data_1PAE # _entry.id 1PAE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.351 _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 1PAE pdb_00001pae 10.2210/pdb1pae/pdb RCSB RCSB019203 ? ? WWPDB D_1000019203 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1PAE _pdbx_database_status.recvd_initial_deposition_date 2003-05-14 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Strub, M.-P.' 1 'Hoh, F.' 2 'Sanchez, J.-F.' 3 'Strub, J.M.' 4 'Bock, A.' 5 'Aumelas, A.' 6 'Dumas, C.' 7 # loop_ _citation.id _citation.title _citation.journal_abbrev _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 _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Selenomethionine and Selenocysteine Double Labeling Strategy for Crystallographic Phasing' Structure 11 1359 1367 2003 STRUE6 UK 0969-2126 2005 ? 14604526 10.1016/j.str.2003.09.014 1 ;Structure of the cathelicidin motif of protegrin-3 precursor: structural insights into the activation mechanism of an antimicrobial protein. ; Structure 10 1363 1370 2002 STRUE6 UK 0969-2126 2005 ? ? '10.1016/S0969-2126(02)00859-6' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Strub, M.-P.' 1 ? primary 'Hoh, F.' 2 ? primary 'Sanchez, J.-F.' 3 ? primary 'Strub, J.M.' 4 ? primary 'Bock, A.' 5 ? primary 'Aumelas, A.' 6 ? primary 'Dumas, C.' 7 ? 1 'Sanchez, J.-F.' 8 ? 1 'Hoh, F.' 9 ? 1 'Strub, M.-P.' 10 ? 1 'Aumelas, A.' 11 ? 1 'Dumas, C.' 12 ? # _cell.entry_id 1PAE _cell.length_a 76.633 _cell.length_b 76.633 _cell.length_c 106.510 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PAE _symmetry.space_group_name_H-M 'P 63 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 # 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 'Nucleoside diphosphate kinase, cytosolic' 16968.912 1 2.7.4.6 H122C ? ? 2 non-polymer syn 'SELENIUM ATOM' 78.960 2 ? ? ? ? 3 water nat water 18.015 15 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'NDK, NDP kinase' # _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)STNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGP VVA(MSE)VFEGKGVVASARL(MSE)IGVTNPLASAPGSIRGDFGVDVGRNIIUGSDSVESANREIALWFKPEELLTEVK PNPNLYE ; _entity_poly.pdbx_seq_one_letter_code_can ;MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIUGSDSVESANREIALWFKPEELLTEVKPNPNLYE ; _entity_poly.pdbx_strand_id X _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 SER n 1 3 THR n 1 4 ASN n 1 5 LYS n 1 6 VAL n 1 7 ASN n 1 8 LYS n 1 9 GLU n 1 10 ARG n 1 11 THR n 1 12 PHE n 1 13 LEU n 1 14 ALA n 1 15 VAL n 1 16 LYS n 1 17 PRO n 1 18 ASP n 1 19 GLY n 1 20 VAL n 1 21 ALA n 1 22 ARG n 1 23 GLY n 1 24 LEU n 1 25 VAL n 1 26 GLY n 1 27 GLU n 1 28 ILE n 1 29 ILE n 1 30 ALA n 1 31 ARG n 1 32 TYR n 1 33 GLU n 1 34 LYS n 1 35 LYS n 1 36 GLY n 1 37 PHE n 1 38 VAL n 1 39 LEU n 1 40 VAL n 1 41 GLY n 1 42 LEU n 1 43 LYS n 1 44 GLN n 1 45 LEU n 1 46 VAL n 1 47 PRO n 1 48 THR n 1 49 LYS n 1 50 ASP n 1 51 LEU n 1 52 ALA n 1 53 GLU n 1 54 SER n 1 55 HIS n 1 56 TYR n 1 57 ALA n 1 58 GLU n 1 59 HIS n 1 60 LYS n 1 61 GLU n 1 62 ARG n 1 63 PRO n 1 64 PHE n 1 65 PHE n 1 66 GLY n 1 67 GLY n 1 68 LEU n 1 69 VAL n 1 70 SER n 1 71 PHE n 1 72 ILE n 1 73 THR n 1 74 SER n 1 75 GLY n 1 76 PRO n 1 77 VAL n 1 78 VAL n 1 79 ALA n 1 80 MSE n 1 81 VAL n 1 82 PHE n 1 83 GLU n 1 84 GLY n 1 85 LYS n 1 86 GLY n 1 87 VAL n 1 88 VAL n 1 89 ALA n 1 90 SER n 1 91 ALA n 1 92 ARG n 1 93 LEU n 1 94 MSE n 1 95 ILE n 1 96 GLY n 1 97 VAL n 1 98 THR n 1 99 ASN n 1 100 PRO n 1 101 LEU n 1 102 ALA n 1 103 SER n 1 104 ALA n 1 105 PRO n 1 106 GLY n 1 107 SER n 1 108 ILE n 1 109 ARG n 1 110 GLY n 1 111 ASP n 1 112 PHE n 1 113 GLY n 1 114 VAL n 1 115 ASP n 1 116 VAL n 1 117 GLY n 1 118 ARG n 1 119 ASN n 1 120 ILE n 1 121 ILE n 1 122 SEC n 1 123 GLY n 1 124 SER n 1 125 ASP n 1 126 SER n 1 127 VAL n 1 128 GLU n 1 129 SER n 1 130 ALA n 1 131 ASN n 1 132 ARG n 1 133 GLU n 1 134 ILE n 1 135 ALA n 1 136 LEU n 1 137 TRP n 1 138 PHE n 1 139 LYS n 1 140 PRO n 1 141 GLU n 1 142 GLU n 1 143 LEU n 1 144 LEU n 1 145 THR n 1 146 GLU n 1 147 VAL n 1 148 LYS n 1 149 PRO n 1 150 ASN n 1 151 PRO n 1 152 ASN n 1 153 LEU n 1 154 TYR n 1 155 GLU 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 Dictyostelium _entity_src_gen.pdbx_gene_src_gene ndk _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 'Dictyostelium discoideum' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 44689 _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 Escherichia _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 'BL21(DE3) selB::kan Cys51E' _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 pET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code NDKC_DICDI _struct_ref.pdbx_db_accession P22887 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE ; _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 1PAE _struct_ref_seq.pdbx_strand_id X _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 155 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P22887 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 155 _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 155 # 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 1PAE MSE X 1 ? UNP P22887 MET 1 'modified residue' 1 1 1 1PAE MSE X 80 ? UNP P22887 MET 80 'modified residue' 80 2 1 1PAE MSE X 94 ? UNP P22887 MET 94 'modified residue' 94 3 1 1PAE SEC X 122 ? UNP P22887 HIS 122 'engineered mutation' 122 4 # 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 SE non-polymer . 'SELENIUM ATOM' ? Se 78.960 SEC 'L-peptide linking' y SELENOCYSTEINE ? 'C3 H7 N O2 Se' 168.053 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 1PAE _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.66 _exptl_crystal.density_percent_sol 53.74 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_details 'PEG 6000, magnesium chloride,Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 293.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2003-03-15 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator mirrors _diffrn_radiation.pdbx_diffrn_protocol SAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9754 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'LURE BEAMLINE DW32' _diffrn_source.pdbx_synchrotron_site LURE _diffrn_source.pdbx_synchrotron_beamline DW32 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9754 # _reflns.entry_id 1PAE _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 2.70 _reflns.d_resolution_low 24.71 _reflns.number_all 5418 _reflns.number_obs 5418 _reflns.percent_possible_obs 98.4 _reflns.pdbx_Rmerge_I_obs 0.074 _reflns.pdbx_Rsym_value 0.074 _reflns.pdbx_netI_over_sigmaI 18.7 _reflns.B_iso_Wilson_estimate 40. _reflns.pdbx_redundancy 23.0 _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.70 _reflns_shell.d_res_low 2.77 _reflns_shell.percent_possible_all 97.4 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1PAE _refine.ls_number_reflns_obs 4823 _refine.ls_number_reflns_all 4823 _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 24.71 _refine.ls_d_res_high 2.70 _refine.ls_percent_reflns_obs 98.42 _refine.ls_R_factor_obs 0.18787 _refine.ls_R_factor_all 0.1878 _refine.ls_R_factor_R_work 0.18215 _refine.ls_R_factor_R_free 0.23216 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 11.0 _refine.ls_number_reflns_R_free 595 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.952 _refine.correlation_coeff_Fo_to_Fc_free 0.927 _refine.B_iso_mean 37.258 _refine.aniso_B[1][1] 1.14 _refine.aniso_B[2][2] 1.14 _refine.aniso_B[3][3] -1.72 _refine.aniso_B[1][2] 0.57 _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 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _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 0.486 _refine.pdbx_overall_ESU_R_Free 0.320 _refine.overall_SU_ML 0.220 _refine.overall_SU_B 10.980 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 1127 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 15 _refine_hist.number_atoms_total 1144 _refine_hist.d_res_high 2.70 _refine_hist.d_res_low 24.71 # 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 0.015 0.022 ? 1151 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 1089 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.544 1.979 ? 1555 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.958 3.000 ? 2530 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.445 5.000 ? 147 'X-RAY DIFFRACTION' ? r_chiral_restr 0.105 0.200 ? 175 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 1275 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.002 0.020 ? 232 'X-RAY DIFFRACTION' ? r_nbd_refined 0.196 0.200 ? 205 'X-RAY DIFFRACTION' ? r_nbd_other 0.226 0.200 ? 1141 'X-RAY DIFFRACTION' ? r_nbtor_other 0.094 0.200 ? 687 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.141 0.200 ? 22 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.065 0.200 ? 7 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.256 0.200 ? 32 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.076 0.200 ? 5 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.700 _refine_ls_shell.d_res_low 2.769 _refine_ls_shell.number_reflns_R_work 336 _refine_ls_shell.R_factor_R_work 0.277 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.375 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 39 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # _struct.entry_id 1PAE _struct.title 'nucleoside diphosphate kinase' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1PAE _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text 'selenocysteine selenomethionine, TRANSFERASE' # 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 ? # _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 LYS A 16 ? ARG A 22 ? LYS X 16 ARG X 22 1 ? 7 HELX_P HELX_P2 2 LEU A 24 ? GLY A 36 ? LEU X 24 GLY X 36 1 ? 13 HELX_P HELX_P3 3 THR A 48 ? TYR A 56 ? THR X 48 TYR X 56 1 ? 9 HELX_P HELX_P4 4 ALA A 57 ? LYS A 60 ? ALA X 57 LYS X 60 5 ? 4 HELX_P HELX_P5 5 PHE A 64 ? THR A 73 ? PHE X 64 THR X 73 1 ? 10 HELX_P HELX_P6 6 GLY A 86 ? GLY A 96 ? GLY X 86 GLY X 96 1 ? 11 HELX_P HELX_P7 7 ASN A 99 ? SER A 103 ? ASN X 99 SER X 103 5 ? 5 HELX_P HELX_P8 8 SER A 107 ? GLY A 113 ? SER X 107 GLY X 113 1 ? 7 HELX_P HELX_P9 9 ASP A 115 ? ASN A 119 ? ASP X 115 ASN X 119 5 ? 5 HELX_P HELX_P10 10 SER A 126 ? PHE A 138 ? SER X 126 PHE X 138 1 ? 13 HELX_P HELX_P11 11 LYS A 139 ? LEU A 143 ? LYS X 139 LEU X 143 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A ALA 79 C ? ? ? 1_555 A MSE 80 N ? ? X ALA 79 X MSE 80 1_555 ? ? ? ? ? ? ? 1.312 ? ? covale2 covale both ? A MSE 80 C ? ? ? 1_555 A VAL 81 N ? ? X MSE 80 X VAL 81 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale3 covale both ? A LEU 93 C ? ? ? 1_555 A MSE 94 N ? ? X LEU 93 X MSE 94 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale4 covale both ? A MSE 94 C ? ? ? 1_555 A ILE 95 N ? ? X MSE 94 X ILE 95 1_555 ? ? ? ? ? ? ? 1.333 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 4 _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 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 VAL A 38 ? LEU A 45 ? VAL X 38 LEU X 45 A 2 VAL A 77 ? GLU A 83 ? VAL X 77 GLU X 83 A 3 ARG A 10 ? VAL A 15 ? ARG X 10 VAL X 15 A 4 ILE A 121 ? GLY A 123 ? ILE X 121 GLY X 123 # 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 LYS A 43 ? N LYS X 43 O ALA A 79 ? O ALA X 79 A 2 3 O MSE A 80 ? O MSE X 80 N LEU A 13 ? N LEU X 13 A 3 4 N ALA A 14 ? N ALA X 14 O SEC A 122 ? O SEC X 122 # 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 X SE 156 ? 2 'BINDING SITE FOR RESIDUE SE X 156' AC2 Software X SE 157 ? 1 'BINDING SITE FOR RESIDUE SE X 157' # 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 SEC A 122 ? SEC X 122 . ? 1_555 ? 2 AC1 2 GLY A 123 ? GLY X 123 . ? 1_555 ? 3 AC2 1 SEC A 122 ? SEC X 122 . ? 1_555 ? # _database_PDB_matrix.entry_id 1PAE _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 1PAE _atom_sites.fract_transf_matrix[1][1] 0.013049 _atom_sites.fract_transf_matrix[1][2] 0.007534 _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] 0.015068 _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] 0.009389 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MSE 1 1 ? ? ? X . n A 1 2 SER 2 2 ? ? ? X . n A 1 3 THR 3 3 ? ? ? X . n A 1 4 ASN 4 4 ? ? ? X . n A 1 5 LYS 5 5 ? ? ? X . n A 1 6 VAL 6 6 ? ? ? X . n A 1 7 ASN 7 7 ? ? ? X . n A 1 8 LYS 8 8 8 LYS LYS X . n A 1 9 GLU 9 9 9 GLU GLU X . n A 1 10 ARG 10 10 10 ARG ARG X . n A 1 11 THR 11 11 11 THR THR X . n A 1 12 PHE 12 12 12 PHE PHE X . n A 1 13 LEU 13 13 13 LEU LEU X . n A 1 14 ALA 14 14 14 ALA ALA X . n A 1 15 VAL 15 15 15 VAL VAL X . n A 1 16 LYS 16 16 16 LYS LYS X . n A 1 17 PRO 17 17 17 PRO PRO X . n A 1 18 ASP 18 18 18 ASP ASP X . n A 1 19 GLY 19 19 19 GLY GLY X . n A 1 20 VAL 20 20 20 VAL VAL X . n A 1 21 ALA 21 21 21 ALA ALA X . n A 1 22 ARG 22 22 22 ARG ARG X . n A 1 23 GLY 23 23 23 GLY GLY X . n A 1 24 LEU 24 24 24 LEU LEU X . n A 1 25 VAL 25 25 25 VAL VAL X . n A 1 26 GLY 26 26 26 GLY GLY X . n A 1 27 GLU 27 27 27 GLU GLU X . n A 1 28 ILE 28 28 28 ILE ILE X . n A 1 29 ILE 29 29 29 ILE ILE X . n A 1 30 ALA 30 30 30 ALA ALA X . n A 1 31 ARG 31 31 31 ARG ARG X . n A 1 32 TYR 32 32 32 TYR TYR X . n A 1 33 GLU 33 33 33 GLU GLU X . n A 1 34 LYS 34 34 34 LYS LYS X . n A 1 35 LYS 35 35 35 LYS LYS X . n A 1 36 GLY 36 36 36 GLY GLY X . n A 1 37 PHE 37 37 37 PHE PHE X . n A 1 38 VAL 38 38 38 VAL VAL X . n A 1 39 LEU 39 39 39 LEU LEU X . n A 1 40 VAL 40 40 40 VAL VAL X . n A 1 41 GLY 41 41 41 GLY GLY X . n A 1 42 LEU 42 42 42 LEU LEU X . n A 1 43 LYS 43 43 43 LYS LYS X . n A 1 44 GLN 44 44 44 GLN GLN X . n A 1 45 LEU 45 45 45 LEU LEU X . n A 1 46 VAL 46 46 46 VAL VAL X . n A 1 47 PRO 47 47 47 PRO PRO X . n A 1 48 THR 48 48 48 THR THR X . n A 1 49 LYS 49 49 49 LYS LYS X . n A 1 50 ASP 50 50 50 ASP ASP X . n A 1 51 LEU 51 51 51 LEU LEU X . n A 1 52 ALA 52 52 52 ALA ALA X . n A 1 53 GLU 53 53 53 GLU GLU X . n A 1 54 SER 54 54 54 SER SER X . n A 1 55 HIS 55 55 55 HIS HIS X . n A 1 56 TYR 56 56 56 TYR TYR X . n A 1 57 ALA 57 57 57 ALA ALA X . n A 1 58 GLU 58 58 58 GLU GLU X . n A 1 59 HIS 59 59 59 HIS HIS X . n A 1 60 LYS 60 60 60 LYS LYS X . n A 1 61 GLU 61 61 61 GLU GLU X . n A 1 62 ARG 62 62 62 ARG ARG X . n A 1 63 PRO 63 63 63 PRO PRO X . n A 1 64 PHE 64 64 64 PHE PHE X . n A 1 65 PHE 65 65 65 PHE PHE X . n A 1 66 GLY 66 66 66 GLY GLY X . n A 1 67 GLY 67 67 67 GLY GLY X . n A 1 68 LEU 68 68 68 LEU LEU X . n A 1 69 VAL 69 69 69 VAL VAL X . n A 1 70 SER 70 70 70 SER SER X . n A 1 71 PHE 71 71 71 PHE PHE X . n A 1 72 ILE 72 72 72 ILE ILE X . n A 1 73 THR 73 73 73 THR THR X . n A 1 74 SER 74 74 74 SER SER X . n A 1 75 GLY 75 75 75 GLY GLY X . n A 1 76 PRO 76 76 76 PRO PRO X . n A 1 77 VAL 77 77 77 VAL VAL X . n A 1 78 VAL 78 78 78 VAL VAL X . n A 1 79 ALA 79 79 79 ALA ALA X . n A 1 80 MSE 80 80 80 MSE MSE X . n A 1 81 VAL 81 81 81 VAL VAL X . n A 1 82 PHE 82 82 82 PHE PHE X . n A 1 83 GLU 83 83 83 GLU GLU X . n A 1 84 GLY 84 84 84 GLY GLY X . n A 1 85 LYS 85 85 85 LYS LYS X . n A 1 86 GLY 86 86 86 GLY GLY X . n A 1 87 VAL 87 87 87 VAL VAL X . n A 1 88 VAL 88 88 88 VAL VAL X . n A 1 89 ALA 89 89 89 ALA ALA X . n A 1 90 SER 90 90 90 SER SER X . n A 1 91 ALA 91 91 91 ALA ALA X . n A 1 92 ARG 92 92 92 ARG ARG X . n A 1 93 LEU 93 93 93 LEU LEU X . n A 1 94 MSE 94 94 94 MSE MSE X . n A 1 95 ILE 95 95 95 ILE ILE X . n A 1 96 GLY 96 96 96 GLY GLY X . n A 1 97 VAL 97 97 97 VAL VAL X . n A 1 98 THR 98 98 98 THR THR X . n A 1 99 ASN 99 99 99 ASN ASN X . n A 1 100 PRO 100 100 100 PRO PRO X . n A 1 101 LEU 101 101 101 LEU LEU X . n A 1 102 ALA 102 102 102 ALA ALA X . n A 1 103 SER 103 103 103 SER SER X . n A 1 104 ALA 104 104 104 ALA ALA X . n A 1 105 PRO 105 105 105 PRO PRO X . n A 1 106 GLY 106 106 106 GLY GLY X . n A 1 107 SER 107 107 107 SER SER X . n A 1 108 ILE 108 108 108 ILE ILE X . n A 1 109 ARG 109 109 109 ARG ARG X . n A 1 110 GLY 110 110 110 GLY GLY X . n A 1 111 ASP 111 111 111 ASP ASP X . n A 1 112 PHE 112 112 112 PHE PHE X . n A 1 113 GLY 113 113 113 GLY GLY X . n A 1 114 VAL 114 114 114 VAL VAL X . n A 1 115 ASP 115 115 115 ASP ASP X . n A 1 116 VAL 116 116 116 VAL VAL X . n A 1 117 GLY 117 117 117 GLY GLY X . n A 1 118 ARG 118 118 118 ARG ARG X . n A 1 119 ASN 119 119 119 ASN ASN X . n A 1 120 ILE 120 120 120 ILE ILE X . n A 1 121 ILE 121 121 121 ILE ILE X . n A 1 122 SEC 122 122 122 SEC SEC X . n A 1 123 GLY 123 123 123 GLY GLY X . n A 1 124 SER 124 124 124 SER SER X . n A 1 125 ASP 125 125 125 ASP ASP X . n A 1 126 SER 126 126 126 SER SER X . n A 1 127 VAL 127 127 127 VAL VAL X . n A 1 128 GLU 128 128 128 GLU GLU X . n A 1 129 SER 129 129 129 SER SER X . n A 1 130 ALA 130 130 130 ALA ALA X . n A 1 131 ASN 131 131 131 ASN ASN X . n A 1 132 ARG 132 132 132 ARG ARG X . n A 1 133 GLU 133 133 133 GLU GLU X . n A 1 134 ILE 134 134 134 ILE ILE X . n A 1 135 ALA 135 135 135 ALA ALA X . n A 1 136 LEU 136 136 136 LEU LEU X . n A 1 137 TRP 137 137 137 TRP TRP X . n A 1 138 PHE 138 138 138 PHE PHE X . n A 1 139 LYS 139 139 139 LYS LYS X . n A 1 140 PRO 140 140 140 PRO PRO X . n A 1 141 GLU 141 141 141 GLU GLU X . n A 1 142 GLU 142 142 142 GLU GLU X . n A 1 143 LEU 143 143 143 LEU LEU X . n A 1 144 LEU 144 144 144 LEU LEU X . n A 1 145 THR 145 145 145 THR THR X . n A 1 146 GLU 146 146 146 GLU GLU X . n A 1 147 VAL 147 147 147 VAL VAL X . n A 1 148 LYS 148 148 148 LYS LYS X . n A 1 149 PRO 149 149 149 PRO PRO X . n A 1 150 ASN 150 150 150 ASN ASN X . n A 1 151 PRO 151 151 151 PRO PRO X . n A 1 152 ASN 152 152 152 ASN ASN X . n A 1 153 LEU 153 153 153 LEU LEU X . n A 1 154 TYR 154 154 154 TYR TYR X . n A 1 155 GLU 155 155 155 GLU GLU X . 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 SE 1 156 121 SE SE X . C 2 SE 1 157 123 SE SE X . D 3 HOH 1 158 1 HOH HOH X . D 3 HOH 2 159 2 HOH HOH X . D 3 HOH 3 160 3 HOH HOH X . D 3 HOH 4 161 4 HOH HOH X . D 3 HOH 5 162 5 HOH HOH X . D 3 HOH 6 163 6 HOH HOH X . D 3 HOH 7 164 7 HOH HOH X . D 3 HOH 8 165 8 HOH HOH X . D 3 HOH 9 166 9 HOH HOH X . D 3 HOH 10 167 10 HOH HOH X . D 3 HOH 11 168 11 HOH HOH X . D 3 HOH 12 169 12 HOH HOH X . D 3 HOH 13 170 13 HOH HOH X . D 3 HOH 14 171 14 HOH HOH X . D 3 HOH 15 172 15 HOH HOH X . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 80 X MSE 80 ? MET SELENOMETHIONINE 2 A MSE 94 X MSE 94 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # 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)' 14810 ? 1 MORE -115 ? 1 'SSA (A^2)' 36410 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5000000000 -0.8660254038 0.0000000000 38.3165000000 0.8660254038 -0.5000000000 0.0000000000 66.3661247682 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5000000000 0.8660254038 0.0000000000 -38.3165000000 -0.8660254038 -0.5000000000 0.0000000000 66.3661247682 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5000000000 -0.8660254038 0.0000000000 38.3165000000 -0.8660254038 -0.5000000000 0.0000000000 66.3661247682 0.0000000000 0.0000000000 -1.0000000000 53.2550000000 5 'crystal symmetry operation' 11_555 -x+y,y,-z+1/2 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 53.2550000000 6 'crystal symmetry operation' 12_565 x,x-y+1,-z+1/2 0.5000000000 0.8660254038 0.0000000000 -38.3165000000 0.8660254038 -0.5000000000 0.0000000000 66.3661247682 0.0000000000 0.0000000000 -1.0000000000 53.2550000000 # 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 2003-11-11 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2014-02-19 5 'Structure model' 1 4 2014-08-06 6 'Structure model' 1 5 2021-10-27 # _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' 'Derived calculations' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Atomic model' 5 4 'Structure model' 'Structure summary' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' 'Structure summary' 8 6 'Structure model' 'Database references' 9 6 '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 6 'Structure model' database_2 2 6 'Structure model' struct_conn 3 6 'Structure model' struct_ref_seq_dif 4 6 '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 6 'Structure model' '_database_2.pdbx_DOI' 2 6 'Structure model' '_database_2.pdbx_database_accession' 3 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 6 'Structure model' '_struct_ref_seq_dif.details' 5 6 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 6 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 6 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.24 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 SHARP phasing . ? 4 # _pdbx_database_remark.id 600 _pdbx_database_remark.text ;HETEROGEN THE HETATM ENTRY SE 121 CORRESPONDS TO A SELENOCYSTEINE ADDUCT TO SEC 122 (NOT VISIBLE IN THE ELECTRON DENSITY MAP EXCEPT SELENIUM ATOM) WITH A DISELENIDE BRIDGE BETWEEN SE 121 AND SE SEC X 122 ; # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE X ARG 31 ? ? CZ X ARG 31 ? ? NH1 X ARG 31 ? ? 123.71 120.30 3.41 0.50 N 2 1 NE X ARG 109 ? ? CZ X ARG 109 ? ? NH1 X ARG 109 ? ? 123.57 120.30 3.27 0.50 N # 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 X 56 ? ? -103.52 42.02 2 1 ILE X 120 ? ? 78.86 -55.67 3 1 ASN X 150 ? ? -28.42 125.24 # 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 X MSE 1 ? A MSE 1 2 1 Y 1 X SER 2 ? A SER 2 3 1 Y 1 X THR 3 ? A THR 3 4 1 Y 1 X ASN 4 ? A ASN 4 5 1 Y 1 X LYS 5 ? A LYS 5 6 1 Y 1 X VAL 6 ? A VAL 6 7 1 Y 1 X ASN 7 ? A ASN 7 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SELENIUM ATOM' SE 3 water HOH #