data_5ZWZ # _entry.id 5ZWZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.299 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5ZWZ WWPDB D_1300007807 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5ZWZ _pdbx_database_status.recvd_initial_deposition_date 2018-05-17 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Du, X.' 1 ? 'Du, J.' 2 0000-0002-1337-0786 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 9 _citation.language ? _citation.page_first 4547 _citation.page_last 4547 _citation.title 'Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-018-06965-w _citation.pdbx_database_id_PubMed 30382101 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhang, C.' 1 ? primary 'Du, X.' 2 ? primary 'Tang, K.' 3 0000-0003-3913-6426 primary 'Yang, Z.' 4 ? primary 'Pan, L.' 5 ? primary 'Zhu, P.' 6 ? primary 'Luo, J.' 7 ? primary 'Jiang, Y.' 8 ? primary 'Zhang, H.' 9 ? primary 'Wan, H.' 10 ? primary 'Wang, X.' 11 ? primary 'Wu, F.' 12 ? primary 'Tao, W.A.' 13 ? primary 'He, X.J.' 14 0000-0002-2878-7461 primary 'Zhang, H.' 15 0000-0002-1541-3890 primary 'Bressan, R.A.' 16 ? primary 'Du, J.' 17 0000-0002-1337-0786 primary 'Zhu, J.K.' 18 0000-0001-5134-731X # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 5ZWZ _cell.details ? _cell.formula_units_Z ? _cell.length_a 57.177 _cell.length_a_esd ? _cell.length_b 57.177 _cell.length_b_esd ? _cell.length_c 206.430 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZWZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? # 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 'Agenet domain-containing protein' 19301.209 1 ? ? ? ? 2 water nat water 18.015 87 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name At1g09320 # _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 ;SEDEEDILARVDLETTRAIAKQ(MSE)FSSGTVVEVSSDEEGFQGCWFAAKVVEPVGEDKFLVEYRDLREKDGIEPLKEE TDFLHIRPPPPRDEDIDFAVGDKINAFYNDGWWVGVVIDG(MSE)KHGTVGIYFRQSQEK(MSE)RFGRQGLRLHKDWVD GTWQLPLKGGKIKREKTVS ; _entity_poly.pdbx_seq_one_letter_code_can ;SEDEEDILARVDLETTRAIAKQMFSSGTVVEVSSDEEGFQGCWFAAKVVEPVGEDKFLVEYRDLREKDGIEPLKEETDFL HIRPPPPRDEDIDFAVGDKINAFYNDGWWVGVVIDGMKHGTVGIYFRQSQEKMRFGRQGLRLHKDWVDGTWQLPLKGGKI KREKTVS ; _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 SER n 1 2 GLU n 1 3 ASP n 1 4 GLU n 1 5 GLU n 1 6 ASP n 1 7 ILE n 1 8 LEU n 1 9 ALA n 1 10 ARG n 1 11 VAL n 1 12 ASP n 1 13 LEU n 1 14 GLU n 1 15 THR n 1 16 THR n 1 17 ARG n 1 18 ALA n 1 19 ILE n 1 20 ALA n 1 21 LYS n 1 22 GLN n 1 23 MSE n 1 24 PHE n 1 25 SER n 1 26 SER n 1 27 GLY n 1 28 THR n 1 29 VAL n 1 30 VAL n 1 31 GLU n 1 32 VAL n 1 33 SER n 1 34 SER n 1 35 ASP n 1 36 GLU n 1 37 GLU n 1 38 GLY n 1 39 PHE n 1 40 GLN n 1 41 GLY n 1 42 CYS n 1 43 TRP n 1 44 PHE n 1 45 ALA n 1 46 ALA n 1 47 LYS n 1 48 VAL n 1 49 VAL n 1 50 GLU n 1 51 PRO n 1 52 VAL n 1 53 GLY n 1 54 GLU n 1 55 ASP n 1 56 LYS n 1 57 PHE n 1 58 LEU n 1 59 VAL n 1 60 GLU n 1 61 TYR n 1 62 ARG n 1 63 ASP n 1 64 LEU n 1 65 ARG n 1 66 GLU n 1 67 LYS n 1 68 ASP n 1 69 GLY n 1 70 ILE n 1 71 GLU n 1 72 PRO n 1 73 LEU n 1 74 LYS n 1 75 GLU n 1 76 GLU n 1 77 THR n 1 78 ASP n 1 79 PHE n 1 80 LEU n 1 81 HIS n 1 82 ILE n 1 83 ARG n 1 84 PRO n 1 85 PRO n 1 86 PRO n 1 87 PRO n 1 88 ARG n 1 89 ASP n 1 90 GLU n 1 91 ASP n 1 92 ILE n 1 93 ASP n 1 94 PHE n 1 95 ALA n 1 96 VAL n 1 97 GLY n 1 98 ASP n 1 99 LYS n 1 100 ILE n 1 101 ASN n 1 102 ALA n 1 103 PHE n 1 104 TYR n 1 105 ASN n 1 106 ASP n 1 107 GLY n 1 108 TRP n 1 109 TRP n 1 110 VAL n 1 111 GLY n 1 112 VAL n 1 113 VAL n 1 114 ILE n 1 115 ASP n 1 116 GLY n 1 117 MSE n 1 118 LYS n 1 119 HIS n 1 120 GLY n 1 121 THR n 1 122 VAL n 1 123 GLY n 1 124 ILE n 1 125 TYR n 1 126 PHE n 1 127 ARG n 1 128 GLN n 1 129 SER n 1 130 GLN n 1 131 GLU n 1 132 LYS n 1 133 MSE n 1 134 ARG n 1 135 PHE n 1 136 GLY n 1 137 ARG n 1 138 GLN n 1 139 GLY n 1 140 LEU n 1 141 ARG n 1 142 LEU n 1 143 HIS n 1 144 LYS n 1 145 ASP n 1 146 TRP n 1 147 VAL n 1 148 ASP n 1 149 GLY n 1 150 THR n 1 151 TRP n 1 152 GLN n 1 153 LEU n 1 154 PRO n 1 155 LEU n 1 156 LYS n 1 157 GLY n 1 158 GLY n 1 159 LYS n 1 160 ILE n 1 161 LYS n 1 162 ARG n 1 163 GLU n 1 164 LYS n 1 165 THR n 1 166 VAL n 1 167 SER 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 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 167 _entity_src_gen.gene_src_common_name 'Mouse-ear cress' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'At1g09320, T31J12.4, T31J12_4' _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 'Arabidopsis thaliana' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 3702 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant RIL _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 pMBP _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q500V5_ARATH _struct_ref.pdbx_db_accession Q500V5 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;SEDEEDILARVDLETTRAIAKQMFSSGTVVEVSSDEEGFQGCWFAAKVVEPVGEDKFLVEYRDLREKDGIEPLKEETDFL HIRPPPPRDEDIDFAVGDKINAFYNDGWWVGVVIDGMKHGTVGIYFRQSQEKMRFGRQGLRLHKDWVDGTWQLPLKGGKI KREKTVS ; _struct_ref.pdbx_align_begin 198 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5ZWZ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 167 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q500V5 _struct_ref_seq.db_align_beg 198 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 364 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 198 _struct_ref_seq.pdbx_auth_seq_align_end 364 # 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 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.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5ZWZ _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.54 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 51.61 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '3.5M sodium formate, 0.1M HEPES, pH 7.5' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-03-08 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9778 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'SSRF BEAMLINE BL18U1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9778 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL18U1 _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5ZWZ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.00 _reflns.d_resolution_low 50.0 _reflns.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.number_all ? _reflns.number_obs 14321 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.4 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 15.6 _reflns.pdbx_Rmerge_I_obs 0.097 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 56.0 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.0 _reflns_shell.d_res_low 2.07 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 17.8 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 1369 _reflns_shell.percent_possible_all 98.6 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.241 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 17.8 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 5ZWZ _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.000 _refine.ls_d_res_low 40.192 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 14321 _refine.ls_number_reflns_R_free 722 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.66 _refine.ls_percent_reflns_R_free 5.07 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2007 _refine.ls_R_factor_R_free 0.2185 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1998 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.77 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 21.09 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.16 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1185 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 87 _refine_hist.number_atoms_total 1272 _refine_hist.d_res_high 2.000 _refine_hist.d_res_low 40.192 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.004 ? 1216 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.845 ? 1644 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 14.906 ? 449 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.033 ? 167 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.003 ? 217 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.0001 2.0801 . . 144 2645 98.00 . . . 0.2539 . 0.2291 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.0801 2.1748 . . 142 2673 100.00 . . . 0.2109 . 0.2110 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.1748 2.2895 . . 159 2709 100.00 . . . 0.2454 . 0.2205 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.2895 2.4329 . . 185 2613 100.00 . . . 0.2310 . 0.2232 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.4329 2.6207 . . 135 2708 100.00 . . . 0.2586 . 0.2267 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.6207 2.8844 . . 115 2711 100.00 . . . 0.2072 . 0.2506 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.8844 3.3016 . . 158 2674 100.00 . . . 0.2390 . 0.2175 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.3016 4.1589 . . 126 2698 100.00 . . . 0.2261 . 0.1817 . . . . . . . . . . 'X-RAY DIFFRACTION' 4.1589 40.2000 . . 124 2709 100.00 . . . 0.1821 . 0.1736 . . . . . . . . . . # _struct.entry_id 5ZWZ _struct.title 'Crystal structure of Arabidopsis thaliana AGDP1 AGD34' _struct.pdbx_descriptor 'Agenet domain-containing protein' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 5ZWZ _struct_keywords.text 'AGENET domain, AGDP1, epigenetics, H3K9me2, GENE REGULATION' _struct_keywords.pdbx_keywords 'GENE REGULATION' # 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 ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id ASP _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 12 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id PHE _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 24 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ASP _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 209 _struct_conf.end_auth_comp_id PHE _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 221 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 13 # _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 both ? A GLN 22 C ? ? ? 1_555 A MSE 23 N ? ? A GLN 219 A MSE 220 1_555 ? ? ? ? ? ? ? 1.327 ? covale2 covale both ? A MSE 23 C ? ? ? 1_555 A PHE 24 N ? ? A MSE 220 A PHE 221 1_555 ? ? ? ? ? ? ? 1.327 ? covale3 covale both ? A GLY 116 C ? ? ? 1_555 A MSE 117 N ? ? A GLY 313 A MSE 314 1_555 ? ? ? ? ? ? ? 1.329 ? covale4 covale both ? A MSE 117 C ? ? ? 1_555 A LYS 118 N ? ? A MSE 314 A LYS 315 1_555 ? ? ? ? ? ? ? 1.327 ? covale5 covale both ? A LYS 132 C ? ? ? 1_555 A MSE 133 N ? ? A LYS 329 A MSE 330 1_555 ? ? ? ? ? ? ? 1.330 ? covale6 covale both ? A MSE 133 C ? ? ? 1_555 A ARG 134 N ? ? A MSE 330 A ARG 331 1_555 ? ? ? ? ? ? ? 1.328 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 6 ? AA2 ? 6 ? AA3 ? 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 AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel AA1 4 5 ? anti-parallel AA1 5 6 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA2 4 5 ? anti-parallel AA2 5 6 ? anti-parallel AA3 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 AA1 1 PRO A 72 ? ASP A 78 ? PRO A 269 ASP A 275 AA1 2 LYS A 56 ? ARG A 65 ? LYS A 253 ARG A 262 AA1 3 CYS A 42 ? VAL A 52 ? CYS A 239 VAL A 249 AA1 4 GLY A 107 ? LYS A 118 ? GLY A 304 LYS A 315 AA1 5 THR A 121 ? PHE A 126 ? THR A 318 PHE A 323 AA1 6 GLU A 131 ? GLY A 136 ? GLU A 328 GLY A 333 AA2 1 ILE A 82 ? ARG A 83 ? ILE A 279 ARG A 280 AA2 2 VAL A 29 ? VAL A 32 ? VAL A 226 VAL A 229 AA2 3 CYS A 42 ? VAL A 52 ? CYS A 239 VAL A 249 AA2 4 GLY A 107 ? LYS A 118 ? GLY A 304 LYS A 315 AA2 5 LYS A 99 ? TYR A 104 ? LYS A 296 TYR A 301 AA2 6 LEU A 140 ? LEU A 142 ? LEU A 337 LEU A 339 AA3 1 ASP A 145 ? VAL A 147 ? ASP A 342 VAL A 344 AA3 2 THR A 150 ? GLN A 152 ? THR A 347 GLN A 349 # 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 AA1 1 2 O LEU A 73 ? O LEU A 270 N TYR A 61 ? N TYR A 258 AA1 2 3 O LYS A 56 ? O LYS A 253 N VAL A 52 ? N VAL A 249 AA1 3 4 N TRP A 43 ? N TRP A 240 O TRP A 108 ? O TRP A 305 AA1 4 5 N LYS A 118 ? N LYS A 315 O THR A 121 ? O THR A 318 AA1 5 6 N PHE A 126 ? N PHE A 323 O GLU A 131 ? O GLU A 328 AA2 1 2 O ARG A 83 ? O ARG A 280 N GLU A 31 ? N GLU A 228 AA2 2 3 N VAL A 32 ? N VAL A 229 O PHE A 44 ? O PHE A 241 AA2 3 4 N TRP A 43 ? N TRP A 240 O TRP A 108 ? O TRP A 305 AA2 4 5 O TRP A 109 ? O TRP A 306 N ALA A 102 ? N ALA A 299 AA2 5 6 N ASN A 101 ? N ASN A 298 O ARG A 141 ? O ARG A 338 AA3 1 2 N VAL A 147 ? N VAL A 344 O THR A 150 ? O THR A 347 # _atom_sites.entry_id 5ZWZ _atom_sites.fract_transf_matrix[1][1] 0.017490 _atom_sites.fract_transf_matrix[1][2] 0.010098 _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] 0.020195 _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] 0.004844 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S 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 SER 1 198 ? ? ? A . n A 1 2 GLU 2 199 ? ? ? A . n A 1 3 ASP 3 200 ? ? ? A . n A 1 4 GLU 4 201 ? ? ? A . n A 1 5 GLU 5 202 ? ? ? A . n A 1 6 ASP 6 203 ? ? ? A . n A 1 7 ILE 7 204 ? ? ? A . n A 1 8 LEU 8 205 ? ? ? A . n A 1 9 ALA 9 206 206 ALA ALA A . n A 1 10 ARG 10 207 207 ARG ARG A . n A 1 11 VAL 11 208 208 VAL VAL A . n A 1 12 ASP 12 209 209 ASP ASP A . n A 1 13 LEU 13 210 210 LEU LEU A . n A 1 14 GLU 14 211 211 GLU GLU A . n A 1 15 THR 15 212 212 THR THR A . n A 1 16 THR 16 213 213 THR THR A . n A 1 17 ARG 17 214 214 ARG ARG A . n A 1 18 ALA 18 215 215 ALA ALA A . n A 1 19 ILE 19 216 216 ILE ILE A . n A 1 20 ALA 20 217 217 ALA ALA A . n A 1 21 LYS 21 218 218 LYS LYS A . n A 1 22 GLN 22 219 219 GLN GLN A . n A 1 23 MSE 23 220 220 MSE MSE A . n A 1 24 PHE 24 221 221 PHE PHE A . n A 1 25 SER 25 222 222 SER SER A . n A 1 26 SER 26 223 223 SER SER A . n A 1 27 GLY 27 224 224 GLY GLY A . n A 1 28 THR 28 225 225 THR THR A . n A 1 29 VAL 29 226 226 VAL VAL A . n A 1 30 VAL 30 227 227 VAL VAL A . n A 1 31 GLU 31 228 228 GLU GLU A . n A 1 32 VAL 32 229 229 VAL VAL A . n A 1 33 SER 33 230 230 SER SER A . n A 1 34 SER 34 231 231 SER SER A . n A 1 35 ASP 35 232 232 ASP ASP A . n A 1 36 GLU 36 233 233 GLU GLU A . n A 1 37 GLU 37 234 234 GLU GLU A . n A 1 38 GLY 38 235 235 GLY GLY A . n A 1 39 PHE 39 236 236 PHE PHE A . n A 1 40 GLN 40 237 237 GLN GLN A . n A 1 41 GLY 41 238 238 GLY GLY A . n A 1 42 CYS 42 239 239 CYS CYS A . n A 1 43 TRP 43 240 240 TRP TRP A . n A 1 44 PHE 44 241 241 PHE PHE A . n A 1 45 ALA 45 242 242 ALA ALA A . n A 1 46 ALA 46 243 243 ALA ALA A . n A 1 47 LYS 47 244 244 LYS LYS A . n A 1 48 VAL 48 245 245 VAL VAL A . n A 1 49 VAL 49 246 246 VAL VAL A . n A 1 50 GLU 50 247 247 GLU GLU A . n A 1 51 PRO 51 248 248 PRO PRO A . n A 1 52 VAL 52 249 249 VAL VAL A . n A 1 53 GLY 53 250 250 GLY GLY A . n A 1 54 GLU 54 251 251 GLU GLU A . n A 1 55 ASP 55 252 252 ASP ASP A . n A 1 56 LYS 56 253 253 LYS LYS A . n A 1 57 PHE 57 254 254 PHE PHE A . n A 1 58 LEU 58 255 255 LEU LEU A . n A 1 59 VAL 59 256 256 VAL VAL A . n A 1 60 GLU 60 257 257 GLU GLU A . n A 1 61 TYR 61 258 258 TYR TYR A . n A 1 62 ARG 62 259 259 ARG ARG A . n A 1 63 ASP 63 260 260 ASP ASP A . n A 1 64 LEU 64 261 261 LEU LEU A . n A 1 65 ARG 65 262 262 ARG ARG A . n A 1 66 GLU 66 263 263 GLU GLU A . n A 1 67 LYS 67 264 264 LYS LYS A . n A 1 68 ASP 68 265 265 ASP ASP A . n A 1 69 GLY 69 266 266 GLY GLY A . n A 1 70 ILE 70 267 267 ILE ILE A . n A 1 71 GLU 71 268 268 GLU GLU A . n A 1 72 PRO 72 269 269 PRO PRO A . n A 1 73 LEU 73 270 270 LEU LEU A . n A 1 74 LYS 74 271 271 LYS LYS A . n A 1 75 GLU 75 272 272 GLU GLU A . n A 1 76 GLU 76 273 273 GLU GLU A . n A 1 77 THR 77 274 274 THR THR A . n A 1 78 ASP 78 275 275 ASP ASP A . n A 1 79 PHE 79 276 276 PHE PHE A . n A 1 80 LEU 80 277 277 LEU LEU A . n A 1 81 HIS 81 278 278 HIS HIS A . n A 1 82 ILE 82 279 279 ILE ILE A . n A 1 83 ARG 83 280 280 ARG ARG A . n A 1 84 PRO 84 281 281 PRO PRO A . n A 1 85 PRO 85 282 282 PRO PRO A . n A 1 86 PRO 86 283 283 PRO PRO A . n A 1 87 PRO 87 284 284 PRO PRO A . n A 1 88 ARG 88 285 285 ARG ARG A . n A 1 89 ASP 89 286 286 ASP ASP A . n A 1 90 GLU 90 287 287 GLU GLU A . n A 1 91 ASP 91 288 288 ASP ASP A . n A 1 92 ILE 92 289 289 ILE ILE A . n A 1 93 ASP 93 290 290 ASP ASP A . n A 1 94 PHE 94 291 291 PHE PHE A . n A 1 95 ALA 95 292 292 ALA ALA A . n A 1 96 VAL 96 293 293 VAL VAL A . n A 1 97 GLY 97 294 294 GLY GLY A . n A 1 98 ASP 98 295 295 ASP ASP A . n A 1 99 LYS 99 296 296 LYS LYS A . n A 1 100 ILE 100 297 297 ILE ILE A . n A 1 101 ASN 101 298 298 ASN ASN A . n A 1 102 ALA 102 299 299 ALA ALA A . n A 1 103 PHE 103 300 300 PHE PHE A . n A 1 104 TYR 104 301 301 TYR TYR A . n A 1 105 ASN 105 302 302 ASN ASN A . n A 1 106 ASP 106 303 303 ASP ASP A . n A 1 107 GLY 107 304 304 GLY GLY A . n A 1 108 TRP 108 305 305 TRP TRP A . n A 1 109 TRP 109 306 306 TRP TRP A . n A 1 110 VAL 110 307 307 VAL VAL A . n A 1 111 GLY 111 308 308 GLY GLY A . n A 1 112 VAL 112 309 309 VAL VAL A . n A 1 113 VAL 113 310 310 VAL VAL A . n A 1 114 ILE 114 311 311 ILE ILE A . n A 1 115 ASP 115 312 312 ASP ASP A . n A 1 116 GLY 116 313 313 GLY GLY A . n A 1 117 MSE 117 314 314 MSE MSE A . n A 1 118 LYS 118 315 315 LYS LYS A . n A 1 119 HIS 119 316 316 HIS HIS A . n A 1 120 GLY 120 317 317 GLY GLY A . n A 1 121 THR 121 318 318 THR THR A . n A 1 122 VAL 122 319 319 VAL VAL A . n A 1 123 GLY 123 320 320 GLY GLY A . n A 1 124 ILE 124 321 321 ILE ILE A . n A 1 125 TYR 125 322 322 TYR TYR A . n A 1 126 PHE 126 323 323 PHE PHE A . n A 1 127 ARG 127 324 324 ARG ARG A . n A 1 128 GLN 128 325 325 GLN GLN A . n A 1 129 SER 129 326 326 SER SER A . n A 1 130 GLN 130 327 327 GLN GLN A . n A 1 131 GLU 131 328 328 GLU GLU A . n A 1 132 LYS 132 329 329 LYS LYS A . n A 1 133 MSE 133 330 330 MSE MSE A . n A 1 134 ARG 134 331 331 ARG ARG A . n A 1 135 PHE 135 332 332 PHE PHE A . n A 1 136 GLY 136 333 333 GLY GLY A . n A 1 137 ARG 137 334 334 ARG ARG A . n A 1 138 GLN 138 335 335 GLN GLN A . n A 1 139 GLY 139 336 336 GLY GLY A . n A 1 140 LEU 140 337 337 LEU LEU A . n A 1 141 ARG 141 338 338 ARG ARG A . n A 1 142 LEU 142 339 339 LEU LEU A . n A 1 143 HIS 143 340 340 HIS HIS A . n A 1 144 LYS 144 341 341 LYS LYS A . n A 1 145 ASP 145 342 342 ASP ASP A . n A 1 146 TRP 146 343 343 TRP TRP A . n A 1 147 VAL 147 344 344 VAL VAL A . n A 1 148 ASP 148 345 345 ASP ASP A . n A 1 149 GLY 149 346 346 GLY GLY A . n A 1 150 THR 150 347 347 THR THR A . n A 1 151 TRP 151 348 348 TRP TRP A . n A 1 152 GLN 152 349 349 GLN GLN A . n A 1 153 LEU 153 350 350 LEU LEU A . n A 1 154 PRO 154 351 351 PRO PRO A . n A 1 155 LEU 155 352 ? ? ? A . n A 1 156 LYS 156 353 ? ? ? A . n A 1 157 GLY 157 354 ? ? ? A . n A 1 158 GLY 158 355 ? ? ? A . n A 1 159 LYS 159 356 ? ? ? A . n A 1 160 ILE 160 357 ? ? ? A . n A 1 161 LYS 161 358 ? ? ? A . n A 1 162 ARG 162 359 ? ? ? A . n A 1 163 GLU 163 360 ? ? ? A . n A 1 164 LYS 164 361 ? ? ? A . n A 1 165 THR 165 362 ? ? ? A . n A 1 166 VAL 166 363 ? ? ? A . n A 1 167 SER 167 364 ? ? ? 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 HOH 1 401 64 HOH HOH A . B 2 HOH 2 402 58 HOH HOH A . B 2 HOH 3 403 79 HOH HOH A . B 2 HOH 4 404 33 HOH HOH A . B 2 HOH 5 405 1 HOH HOH A . B 2 HOH 6 406 2 HOH HOH A . B 2 HOH 7 407 46 HOH HOH A . B 2 HOH 8 408 11 HOH HOH A . B 2 HOH 9 409 32 HOH HOH A . B 2 HOH 10 410 34 HOH HOH A . B 2 HOH 11 411 82 HOH HOH A . B 2 HOH 12 412 21 HOH HOH A . B 2 HOH 13 413 20 HOH HOH A . B 2 HOH 14 414 19 HOH HOH A . B 2 HOH 15 415 44 HOH HOH A . B 2 HOH 16 416 3 HOH HOH A . B 2 HOH 17 417 40 HOH HOH A . B 2 HOH 18 418 75 HOH HOH A . B 2 HOH 19 419 6 HOH HOH A . B 2 HOH 20 420 14 HOH HOH A . B 2 HOH 21 421 10 HOH HOH A . B 2 HOH 22 422 23 HOH HOH A . B 2 HOH 23 423 35 HOH HOH A . B 2 HOH 24 424 63 HOH HOH A . B 2 HOH 25 425 18 HOH HOH A . B 2 HOH 26 426 66 HOH HOH A . B 2 HOH 27 427 68 HOH HOH A . B 2 HOH 28 428 80 HOH HOH A . B 2 HOH 29 429 45 HOH HOH A . B 2 HOH 30 430 36 HOH HOH A . B 2 HOH 31 431 47 HOH HOH A . B 2 HOH 32 432 31 HOH HOH A . B 2 HOH 33 433 59 HOH HOH A . B 2 HOH 34 434 13 HOH HOH A . B 2 HOH 35 435 76 HOH HOH A . B 2 HOH 36 436 38 HOH HOH A . B 2 HOH 37 437 5 HOH HOH A . B 2 HOH 38 438 71 HOH HOH A . B 2 HOH 39 439 12 HOH HOH A . B 2 HOH 40 440 53 HOH HOH A . B 2 HOH 41 441 69 HOH HOH A . B 2 HOH 42 442 16 HOH HOH A . B 2 HOH 43 443 15 HOH HOH A . B 2 HOH 44 444 62 HOH HOH A . B 2 HOH 45 445 50 HOH HOH A . B 2 HOH 46 446 78 HOH HOH A . B 2 HOH 47 447 30 HOH HOH A . B 2 HOH 48 448 8 HOH HOH A . B 2 HOH 49 449 85 HOH HOH A . B 2 HOH 50 450 25 HOH HOH A . B 2 HOH 51 451 41 HOH HOH A . B 2 HOH 52 452 52 HOH HOH A . B 2 HOH 53 453 24 HOH HOH A . B 2 HOH 54 454 9 HOH HOH A . B 2 HOH 55 455 4 HOH HOH A . B 2 HOH 56 456 87 HOH HOH A . B 2 HOH 57 457 7 HOH HOH A . B 2 HOH 58 458 43 HOH HOH A . B 2 HOH 59 459 49 HOH HOH A . B 2 HOH 60 460 54 HOH HOH A . B 2 HOH 61 461 84 HOH HOH A . B 2 HOH 62 462 55 HOH HOH A . B 2 HOH 63 463 39 HOH HOH A . B 2 HOH 64 464 27 HOH HOH A . B 2 HOH 65 465 61 HOH HOH A . B 2 HOH 66 466 17 HOH HOH A . B 2 HOH 67 467 56 HOH HOH A . B 2 HOH 68 468 57 HOH HOH A . B 2 HOH 69 469 60 HOH HOH A . B 2 HOH 70 470 22 HOH HOH A . B 2 HOH 71 471 26 HOH HOH A . B 2 HOH 72 472 37 HOH HOH A . B 2 HOH 73 473 28 HOH HOH A . B 2 HOH 74 474 81 HOH HOH A . B 2 HOH 75 475 74 HOH HOH A . B 2 HOH 76 476 70 HOH HOH A . B 2 HOH 77 477 65 HOH HOH A . B 2 HOH 78 478 73 HOH HOH A . B 2 HOH 79 479 86 HOH HOH A . B 2 HOH 80 480 51 HOH HOH A . B 2 HOH 81 481 72 HOH HOH A . B 2 HOH 82 482 29 HOH HOH A . B 2 HOH 83 483 48 HOH HOH A . B 2 HOH 84 484 67 HOH HOH A . B 2 HOH 85 485 83 HOH HOH A . B 2 HOH 86 486 77 HOH HOH A . B 2 HOH 87 487 42 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 23 A MSE 220 ? MET 'modified residue' 2 A MSE 117 A MSE 314 ? MET 'modified residue' 3 A MSE 133 A MSE 330 ? MET 'modified residue' # _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 # 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)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 8540 ? # _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_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 457 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2018-11-14 # _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_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 16.8724 28.7518 95.2933 0.4102 0.2919 0.4974 -0.0152 -0.0435 -0.1093 3.6866 2.0419 2.7340 -0.2434 -0.2725 0.8140 -0.2841 -0.1481 0.7009 0.0375 0.2739 -0.2789 -0.2502 0.1180 -0.4598 'X-RAY DIFFRACTION' 2 ? refined -0.0557 22.1763 89.7571 0.7832 0.7590 1.1176 -0.0173 -0.0954 0.0621 6.6119 3.8251 3.4699 -1.0792 2.1272 -2.6289 -0.0919 0.5529 1.4867 -0.2720 0.3106 1.8860 -0.4106 -1.2277 -0.0286 'X-RAY DIFFRACTION' 3 ? refined 15.7960 23.2094 86.4066 0.5455 0.3551 0.4776 -0.0353 0.1068 -0.0324 5.2807 3.7744 4.5819 0.2381 -1.3138 0.5988 0.1685 0.2247 0.6067 -0.6097 0.1318 -0.5128 -0.5689 0.0946 -0.1467 'X-RAY DIFFRACTION' 4 ? refined 11.1218 18.1316 84.6617 0.4369 0.3615 0.3195 0.0074 -0.0211 -0.0470 2.4643 2.5832 2.4170 0.2936 -0.6053 2.2497 -0.1402 0.4773 0.1750 -0.6296 -0.1502 0.1893 -0.4255 -0.0982 -0.0055 'X-RAY DIFFRACTION' 5 ? refined 8.3345 11.9292 108.8124 0.6590 0.5908 0.5094 0.1740 0.0891 0.0526 2.9053 2.0130 2.6687 2.1915 -2.4282 -1.2287 -0.4501 -1.5150 -0.9622 0.4649 0.0055 -0.5454 0.7721 0.9199 0.2975 'X-RAY DIFFRACTION' 6 ? refined 0.9346 9.8676 101.8812 0.3466 0.2538 0.3901 0.0111 0.0145 -0.0733 3.7121 2.7589 2.7783 0.5255 -1.5256 0.8575 -0.1956 0.0970 -0.1472 0.1439 0.2449 0.2069 0.1468 -0.0475 0.2333 'X-RAY DIFFRACTION' 7 ? refined 2.5315 15.0257 102.7550 0.4308 0.2794 0.3157 0.0064 -0.0023 -0.0891 4.8362 3.4021 1.9292 0.5241 -1.8429 -1.0665 0.0408 -0.1235 0.1632 0.1090 -0.0981 0.4386 -0.0260 -0.0469 0.1494 # 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.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _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 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 206 through 230 ) ; 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 231 through 239 ) ; 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 240 through 258 ) ; 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 259 through 281 ) ; 'X-RAY DIFFRACTION' 5 5 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 282 through 295 ) ; 'X-RAY DIFFRACTION' 6 6 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 296 through 317 ) ; 'X-RAY DIFFRACTION' 7 7 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 318 through 351 ) ; # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.9_1692 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ASP _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 286 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi 14.89 _pdbx_validate_torsion.psi 93.20 # 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 SER 198 ? A SER 1 2 1 Y 1 A GLU 199 ? A GLU 2 3 1 Y 1 A ASP 200 ? A ASP 3 4 1 Y 1 A GLU 201 ? A GLU 4 5 1 Y 1 A GLU 202 ? A GLU 5 6 1 Y 1 A ASP 203 ? A ASP 6 7 1 Y 1 A ILE 204 ? A ILE 7 8 1 Y 1 A LEU 205 ? A LEU 8 9 1 Y 1 A LEU 352 ? A LEU 155 10 1 Y 1 A LYS 353 ? A LYS 156 11 1 Y 1 A GLY 354 ? A GLY 157 12 1 Y 1 A GLY 355 ? A GLY 158 13 1 Y 1 A LYS 356 ? A LYS 159 14 1 Y 1 A ILE 357 ? A ILE 160 15 1 Y 1 A LYS 358 ? A LYS 161 16 1 Y 1 A ARG 359 ? A ARG 162 17 1 Y 1 A GLU 360 ? A GLU 163 18 1 Y 1 A LYS 361 ? A LYS 164 19 1 Y 1 A THR 362 ? A THR 165 20 1 Y 1 A VAL 363 ? A VAL 166 21 1 Y 1 A SER 364 ? A SER 167 # _pdbx_audit_support.funding_organization 'Ministry of Science and Technology (China)' _pdbx_audit_support.country China _pdbx_audit_support.grant_number 2016YFA0503200 _pdbx_audit_support.ordinal 1 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #