data_3KQI # _entry.id 3KQI # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.305 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3KQI RCSB RCSB056320 WWPDB D_1000056320 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3KQI _pdbx_database_status.recvd_initial_deposition_date 2009-11-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Wen, H.' 1 'Li, J.Z.' 2 'Song, T.' 3 'Lu, M.' 4 'Lee, M.' 5 # _citation.id primary _citation.title 'Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation.' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 285 _citation.page_first 9322 _citation.page_last 9326 _citation.year 2010 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20129925 _citation.pdbx_database_id_DOI 10.1074/jbc.C109.097667 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wen, H.' 1 ? primary 'Li, J.' 2 ? primary 'Song, T.' 3 ? primary 'Lu, M.' 4 ? primary 'Kan, P.Y.' 5 ? primary 'Lee, M.G.' 6 ? primary 'Sha, B.' 7 ? primary 'Shi, X.' 8 ? # _cell.entry_id 3KQI _cell.length_a 77.757 _cell.length_b 77.758 _cell.length_c 72.116 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3KQI _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'PHD finger protein 2' 8575.896 1 ? ? 'PHD finger' ? 2 polymer syn 'H3K4Me3 peptide' 1350.568 1 ? ? ? ? 3 non-polymer syn 'ZINC ION' 65.409 2 ? ? ? ? 4 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 5 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 6 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 7 water nat water 18.015 125 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name GRC5 # 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 GPLGSMATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTHGKSTLKKKRTWHK GPLGSMATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTHGKSTLKKKRTWHK A ? 2 'polypeptide(L)' no yes 'ART(M3L)QTARKSTG' ARTKQTARKSTG B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 PRO n 1 3 LEU n 1 4 GLY n 1 5 SER n 1 6 MET n 1 7 ALA n 1 8 THR n 1 9 VAL n 1 10 PRO n 1 11 VAL n 1 12 TYR n 1 13 CYS n 1 14 VAL n 1 15 CYS n 1 16 ARG n 1 17 LEU n 1 18 PRO n 1 19 TYR n 1 20 ASP n 1 21 VAL n 1 22 THR n 1 23 ARG n 1 24 PHE n 1 25 MET n 1 26 ILE n 1 27 GLU n 1 28 CYS n 1 29 ASP n 1 30 ALA n 1 31 CYS n 1 32 LYS n 1 33 ASP n 1 34 TRP n 1 35 PHE n 1 36 HIS n 1 37 GLY n 1 38 SER n 1 39 CYS n 1 40 VAL n 1 41 GLY n 1 42 VAL n 1 43 GLU n 1 44 GLU n 1 45 GLU n 1 46 GLU n 1 47 ALA n 1 48 PRO n 1 49 ASP n 1 50 ILE n 1 51 ASP n 1 52 ILE n 1 53 TYR n 1 54 HIS n 1 55 CYS n 1 56 PRO n 1 57 ASN n 1 58 CYS n 1 59 GLU n 1 60 LYS n 1 61 THR n 1 62 HIS n 1 63 GLY n 1 64 LYS n 1 65 SER n 1 66 THR n 1 67 LEU n 1 68 LYS n 1 69 LYS n 1 70 LYS n 1 71 ARG n 1 72 THR n 1 73 TRP n 1 74 HIS n 1 75 LYS n 2 1 ALA n 2 2 ARG n 2 3 THR n 2 4 M3L n 2 5 GLN n 2 6 THR n 2 7 ALA n 2 8 ARG n 2 9 LYS n 2 10 SER n 2 11 THR n 2 12 GLY n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'KIAA0662, PHF2' _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 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 ? _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 PGEX6P1 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP PHF2_HUMAN O75151 1 MATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTHGKSTLKKKRTWHK 1 ? 2 UNP H31_HUMAN P68431 2 ARTKQTARKSTG 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 3KQI A 6 ? 75 ? O75151 1 ? 70 ? 1 70 2 2 3KQI B 1 ? 12 ? P68431 1 ? 12 ? 1 12 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3KQI GLY A 1 ? UNP O75151 ? ? 'EXPRESSION TAG' -4 1 1 3KQI PRO A 2 ? UNP O75151 ? ? 'EXPRESSION TAG' -3 2 1 3KQI LEU A 3 ? UNP O75151 ? ? 'EXPRESSION TAG' -2 3 1 3KQI GLY A 4 ? UNP O75151 ? ? 'EXPRESSION TAG' -1 4 1 3KQI SER A 5 ? UNP O75151 ? ? 'EXPRESSION TAG' 0 5 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 M3L 'L-peptide linking' n N-TRIMETHYLLYSINE ? 'C9 H21 N2 O2 1' 189.275 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 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 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # _exptl.entry_id 3KQI _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.17 _exptl_crystal.density_percent_sol 61.20 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details '2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 200 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.pdbx_collection_date 2009-07-31 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 22-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 22-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 3KQI _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.78 _reflns.number_obs 11858 _reflns.number_all 11858 _reflns.percent_possible_obs 89.0 _reflns.pdbx_Rmerge_I_obs 0.07 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 0.3896 _reflns.B_iso_Wilson_estimate 31 _reflns.pdbx_redundancy 9.0 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.78 _reflns_shell.d_res_low 1.84 _reflns_shell.percent_possible_all 62.9 _reflns_shell.Rmerge_I_obs 0.381 _reflns_shell.pdbx_Rsym_value 0.381 _reflns_shell.meanI_over_sigI_obs 3.83 _reflns_shell.pdbx_redundancy 4.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 927 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3KQI _refine.ls_number_reflns_obs 11858 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 7.99 _refine.ls_d_res_high 1.78 _refine.ls_percent_reflns_obs 98.48 _refine.ls_R_factor_obs 0.19090 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.18953 _refine.ls_R_factor_R_free 0.21801 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.9 _refine.ls_number_reflns_R_free 617 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.955 _refine.correlation_coeff_Fo_to_Fc_free 0.943 _refine.B_iso_mean 30.438 _refine.aniso_B[1][1] -0.04 _refine.aniso_B[2][2] -0.04 _refine.aniso_B[3][3] 0.05 _refine.aniso_B[1][2] -0.02 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.101 _refine.pdbx_overall_ESU_R_Free 0.100 _refine.overall_SU_ML 0.059 _refine.overall_SU_B 3.070 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 618 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 11 _refine_hist.number_atoms_solvent 125 _refine_hist.number_atoms_total 754 _refine_hist.d_res_high 1.78 _refine_hist.d_res_low 7.99 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.009 0.021 ? 643 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.170 1.951 ? 870 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.224 5.000 ? 77 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 34.997 23.214 ? 28 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 11.329 15.000 ? 107 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 16.791 15.000 ? 4 'X-RAY DIFFRACTION' ? r_chiral_restr 0.080 0.200 ? 94 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 474 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.199 0.200 ? 277 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.300 0.200 ? 433 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.150 0.200 ? 86 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.199 0.200 ? 26 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.120 0.200 ? 16 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.605 1.500 ? 395 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.060 2.000 ? 629 'X-RAY DIFFRACTION' ? r_scbond_it 1.625 3.000 ? 283 'X-RAY DIFFRACTION' ? r_scangle_it 2.691 4.500 ? 240 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.780 _refine_ls_shell.d_res_low 1.824 _refine_ls_shell.number_reflns_R_work 732 _refine_ls_shell.R_factor_R_work 0.224 _refine_ls_shell.percent_reflns_obs 86.89 _refine_ls_shell.R_factor_R_free 0.314 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 37 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3KQI _struct.title 'crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide' _struct.pdbx_descriptor 'PHD finger protein 2' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3KQI _struct_keywords.pdbx_keywords 'NUCLEAR PROTEIN' _struct_keywords.text 'PHD finger, Metal-binding, Zinc-finger, Histone-binding, NUCLEAR PROTEIN' # 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 3 ? E N N 4 ? F N N 5 ? G N N 6 ? H N N 6 ? I N N 7 ? J N N 7 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLY A 37 ? GLY A 41 ? GLY A 32 GLY A 36 1 ? 5 HELX_P HELX_P2 2 GLU A 46 ? ILE A 50 ? GLU A 41 ILE A 45 5 ? 5 HELX_P HELX_P3 3 CYS A 55 ? GLY A 63 ? CYS A 50 GLY A 58 1 ? 9 # _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 ? B THR 3 C ? ? ? 1_555 B M3L 4 N ? ? B THR 3 B M3L 4 1_555 ? ? ? ? ? ? ? 1.332 ? covale2 covale both ? B M3L 4 C ? ? ? 1_555 B GLN 5 N ? ? B M3L 4 B GLN 5 1_555 ? ? ? ? ? ? ? 1.332 ? metalc1 metalc ? ? A CYS 13 SG ? ? ? 1_555 D ZN . ZN ? ? A CYS 8 A ZN 72 1_555 ? ? ? ? ? ? ? 2.343 ? metalc2 metalc ? ? A CYS 15 SG ? ? ? 1_555 D ZN . ZN ? ? A CYS 10 A ZN 72 1_555 ? ? ? ? ? ? ? 2.314 ? metalc3 metalc ? ? A CYS 28 SG ? ? ? 1_555 C ZN . ZN ? ? A CYS 23 A ZN 71 1_555 ? ? ? ? ? ? ? 2.367 ? metalc4 metalc ? ? A CYS 31 SG ? ? ? 1_555 C ZN . ZN ? ? A CYS 26 A ZN 71 1_555 ? ? ? ? ? ? ? 2.345 ? metalc5 metalc ? ? A HIS 36 ND1 ? ? ? 1_555 D ZN . ZN ? ? A HIS 31 A ZN 72 1_555 ? ? ? ? ? ? ? 2.164 ? metalc6 metalc ? ? A CYS 39 SG ? ? ? 1_555 D ZN . ZN ? ? A CYS 34 A ZN 72 1_555 ? ? ? ? ? ? ? 2.311 ? metalc7 metalc ? ? A CYS 55 SG ? ? ? 1_555 C ZN . ZN ? ? A CYS 50 A ZN 71 1_555 ? ? ? ? ? ? ? 2.295 ? metalc8 metalc ? ? A CYS 58 SG ? ? ? 1_555 C ZN . ZN ? ? A CYS 53 A ZN 71 1_555 ? ? ? ? ? ? ? 2.356 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 2 ? B ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel B 1 2 ? anti-parallel B 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 A 1 VAL A 11 ? TYR A 12 ? VAL A 6 TYR A 7 A 2 LEU A 17 ? PRO A 18 ? LEU A 12 PRO A 13 B 1 TRP A 34 ? HIS A 36 ? TRP A 29 HIS A 31 B 2 MET A 25 ? GLU A 27 ? MET A 20 GLU A 22 B 3 THR B 3 ? M3L B 4 ? THR B 3 M3L B 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 A 1 2 N TYR A 12 ? N TYR A 7 O LEU A 17 ? O LEU A 12 B 1 2 O PHE A 35 ? O PHE A 30 N ILE A 26 ? N ILE A 21 B 2 3 N MET A 25 ? N MET A 20 O M3L B 4 ? O M3L B 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 ? ? ? ? 4 'BINDING SITE FOR RESIDUE ZN A 71' AC2 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ZN A 72' AC3 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE GOL A 968' AC4 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE CL A 73' AC5 Software ? ? ? ? 1 'BINDING SITE FOR RESIDUE MG A 74' AC6 Software ? ? ? ? 1 'BINDING SITE FOR RESIDUE MG A 75' # 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 28 ? CYS A 23 . ? 1_555 ? 2 AC1 4 CYS A 31 ? CYS A 26 . ? 1_555 ? 3 AC1 4 CYS A 55 ? CYS A 50 . ? 1_555 ? 4 AC1 4 CYS A 58 ? CYS A 53 . ? 1_555 ? 5 AC2 4 CYS A 13 ? CYS A 8 . ? 1_555 ? 6 AC2 4 CYS A 15 ? CYS A 10 . ? 1_555 ? 7 AC2 4 HIS A 36 ? HIS A 31 . ? 1_555 ? 8 AC2 4 CYS A 39 ? CYS A 34 . ? 1_555 ? 9 AC3 7 CYS A 58 ? CYS A 53 . ? 1_555 ? 10 AC3 7 THR A 61 ? THR A 56 . ? 1_555 ? 11 AC3 7 HIS A 62 ? HIS A 57 . ? 1_555 ? 12 AC3 7 HIS A 62 ? HIS A 57 . ? 10_665 ? 13 AC3 7 HOH I . ? HOH A 83 . ? 1_555 ? 14 AC3 7 HOH I . ? HOH A 154 . ? 10_665 ? 15 AC3 7 HOH I . ? HOH A 154 . ? 1_555 ? 16 AC4 3 LYS A 69 ? LYS A 64 . ? 1_555 ? 17 AC4 3 HOH I . ? HOH A 158 . ? 1_555 ? 18 AC4 3 HOH I . ? HOH A 167 . ? 1_555 ? 19 AC5 1 THR A 72 ? THR A 67 . ? 1_555 ? 20 AC6 1 SER A 38 ? SER A 33 . ? 1_555 ? # _database_PDB_matrix.entry_id 3KQI _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3KQI _atom_sites.fract_transf_matrix[1][1] 0.012861 _atom_sites.fract_transf_matrix[1][2] 0.007425 _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] 0.014850 _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] 0.013867 _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 CL MG 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 GLY 1 -4 ? ? ? A . n A 1 2 PRO 2 -3 ? ? ? A . n A 1 3 LEU 3 -2 ? ? ? A . n A 1 4 GLY 4 -1 -1 GLY GLY A . n A 1 5 SER 5 0 0 SER SER A . n A 1 6 MET 6 1 1 MET MET A . n A 1 7 ALA 7 2 2 ALA ALA A . n A 1 8 THR 8 3 3 THR THR A . n A 1 9 VAL 9 4 4 VAL VAL A . n A 1 10 PRO 10 5 5 PRO PRO A . n A 1 11 VAL 11 6 6 VAL VAL A . n A 1 12 TYR 12 7 7 TYR TYR A . n A 1 13 CYS 13 8 8 CYS CYS A . n A 1 14 VAL 14 9 9 VAL VAL A . n A 1 15 CYS 15 10 10 CYS CYS A . n A 1 16 ARG 16 11 11 ARG ARG A . n A 1 17 LEU 17 12 12 LEU LEU A . n A 1 18 PRO 18 13 13 PRO PRO A . n A 1 19 TYR 19 14 14 TYR TYR A . n A 1 20 ASP 20 15 15 ASP ASP A . n A 1 21 VAL 21 16 16 VAL VAL A . n A 1 22 THR 22 17 17 THR THR A . n A 1 23 ARG 23 18 18 ARG ARG A . n A 1 24 PHE 24 19 19 PHE PHE A . n A 1 25 MET 25 20 20 MET MET A . n A 1 26 ILE 26 21 21 ILE ILE A . n A 1 27 GLU 27 22 22 GLU GLU A . n A 1 28 CYS 28 23 23 CYS CYS A . n A 1 29 ASP 29 24 24 ASP ASP A . n A 1 30 ALA 30 25 25 ALA ALA A . n A 1 31 CYS 31 26 26 CYS CYS A . n A 1 32 LYS 32 27 27 LYS LYS A . n A 1 33 ASP 33 28 28 ASP ASP A . n A 1 34 TRP 34 29 29 TRP TRP A . n A 1 35 PHE 35 30 30 PHE PHE A . n A 1 36 HIS 36 31 31 HIS HIS A . n A 1 37 GLY 37 32 32 GLY GLY A . n A 1 38 SER 38 33 33 SER SER A . n A 1 39 CYS 39 34 34 CYS CYS A . n A 1 40 VAL 40 35 35 VAL VAL A . n A 1 41 GLY 41 36 36 GLY GLY A . n A 1 42 VAL 42 37 37 VAL VAL A . n A 1 43 GLU 43 38 38 GLU GLU A . n A 1 44 GLU 44 39 39 GLU GLU A . n A 1 45 GLU 45 40 40 GLU GLU A . n A 1 46 GLU 46 41 41 GLU GLU A . n A 1 47 ALA 47 42 42 ALA ALA A . n A 1 48 PRO 48 43 43 PRO PRO A . n A 1 49 ASP 49 44 44 ASP ASP A . n A 1 50 ILE 50 45 45 ILE ILE A . n A 1 51 ASP 51 46 46 ASP ASP A . n A 1 52 ILE 52 47 47 ILE ILE A . n A 1 53 TYR 53 48 48 TYR TYR A . n A 1 54 HIS 54 49 49 HIS HIS A . n A 1 55 CYS 55 50 50 CYS CYS A . n A 1 56 PRO 56 51 51 PRO PRO A . n A 1 57 ASN 57 52 52 ASN ASN A . n A 1 58 CYS 58 53 53 CYS CYS A . n A 1 59 GLU 59 54 54 GLU GLU A . n A 1 60 LYS 60 55 55 LYS LYS A . n A 1 61 THR 61 56 56 THR THR A . n A 1 62 HIS 62 57 57 HIS HIS A . n A 1 63 GLY 63 58 58 GLY GLY A . n A 1 64 LYS 64 59 59 LYS LYS A . n A 1 65 SER 65 60 60 SER SER A . n A 1 66 THR 66 61 61 THR THR A . n A 1 67 LEU 67 62 62 LEU LEU A . n A 1 68 LYS 68 63 63 LYS LYS A . n A 1 69 LYS 69 64 64 LYS LYS A . n A 1 70 LYS 70 65 65 LYS LYS A . n A 1 71 ARG 71 66 66 ARG ARG A . n A 1 72 THR 72 67 67 THR THR A . n A 1 73 TRP 73 68 68 TRP TRP A . n A 1 74 HIS 74 69 69 HIS HIS A . n A 1 75 LYS 75 70 ? ? ? A . n B 2 1 ALA 1 1 1 ALA ALA B . n B 2 2 ARG 2 2 2 ARG ARG B . n B 2 3 THR 3 3 3 THR THR B . n B 2 4 M3L 4 4 4 M3L M3L B . n B 2 5 GLN 5 5 5 GLN GLN B . n B 2 6 THR 6 6 6 THR THR B . n B 2 7 ALA 7 7 ? ? ? B . n B 2 8 ARG 8 8 ? ? ? B . n B 2 9 LYS 9 9 ? ? ? B . n B 2 10 SER 10 10 ? ? ? B . n B 2 11 THR 11 11 ? ? ? B . n B 2 12 GLY 12 12 ? ? ? B . 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 71 1 ZN ZN A . D 3 ZN 1 72 2 ZN ZN A . E 4 GOL 1 968 968 GOL GOL A . F 5 CL 1 73 1 CL CL A . G 6 MG 1 74 1 MG MG A . H 6 MG 1 75 1 MG MG A . I 7 HOH 1 76 76 HOH HOH A . I 7 HOH 2 77 77 HOH HOH A . I 7 HOH 3 78 78 HOH HOH A . I 7 HOH 4 79 1 HOH HOH A . I 7 HOH 5 80 2 HOH HOH A . I 7 HOH 6 81 3 HOH HOH A . I 7 HOH 7 82 82 HOH HOH A . I 7 HOH 8 83 83 HOH HOH A . I 7 HOH 9 84 4 HOH HOH A . I 7 HOH 10 85 5 HOH HOH A . I 7 HOH 11 86 6 HOH HOH A . I 7 HOH 12 87 87 HOH HOH A . I 7 HOH 13 88 88 HOH HOH A . I 7 HOH 14 89 7 HOH HOH A . I 7 HOH 15 90 90 HOH HOH A . I 7 HOH 16 91 91 HOH HOH A . I 7 HOH 17 92 92 HOH HOH A . I 7 HOH 18 93 93 HOH HOH A . I 7 HOH 19 94 8 HOH HOH A . I 7 HOH 20 95 95 HOH HOH A . I 7 HOH 21 96 9 HOH HOH A . I 7 HOH 22 97 97 HOH HOH A . I 7 HOH 23 98 98 HOH HOH A . I 7 HOH 24 99 99 HOH HOH A . I 7 HOH 25 100 100 HOH HOH A . I 7 HOH 26 101 10 HOH HOH A . I 7 HOH 27 102 102 HOH HOH A . I 7 HOH 28 103 103 HOH HOH A . I 7 HOH 29 104 104 HOH HOH A . I 7 HOH 30 105 105 HOH HOH A . I 7 HOH 31 106 106 HOH HOH A . I 7 HOH 32 107 107 HOH HOH A . I 7 HOH 33 108 11 HOH HOH A . I 7 HOH 34 109 12 HOH HOH A . I 7 HOH 35 110 110 HOH HOH A . I 7 HOH 36 111 111 HOH HOH A . I 7 HOH 37 112 112 HOH HOH A . I 7 HOH 38 113 13 HOH HOH A . I 7 HOH 39 114 14 HOH HOH A . I 7 HOH 40 115 115 HOH HOH A . I 7 HOH 41 116 116 HOH HOH A . I 7 HOH 42 117 15 HOH HOH A . I 7 HOH 43 118 118 HOH HOH A . I 7 HOH 44 119 16 HOH HOH A . I 7 HOH 45 120 17 HOH HOH A . I 7 HOH 46 121 121 HOH HOH A . I 7 HOH 47 122 18 HOH HOH A . I 7 HOH 48 123 19 HOH HOH A . I 7 HOH 49 124 20 HOH HOH A . I 7 HOH 50 125 21 HOH HOH A . I 7 HOH 51 126 24 HOH HOH A . I 7 HOH 52 127 25 HOH HOH A . I 7 HOH 53 128 128 HOH HOH A . I 7 HOH 54 129 129 HOH HOH A . I 7 HOH 55 130 26 HOH HOH A . I 7 HOH 56 131 131 HOH HOH A . I 7 HOH 57 132 132 HOH HOH A . I 7 HOH 58 133 27 HOH HOH A . I 7 HOH 59 134 28 HOH HOH A . I 7 HOH 60 135 29 HOH HOH A . I 7 HOH 61 136 136 HOH HOH A . I 7 HOH 62 137 30 HOH HOH A . I 7 HOH 63 138 138 HOH HOH A . I 7 HOH 64 139 139 HOH HOH A . I 7 HOH 65 140 31 HOH HOH A . I 7 HOH 66 141 141 HOH HOH A . I 7 HOH 67 142 32 HOH HOH A . I 7 HOH 68 143 143 HOH HOH A . I 7 HOH 69 144 144 HOH HOH A . I 7 HOH 70 145 33 HOH HOH A . I 7 HOH 71 146 35 HOH HOH A . I 7 HOH 72 147 39 HOH HOH A . I 7 HOH 73 148 40 HOH HOH A . I 7 HOH 74 149 149 HOH HOH A . I 7 HOH 75 150 41 HOH HOH A . I 7 HOH 76 151 42 HOH HOH A . I 7 HOH 77 152 43 HOH HOH A . I 7 HOH 78 153 44 HOH HOH A . I 7 HOH 79 154 154 HOH HOH A . I 7 HOH 80 155 45 HOH HOH A . I 7 HOH 81 156 46 HOH HOH A . I 7 HOH 82 157 47 HOH HOH A . I 7 HOH 83 158 158 HOH HOH A . I 7 HOH 84 159 50 HOH HOH A . I 7 HOH 85 160 51 HOH HOH A . I 7 HOH 86 161 52 HOH HOH A . I 7 HOH 87 162 53 HOH HOH A . I 7 HOH 88 163 54 HOH HOH A . I 7 HOH 89 164 55 HOH HOH A . I 7 HOH 90 165 165 HOH HOH A . I 7 HOH 91 166 56 HOH HOH A . I 7 HOH 92 167 167 HOH HOH A . I 7 HOH 93 168 168 HOH HOH A . I 7 HOH 94 169 58 HOH HOH A . I 7 HOH 95 170 59 HOH HOH A . I 7 HOH 96 171 60 HOH HOH A . I 7 HOH 97 172 61 HOH HOH A . I 7 HOH 98 173 62 HOH HOH A . I 7 HOH 99 174 63 HOH HOH A . I 7 HOH 100 175 64 HOH HOH A . I 7 HOH 101 176 65 HOH HOH A . I 7 HOH 102 177 66 HOH HOH A . I 7 HOH 103 178 68 HOH HOH A . I 7 HOH 104 179 69 HOH HOH A . I 7 HOH 105 180 70 HOH HOH A . I 7 HOH 106 181 72 HOH HOH A . I 7 HOH 107 182 75 HOH HOH A . J 7 HOH 1 22 22 HOH HOH B . J 7 HOH 2 23 23 HOH HOH B . J 7 HOH 3 34 34 HOH HOH B . J 7 HOH 4 36 36 HOH HOH B . J 7 HOH 5 37 37 HOH HOH B . J 7 HOH 6 49 49 HOH HOH B . J 7 HOH 7 67 67 HOH HOH B . J 7 HOH 8 71 71 HOH HOH B . J 7 HOH 9 73 73 HOH HOH B . J 7 HOH 10 84 84 HOH HOH B . J 7 HOH 11 96 96 HOH HOH B . J 7 HOH 12 109 109 HOH HOH B . J 7 HOH 13 113 113 HOH HOH B . J 7 HOH 14 124 124 HOH HOH B . J 7 HOH 15 133 133 HOH HOH B . J 7 HOH 16 160 160 HOH HOH B . J 7 HOH 17 164 164 HOH HOH B . J 7 HOH 18 171 171 HOH HOH B . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id B _pdbx_struct_mod_residue.label_comp_id M3L _pdbx_struct_mod_residue.label_seq_id 4 _pdbx_struct_mod_residue.auth_asym_id B _pdbx_struct_mod_residue.auth_comp_id M3L _pdbx_struct_mod_residue.auth_seq_id 4 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id LYS _pdbx_struct_mod_residue.details N-TRIMETHYLLYSINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 software_defined_assembly PISA tetrameric 4 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D,E,F,G,H,I,J 2 1,2 A,B,C,D,E,F,G,H,I,J # 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)' 1540 ? 1 MORE -30 ? 1 'SSA (A^2)' 5810 ? 2 'ABSA (A^2)' 4390 ? 2 MORE -76 ? 2 'SSA (A^2)' 10500 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 12_564 x,x-y+1,-z-1/6 0.4999935697 0.8660216913 0.0000000000 -38.8790000000 0.8660365414 -0.4999935697 0.0000000000 67.3404033475 0.0000000000 0.0000000000 -1.0000000000 -12.0193333333 # _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 154 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id I _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 13 ? A CYS 8 ? 1_555 ZN ? D ZN . ? A ZN 72 ? 1_555 SG ? A CYS 15 ? A CYS 10 ? 1_555 112.2 ? 2 SG ? A CYS 13 ? A CYS 8 ? 1_555 ZN ? D ZN . ? A ZN 72 ? 1_555 ND1 ? A HIS 36 ? A HIS 31 ? 1_555 105.4 ? 3 SG ? A CYS 15 ? A CYS 10 ? 1_555 ZN ? D ZN . ? A ZN 72 ? 1_555 ND1 ? A HIS 36 ? A HIS 31 ? 1_555 97.5 ? 4 SG ? A CYS 13 ? A CYS 8 ? 1_555 ZN ? D ZN . ? A ZN 72 ? 1_555 SG ? A CYS 39 ? A CYS 34 ? 1_555 109.0 ? 5 SG ? A CYS 15 ? A CYS 10 ? 1_555 ZN ? D ZN . ? A ZN 72 ? 1_555 SG ? A CYS 39 ? A CYS 34 ? 1_555 119.5 ? 6 ND1 ? A HIS 36 ? A HIS 31 ? 1_555 ZN ? D ZN . ? A ZN 72 ? 1_555 SG ? A CYS 39 ? A CYS 34 ? 1_555 112.1 ? 7 SG ? A CYS 28 ? A CYS 23 ? 1_555 ZN ? C ZN . ? A ZN 71 ? 1_555 SG ? A CYS 31 ? A CYS 26 ? 1_555 105.8 ? 8 SG ? A CYS 28 ? A CYS 23 ? 1_555 ZN ? C ZN . ? A ZN 71 ? 1_555 SG ? A CYS 55 ? A CYS 50 ? 1_555 112.7 ? 9 SG ? A CYS 31 ? A CYS 26 ? 1_555 ZN ? C ZN . ? A ZN 71 ? 1_555 SG ? A CYS 55 ? A CYS 50 ? 1_555 118.3 ? 10 SG ? A CYS 28 ? A CYS 23 ? 1_555 ZN ? C ZN . ? A ZN 71 ? 1_555 SG ? A CYS 58 ? A CYS 53 ? 1_555 106.9 ? 11 SG ? A CYS 31 ? A CYS 26 ? 1_555 ZN ? C ZN . ? A ZN 71 ? 1_555 SG ? A CYS 58 ? A CYS 53 ? 1_555 109.3 ? 12 SG ? A CYS 55 ? A CYS 50 ? 1_555 ZN ? C ZN . ? A ZN 71 ? 1_555 SG ? A CYS 58 ? A CYS 53 ? 1_555 103.3 ? # 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 2010-02-02 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2019-02-13 # _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' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' Advisory 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' pdbx_distant_solvent_atoms 2 3 'Structure model' pdbx_struct_assembly 3 3 'Structure model' pdbx_struct_assembly_gen 4 3 'Structure model' pdbx_struct_assembly_prop 5 3 'Structure model' pdbx_struct_oper_list 6 3 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_pdbx_struct_assembly.oligomeric_count' 2 3 'Structure model' '_pdbx_struct_assembly.oligomeric_details' 3 3 'Structure model' '_pdbx_struct_assembly_prop.value' 4 3 'Structure model' '_pdbx_struct_oper_list.matrix[1][1]' 5 3 'Structure model' '_pdbx_struct_oper_list.matrix[1][2]' 6 3 'Structure model' '_pdbx_struct_oper_list.matrix[2][1]' 7 3 'Structure model' '_pdbx_struct_oper_list.matrix[2][2]' 8 3 'Structure model' '_pdbx_struct_oper_list.matrix[3][3]' 9 3 'Structure model' '_pdbx_struct_oper_list.name' 10 3 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 11 3 'Structure model' '_pdbx_struct_oper_list.type' 12 3 'Structure model' '_pdbx_struct_oper_list.vector[1]' 13 3 'Structure model' '_pdbx_struct_oper_list.vector[2]' 14 3 'Structure model' '_pdbx_struct_oper_list.vector[3]' 15 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # 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 -15.6940 52.1790 -7.1650 -0.0224 -0.0290 -0.0611 0.0005 0.0010 0.0136 1.5558 3.7525 0.6473 1.1310 -0.4784 -0.6032 0.0049 -0.0131 0.0565 -0.1549 -0.0411 0.0519 -0.0155 -0.0543 0.0361 'X-RAY DIFFRACTION' 2 ? refined -9.0030 49.5740 -7.6060 -0.0213 -0.0213 -0.0481 -0.0095 0.0370 0.0254 7.6247 18.6380 1.7809 0.6033 2.3830 3.8857 -0.0020 0.2063 0.0149 -0.1502 0.1451 -0.9171 -0.1679 0.2841 -0.1431 # 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 A -1 ? ? A 69 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 B 1 ? ? B 6 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 SOLVE phasing . ? 2 REFMAC refinement 5.2.0019 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _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 TRP _pdbx_validate_close_contact.auth_seq_id_1 68 _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_2 180 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.97 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 CYS A 8 ? ? 72.78 179.27 2 1 ASP A 46 ? ? -85.32 -80.28 # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 148 ? 6.43 . 2 1 O ? A HOH 149 ? 6.17 . 3 1 O ? A HOH 176 ? 8.02 . 4 1 O ? A HOH 177 ? 7.87 . # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY -4 ? A GLY 1 2 1 Y 1 A PRO -3 ? A PRO 2 3 1 Y 1 A LEU -2 ? A LEU 3 4 1 Y 1 A LYS 70 ? A LYS 75 5 1 Y 1 B ALA 7 ? B ALA 7 6 1 Y 1 B ARG 8 ? B ARG 8 7 1 Y 1 B LYS 9 ? B LYS 9 8 1 Y 1 B SER 10 ? B SER 10 9 1 Y 1 B THR 11 ? B THR 11 10 1 Y 1 B GLY 12 ? B GLY 12 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'ZINC ION' ZN 4 GLYCEROL GOL 5 'CHLORIDE ION' CL 6 'MAGNESIUM ION' MG 7 water HOH #