data_5YVX # _entry.id 5YVX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.291 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5YVX WWPDB D_1300005913 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5YVX _pdbx_database_status.recvd_initial_deposition_date 2017-11-27 _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 'Liu, Y.' 1 ? 'Huang, Y.' 2 ? # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'J. Biol. Chem.' _citation.journal_id_ASTM JBCHA3 _citation.journal_id_CSD 0071 _citation.journal_id_ISSN 1083-351X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 293 _citation.language ? _citation.page_first 6470 _citation.page_last 6481 _citation.title ;Uncovering the mechanistic basis for specific recognition of monomethylated H3K4 by the CW domain ofArabidopsishistone methyltransferase SDG8. ; _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1074/jbc.RA117.001390 _citation.pdbx_database_id_PubMed 29496997 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Liu, Y.' 1 primary 'Huang, Y.' 2 # _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 5YVX _cell.details ? _cell.formula_units_Z ? _cell.length_a 66.421 _cell.length_a_esd ? _cell.length_b 66.421 _cell.length_b_esd ? _cell.length_c 29.241 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 6 _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 5YVX _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' _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 'Histone-lysine N-methyltransferase ASHH2' 6909.692 1 2.1.1.43 E917A ? ? 2 polymer syn H3K4me1 1076.273 1 ? ? ? ? 3 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ? 4 water nat water 18.015 84 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;ASH1 homolog 2,H3-K4-HMTase,Histone H3-K36 methyltransferase 8,H3-K36-HMTase 8,Protein EARLY FLOWERING IN SHORT DAYS,Protein LAZARUS 2,Protein SET DOMAIN GROUP 8 ; # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ESAWVRCDDCFKWRRIPASVVGSIDESSRWICMNNSDKRFADCSKSQEMSNEEINAELGI ESAWVRCDDCFKWRRIPASVVGSIDESSRWICMNNSDKRFADCSKSQEMSNEEINAELGI A ? 2 'polypeptide(L)' no yes 'ART(MLZ)QTARK' ARTKQTARK C ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLU n 1 2 SER n 1 3 ALA n 1 4 TRP n 1 5 VAL n 1 6 ARG n 1 7 CYS n 1 8 ASP n 1 9 ASP n 1 10 CYS n 1 11 PHE n 1 12 LYS n 1 13 TRP n 1 14 ARG n 1 15 ARG n 1 16 ILE n 1 17 PRO n 1 18 ALA n 1 19 SER n 1 20 VAL n 1 21 VAL n 1 22 GLY n 1 23 SER n 1 24 ILE n 1 25 ASP n 1 26 GLU n 1 27 SER n 1 28 SER n 1 29 ARG n 1 30 TRP n 1 31 ILE n 1 32 CYS n 1 33 MET n 1 34 ASN n 1 35 ASN n 1 36 SER n 1 37 ASP n 1 38 LYS n 1 39 ARG n 1 40 PHE n 1 41 ALA n 1 42 ASP n 1 43 CYS n 1 44 SER n 1 45 LYS n 1 46 SER n 1 47 GLN n 1 48 GLU n 1 49 MET n 1 50 SER n 1 51 ASN n 1 52 GLU n 1 53 GLU n 1 54 ILE n 1 55 ASN n 1 56 ALA n 1 57 GLU n 1 58 LEU n 1 59 GLY n 1 60 ILE n 2 1 ALA n 2 2 ARG n 2 3 THR n 2 4 MLZ n 2 5 GLN n 2 6 THR n 2 7 ALA n 2 8 ARG n 2 9 LYS 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 60 _entity_src_gen.gene_src_common_name 'Mouse-ear cress' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'ASHH2, EFS, LAZ2, SDG8, SET8, At1g77300, T14N5.15' _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' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _pdbx_entity_src_syn.entity_id 2 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 9 _pdbx_entity_src_syn.organism_scientific 'Arabidopsis thaliana' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 3702 _pdbx_entity_src_syn.details ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 UNP ASHH2_ARATH Q2LAE1 ? 1 ESAWVRCDDCFKWRRIPASVVGSIDESSRWICMNNSDKRFADCSKSQEMSNEEINEELGI 862 2 PDB 5YVX 5YVX ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 5YVX A 1 ? 60 ? Q2LAE1 862 ? 921 ? 862 921 2 2 5YVX C 1 ? 9 ? 5YVX 1 ? 9 ? 1 9 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 5YVX _struct_ref_seq_dif.mon_id ALA _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 56 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q2LAE1 _struct_ref_seq_dif.db_mon_id GLU _struct_ref_seq_dif.pdbx_seq_db_seq_num 917 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 917 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MLZ 'L-peptide linking' n N-METHYL-LYSINE ? 'C7 H16 N2 O2' 160.214 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 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # _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 5YVX _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 2.44 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 49.52 _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, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.1 M Tris pH 8.5, 30% PEG 3350, 30% iso-propanol' _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 CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'RAYONIX MX-225' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-08-03 # _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 1.2824 _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 BL19U1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.2824 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL19U1 _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5YVX _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.59 _reflns.d_resolution_low 30 _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 19136 _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 98.6 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.4 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 26.6 _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 1.59 _reflns_shell.d_res_low 1.65 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all ? _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 ? _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 ? _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 5YVX _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 1.591 _refine.ls_d_res_low 28.761 _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 19132 _refine.ls_number_reflns_R_free 1900 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.64 _refine.ls_percent_reflns_R_free 9.93 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1692 _refine.ls_R_factor_R_free 0.1845 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1675 _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 1.51 _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 17.87 _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 0.18 _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 529 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 84 _refine_hist.number_atoms_total 614 _refine_hist.d_res_high 1.591 _refine_hist.d_res_low 28.761 # 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' ? 0.007 ? 536 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.991 ? 718 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 15.524 ? 199 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.045 ? 76 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.005 ? 93 ? 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' 1.5913 1.6311 . . 117 1103 87.00 . . . 0.3191 . 0.2700 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.6311 1.6752 . . 132 1222 98.00 . . . 0.2697 . 0.2412 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.6752 1.7245 . . 144 1240 99.00 . . . 0.2489 . 0.2365 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.7245 1.7801 . . 136 1198 99.00 . . . 0.2374 . 0.2055 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.7801 1.8437 . . 143 1279 100.00 . . . 0.2220 . 0.1887 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.8437 1.9175 . . 126 1247 100.00 . . . 0.2044 . 0.1885 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.9175 2.0048 . . 140 1226 100.00 . . . 0.2130 . 0.1720 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.0048 2.1104 . . 135 1240 100.00 . . . 0.1770 . 0.1645 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.1104 2.2426 . . 142 1249 100.00 . . . 0.2083 . 0.1726 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.2426 2.4157 . . 141 1236 100.00 . . . 0.2097 . 0.1623 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.4157 2.6586 . . 139 1254 100.00 . . . 0.1723 . 0.1787 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.6586 3.0430 . . 136 1243 100.00 . . . 0.1648 . 0.1823 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.0430 3.8324 . . 131 1252 100.00 . . . 0.1838 . 0.1501 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.8324 28.7658 . . 138 1243 100.00 . . . 0.1482 . 0.1379 . . . . . . . . . . # _struct.entry_id 5YVX _struct.title 'Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide' _struct.pdbx_descriptor 'Histone-lysine N-methyltransferase ASHH2 (E.C.2.1.1.43), H3K4me1' _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 5YVX _struct_keywords.text 'SDG8, CW domain, H3K4me1, TRANSFERASE' _struct_keywords.pdbx_keywords TRANSFERASE # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? # 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 AA1 ALA A 18 ? GLY A 22 ? ALA A 879 GLY A 883 1 ? 5 HELX_P HELX_P2 AA2 ILE A 31 ? ASN A 35 ? ILE A 892 ASN A 896 5 ? 5 HELX_P HELX_P3 AA3 SER A 50 ? GLY A 59 ? SER A 911 GLY A 920 1 ? 10 # _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 metalc1 metalc ? ? A CYS 7 SG ? ? ? 1_555 C ZN . ZN L ? A CYS 868 A ZN 1001 1_555 ? ? ? ? ? ? ? 2.363 ? metalc2 metalc ? ? A CYS 10 SG ? ? ? 1_555 C ZN . ZN L ? A CYS 871 A ZN 1001 1_555 ? ? ? ? ? ? ? 2.313 ? metalc3 metalc ? ? A CYS 32 SG ? ? ? 1_555 C ZN . ZN L ? A CYS 893 A ZN 1001 1_555 ? ? ? ? ? ? ? 2.336 ? metalc4 metalc ? ? A CYS 43 SG ? ? ? 1_555 C ZN . ZN L ? A CYS 904 A ZN 1001 1_555 ? ? ? ? ? ? ? 2.311 ? covale1 covale both ? B THR 3 C ? ? ? 1_555 B MLZ 4 N ? ? C THR 3 C MLZ 4 1_555 ? ? ? ? ? ? ? 1.331 ? covale2 covale both ? B MLZ 4 C ? ? ? 1_555 B GLN 5 N ? ? C MLZ 4 C GLN 5 1_555 ? ? ? ? ? ? ? 1.331 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? covale ? ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 3 _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 AA1 1 2 ? anti-parallel AA1 2 3 ? 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 TRP A 13 ? PRO A 17 ? TRP A 874 PRO A 878 AA1 2 SER A 2 ? ARG A 6 ? SER A 863 ARG A 867 AA1 3 THR B 3 ? MLZ B 4 ? THR C 3 MLZ C 4 # 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 ILE A 16 ? O ILE A 877 N ALA A 3 ? N ALA A 864 AA1 2 3 N TRP A 4 ? N TRP A 865 O MLZ B 4 ? O MLZ C 4 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A ZN 1001 ? 4 'binding site for residue ZN A 1001' AC2 Software C MLZ 4 ? 11 'binding site for Ligand residues MLZ C 4 through GLN C 5 bound to THR C 3' # 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 4 CYS A 7 ? CYS A 868 . ? 1_555 ? 2 AC1 4 CYS A 10 ? CYS A 871 . ? 1_555 ? 3 AC1 4 CYS A 32 ? CYS A 893 . ? 1_555 ? 4 AC1 4 CYS A 43 ? CYS A 904 . ? 1_555 ? 5 AC2 11 ALA A 3 ? ALA A 864 . ? 1_555 ? 6 AC2 11 TRP A 4 ? TRP A 865 . ? 1_555 ? 7 AC2 11 VAL A 21 ? VAL A 882 . ? 1_555 ? 8 AC2 11 ASN A 55 ? ASN A 916 . ? 1_555 ? 9 AC2 11 LEU A 58 ? LEU A 919 . ? 1_555 ? 10 AC2 11 THR B 3 ? THR C 3 . ? 1_555 ? 11 AC2 11 THR B 6 ? THR C 6 . ? 1_555 ? 12 AC2 11 ALA B 7 ? ALA C 7 . ? 1_555 ? 13 AC2 11 HOH E . ? HOH C 102 . ? 1_555 ? 14 AC2 11 HOH E . ? HOH C 103 . ? 1_555 ? 15 AC2 11 HOH E . ? HOH C 106 . ? 1_555 ? # _atom_sites.entry_id 5YVX _atom_sites.fract_transf_matrix[1][1] 0.015055 _atom_sites.fract_transf_matrix[1][2] 0.008692 _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] 0.017385 _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] 0.034199 _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 ZN # 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 GLU 1 862 862 GLU ALA A . n A 1 2 SER 2 863 863 SER SER A . n A 1 3 ALA 3 864 864 ALA ALA A . n A 1 4 TRP 4 865 865 TRP TRP A . n A 1 5 VAL 5 866 866 VAL VAL A . n A 1 6 ARG 6 867 867 ARG ARG A . n A 1 7 CYS 7 868 868 CYS CYS A . n A 1 8 ASP 8 869 869 ASP ASP A . n A 1 9 ASP 9 870 870 ASP ASP A . n A 1 10 CYS 10 871 871 CYS CYS A . n A 1 11 PHE 11 872 872 PHE PHE A . n A 1 12 LYS 12 873 873 LYS LYS A . n A 1 13 TRP 13 874 874 TRP TRP A . n A 1 14 ARG 14 875 875 ARG ARG A . n A 1 15 ARG 15 876 876 ARG ARG A . n A 1 16 ILE 16 877 877 ILE ILE A . n A 1 17 PRO 17 878 878 PRO PRO A . n A 1 18 ALA 18 879 879 ALA ALA A . n A 1 19 SER 19 880 880 SER SER A . n A 1 20 VAL 20 881 881 VAL VAL A . n A 1 21 VAL 21 882 882 VAL VAL A . n A 1 22 GLY 22 883 883 GLY GLY A . n A 1 23 SER 23 884 884 SER SER A . n A 1 24 ILE 24 885 885 ILE ILE A . n A 1 25 ASP 25 886 886 ASP ASP A . n A 1 26 GLU 26 887 887 GLU GLU A . n A 1 27 SER 27 888 888 SER SER A . n A 1 28 SER 28 889 889 SER SER A . n A 1 29 ARG 29 890 890 ARG ARG A . n A 1 30 TRP 30 891 891 TRP TRP A . n A 1 31 ILE 31 892 892 ILE ILE A . n A 1 32 CYS 32 893 893 CYS CYS A . n A 1 33 MET 33 894 894 MET MET A . n A 1 34 ASN 34 895 895 ASN ASN A . n A 1 35 ASN 35 896 896 ASN ASN A . n A 1 36 SER 36 897 897 SER SER A . n A 1 37 ASP 37 898 898 ASP ASP A . n A 1 38 LYS 38 899 899 LYS LYS A . n A 1 39 ARG 39 900 900 ARG ARG A . n A 1 40 PHE 40 901 901 PHE PHE A . n A 1 41 ALA 41 902 902 ALA ALA A . n A 1 42 ASP 42 903 903 ASP ASP A . n A 1 43 CYS 43 904 904 CYS CYS A . n A 1 44 SER 44 905 905 SER SER A . n A 1 45 LYS 45 906 906 LYS LYS A . n A 1 46 SER 46 907 907 SER SER A . n A 1 47 GLN 47 908 908 GLN GLN A . n A 1 48 GLU 48 909 909 GLU GLU A . n A 1 49 MET 49 910 910 MET MET A . n A 1 50 SER 50 911 911 SER SER A . n A 1 51 ASN 51 912 912 ASN ASN A . n A 1 52 GLU 52 913 913 GLU GLU A . n A 1 53 GLU 53 914 914 GLU GLU A . n A 1 54 ILE 54 915 915 ILE ILE A . n A 1 55 ASN 55 916 916 ASN ASN A . n A 1 56 ALA 56 917 917 ALA ALA A . n A 1 57 GLU 57 918 918 GLU GLU A . n A 1 58 LEU 58 919 919 LEU LEU A . n A 1 59 GLY 59 920 920 GLY GLY A . n A 1 60 ILE 60 921 921 ILE ILE A . n B 2 1 ALA 1 1 1 ALA ALA C . n B 2 2 ARG 2 2 2 ARG ARG C . n B 2 3 THR 3 3 3 THR THR C . n B 2 4 MLZ 4 4 4 MLZ MLZ C . n B 2 5 GLN 5 5 5 GLN GLN C . n B 2 6 THR 6 6 6 THR THR C . n B 2 7 ALA 7 7 7 ALA ALA C . n B 2 8 ARG 8 8 ? ? ? C . n B 2 9 LYS 9 9 ? ? ? C . 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 C 3 ZN 1 1001 1 ZN ZN A . D 4 HOH 1 1101 42 HOH HOH A . D 4 HOH 2 1102 49 HOH HOH A . D 4 HOH 3 1103 43 HOH HOH A . D 4 HOH 4 1104 53 HOH HOH A . D 4 HOH 5 1105 29 HOH HOH A . D 4 HOH 6 1106 18 HOH HOH A . D 4 HOH 7 1107 4 HOH HOH A . D 4 HOH 8 1108 81 HOH HOH A . D 4 HOH 9 1109 47 HOH HOH A . D 4 HOH 10 1110 28 HOH HOH A . D 4 HOH 11 1111 14 HOH HOH A . D 4 HOH 12 1112 24 HOH HOH A . D 4 HOH 13 1113 77 HOH HOH A . D 4 HOH 14 1114 7 HOH HOH A . D 4 HOH 15 1115 46 HOH HOH A . D 4 HOH 16 1116 16 HOH HOH A . D 4 HOH 17 1117 32 HOH HOH A . D 4 HOH 18 1118 8 HOH HOH A . D 4 HOH 19 1119 30 HOH HOH A . D 4 HOH 20 1120 21 HOH HOH A . D 4 HOH 21 1121 64 HOH HOH A . D 4 HOH 22 1122 25 HOH HOH A . D 4 HOH 23 1123 45 HOH HOH A . D 4 HOH 24 1124 5 HOH HOH A . D 4 HOH 25 1125 63 HOH HOH A . D 4 HOH 26 1126 76 HOH HOH A . D 4 HOH 27 1127 34 HOH HOH A . D 4 HOH 28 1128 36 HOH HOH A . D 4 HOH 29 1129 10 HOH HOH A . D 4 HOH 30 1130 59 HOH HOH A . D 4 HOH 31 1131 6 HOH HOH A . D 4 HOH 32 1132 73 HOH HOH A . D 4 HOH 33 1133 13 HOH HOH A . D 4 HOH 34 1134 35 HOH HOH A . D 4 HOH 35 1135 62 HOH HOH A . D 4 HOH 36 1136 31 HOH HOH A . D 4 HOH 37 1137 22 HOH HOH A . D 4 HOH 38 1138 23 HOH HOH A . D 4 HOH 39 1139 27 HOH HOH A . D 4 HOH 40 1140 50 HOH HOH A . D 4 HOH 41 1141 1 HOH HOH A . D 4 HOH 42 1142 2 HOH HOH A . D 4 HOH 43 1143 15 HOH HOH A . D 4 HOH 44 1144 79 HOH HOH A . D 4 HOH 45 1145 40 HOH HOH A . D 4 HOH 46 1146 11 HOH HOH A . D 4 HOH 47 1147 69 HOH HOH A . D 4 HOH 48 1148 12 HOH HOH A . D 4 HOH 49 1149 3 HOH HOH A . D 4 HOH 50 1150 66 HOH HOH A . D 4 HOH 51 1151 61 HOH HOH A . D 4 HOH 52 1152 44 HOH HOH A . D 4 HOH 53 1153 9 HOH HOH A . D 4 HOH 54 1154 74 HOH HOH A . D 4 HOH 55 1155 20 HOH HOH A . D 4 HOH 56 1156 54 HOH HOH A . D 4 HOH 57 1157 48 HOH HOH A . D 4 HOH 58 1158 78 HOH HOH A . D 4 HOH 59 1159 84 HOH HOH A . D 4 HOH 60 1160 52 HOH HOH A . D 4 HOH 61 1161 19 HOH HOH A . D 4 HOH 62 1162 80 HOH HOH A . D 4 HOH 63 1163 38 HOH HOH A . D 4 HOH 64 1164 57 HOH HOH A . D 4 HOH 65 1165 83 HOH HOH A . D 4 HOH 66 1166 58 HOH HOH A . D 4 HOH 67 1167 41 HOH HOH A . D 4 HOH 68 1168 67 HOH HOH A . D 4 HOH 69 1169 55 HOH HOH A . D 4 HOH 70 1170 71 HOH HOH A . D 4 HOH 71 1171 51 HOH HOH A . D 4 HOH 72 1172 65 HOH HOH A . D 4 HOH 73 1173 39 HOH HOH A . D 4 HOH 74 1174 37 HOH HOH A . D 4 HOH 75 1175 82 HOH HOH A . E 4 HOH 1 101 60 HOH HOH C . E 4 HOH 2 102 33 HOH HOH C . E 4 HOH 3 103 68 HOH HOH C . E 4 HOH 4 104 26 HOH HOH C . E 4 HOH 5 105 72 HOH HOH C . E 4 HOH 6 106 17 HOH HOH C . E 4 HOH 7 107 75 HOH HOH C . E 4 HOH 8 108 56 HOH HOH C . E 4 HOH 9 109 70 HOH HOH C . # _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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)' 1130 ? 1 MORE -9 ? 1 'SSA (A^2)' 4220 ? # _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_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 1173 ? D HOH . 2 1 C HOH 105 ? E HOH . 3 1 C HOH 108 ? E HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 SG ? A CYS 7 ? A CYS 868 ? 1_555 ZN L C ZN . ? A ZN 1001 ? 1_555 SG ? A CYS 10 ? A CYS 871 ? 1_555 109.8 ? 2 SG ? A CYS 7 ? A CYS 868 ? 1_555 ZN L C ZN . ? A ZN 1001 ? 1_555 SG ? A CYS 32 ? A CYS 893 ? 1_555 102.6 ? 3 SG ? A CYS 10 ? A CYS 871 ? 1_555 ZN L C ZN . ? A ZN 1001 ? 1_555 SG ? A CYS 32 ? A CYS 893 ? 1_555 107.1 ? 4 SG ? A CYS 7 ? A CYS 868 ? 1_555 ZN L C ZN . ? A ZN 1001 ? 1_555 SG ? A CYS 43 ? A CYS 904 ? 1_555 107.7 ? 5 SG ? A CYS 10 ? A CYS 871 ? 1_555 ZN L C ZN . ? A ZN 1001 ? 1_555 SG ? A CYS 43 ? A CYS 904 ? 1_555 111.3 ? 6 SG ? A CYS 32 ? A CYS 893 ? 1_555 ZN L C ZN . ? A ZN 1001 ? 1_555 SG ? A CYS 43 ? A CYS 904 ? 1_555 117.9 ? # 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 2018-03-14 2 'Structure model' 1 1 2018-05-09 # _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' 'Data collection' 2 2 'Structure model' 'Database references' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category citation # 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 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.title' # 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 ? ? ? 1.8.4_1496 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 1132 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 1165 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.91 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 1157 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 1169 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 1_556 _pdbx_validate_symm_contact.dist 1.84 # 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 862 ? CG ? A GLU 1 CG 2 1 Y 1 A GLU 862 ? CD ? A GLU 1 CD 3 1 Y 1 A GLU 862 ? OE1 ? A GLU 1 OE1 4 1 Y 1 A GLU 862 ? OE2 ? A GLU 1 OE2 # 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 C ARG 8 ? B ARG 8 2 1 Y 1 C LYS 9 ? B LYS 9 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'ZINC ION' ZN 4 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'isothermal titration calorimetry' _pdbx_struct_assembly_auth_evidence.details 'the equilibrium disassociation constants (Kd) of SDG8 CW domain to H3K4me1 is 1.29 uM.' #