data_2WC9 # _entry.id 2WC9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.280 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2WC9 PDBE EBI-39013 WWPDB D_1290039013 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2WBN _pdbx_database_related.content_type unspecified _pdbx_database_related.details 'CRYSTAL STRUCTURE OF THE G2P (LARGE TERMINASE) NUCLEASE DOMAIN FROM THE BACTERIOPHAGE SPP1' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2WC9 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2009-03-10 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Smits, C.' 1 'Chechik, M.' 2 'Kovalevskiy, O.V.' 3 'Shevtsov, M.B.' 4 'Foster, A.W.' 5 'Alonso, J.C.' 6 'Antson, A.A.' 7 # _citation.id primary _citation.title 'Structural Basis for the Nuclease Activity of a Bacteriophage Large Terminase.' _citation.journal_abbrev 'Embo Rep.' _citation.journal_volume 10 _citation.page_first 592 _citation.page_last ? _citation.year 2009 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1469-221X _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19444313 _citation.pdbx_database_id_DOI 10.1038/EMBOR.2009.53 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Smits, C.' 1 primary 'Chechik, M.' 2 primary 'Kovalevskiy, O.V.' 3 primary 'Shevtsov, M.B.' 4 primary 'Foster, A.W.' 5 primary 'Alonso, J.C.' 6 primary 'Antson, A.A.' 7 # _cell.entry_id 2WC9 _cell.length_a 69.710 _cell.length_b 69.710 _cell.length_c 73.801 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2WC9 _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 # 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 'TERMINASE LARGE SUBUNIT' 24296.648 1 ? ? 'NUCLEASE DOMAIN, RESIDUES 232-422' ? 2 non-polymer syn 'MANGANESE (II) ION' 54.938 2 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 4 water nat water 18.015 24 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name G2P # _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 ;(MSE)GSSHHHHHHSSGLVPRGSH(MSE)ALGSGVVPFENLQIEEGIITDAEVARFDNIRQGLDFGYGPDPLAFVRWHYD KRKNRIYAIDELVDHKVSLKRTADFVRKNKYESARIIADSSEPRSIDALKLEHGINRIEGAKKGPDSVEHGERWLDELDA IVIDPLRTPNIAREFENIDYQTDKNGDPIPRLEDKDNHTIDATRYAFERD(MSE)KKGGVSLWG ; _entity_poly.pdbx_seq_one_letter_code_can ;MGSSHHHHHHSSGLVPRGSHMALGSGVVPFENLQIEEGIITDAEVARFDNIRQGLDFGYGPDPLAFVRWHYDKRKNRIYA IDELVDHKVSLKRTADFVRKNKYESARIIADSSEPRSIDALKLEHGINRIEGAKKGPDSVEHGERWLDELDAIVIDPLRT PNIAREFENIDYQTDKNGDPIPRLEDKDNHTIDATRYAFERDMKKGGVSLWG ; _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 MSE n 1 2 GLY n 1 3 SER n 1 4 SER n 1 5 HIS n 1 6 HIS n 1 7 HIS n 1 8 HIS n 1 9 HIS n 1 10 HIS n 1 11 SER n 1 12 SER n 1 13 GLY n 1 14 LEU n 1 15 VAL n 1 16 PRO n 1 17 ARG n 1 18 GLY n 1 19 SER n 1 20 HIS n 1 21 MSE n 1 22 ALA n 1 23 LEU n 1 24 GLY n 1 25 SER n 1 26 GLY n 1 27 VAL n 1 28 VAL n 1 29 PRO n 1 30 PHE n 1 31 GLU n 1 32 ASN n 1 33 LEU n 1 34 GLN n 1 35 ILE n 1 36 GLU n 1 37 GLU n 1 38 GLY n 1 39 ILE n 1 40 ILE n 1 41 THR n 1 42 ASP n 1 43 ALA n 1 44 GLU n 1 45 VAL n 1 46 ALA n 1 47 ARG n 1 48 PHE n 1 49 ASP n 1 50 ASN n 1 51 ILE n 1 52 ARG n 1 53 GLN n 1 54 GLY n 1 55 LEU n 1 56 ASP n 1 57 PHE n 1 58 GLY n 1 59 TYR n 1 60 GLY n 1 61 PRO n 1 62 ASP n 1 63 PRO n 1 64 LEU n 1 65 ALA n 1 66 PHE n 1 67 VAL n 1 68 ARG n 1 69 TRP n 1 70 HIS n 1 71 TYR n 1 72 ASP n 1 73 LYS n 1 74 ARG n 1 75 LYS n 1 76 ASN n 1 77 ARG n 1 78 ILE n 1 79 TYR n 1 80 ALA n 1 81 ILE n 1 82 ASP n 1 83 GLU n 1 84 LEU n 1 85 VAL n 1 86 ASP n 1 87 HIS n 1 88 LYS n 1 89 VAL n 1 90 SER n 1 91 LEU n 1 92 LYS n 1 93 ARG n 1 94 THR n 1 95 ALA n 1 96 ASP n 1 97 PHE n 1 98 VAL n 1 99 ARG n 1 100 LYS n 1 101 ASN n 1 102 LYS n 1 103 TYR n 1 104 GLU n 1 105 SER n 1 106 ALA n 1 107 ARG n 1 108 ILE n 1 109 ILE n 1 110 ALA n 1 111 ASP n 1 112 SER n 1 113 SER n 1 114 GLU n 1 115 PRO n 1 116 ARG n 1 117 SER n 1 118 ILE n 1 119 ASP n 1 120 ALA n 1 121 LEU n 1 122 LYS n 1 123 LEU n 1 124 GLU n 1 125 HIS n 1 126 GLY n 1 127 ILE n 1 128 ASN n 1 129 ARG n 1 130 ILE n 1 131 GLU n 1 132 GLY n 1 133 ALA n 1 134 LYS n 1 135 LYS n 1 136 GLY n 1 137 PRO n 1 138 ASP n 1 139 SER n 1 140 VAL n 1 141 GLU n 1 142 HIS n 1 143 GLY n 1 144 GLU n 1 145 ARG n 1 146 TRP n 1 147 LEU n 1 148 ASP n 1 149 GLU n 1 150 LEU n 1 151 ASP n 1 152 ALA n 1 153 ILE n 1 154 VAL n 1 155 ILE n 1 156 ASP n 1 157 PRO n 1 158 LEU n 1 159 ARG n 1 160 THR n 1 161 PRO n 1 162 ASN n 1 163 ILE n 1 164 ALA n 1 165 ARG n 1 166 GLU n 1 167 PHE n 1 168 GLU n 1 169 ASN n 1 170 ILE n 1 171 ASP n 1 172 TYR n 1 173 GLN n 1 174 THR n 1 175 ASP n 1 176 LYS n 1 177 ASN n 1 178 GLY n 1 179 ASP n 1 180 PRO n 1 181 ILE n 1 182 PRO n 1 183 ARG n 1 184 LEU n 1 185 GLU n 1 186 ASP n 1 187 LYS n 1 188 ASP n 1 189 ASN n 1 190 HIS n 1 191 THR n 1 192 ILE n 1 193 ASP n 1 194 ALA n 1 195 THR n 1 196 ARG n 1 197 TYR n 1 198 ALA n 1 199 PHE n 1 200 GLU n 1 201 ARG n 1 202 ASP n 1 203 MSE n 1 204 LYS n 1 205 LYS n 1 206 GLY n 1 207 GLY n 1 208 VAL n 1 209 SER n 1 210 LEU n 1 211 TRP n 1 212 GLY 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 'BACTERIOPHAGE SPP1' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _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 'BACILLUS PHAGE SPP1' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10724 _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 'B834 (DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector PET28A _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PYM20 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TERL_BPSPP _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P54308 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2WC9 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 22 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 212 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P54308 _struct_ref_seq.db_align_beg 232 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 422 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 232 _struct_ref_seq.pdbx_auth_seq_align_end 422 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 2WC9 MSE A 1 ? UNP P54308 ? ? 'expression tag' 211 1 1 2WC9 GLY A 2 ? UNP P54308 ? ? 'expression tag' 212 2 1 2WC9 SER A 3 ? UNP P54308 ? ? 'expression tag' 213 3 1 2WC9 SER A 4 ? UNP P54308 ? ? 'expression tag' 214 4 1 2WC9 HIS A 5 ? UNP P54308 ? ? 'expression tag' 215 5 1 2WC9 HIS A 6 ? UNP P54308 ? ? 'expression tag' 216 6 1 2WC9 HIS A 7 ? UNP P54308 ? ? 'expression tag' 217 7 1 2WC9 HIS A 8 ? UNP P54308 ? ? 'expression tag' 218 8 1 2WC9 HIS A 9 ? UNP P54308 ? ? 'expression tag' 219 9 1 2WC9 HIS A 10 ? UNP P54308 ? ? 'expression tag' 220 10 1 2WC9 SER A 11 ? UNP P54308 ? ? 'expression tag' 221 11 1 2WC9 SER A 12 ? UNP P54308 ? ? 'expression tag' 222 12 1 2WC9 GLY A 13 ? UNP P54308 ? ? 'expression tag' 223 13 1 2WC9 LEU A 14 ? UNP P54308 ? ? 'expression tag' 224 14 1 2WC9 VAL A 15 ? UNP P54308 ? ? 'expression tag' 225 15 1 2WC9 PRO A 16 ? UNP P54308 ? ? 'expression tag' 226 16 1 2WC9 ARG A 17 ? UNP P54308 ? ? 'expression tag' 227 17 1 2WC9 GLY A 18 ? UNP P54308 ? ? 'expression tag' 228 18 1 2WC9 SER A 19 ? UNP P54308 ? ? 'expression tag' 229 19 1 2WC9 HIS A 20 ? UNP P54308 ? ? 'expression tag' 230 20 1 2WC9 MSE A 21 ? UNP P54308 ? ? 'expression tag' 231 21 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 2WC9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.1 _exptl_crystal.density_percent_sol 42 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '80 MM TRIS PH 8.5, 2.3 M LI2SO4' # _diffrn.id 1 _diffrn.ambient_temp 120 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type ? _diffrn_detector.pdbx_collection_date 2008-09-20 _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU MICROMAX-007 HF' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2WC9 _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 60.40 _reflns.d_resolution_high 2.50 _reflns.number_obs 7520 _reflns.number_all ? _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 32.40 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.8 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.50 _reflns_shell.d_res_low 2.64 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.54 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.40 _reflns_shell.pdbx_redundancy 11.8 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2WC9 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 7142 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 24.60 _refine.ls_d_res_high 2.50 _refine.ls_percent_reflns_obs 100.00 _refine.ls_R_factor_obs 0.19781 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.19502 _refine.ls_R_factor_R_free 0.25862 _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 349 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.954 _refine.correlation_coeff_Fo_to_Fc_free 0.924 _refine.B_iso_mean 32.121 _refine.aniso_B[1][1] -0.21 _refine.aniso_B[2][2] -0.21 _refine.aniso_B[3][3] 0.31 _refine.aniso_B[1][2] -0.10 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH 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 NONE _refine.pdbx_method_to_determine_struct OTHER _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 0.546 _refine.pdbx_overall_ESU_R_Free 0.299 _refine.overall_SU_ML 0.211 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 21.218 _refine.overall_SU_R_Cruickshank_DPI ? _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 1450 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 7 _refine_hist.number_atoms_solvent 24 _refine_hist.number_atoms_total 1481 _refine_hist.d_res_high 2.50 _refine_hist.d_res_low 24.60 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.010 0.022 ? 1484 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 1043 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.217 1.958 ? 2007 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.814 3.000 ? 2517 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.501 5.000 ? 176 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 33.686 23.882 ? 85 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 14.216 15.000 ? 260 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 17.605 15.000 ? 16 'X-RAY DIFFRACTION' ? r_chiral_restr 0.069 0.200 ? 211 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.004 0.021 ? 1664 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 310 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.316 1.500 ? 884 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 0.624 2.000 ? 1432 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 1.075 3.000 ? 600 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 1.768 4.500 ? 575 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? '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 2.500 _refine_ls_shell.d_res_low 2.564 _refine_ls_shell.number_reflns_R_work 512 _refine_ls_shell.R_factor_R_work 0.278 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.276 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 21 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2WC9 _struct.title 'Crystal structure of the g2p (large terminase) nuclease domain from the bacteriophage SPP1 with bound Mn' _struct.pdbx_descriptor 'TERMINASE LARGE SUBUNIT' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2WC9 _struct_keywords.pdbx_keywords 'VIRAL PROTEIN' _struct_keywords.text 'VIRAL PROTEIN, DNA TRANSLOCATION' # 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 # 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 THR A 41 ? PHE A 48 ? THR A 251 PHE A 258 1 ? 8 HELX_P HELX_P2 2 SER A 90 ? ASN A 101 ? SER A 300 ASN A 311 1 ? 12 HELX_P HELX_P3 3 GLU A 114 ? GLU A 124 ? GLU A 324 GLU A 334 1 ? 11 HELX_P HELX_P4 4 SER A 139 ? GLU A 149 ? SER A 349 GLU A 359 1 ? 11 HELX_P HELX_P5 5 THR A 160 ? ILE A 170 ? THR A 370 ILE A 380 1 ? 11 HELX_P HELX_P6 6 ASN A 189 ? PHE A 199 ? ASN A 399 PHE A 409 1 ? 11 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A ASP 202 C ? ? ? 1_555 A MSE 203 N ? ? A ASP 412 A MSE 413 1_555 ? ? ? ? ? ? ? 1.340 ? metalc1 metalc ? ? C MN . MN ? ? ? 1_555 A ASP 56 OD1 ? ? A MN 1414 A ASP 266 1_555 ? ? ? ? ? ? ? 2.203 ? metalc2 metalc ? ? C MN . MN ? ? ? 1_555 A ASP 56 OD2 ? ? A MN 1414 A ASP 266 1_555 ? ? ? ? ? ? ? 1.892 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 7 ? AB ? 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 AA 1 2 ? parallel AA 2 3 ? parallel AA 3 4 ? anti-parallel AA 4 5 ? anti-parallel AA 5 6 ? parallel AA 6 7 ? parallel AB 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 AA 1 LEU A 33 ? ILE A 35 ? LEU A 243 ILE A 245 AA 2 ALA A 152 ? ILE A 155 ? ALA A 362 ILE A 365 AA 3 ARG A 77 ? ASP A 86 ? ARG A 287 ASP A 296 AA 4 LEU A 64 ? ASP A 72 ? LEU A 274 ASP A 282 AA 5 ILE A 51 ? ASP A 56 ? ILE A 261 ASP A 266 AA 6 ILE A 108 ? ALA A 110 ? ILE A 318 ALA A 320 AA 7 ILE A 130 ? GLY A 132 ? ILE A 340 GLY A 342 AB 1 TYR A 172 ? THR A 174 ? TYR A 382 THR A 384 AB 2 PRO A 180 ? LEU A 184 ? PRO A 390 LEU A 394 # 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 AA 1 2 N GLN A 34 ? N GLN A 244 O ILE A 153 ? O ILE A 363 AA 2 3 N VAL A 154 ? N VAL A 364 O ILE A 78 ? O ILE A 288 AA 3 4 N ASP A 86 ? N ASP A 296 O LEU A 64 ? O LEU A 274 AA 4 5 N TRP A 69 ? N TRP A 279 O ARG A 52 ? O ARG A 262 AA 5 6 N LEU A 55 ? N LEU A 265 O ILE A 109 ? O ILE A 319 AA 6 7 N ALA A 110 ? N ALA A 320 O GLU A 131 ? O GLU A 341 AB 1 2 O GLN A 173 ? O GLN A 383 N ILE A 181 ? N ILE A 391 # 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 ? ? ? ? 2 'BINDING SITE FOR RESIDUE MN A 1413' AC2 Software ? ? ? ? 2 'BINDING SITE FOR RESIDUE MN A 1414' AC3 Software ? ? ? ? 2 'BINDING SITE FOR RESIDUE SO4 A 1415' # 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 56 ? ASP A 266 . ? 1_555 ? 2 AC1 2 HIS A 190 ? HIS A 400 . ? 1_555 ? 3 AC2 2 ASP A 56 ? ASP A 266 . ? 1_555 ? 4 AC2 2 ASP A 111 ? ASP A 321 . ? 1_555 ? 5 AC3 2 ARG A 107 ? ARG A 317 . ? 1_555 ? 6 AC3 2 ARG A 201 ? ARG A 411 . ? 1_555 ? # _database_PDB_matrix.entry_id 2WC9 _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 2WC9 _atom_sites.fract_transf_matrix[1][1] 0.014345 _atom_sites.fract_transf_matrix[1][2] 0.008282 _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] 0.016564 _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] 0.013550 _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 MN N O S 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 MSE 1 211 ? ? ? A . n A 1 2 GLY 2 212 ? ? ? A . n A 1 3 SER 3 213 ? ? ? A . n A 1 4 SER 4 214 ? ? ? A . n A 1 5 HIS 5 215 ? ? ? A . n A 1 6 HIS 6 216 ? ? ? A . n A 1 7 HIS 7 217 ? ? ? A . n A 1 8 HIS 8 218 ? ? ? A . n A 1 9 HIS 9 219 ? ? ? A . n A 1 10 HIS 10 220 ? ? ? A . n A 1 11 SER 11 221 ? ? ? A . n A 1 12 SER 12 222 ? ? ? A . n A 1 13 GLY 13 223 ? ? ? A . n A 1 14 LEU 14 224 ? ? ? A . n A 1 15 VAL 15 225 ? ? ? A . n A 1 16 PRO 16 226 ? ? ? A . n A 1 17 ARG 17 227 ? ? ? A . n A 1 18 GLY 18 228 ? ? ? A . n A 1 19 SER 19 229 ? ? ? A . n A 1 20 HIS 20 230 ? ? ? A . n A 1 21 MSE 21 231 ? ? ? A . n A 1 22 ALA 22 232 ? ? ? A . n A 1 23 LEU 23 233 ? ? ? A . n A 1 24 GLY 24 234 ? ? ? A . n A 1 25 SER 25 235 ? ? ? A . n A 1 26 GLY 26 236 ? ? ? A . n A 1 27 VAL 27 237 237 VAL VAL A . n A 1 28 VAL 28 238 238 VAL VAL A . n A 1 29 PRO 29 239 239 PRO PRO A . n A 1 30 PHE 30 240 240 PHE PHE A . n A 1 31 GLU 31 241 241 GLU GLU A . n A 1 32 ASN 32 242 242 ASN ASN A . n A 1 33 LEU 33 243 243 LEU LEU A . n A 1 34 GLN 34 244 244 GLN GLN A . n A 1 35 ILE 35 245 245 ILE ILE A . n A 1 36 GLU 36 246 246 GLU GLU A . n A 1 37 GLU 37 247 247 GLU GLU A . n A 1 38 GLY 38 248 248 GLY GLY A . n A 1 39 ILE 39 249 249 ILE ILE A . n A 1 40 ILE 40 250 250 ILE ILE A . n A 1 41 THR 41 251 251 THR THR A . n A 1 42 ASP 42 252 252 ASP ASP A . n A 1 43 ALA 43 253 253 ALA ALA A . n A 1 44 GLU 44 254 254 GLU GLU A . n A 1 45 VAL 45 255 255 VAL VAL A . n A 1 46 ALA 46 256 256 ALA ALA A . n A 1 47 ARG 47 257 257 ARG ARG A . n A 1 48 PHE 48 258 258 PHE PHE A . n A 1 49 ASP 49 259 259 ASP ASP A . n A 1 50 ASN 50 260 260 ASN ASN A . n A 1 51 ILE 51 261 261 ILE ILE A . n A 1 52 ARG 52 262 262 ARG ARG A . n A 1 53 GLN 53 263 263 GLN GLN A . n A 1 54 GLY 54 264 264 GLY GLY A . n A 1 55 LEU 55 265 265 LEU LEU A . n A 1 56 ASP 56 266 266 ASP ASP A . n A 1 57 PHE 57 267 267 PHE PHE A . n A 1 58 GLY 58 268 268 GLY GLY A . n A 1 59 TYR 59 269 269 TYR TYR A . n A 1 60 GLY 60 270 270 GLY GLY A . n A 1 61 PRO 61 271 271 PRO PRO A . n A 1 62 ASP 62 272 272 ASP ASP A . n A 1 63 PRO 63 273 273 PRO PRO A . n A 1 64 LEU 64 274 274 LEU LEU A . n A 1 65 ALA 65 275 275 ALA ALA A . n A 1 66 PHE 66 276 276 PHE PHE A . n A 1 67 VAL 67 277 277 VAL VAL A . n A 1 68 ARG 68 278 278 ARG ARG A . n A 1 69 TRP 69 279 279 TRP TRP A . n A 1 70 HIS 70 280 280 HIS HIS A . n A 1 71 TYR 71 281 281 TYR TYR A . n A 1 72 ASP 72 282 282 ASP ASP A . n A 1 73 LYS 73 283 283 LYS LYS A . n A 1 74 ARG 74 284 284 ARG ARG A . n A 1 75 LYS 75 285 285 LYS LYS A . n A 1 76 ASN 76 286 286 ASN ASN A . n A 1 77 ARG 77 287 287 ARG ARG A . n A 1 78 ILE 78 288 288 ILE ILE A . n A 1 79 TYR 79 289 289 TYR TYR A . n A 1 80 ALA 80 290 290 ALA ALA A . n A 1 81 ILE 81 291 291 ILE ILE A . n A 1 82 ASP 82 292 292 ASP ASP A . n A 1 83 GLU 83 293 293 GLU GLU A . n A 1 84 LEU 84 294 294 LEU LEU A . n A 1 85 VAL 85 295 295 VAL VAL A . n A 1 86 ASP 86 296 296 ASP ASP A . n A 1 87 HIS 87 297 297 HIS HIS A . n A 1 88 LYS 88 298 298 LYS LYS A . n A 1 89 VAL 89 299 299 VAL VAL A . n A 1 90 SER 90 300 300 SER SER A . n A 1 91 LEU 91 301 301 LEU LEU A . n A 1 92 LYS 92 302 302 LYS LYS A . n A 1 93 ARG 93 303 303 ARG ARG A . n A 1 94 THR 94 304 304 THR THR A . n A 1 95 ALA 95 305 305 ALA ALA A . n A 1 96 ASP 96 306 306 ASP ASP A . n A 1 97 PHE 97 307 307 PHE PHE A . n A 1 98 VAL 98 308 308 VAL VAL A . n A 1 99 ARG 99 309 309 ARG ARG A . n A 1 100 LYS 100 310 310 LYS LYS A . n A 1 101 ASN 101 311 311 ASN ASN A . n A 1 102 LYS 102 312 312 LYS LYS A . n A 1 103 TYR 103 313 313 TYR TYR A . n A 1 104 GLU 104 314 314 GLU GLU A . n A 1 105 SER 105 315 315 SER SER A . n A 1 106 ALA 106 316 316 ALA ALA A . n A 1 107 ARG 107 317 317 ARG ARG A . n A 1 108 ILE 108 318 318 ILE ILE A . n A 1 109 ILE 109 319 319 ILE ILE A . n A 1 110 ALA 110 320 320 ALA ALA A . n A 1 111 ASP 111 321 321 ASP ASP A . n A 1 112 SER 112 322 322 SER SER A . n A 1 113 SER 113 323 323 SER SER A . n A 1 114 GLU 114 324 324 GLU GLU A . n A 1 115 PRO 115 325 325 PRO PRO A . n A 1 116 ARG 116 326 326 ARG ARG A . n A 1 117 SER 117 327 327 SER SER A . n A 1 118 ILE 118 328 328 ILE ILE A . n A 1 119 ASP 119 329 329 ASP ASP A . n A 1 120 ALA 120 330 330 ALA ALA A . n A 1 121 LEU 121 331 331 LEU LEU A . n A 1 122 LYS 122 332 332 LYS LYS A . n A 1 123 LEU 123 333 333 LEU LEU A . n A 1 124 GLU 124 334 334 GLU GLU A . n A 1 125 HIS 125 335 335 HIS HIS A . n A 1 126 GLY 126 336 336 GLY GLY A . n A 1 127 ILE 127 337 337 ILE ILE A . n A 1 128 ASN 128 338 338 ASN ASN A . n A 1 129 ARG 129 339 339 ARG ARG A . n A 1 130 ILE 130 340 340 ILE ILE A . n A 1 131 GLU 131 341 341 GLU GLU A . n A 1 132 GLY 132 342 342 GLY GLY A . n A 1 133 ALA 133 343 343 ALA ALA A . n A 1 134 LYS 134 344 344 LYS LYS A . n A 1 135 LYS 135 345 345 LYS LYS A . n A 1 136 GLY 136 346 346 GLY GLY A . n A 1 137 PRO 137 347 347 PRO PRO A . n A 1 138 ASP 138 348 348 ASP ASP A . n A 1 139 SER 139 349 349 SER SER A . n A 1 140 VAL 140 350 350 VAL VAL A . n A 1 141 GLU 141 351 351 GLU GLU A . n A 1 142 HIS 142 352 352 HIS HIS A . n A 1 143 GLY 143 353 353 GLY GLY A . n A 1 144 GLU 144 354 354 GLU GLU A . n A 1 145 ARG 145 355 355 ARG ARG A . n A 1 146 TRP 146 356 356 TRP TRP A . n A 1 147 LEU 147 357 357 LEU LEU A . n A 1 148 ASP 148 358 358 ASP ASP A . n A 1 149 GLU 149 359 359 GLU GLU A . n A 1 150 LEU 150 360 360 LEU LEU A . n A 1 151 ASP 151 361 361 ASP ASP A . n A 1 152 ALA 152 362 362 ALA ALA A . n A 1 153 ILE 153 363 363 ILE ILE A . n A 1 154 VAL 154 364 364 VAL VAL A . n A 1 155 ILE 155 365 365 ILE ILE A . n A 1 156 ASP 156 366 366 ASP ASP A . n A 1 157 PRO 157 367 367 PRO PRO A . n A 1 158 LEU 158 368 368 LEU LEU A . n A 1 159 ARG 159 369 369 ARG ARG A . n A 1 160 THR 160 370 370 THR THR A . n A 1 161 PRO 161 371 371 PRO PRO A . n A 1 162 ASN 162 372 372 ASN ASN A . n A 1 163 ILE 163 373 373 ILE ILE A . n A 1 164 ALA 164 374 374 ALA ALA A . n A 1 165 ARG 165 375 375 ARG ARG A . n A 1 166 GLU 166 376 376 GLU GLU A . n A 1 167 PHE 167 377 377 PHE PHE A . n A 1 168 GLU 168 378 378 GLU GLU A . n A 1 169 ASN 169 379 379 ASN ASN A . n A 1 170 ILE 170 380 380 ILE ILE A . n A 1 171 ASP 171 381 381 ASP ASP A . n A 1 172 TYR 172 382 382 TYR TYR A . n A 1 173 GLN 173 383 383 GLN GLN A . n A 1 174 THR 174 384 384 THR THR A . n A 1 175 ASP 175 385 385 ASP ASP A . n A 1 176 LYS 176 386 386 LYS LYS A . n A 1 177 ASN 177 387 387 ASN ASN A . n A 1 178 GLY 178 388 388 GLY GLY A . n A 1 179 ASP 179 389 389 ASP ASP A . n A 1 180 PRO 180 390 390 PRO PRO A . n A 1 181 ILE 181 391 391 ILE ILE A . n A 1 182 PRO 182 392 392 PRO PRO A . n A 1 183 ARG 183 393 393 ARG ARG A . n A 1 184 LEU 184 394 394 LEU LEU A . n A 1 185 GLU 185 395 395 GLU GLU A . n A 1 186 ASP 186 396 396 ASP ASP A . n A 1 187 LYS 187 397 397 LYS LYS A . n A 1 188 ASP 188 398 398 ASP ASP A . n A 1 189 ASN 189 399 399 ASN ASN A . n A 1 190 HIS 190 400 400 HIS HIS A . n A 1 191 THR 191 401 401 THR THR A . n A 1 192 ILE 192 402 402 ILE ILE A . n A 1 193 ASP 193 403 403 ASP ASP A . n A 1 194 ALA 194 404 404 ALA ALA A . n A 1 195 THR 195 405 405 THR THR A . n A 1 196 ARG 196 406 406 ARG ARG A . n A 1 197 TYR 197 407 407 TYR TYR A . n A 1 198 ALA 198 408 408 ALA ALA A . n A 1 199 PHE 199 409 409 PHE PHE A . n A 1 200 GLU 200 410 410 GLU GLU A . n A 1 201 ARG 201 411 411 ARG ARG A . n A 1 202 ASP 202 412 412 ASP ASP A . n A 1 203 MSE 203 413 413 MSE MSE A . n A 1 204 LYS 204 414 ? ? ? A . n A 1 205 LYS 205 415 ? ? ? A . n A 1 206 GLY 206 416 ? ? ? A . n A 1 207 GLY 207 417 ? ? ? A . n A 1 208 VAL 208 418 ? ? ? A . n A 1 209 SER 209 419 ? ? ? A . n A 1 210 LEU 210 420 ? ? ? A . n A 1 211 TRP 211 421 ? ? ? A . n A 1 212 GLY 212 422 ? ? ? 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 MN 1 1413 1413 MN MN A . C 2 MN 1 1414 1414 MN MN A . D 3 SO4 1 1415 1415 SO4 SO4 A . E 4 HOH 1 2001 2001 HOH HOH A . E 4 HOH 2 2002 2002 HOH HOH A . E 4 HOH 3 2003 2003 HOH HOH A . E 4 HOH 4 2004 2004 HOH HOH A . E 4 HOH 5 2005 2005 HOH HOH A . E 4 HOH 6 2006 2006 HOH HOH A . E 4 HOH 7 2007 2007 HOH HOH A . E 4 HOH 8 2008 2008 HOH HOH A . E 4 HOH 9 2009 2009 HOH HOH A . E 4 HOH 10 2010 2010 HOH HOH A . E 4 HOH 11 2011 2011 HOH HOH A . E 4 HOH 12 2012 2012 HOH HOH A . E 4 HOH 13 2013 2013 HOH HOH A . E 4 HOH 14 2014 2014 HOH HOH A . E 4 HOH 15 2015 2015 HOH HOH A . E 4 HOH 16 2016 2016 HOH HOH A . E 4 HOH 17 2017 2017 HOH HOH A . E 4 HOH 18 2018 2018 HOH HOH A . E 4 HOH 19 2019 2019 HOH HOH A . E 4 HOH 20 2020 2020 HOH HOH A . E 4 HOH 21 2021 2021 HOH HOH A . E 4 HOH 22 2022 2022 HOH HOH A . E 4 HOH 23 2023 2023 HOH HOH A . E 4 HOH 24 2024 2024 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id MSE _pdbx_struct_mod_residue.label_seq_id 203 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id MSE _pdbx_struct_mod_residue.auth_seq_id 413 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id MET _pdbx_struct_mod_residue.details SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 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_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id OD1 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id A _pdbx_struct_conn_angle.ptnr1_label_comp_id ASP _pdbx_struct_conn_angle.ptnr1_label_seq_id 56 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id ASP _pdbx_struct_conn_angle.ptnr1_auth_seq_id 266 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id MN _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id C _pdbx_struct_conn_angle.ptnr2_label_comp_id MN _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id MN _pdbx_struct_conn_angle.ptnr2_auth_seq_id 1414 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id OD2 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id A _pdbx_struct_conn_angle.ptnr3_label_comp_id ASP _pdbx_struct_conn_angle.ptnr3_label_seq_id 56 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id A _pdbx_struct_conn_angle.ptnr3_auth_comp_id ASP _pdbx_struct_conn_angle.ptnr3_auth_seq_id 266 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 64.5 _pdbx_struct_conn_angle.value_esd ? # 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 2009-03-24 2 'Structure model' 1 1 2011-06-23 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-06-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 4 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category diffrn_source # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 4 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_diffrn_source.type' # _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 15.2930 _pdbx_refine_tls.origin_y 26.7420 _pdbx_refine_tls.origin_z 21.8770 _pdbx_refine_tls.T[1][1] 0.2141 _pdbx_refine_tls.T[2][2] 0.1527 _pdbx_refine_tls.T[3][3] 0.0759 _pdbx_refine_tls.T[1][2] 0.1099 _pdbx_refine_tls.T[1][3] -0.0700 _pdbx_refine_tls.T[2][3] -0.0756 _pdbx_refine_tls.L[1][1] 2.3011 _pdbx_refine_tls.L[2][2] 7.5522 _pdbx_refine_tls.L[3][3] 3.8026 _pdbx_refine_tls.L[1][2] -1.1015 _pdbx_refine_tls.L[1][3] 0.8874 _pdbx_refine_tls.L[2][3] 0.5877 _pdbx_refine_tls.S[1][1] 0.0140 _pdbx_refine_tls.S[1][2] 0.1473 _pdbx_refine_tls.S[1][3] -0.0820 _pdbx_refine_tls.S[2][1] -0.7741 _pdbx_refine_tls.S[2][2] 0.0772 _pdbx_refine_tls.S[2][3] -0.1136 _pdbx_refine_tls.S[3][1] -0.0349 _pdbx_refine_tls.S[3][2] 0.1882 _pdbx_refine_tls.S[3][3] -0.0912 # _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 237 _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 414 _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.5.0082 ? 1 MOSFLM 'data reduction' . ? 2 SCALA 'data scaling' . ? 3 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 NH2 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 ARG _pdbx_validate_symm_contact.auth_seq_id_1 326 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 ILE _pdbx_validate_symm_contact.auth_seq_id_2 380 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 6_655 _pdbx_validate_symm_contact.dist 2.17 # 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 TYR A 269 ? ? -176.14 135.17 2 1 ASP A 321 ? ? -31.46 113.94 3 1 PRO A 347 ? ? -67.94 0.02 4 1 PRO A 392 ? ? -75.20 23.82 5 1 ASP A 396 ? ? -90.39 58.70 # 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 MSE 211 ? A MSE 1 2 1 Y 1 A GLY 212 ? A GLY 2 3 1 Y 1 A SER 213 ? A SER 3 4 1 Y 1 A SER 214 ? A SER 4 5 1 Y 1 A HIS 215 ? A HIS 5 6 1 Y 1 A HIS 216 ? A HIS 6 7 1 Y 1 A HIS 217 ? A HIS 7 8 1 Y 1 A HIS 218 ? A HIS 8 9 1 Y 1 A HIS 219 ? A HIS 9 10 1 Y 1 A HIS 220 ? A HIS 10 11 1 Y 1 A SER 221 ? A SER 11 12 1 Y 1 A SER 222 ? A SER 12 13 1 Y 1 A GLY 223 ? A GLY 13 14 1 Y 1 A LEU 224 ? A LEU 14 15 1 Y 1 A VAL 225 ? A VAL 15 16 1 Y 1 A PRO 226 ? A PRO 16 17 1 Y 1 A ARG 227 ? A ARG 17 18 1 Y 1 A GLY 228 ? A GLY 18 19 1 Y 1 A SER 229 ? A SER 19 20 1 Y 1 A HIS 230 ? A HIS 20 21 1 Y 1 A MSE 231 ? A MSE 21 22 1 Y 1 A ALA 232 ? A ALA 22 23 1 Y 1 A LEU 233 ? A LEU 23 24 1 Y 1 A GLY 234 ? A GLY 24 25 1 Y 1 A SER 235 ? A SER 25 26 1 Y 1 A GLY 236 ? A GLY 26 27 1 Y 1 A LYS 414 ? A LYS 204 28 1 Y 1 A LYS 415 ? A LYS 205 29 1 Y 1 A GLY 416 ? A GLY 206 30 1 Y 1 A GLY 417 ? A GLY 207 31 1 Y 1 A VAL 418 ? A VAL 208 32 1 Y 1 A SER 419 ? A SER 209 33 1 Y 1 A LEU 420 ? A LEU 210 34 1 Y 1 A TRP 421 ? A TRP 211 35 1 Y 1 A GLY 422 ? A GLY 212 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MANGANESE (II) ION' MN 3 'SULFATE ION' SO4 4 water HOH #