data_4GEN # _entry.id 4GEN # _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 4GEN RCSB RCSB074087 WWPDB D_1000074087 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4GEL . unspecified PDB 4GEM . unspecified # _pdbx_database_status.entry_id 4GEN _pdbx_database_status.status_code REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2012-08-02 _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 'Nishimasu, H.' 1 'Fukuhara, S.' 2 'Ishitani, R.' 3 'Nureki, O.' 4 # _citation.id primary _citation.title 'Structure and function of Zucchini endoribonuclease in piRNA biogenesis' _citation.journal_abbrev Nature _citation.journal_volume 491 _citation.page_first 284 _citation.page_last 287 _citation.year 2012 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23064230 _citation.pdbx_database_id_DOI 10.1038/nature11509 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Nishimasu, H.' 1 primary 'Ishizu, H.' 2 primary 'Saito, K.' 3 primary 'Fukuhara, S.' 4 primary 'Kamatani, M.K.' 5 primary 'Bonnefond, L.' 6 primary 'Matsumoto, N.' 7 primary 'Nishizawa, T.' 8 primary 'Nakanaga, K.' 9 primary 'Aoki, J.' 10 primary 'Ishitani, R.' 11 primary 'Siomi, H.' 12 primary 'Siomi, M.C.' 13 primary 'Nureki, O.' 14 # _cell.length_a 35.277 _cell.length_b 52.396 _cell.length_c 38.791 _cell.angle_alpha 90.000 _cell.angle_beta 104.940 _cell.angle_gamma 90.000 _cell.entry_id 4GEN _cell.pdbx_unique_axis ? _cell.Z_PDB 2 _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.space_group_name_H-M 'P 1 21 1' _symmetry.entry_id 4GEN _symmetry.Int_Tables_number 4 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Mitochondrial cardiolipin hydrolase' 19348.615 1 3.1.4.- ? 'DmZuc UNP residues 89-250' ? 2 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 3 water nat water 18.015 16 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Mitochondrial phospholipase homolog, MitoPLD, Protein zucchini' # _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 ;GPGH(MSE)ELSLRNVAKIVEQIDRAVYSIDLAIYTFTSLFLADSIKRALQRGVIIRIISDGE(MSE)VYSKGSQIS (MSE)LAQLGVPVRVPITTNL(MSE)HNKFCIIDGFERVEEIRLLRKLKF(MSE)RPCYSIVISGSVNWTALGLGGNWEN CIITADDKLTATFQAEFQR(MSE)WRAFAKTEGSQI ; _entity_poly.pdbx_seq_one_letter_code_can ;GPGHMELSLRNVAKIVEQIDRAVYSIDLAIYTFTSLFLADSIKRALQRGVIIRIISDGEMVYSKGSQISMLAQLGVPVRV PITTNLMHNKFCIIDGFERVEEIRLLRKLKFMRPCYSIVISGSVNWTALGLGGNWENCIITADDKLTATFQAEFQRMWRA FAKTEGSQI ; _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 GLY n 1 2 PRO n 1 3 GLY n 1 4 HIS n 1 5 MSE n 1 6 GLU n 1 7 LEU n 1 8 SER n 1 9 LEU n 1 10 ARG n 1 11 ASN n 1 12 VAL n 1 13 ALA n 1 14 LYS n 1 15 ILE n 1 16 VAL n 1 17 GLU n 1 18 GLN n 1 19 ILE n 1 20 ASP n 1 21 ARG n 1 22 ALA n 1 23 VAL n 1 24 TYR n 1 25 SER n 1 26 ILE n 1 27 ASP n 1 28 LEU n 1 29 ALA n 1 30 ILE n 1 31 TYR n 1 32 THR n 1 33 PHE n 1 34 THR n 1 35 SER n 1 36 LEU n 1 37 PHE n 1 38 LEU n 1 39 ALA n 1 40 ASP n 1 41 SER n 1 42 ILE n 1 43 LYS n 1 44 ARG n 1 45 ALA n 1 46 LEU n 1 47 GLN n 1 48 ARG n 1 49 GLY n 1 50 VAL n 1 51 ILE n 1 52 ILE n 1 53 ARG n 1 54 ILE n 1 55 ILE n 1 56 SER n 1 57 ASP n 1 58 GLY n 1 59 GLU n 1 60 MSE n 1 61 VAL n 1 62 TYR n 1 63 SER n 1 64 LYS n 1 65 GLY n 1 66 SER n 1 67 GLN n 1 68 ILE n 1 69 SER n 1 70 MSE n 1 71 LEU n 1 72 ALA n 1 73 GLN n 1 74 LEU n 1 75 GLY n 1 76 VAL n 1 77 PRO n 1 78 VAL n 1 79 ARG n 1 80 VAL n 1 81 PRO n 1 82 ILE n 1 83 THR n 1 84 THR n 1 85 ASN n 1 86 LEU n 1 87 MSE n 1 88 HIS n 1 89 ASN n 1 90 LYS n 1 91 PHE n 1 92 CYS n 1 93 ILE n 1 94 ILE n 1 95 ASP n 1 96 GLY n 1 97 PHE n 1 98 GLU n 1 99 ARG n 1 100 VAL n 1 101 GLU n 1 102 GLU n 1 103 ILE n 1 104 ARG n 1 105 LEU n 1 106 LEU n 1 107 ARG n 1 108 LYS n 1 109 LEU n 1 110 LYS n 1 111 PHE n 1 112 MSE n 1 113 ARG n 1 114 PRO n 1 115 CYS n 1 116 TYR n 1 117 SER n 1 118 ILE n 1 119 VAL n 1 120 ILE n 1 121 SER n 1 122 GLY n 1 123 SER n 1 124 VAL n 1 125 ASN n 1 126 TRP n 1 127 THR n 1 128 ALA n 1 129 LEU n 1 130 GLY n 1 131 LEU n 1 132 GLY n 1 133 GLY n 1 134 ASN n 1 135 TRP n 1 136 GLU n 1 137 ASN n 1 138 CYS n 1 139 ILE n 1 140 ILE n 1 141 THR n 1 142 ALA n 1 143 ASP n 1 144 ASP n 1 145 LYS n 1 146 LEU n 1 147 THR n 1 148 ALA n 1 149 THR n 1 150 PHE n 1 151 GLN n 1 152 ALA n 1 153 GLU n 1 154 PHE n 1 155 GLN n 1 156 ARG n 1 157 MSE n 1 158 TRP n 1 159 ARG n 1 160 ALA n 1 161 PHE n 1 162 ALA n 1 163 LYS n 1 164 THR n 1 165 GLU n 1 166 GLY n 1 167 SER n 1 168 GLN n 1 169 ILE 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 'Fruit fly' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'zuc, CG12314' _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 'Drosophila melanogaster' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 7227 _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 'Rosetta2(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 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 pCold-GST _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code ZUC_DROME _struct_ref.pdbx_db_accession Q9VKD7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;SLRNVAKIVEQIDRAVYSIDLAIYTFTSLFLADSIKRALQRGVIIRIISDGEMVYSKGSQISMLAQLGVPVRVPITTNLM HNKFCIIDGFERVEEIRLLRKLKFMRPCYSIVISGSVNWTALGLGGNWENCIITADDKLTATFQAEFQRMWRAFAKTEGS QI ; _struct_ref.pdbx_align_begin 89 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4GEN _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 8 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 169 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9VKD7 _struct_ref_seq.db_align_beg 89 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 250 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 89 _struct_ref_seq.pdbx_auth_seq_align_end 250 # 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 4GEN GLY A 1 ? UNP Q9VKD7 ? ? 'EXPRESSION TAG' 82 1 1 4GEN PRO A 2 ? UNP Q9VKD7 ? ? 'EXPRESSION TAG' 83 2 1 4GEN GLY A 3 ? UNP Q9VKD7 ? ? 'EXPRESSION TAG' 84 3 1 4GEN HIS A 4 ? UNP Q9VKD7 ? ? 'EXPRESSION TAG' 85 4 1 4GEN MSE A 5 ? UNP Q9VKD7 ? ? 'EXPRESSION TAG' 86 5 1 4GEN GLU A 6 ? UNP Q9VKD7 ? ? 'EXPRESSION TAG' 87 6 1 4GEN LEU A 7 ? UNP Q9VKD7 ? ? 'EXPRESSION TAG' 88 7 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 4GEN _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity 0.871 _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 1.8 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 31.29 _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.pH ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.pdbx_details 'vapor diffusion' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector ? _diffrn_detector.type ? _diffrn_detector.pdbx_collection_date 2011-12-07 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9793 1.0 2 0.9800 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL32XU' _diffrn_source.pdbx_wavelength_list '0.9793, 0.9800' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL32XU # _reflns.entry_id 4GEN _reflns.d_resolution_high 2.200 _reflns.d_resolution_low 50.000 _reflns.number_obs 6839 _reflns.pdbx_Rmerge_I_obs 0.097 _reflns.pdbx_netI_over_sigmaI 10.800 _reflns.pdbx_chi_squared 1.884 _reflns.pdbx_redundancy 5.400 _reflns.percent_possible_obs 97.100 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _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_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.200 2.240 ? ? ? ? 0.354 ? ? 1.037 3.600 ? ? ? 335 ? ? ? ? 94.600 ? ? 1 1 2.240 2.280 ? ? ? ? 0.333 ? ? 0.950 4.000 ? ? ? 333 ? ? ? ? 94.100 ? ? 2 1 2.280 2.320 ? ? ? ? 0.307 ? ? 1.013 4.300 ? ? ? 328 ? ? ? ? 93.700 ? ? 3 1 2.320 2.370 ? ? ? ? 0.275 ? ? 0.884 4.300 ? ? ? 330 ? ? ? ? 94.300 ? ? 4 1 2.370 2.420 ? ? ? ? 0.263 ? ? 1.027 4.200 ? ? ? 319 ? ? ? ? 95.200 ? ? 5 1 2.420 2.480 ? ? ? ? 0.225 ? ? 1.102 4.600 ? ? ? 331 ? ? ? ? 95.100 ? ? 6 1 2.480 2.540 ? ? ? ? 0.214 ? ? 0.946 4.600 ? ? ? 347 ? ? ? ? 95.600 ? ? 7 1 2.540 2.610 ? ? ? ? 0.202 ? ? 1.114 4.700 ? ? ? 342 ? ? ? ? 98.000 ? ? 8 1 2.610 2.690 ? ? ? ? 0.229 ? ? 1.159 5.000 ? ? ? 335 ? ? ? ? 97.400 ? ? 9 1 2.690 2.770 ? ? ? ? 0.175 ? ? 1.242 5.000 ? ? ? 341 ? ? ? ? 96.600 ? ? 10 1 2.770 2.870 ? ? ? ? 0.165 ? ? 1.316 5.300 ? ? ? 335 ? ? ? ? 97.700 ? ? 11 1 2.870 2.990 ? ? ? ? 0.147 ? ? 1.397 5.500 ? ? ? 349 ? ? ? ? 96.400 ? ? 12 1 2.990 3.120 ? ? ? ? 0.124 ? ? 1.596 5.800 ? ? ? 340 ? ? ? ? 98.300 ? ? 13 1 3.120 3.290 ? ? ? ? 0.109 ? ? 1.687 6.100 ? ? ? 347 ? ? ? ? 99.400 ? ? 14 1 3.290 3.490 ? ? ? ? 0.102 ? ? 2.053 6.400 ? ? ? 358 ? ? ? ? 99.200 ? ? 15 1 3.490 3.760 ? ? ? ? 0.084 ? ? 2.234 6.700 ? ? ? 333 ? ? ? ? 99.100 ? ? 16 1 3.760 4.140 ? ? ? ? 0.077 ? ? 2.603 6.900 ? ? ? 355 ? ? ? ? 99.400 ? ? 17 1 4.140 4.740 ? ? ? ? 0.067 ? ? 3.146 7.100 ? ? ? 353 ? ? ? ? 99.700 ? ? 18 1 4.740 5.970 ? ? ? ? 0.071 ? ? 3.139 7.100 ? ? ? 362 ? ? ? ? 99.200 ? ? 19 1 5.970 50.000 ? ? ? ? 0.061 ? ? 3.715 6.900 ? ? ? 366 ? ? ? ? 98.400 ? ? 20 1 # _refine.entry_id 4GEN _refine.ls_d_res_high 2.2000 _refine.ls_d_res_low 37.4800 _refine.pdbx_ls_sigma_F 1.490 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 97.1700 _refine.ls_number_reflns_obs 6836 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2250 _refine.ls_R_factor_R_work 0.2226 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2699 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.7700 _refine.ls_number_reflns_R_free 326 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 38.8704 _refine.solvent_model_param_bsol 37.3720 _refine.solvent_model_param_ksol 0.3260 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -2.5088 _refine.aniso_B[2][2] -3.0200 _refine.aniso_B[3][3] 5.5287 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] -2.5467 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.6300 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.8077 _refine.B_iso_max 207.240 _refine.B_iso_min 6.650 _refine.pdbx_overall_phase_error 26.5800 _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_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 1173 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 16 _refine_hist.number_atoms_total 1190 _refine_hist.d_res_high 2.2000 _refine_hist.d_res_low 37.4800 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 1192 0.002 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 1615 0.566 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 194 0.041 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 200 0.002 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 426 13.255 ? ? ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.redundancy_reflns_obs 2.200 2.7718 2 95.0000 3183 . 0.2445 0.2760 . 155 . 3338 . 'X-RAY DIFFRACTION' . 2.7718 37.4855 2 99.0000 3327 . 0.2138 0.2675 . 171 . 3498 . 'X-RAY DIFFRACTION' . # _struct.entry_id 4GEN _struct.title 'Crystal structure of Zucchini (monomer)' _struct.pdbx_descriptor 'Mitochondrial cardiolipin hydrolase (E.C.3.1.4.-)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4GEN _struct_keywords.text 'piRNA, Phospholipase D, Nuclease, HYDROLASE' _struct_keywords.pdbx_keywords 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 MSE A 5 ? ARG A 21 ? MSE A 86 ARG A 102 1 ? 17 HELX_P HELX_P2 2 SER A 35 ? ARG A 48 ? SER A 116 ARG A 129 1 ? 14 HELX_P HELX_P3 3 GLU A 59 ? SER A 63 ? GLU A 140 SER A 144 5 ? 5 HELX_P HELX_P4 4 GLN A 67 ? GLN A 73 ? GLN A 148 GLN A 154 1 ? 7 HELX_P HELX_P5 5 GLY A 96 ? LYS A 108 ? GLY A 177 LYS A 189 1 ? 13 HELX_P HELX_P6 6 ASP A 143 ? ALA A 160 ? ASP A 224 ALA A 241 1 ? 18 # _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 MSE 5 C ? ? ? 1_555 A GLU 6 N ? ? A MSE 86 A GLU 87 1_555 ? ? ? ? ? ? ? 1.329 ? covale2 covale ? ? A GLU 59 C ? ? ? 1_555 A MSE 60 N ? ? A GLU 140 A MSE 141 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? A MSE 60 C ? ? ? 1_555 A VAL 61 N ? ? A MSE 141 A VAL 142 1_555 ? ? ? ? ? ? ? 1.329 ? covale4 covale ? ? A SER 69 C ? ? ? 1_555 A MSE 70 N ? ? A SER 150 A MSE 151 1_555 ? ? ? ? ? ? ? 1.329 ? covale5 covale ? ? A MSE 70 C ? ? ? 1_555 A LEU 71 N ? ? A MSE 151 A LEU 152 1_555 ? ? ? ? ? ? ? 1.329 ? covale6 covale ? ? A LEU 86 C ? ? ? 1_555 A MSE 87 N ? ? A LEU 167 A MSE 168 1_555 ? ? ? ? ? ? ? 1.328 ? covale7 covale ? ? A MSE 87 C ? ? ? 1_555 A HIS 88 N ? ? A MSE 168 A HIS 169 1_555 ? ? ? ? ? ? ? 1.330 ? covale8 covale ? ? A PHE 111 C ? ? ? 1_555 A MSE 112 N ? ? A PHE 192 A MSE 193 1_555 ? ? ? ? ? ? ? 1.329 ? covale9 covale ? ? A MSE 112 C ? ? ? 1_555 A ARG 113 N ? ? A MSE 193 A ARG 194 1_555 ? ? ? ? ? ? ? 1.329 ? covale10 covale ? ? A ARG 156 C ? ? ? 1_555 A MSE 157 N ? ? A ARG 237 A MSE 238 1_555 ? ? ? ? ? ? ? 1.330 ? covale11 covale ? ? A MSE 157 C ? ? ? 1_555 A TRP 158 N ? ? A MSE 238 A TRP 239 1_555 ? ? ? ? ? ? ? 1.331 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_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 LYS 64 A . ? LYS 145 A GLY 65 A ? GLY 146 A 1 -0.30 2 ILE 82 A . ? ILE 163 A THR 83 A ? THR 164 A 1 -3.82 3 THR 83 A . ? THR 164 A THR 84 A ? THR 165 A 1 -7.91 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 6 _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 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? 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 78 ? ARG A 79 ? VAL A 159 ARG A 160 A 2 ILE A 51 ? ILE A 55 ? ILE A 132 ILE A 136 A 3 SER A 25 ? ALA A 29 ? SER A 106 ALA A 110 A 4 LYS A 90 ? ILE A 94 ? LYS A 171 ILE A 175 A 5 ILE A 118 ? GLY A 122 ? ILE A 199 GLY A 203 A 6 ILE A 139 ? THR A 141 ? ILE A 220 THR A 222 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O ARG A 79 ? O ARG A 160 N ILE A 54 ? N ILE A 135 A 2 3 O ILE A 55 ? O ILE A 136 N LEU A 28 ? N LEU A 109 A 3 4 N ASP A 27 ? N ASP A 108 O ILE A 93 ? O ILE A 174 A 4 5 N ILE A 94 ? N ILE A 175 O ILE A 118 ? O ILE A 199 A 5 6 N VAL A 119 ? N VAL A 200 O THR A 141 ? O THR A 222 # _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 5 _struct_site.details 'BINDING SITE FOR RESIDUE CL 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 5 ILE A 30 ? ILE A 111 . ? 1_555 ? 2 AC1 5 TYR A 31 ? TYR A 112 . ? 1_555 ? 3 AC1 5 THR A 32 ? THR A 113 . ? 1_555 ? 4 AC1 5 LYS A 90 ? LYS A 171 . ? 1_555 ? 5 AC1 5 ASN A 125 ? ASN A 206 . ? 1_555 ? # _atom_sites.entry_id 4GEN _atom_sites.fract_transf_matrix[1][1] 0.028347 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.007563 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.019085 _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] 0.026681 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C CL N O 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 GLY 1 82 ? ? ? A . n A 1 2 PRO 2 83 ? ? ? A . n A 1 3 GLY 3 84 ? ? ? A . n A 1 4 HIS 4 85 ? ? ? A . n A 1 5 MSE 5 86 86 MSE MSE A . n A 1 6 GLU 6 87 87 GLU GLU A . n A 1 7 LEU 7 88 88 LEU LEU A . n A 1 8 SER 8 89 89 SER SER A . n A 1 9 LEU 9 90 90 LEU LEU A . n A 1 10 ARG 10 91 91 ARG ARG A . n A 1 11 ASN 11 92 92 ASN ASN A . n A 1 12 VAL 12 93 93 VAL VAL A . n A 1 13 ALA 13 94 94 ALA ALA A . n A 1 14 LYS 14 95 95 LYS LYS A . n A 1 15 ILE 15 96 96 ILE ILE A . n A 1 16 VAL 16 97 97 VAL VAL A . n A 1 17 GLU 17 98 98 GLU GLU A . n A 1 18 GLN 18 99 99 GLN GLN A . n A 1 19 ILE 19 100 100 ILE ILE A . n A 1 20 ASP 20 101 101 ASP ASP A . n A 1 21 ARG 21 102 102 ARG ARG A . n A 1 22 ALA 22 103 103 ALA ALA A . n A 1 23 VAL 23 104 104 VAL VAL A . n A 1 24 TYR 24 105 105 TYR TYR A . n A 1 25 SER 25 106 106 SER SER A . n A 1 26 ILE 26 107 107 ILE ILE A . n A 1 27 ASP 27 108 108 ASP ASP A . n A 1 28 LEU 28 109 109 LEU LEU A . n A 1 29 ALA 29 110 110 ALA ALA A . n A 1 30 ILE 30 111 111 ILE ILE A . n A 1 31 TYR 31 112 112 TYR TYR A . n A 1 32 THR 32 113 113 THR THR A . n A 1 33 PHE 33 114 114 PHE PHE A . n A 1 34 THR 34 115 115 THR THR A . n A 1 35 SER 35 116 116 SER SER A . n A 1 36 LEU 36 117 117 LEU LEU A . n A 1 37 PHE 37 118 118 PHE PHE A . n A 1 38 LEU 38 119 119 LEU LEU A . n A 1 39 ALA 39 120 120 ALA ALA A . n A 1 40 ASP 40 121 121 ASP ASP A . n A 1 41 SER 41 122 122 SER SER A . n A 1 42 ILE 42 123 123 ILE ILE A . n A 1 43 LYS 43 124 124 LYS LYS A . n A 1 44 ARG 44 125 125 ARG ARG A . n A 1 45 ALA 45 126 126 ALA ALA A . n A 1 46 LEU 46 127 127 LEU LEU A . n A 1 47 GLN 47 128 128 GLN GLN A . n A 1 48 ARG 48 129 129 ARG ARG A . n A 1 49 GLY 49 130 130 GLY GLY A . n A 1 50 VAL 50 131 131 VAL VAL A . n A 1 51 ILE 51 132 132 ILE ILE A . n A 1 52 ILE 52 133 133 ILE ILE A . n A 1 53 ARG 53 134 134 ARG ARG A . n A 1 54 ILE 54 135 135 ILE ILE A . n A 1 55 ILE 55 136 136 ILE ILE A . n A 1 56 SER 56 137 137 SER SER A . n A 1 57 ASP 57 138 138 ASP ASP A . n A 1 58 GLY 58 139 139 GLY GLY A . n A 1 59 GLU 59 140 140 GLU GLU A . n A 1 60 MSE 60 141 141 MSE MSE A . n A 1 61 VAL 61 142 142 VAL VAL A . n A 1 62 TYR 62 143 143 TYR TYR A . n A 1 63 SER 63 144 144 SER SER A . n A 1 64 LYS 64 145 145 LYS LYS A . n A 1 65 GLY 65 146 146 GLY GLY A . n A 1 66 SER 66 147 147 SER SER A . n A 1 67 GLN 67 148 148 GLN GLN A . n A 1 68 ILE 68 149 149 ILE ILE A . n A 1 69 SER 69 150 150 SER SER A . n A 1 70 MSE 70 151 151 MSE MSE A . n A 1 71 LEU 71 152 152 LEU LEU A . n A 1 72 ALA 72 153 153 ALA ALA A . n A 1 73 GLN 73 154 154 GLN GLN A . n A 1 74 LEU 74 155 155 LEU LEU A . n A 1 75 GLY 75 156 156 GLY GLY A . n A 1 76 VAL 76 157 157 VAL VAL A . n A 1 77 PRO 77 158 158 PRO PRO A . n A 1 78 VAL 78 159 159 VAL VAL A . n A 1 79 ARG 79 160 160 ARG ARG A . n A 1 80 VAL 80 161 161 VAL VAL A . n A 1 81 PRO 81 162 162 PRO PRO A . n A 1 82 ILE 82 163 163 ILE ILE A . n A 1 83 THR 83 164 164 THR THR A . n A 1 84 THR 84 165 165 THR THR A . n A 1 85 ASN 85 166 166 ASN ASN A . n A 1 86 LEU 86 167 167 LEU LEU A . n A 1 87 MSE 87 168 168 MSE MSE A . n A 1 88 HIS 88 169 169 HIS HIS A . n A 1 89 ASN 89 170 170 ASN ASN A . n A 1 90 LYS 90 171 171 LYS LYS A . n A 1 91 PHE 91 172 172 PHE PHE A . n A 1 92 CYS 92 173 173 CYS CYS A . n A 1 93 ILE 93 174 174 ILE ILE A . n A 1 94 ILE 94 175 175 ILE ILE A . n A 1 95 ASP 95 176 176 ASP ASP A . n A 1 96 GLY 96 177 177 GLY GLY A . n A 1 97 PHE 97 178 178 PHE PHE A . n A 1 98 GLU 98 179 179 GLU GLU A . n A 1 99 ARG 99 180 180 ARG ARG A . n A 1 100 VAL 100 181 181 VAL VAL A . n A 1 101 GLU 101 182 182 GLU GLU A . n A 1 102 GLU 102 183 183 GLU GLU A . n A 1 103 ILE 103 184 184 ILE ILE A . n A 1 104 ARG 104 185 185 ARG ARG A . n A 1 105 LEU 105 186 186 LEU LEU A . n A 1 106 LEU 106 187 187 LEU LEU A . n A 1 107 ARG 107 188 188 ARG ARG A . n A 1 108 LYS 108 189 189 LYS LYS A . n A 1 109 LEU 109 190 190 LEU LEU A . n A 1 110 LYS 110 191 191 LYS LYS A . n A 1 111 PHE 111 192 192 PHE PHE A . n A 1 112 MSE 112 193 193 MSE MSE A . n A 1 113 ARG 113 194 194 ARG ARG A . n A 1 114 PRO 114 195 195 PRO PRO A . n A 1 115 CYS 115 196 196 CYS CYS A . n A 1 116 TYR 116 197 197 TYR TYR A . n A 1 117 SER 117 198 198 SER SER A . n A 1 118 ILE 118 199 199 ILE ILE A . n A 1 119 VAL 119 200 200 VAL VAL A . n A 1 120 ILE 120 201 201 ILE ILE A . n A 1 121 SER 121 202 202 SER SER A . n A 1 122 GLY 122 203 203 GLY GLY A . n A 1 123 SER 123 204 204 SER SER A . n A 1 124 VAL 124 205 205 VAL VAL A . n A 1 125 ASN 125 206 206 ASN ASN A . n A 1 126 TRP 126 207 207 TRP TRP A . n A 1 127 THR 127 208 208 THR THR A . n A 1 128 ALA 128 209 ? ? ? A . n A 1 129 LEU 129 210 ? ? ? A . n A 1 130 GLY 130 211 ? ? ? A . n A 1 131 LEU 131 212 ? ? ? A . n A 1 132 GLY 132 213 ? ? ? A . n A 1 133 GLY 133 214 214 GLY GLY A . n A 1 134 ASN 134 215 215 ASN ASN A . n A 1 135 TRP 135 216 216 TRP TRP A . n A 1 136 GLU 136 217 217 GLU GLU A . n A 1 137 ASN 137 218 218 ASN ASN A . n A 1 138 CYS 138 219 219 CYS CYS A . n A 1 139 ILE 139 220 220 ILE ILE A . n A 1 140 ILE 140 221 221 ILE ILE A . n A 1 141 THR 141 222 222 THR THR A . n A 1 142 ALA 142 223 223 ALA ALA A . n A 1 143 ASP 143 224 224 ASP ASP A . n A 1 144 ASP 144 225 225 ASP ASP A . n A 1 145 LYS 145 226 226 LYS LYS A . n A 1 146 LEU 146 227 227 LEU LEU A . n A 1 147 THR 147 228 228 THR THR A . n A 1 148 ALA 148 229 229 ALA ALA A . n A 1 149 THR 149 230 230 THR THR A . n A 1 150 PHE 150 231 231 PHE PHE A . n A 1 151 GLN 151 232 232 GLN GLN A . n A 1 152 ALA 152 233 233 ALA ALA A . n A 1 153 GLU 153 234 234 GLU GLU A . n A 1 154 PHE 154 235 235 PHE PHE A . n A 1 155 GLN 155 236 236 GLN GLN A . n A 1 156 ARG 156 237 237 ARG ARG A . n A 1 157 MSE 157 238 238 MSE MSE A . n A 1 158 TRP 158 239 239 TRP TRP A . n A 1 159 ARG 159 240 240 ARG ARG A . n A 1 160 ALA 160 241 241 ALA ALA A . n A 1 161 PHE 161 242 ? ? ? A . n A 1 162 ALA 162 243 ? ? ? A . n A 1 163 LYS 163 244 ? ? ? A . n A 1 164 THR 164 245 ? ? ? A . n A 1 165 GLU 165 246 ? ? ? A . n A 1 166 GLY 166 247 ? ? ? A . n A 1 167 SER 167 248 ? ? ? A . n A 1 168 GLN 168 249 ? ? ? A . n A 1 169 ILE 169 250 ? ? ? 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 CL 1 301 301 CL CL A . C 3 HOH 1 401 1 HOH HOH A . C 3 HOH 2 402 2 HOH HOH A . C 3 HOH 3 403 3 HOH HOH A . C 3 HOH 4 404 4 HOH HOH A . C 3 HOH 5 405 5 HOH HOH A . C 3 HOH 6 406 6 HOH HOH A . C 3 HOH 7 407 7 HOH HOH A . C 3 HOH 8 408 10 HOH HOH A . C 3 HOH 9 409 11 HOH HOH A . C 3 HOH 10 410 15 HOH HOH A . C 3 HOH 11 411 19 HOH HOH A . C 3 HOH 12 412 21 HOH HOH A . C 3 HOH 13 413 27 HOH HOH A . C 3 HOH 14 414 30 HOH HOH A . C 3 HOH 15 415 34 HOH HOH A . C 3 HOH 16 416 46 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 5 A MSE 86 ? MET SELENOMETHIONINE 2 A MSE 60 A MSE 141 ? MET SELENOMETHIONINE 3 A MSE 70 A MSE 151 ? MET SELENOMETHIONINE 4 A MSE 87 A MSE 168 ? MET SELENOMETHIONINE 5 A MSE 112 A MSE 193 ? MET SELENOMETHIONINE 6 A MSE 157 A MSE 238 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _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 2012-10-17 2 'Structure model' 1 1 2013-03-27 3 'Structure model' 1 2 2017-11-15 # _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' 'Database references' 2 3 'Structure model' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 3 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # 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 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.contact_author' 3 3 'Structure model' '_software.contact_author_email' 4 3 'Structure model' '_software.date' 5 3 'Structure model' '_software.language' 6 3 'Structure model' '_software.location' 7 3 'Structure model' '_software.name' 8 3 'Structure model' '_software.type' 9 3 'Structure model' '_software.version' # _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 -20.2294 _pdbx_refine_tls.origin_y -57.4839 _pdbx_refine_tls.origin_z -12.2660 _pdbx_refine_tls.T[1][1] 0.0094 _pdbx_refine_tls.T[2][2] 0.0599 _pdbx_refine_tls.T[3][3] 0.0536 _pdbx_refine_tls.T[1][2] 0.0102 _pdbx_refine_tls.T[1][3] -0.0150 _pdbx_refine_tls.T[2][3] -0.0210 _pdbx_refine_tls.L[1][1] 3.4622 _pdbx_refine_tls.L[2][2] 3.3202 _pdbx_refine_tls.L[3][3] 2.6531 _pdbx_refine_tls.L[1][2] -1.2300 _pdbx_refine_tls.L[1][3] 0.5981 _pdbx_refine_tls.L[2][3] -1.7453 _pdbx_refine_tls.S[1][1] -0.0256 _pdbx_refine_tls.S[2][2] 0.0505 _pdbx_refine_tls.S[3][3] -0.0141 _pdbx_refine_tls.S[1][2] -0.2038 _pdbx_refine_tls.S[1][3] 0.2457 _pdbx_refine_tls.S[2][3] 0.0070 _pdbx_refine_tls.S[2][1] 0.1699 _pdbx_refine_tls.S[3][1] -0.1626 _pdbx_refine_tls.S[3][2] -0.0704 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 86 A 241 all ? ? ? ? ? 'X-RAY DIFFRACTION' 2 1 A 301 A 301 all ? ? ? ? ? 'X-RAY DIFFRACTION' 3 1 A 1 A 416 all ? ? ? ? ? # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 PHENIX 1.7.2_869 ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 4 PDB_EXTRACT 3.11 'April 22, 2011' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? # 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 THR A 165 ? ? -105.06 -169.55 2 1 ALA A 223 ? ? -116.13 61.08 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A GLU 140 ? CG ? A GLU 59 CG 2 1 Y 1 A GLU 140 ? CD ? A GLU 59 CD 3 1 Y 1 A GLU 140 ? OE1 ? A GLU 59 OE1 4 1 Y 1 A GLU 140 ? OE2 ? A GLU 59 OE2 5 1 Y 1 A LYS 145 ? CG ? A LYS 64 CG 6 1 Y 1 A LYS 145 ? CD ? A LYS 64 CD 7 1 Y 1 A LYS 145 ? CE ? A LYS 64 CE 8 1 Y 1 A LYS 145 ? NZ ? A LYS 64 NZ 9 1 Y 1 A GLN 154 ? CG ? A GLN 73 CG 10 1 Y 1 A GLN 154 ? CD ? A GLN 73 CD 11 1 Y 1 A GLN 154 ? OE1 ? A GLN 73 OE1 12 1 Y 1 A GLN 154 ? NE2 ? A GLN 73 NE2 13 1 Y 1 A LYS 189 ? CG ? A LYS 108 CG 14 1 Y 1 A LYS 189 ? CD ? A LYS 108 CD 15 1 Y 1 A LYS 189 ? CE ? A LYS 108 CE 16 1 Y 1 A LYS 189 ? NZ ? A LYS 108 NZ 17 1 Y 1 A LYS 191 ? CG ? A LYS 110 CG 18 1 Y 1 A LYS 191 ? CD ? A LYS 110 CD 19 1 Y 1 A LYS 191 ? CE ? A LYS 110 CE 20 1 Y 1 A LYS 191 ? NZ ? A LYS 110 NZ 21 1 Y 1 A GLU 217 ? CG ? A GLU 136 CG 22 1 Y 1 A GLU 217 ? CD ? A GLU 136 CD 23 1 Y 1 A GLU 217 ? OE1 ? A GLU 136 OE1 24 1 Y 1 A GLU 217 ? OE2 ? A GLU 136 OE2 25 1 Y 1 A ASP 224 ? CG ? A ASP 143 CG 26 1 Y 1 A ASP 224 ? OD1 ? A ASP 143 OD1 27 1 Y 1 A ASP 224 ? OD2 ? A ASP 143 OD2 28 1 Y 1 A LYS 226 ? CG ? A LYS 145 CG 29 1 Y 1 A LYS 226 ? CD ? A LYS 145 CD 30 1 Y 1 A LYS 226 ? CE ? A LYS 145 CE 31 1 Y 1 A LYS 226 ? NZ ? A LYS 145 NZ 32 1 Y 1 A GLU 234 ? CG ? A GLU 153 CG 33 1 Y 1 A GLU 234 ? CD ? A GLU 153 CD 34 1 Y 1 A GLU 234 ? OE1 ? A GLU 153 OE1 35 1 Y 1 A GLU 234 ? OE2 ? A GLU 153 OE2 36 1 Y 1 A ARG 240 ? CG ? A ARG 159 CG 37 1 Y 1 A ARG 240 ? CD ? A ARG 159 CD 38 1 Y 1 A ARG 240 ? NE ? A ARG 159 NE 39 1 Y 1 A ARG 240 ? CZ ? A ARG 159 CZ 40 1 Y 1 A ARG 240 ? NH1 ? A ARG 159 NH1 41 1 Y 1 A ARG 240 ? NH2 ? A ARG 159 NH2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 82 ? A GLY 1 2 1 Y 1 A PRO 83 ? A PRO 2 3 1 Y 1 A GLY 84 ? A GLY 3 4 1 Y 1 A HIS 85 ? A HIS 4 5 1 Y 1 A ALA 209 ? A ALA 128 6 1 Y 1 A LEU 210 ? A LEU 129 7 1 Y 1 A GLY 211 ? A GLY 130 8 1 Y 1 A LEU 212 ? A LEU 131 9 1 Y 1 A GLY 213 ? A GLY 132 10 1 Y 1 A PHE 242 ? A PHE 161 11 1 Y 1 A ALA 243 ? A ALA 162 12 1 Y 1 A LYS 244 ? A LYS 163 13 1 Y 1 A THR 245 ? A THR 164 14 1 Y 1 A GLU 246 ? A GLU 165 15 1 Y 1 A GLY 247 ? A GLY 166 16 1 Y 1 A SER 248 ? A SER 167 17 1 Y 1 A GLN 249 ? A GLN 168 18 1 Y 1 A ILE 250 ? A ILE 169 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CHLORIDE ION' CL 3 water HOH #