416 80 HOH HOH A . C 3 HOH 17 417 87 HOH HOH A . C 3 HOH 18 418 88 HOH HOH A . C 3 HOH 19 419 102 HOH HOH A . C 3 HOH 20 420 113 HOH HOH A . C 3 HOH 21 421 114 HOH HOH A . C 3 HOH 22 422 131 HOH HOH A . C 3 HOH 23 423 133 HOH HOH A . C 3 HOH 24 424 135 HOH HOH A . C 3 HOH 25 425 136 HOH HOH A . C 3 HOH 26 426 137 HOH HOH A . C 3 HOH 27 427 140 HOH HOH A . C 3 HOH 28 428 142 HOH HOH A . C 3 HOH 29 429 150 HOH HOH A . C 3 HOH 30 430 189 HOH HOH A . C 3 HOH 31 431 230 HOH HOH A . C 3 HOH 32 432 235 HOH HOH A . C 3 HOH 33 433 265 HOH HOH A . C 3 HOH 34 434 268 HOH HOH A . C 3 HOH 35 435 269 HOH HOH A . C 3 HOH 36 436 272 HOH HOH A . C 3 HOH 37 437 273 HOH HOH A . C 3 HOH 38 438 288 HOH HOH A . C 3 HOH 39 439 289 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 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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2015-09-16 2 'Structure model' 1 1 2017-11-22 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOLREP phasing . ? 1 REFMAC refinement 5.8.0049 ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASP A 11 ? ? -104.70 55.26 2 1 GLU A 43 ? ? -159.65 76.12 3 1 ASP A 44 ? ? -123.17 -105.64 4 1 ASP A 47 ? ? 78.99 31.02 5 1 ASN A 84 ? ? 55.66 72.61 6 1 SER A 112 ? ? 49.60 74.46 7 1 ASN A 146 ? ? -100.46 46.98 8 1 ASN A 210 ? ? -115.78 -75.91 # 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 MET 1 ? A MET 1 2 1 Y 1 A SER 2 ? A SER 2 3 1 Y 1 A GLU 3 ? A GLU 3 4 1 Y 1 A GLU 4 ? A GLU 4 5 1 Y 1 A GLU 5 ? A GLU 5 6 1 Y 1 A VAL 6 ? A VAL 6 7 1 Y 1 A SER 7 ? A SER 7 8 1 Y 1 A LEU 220 ? A LEU 220 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 water HOH #