data_3WZH # _entry.id 3WZH # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.360 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3WZH pdb_00003wzh 10.2210/pdb3wzh/pdb RCSB RCSB096987 ? ? WWPDB D_1000096987 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3WZH . unspecified PDB 3WZI . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3WZH _pdbx_database_status.recvd_initial_deposition_date 2014-09-25 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Yuan, Y.A.' 1 'Yan, X.' 2 # _citation.id primary _citation.title 'Crystal structures of CRISPR-associated Csx3 reveal a manganese-dependent deadenylation exoribonuclease.' _citation.journal_abbrev 'Rna Biol.' _citation.journal_volume 12 _citation.page_first 749 _citation.page_last 760 _citation.year 2015 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1555-8584 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 26106927 _citation.pdbx_database_id_DOI 10.1080/15476286.2015.1051300 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yan, X.' 1 ? primary 'Guo, W.' 2 ? primary 'Yuan, Y.A.' 3 ? # _cell.entry_id 3WZH _cell.length_a 86.726 _cell.length_b 86.726 _cell.length_c 112.529 _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 3WZH _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _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 'Uncharacterized protein AF_1864' 12819.334 2 ? 'I49Mse, L51Mse' 'UNP residues 2-104' ? 2 non-polymer syn 'MANGANESE (II) ION' 54.938 5 ? ? ? ? 3 water nat water 18.015 25 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;GSH(MSE)ASAS(MSE)KFAVIDRKNFTLIHFEIEKPIKPEILKEIEIPSVDTRKGVVISGRGP(MSE)W(MSE)HCFLA HKYHHTPFVAVYDPRLGAVVVQSHSELREGDVIDVVVEEILKGGVRHV ; _entity_poly.pdbx_seq_one_letter_code_can ;GSHMASASMKFAVIDRKNFTLIHFEIEKPIKPEILKEIEIPSVDTRKGVVISGRGPMWMHCFLAHKYHHTPFVAVYDPRL GAVVVQSHSELREGDVIDVVVEEILKGGVRHV ; _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 SER n 1 3 HIS n 1 4 MSE n 1 5 ALA n 1 6 SER n 1 7 ALA n 1 8 SER n 1 9 MSE n 1 10 LYS n 1 11 PHE n 1 12 ALA n 1 13 VAL n 1 14 ILE n 1 15 ASP n 1 16 ARG n 1 17 LYS n 1 18 ASN n 1 19 PHE n 1 20 THR n 1 21 LEU n 1 22 ILE n 1 23 HIS n 1 24 PHE n 1 25 GLU n 1 26 ILE n 1 27 GLU n 1 28 LYS n 1 29 PRO n 1 30 ILE n 1 31 LYS n 1 32 PRO n 1 33 GLU n 1 34 ILE n 1 35 LEU n 1 36 LYS n 1 37 GLU n 1 38 ILE n 1 39 GLU n 1 40 ILE n 1 41 PRO n 1 42 SER n 1 43 VAL n 1 44 ASP n 1 45 THR n 1 46 ARG n 1 47 LYS n 1 48 GLY n 1 49 VAL n 1 50 VAL n 1 51 ILE n 1 52 SER n 1 53 GLY n 1 54 ARG n 1 55 GLY n 1 56 PRO n 1 57 MSE n 1 58 TRP n 1 59 MSE n 1 60 HIS n 1 61 CYS n 1 62 PHE n 1 63 LEU n 1 64 ALA n 1 65 HIS n 1 66 LYS n 1 67 TYR n 1 68 HIS n 1 69 HIS n 1 70 THR n 1 71 PRO n 1 72 PHE n 1 73 VAL n 1 74 ALA n 1 75 VAL n 1 76 TYR n 1 77 ASP n 1 78 PRO n 1 79 ARG n 1 80 LEU n 1 81 GLY n 1 82 ALA n 1 83 VAL n 1 84 VAL n 1 85 VAL n 1 86 GLN n 1 87 SER n 1 88 HIS n 1 89 SER n 1 90 GLU n 1 91 LEU n 1 92 ARG n 1 93 GLU n 1 94 GLY n 1 95 ASP n 1 96 VAL n 1 97 ILE n 1 98 ASP n 1 99 VAL n 1 100 VAL n 1 101 VAL n 1 102 GLU n 1 103 GLU n 1 104 ILE n 1 105 LEU n 1 106 LYS n 1 107 GLY n 1 108 GLY n 1 109 VAL n 1 110 ARG n 1 111 HIS n 1 112 VAL n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene AF_1864 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126' _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 'Archaeoglobus fulgidus DSM 4304' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 224325 _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Y1864_ARCFU _struct_ref.pdbx_db_accession O28415 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;KFAVIDRKNFTLIHFEIEKPIKPEILKEIEIPSVDTRKGVVISGRGPIWLHCFLAHKYHHTPFVAVYDPRLGAVVVQSHS ELREGDVIDVVVEEILKGGVRHV ; _struct_ref.pdbx_align_begin 2 _struct_ref.pdbx_db_isoform ? # 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 3WZH A 10 ? 112 ? O28415 2 ? 104 ? 2 104 2 1 3WZH B 10 ? 112 ? O28415 2 ? 104 ? 2 104 # 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 3WZH GLY A 1 ? UNP O28415 ? ? 'expression tag' -7 1 1 3WZH SER A 2 ? UNP O28415 ? ? 'expression tag' -6 2 1 3WZH HIS A 3 ? UNP O28415 ? ? 'expression tag' -5 3 1 3WZH MSE A 4 ? UNP O28415 ? ? 'expression tag' -4 4 1 3WZH ALA A 5 ? UNP O28415 ? ? 'expression tag' -3 5 1 3WZH SER A 6 ? UNP O28415 ? ? 'expression tag' -2 6 1 3WZH ALA A 7 ? UNP O28415 ? ? 'expression tag' -1 7 1 3WZH SER A 8 ? UNP O28415 ? ? 'expression tag' 0 8 1 3WZH MSE A 9 ? UNP O28415 ? ? 'expression tag' 1 9 1 3WZH MSE A 57 ? UNP O28415 ILE 49 'engineered mutation' 49 10 1 3WZH MSE A 59 ? UNP O28415 LEU 51 'engineered mutation' 51 11 2 3WZH GLY B 1 ? UNP O28415 ? ? 'expression tag' -7 12 2 3WZH SER B 2 ? UNP O28415 ? ? 'expression tag' -6 13 2 3WZH HIS B 3 ? UNP O28415 ? ? 'expression tag' -5 14 2 3WZH MSE B 4 ? UNP O28415 ? ? 'expression tag' -4 15 2 3WZH ALA B 5 ? UNP O28415 ? ? 'expression tag' -3 16 2 3WZH SER B 6 ? UNP O28415 ? ? 'expression tag' -2 17 2 3WZH ALA B 7 ? UNP O28415 ? ? 'expression tag' -1 18 2 3WZH SER B 8 ? UNP O28415 ? ? 'expression tag' 0 19 2 3WZH MSE B 9 ? UNP O28415 ? ? 'expression tag' 1 20 2 3WZH MSE B 57 ? UNP O28415 ILE 49 'engineered mutation' 49 21 2 3WZH MSE B 59 ? UNP O28415 LEU 51 'engineered mutation' 51 22 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3WZH _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.76 _exptl_crystal.density_percent_sol 74.19 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4 _exptl_crystal_grow.pdbx_details 'Citrate, Phosphate, Ammonium Sulphate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS HTC' _diffrn_detector.pdbx_collection_date 2013-05-08 _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU MICROMAX-007 HF' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 3WZH _reflns.observed_criterion_sigma_I 2 _reflns.observed_criterion_sigma_F 2 _reflns.d_resolution_low 50 _reflns.d_resolution_high 3.3 _reflns.number_obs 7155 _reflns.number_all 7320 _reflns.percent_possible_obs 97.76 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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 3.3 _reflns_shell.d_res_low 3.4 _reflns_shell.percent_possible_all 98.9 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3WZH _refine.ls_number_reflns_obs 7155 _refine.ls_number_reflns_all 7320 _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 22.88 _refine.ls_d_res_high 3.31 _refine.ls_percent_reflns_obs 97.76 _refine.ls_R_factor_obs 0.22242 _refine.ls_R_factor_all 0.22242 _refine.ls_R_factor_R_work 0.22065 _refine.ls_R_factor_R_free 0.25732 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 348 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.902 _refine.correlation_coeff_Fo_to_Fc_free 0.876 _refine.B_iso_mean 38.300 _refine.aniso_B[1][1] 0.08 _refine.aniso_B[2][2] 0.08 _refine.aniso_B[3][3] -0.27 _refine.aniso_B[1][2] 0.08 _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 'FOURIER SYNTHESIS' _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 1.168 _refine.pdbx_overall_ESU_R_Free 0.415 _refine.overall_SU_ML 0.311 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 38.380 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1593 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 25 _refine_hist.number_atoms_total 1623 _refine_hist.d_res_high 3.31 _refine_hist.d_res_low 22.88 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.015 0.019 ? 1633 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.004 0.020 ? 1620 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.799 1.966 ? 2210 ? 'X-RAY DIFFRACTION' r_angle_other_deg 1.084 3.000 ? 3738 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 6.861 5.000 ? 196 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 26.049 23.143 ? 70 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 15.414 15.000 ? 276 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 18.711 15.000 ? 10 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.091 0.200 ? 251 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.008 0.021 ? 1764 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.004 0.020 ? 358 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_restr_ncs.dom_id _refine_ls_restr_ncs.pdbx_auth_asym_id _refine_ls_restr_ncs.pdbx_number _refine_ls_restr_ncs.rms_dev_position _refine_ls_restr_ncs.weight_position _refine_ls_restr_ncs.pdbx_type _refine_ls_restr_ncs.pdbx_ens_id _refine_ls_restr_ncs.pdbx_ordinal _refine_ls_restr_ncs.pdbx_refine_id _refine_ls_restr_ncs.ncs_model_details _refine_ls_restr_ncs.rms_dev_B_iso _refine_ls_restr_ncs.weight_B_iso 1 A 5422 0.14 0.05 'interatomic distance' 1 1 'X-RAY DIFFRACTION' ? ? ? 2 B 5422 0.14 0.05 'interatomic distance' 1 2 'X-RAY DIFFRACTION' ? ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 3.306 _refine_ls_shell.d_res_low 3.392 _refine_ls_shell.number_reflns_R_work 518 _refine_ls_shell.R_factor_R_work 0.277 _refine_ls_shell.percent_reflns_obs 98.90 _refine_ls_shell.R_factor_R_free 0.464 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 21 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # loop_ _struct_ncs_dom.id _struct_ncs_dom.details _struct_ncs_dom.pdbx_ens_id 1 A 1 2 B 1 # loop_ _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.beg_auth_asym_id _struct_ncs_dom_lim.beg_auth_seq_id _struct_ncs_dom_lim.end_auth_asym_id _struct_ncs_dom_lim.end_auth_seq_id _struct_ncs_dom_lim.pdbx_component_id _struct_ncs_dom_lim.pdbx_refine_code _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.pdbx_ens_id _struct_ncs_dom_lim.selection_details 1 A -1 A 95 0 0 ? ? ? ? ? ? ? ? 1 ? 2 B -1 B 95 0 0 ? ? ? ? ? ? ? ? 1 ? # _struct_ncs_ens.id 1 _struct_ncs_ens.details ? # _struct.entry_id 3WZH _struct.title 'Crystal structure of AfCsx3' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3WZH _struct_keywords.pdbx_keywords TRANSCRIPTION _struct_keywords.text 'endonuclease, deadenylation, TRANSCRIPTION' # 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 1 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 3 ? I N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 LYS A 31 ? GLU A 37 ? LYS A 23 GLU A 29 5 ? 7 HELX_P HELX_P2 2 PRO A 56 ? TYR A 67 ? PRO A 48 TYR A 59 1 ? 12 HELX_P HELX_P3 3 LYS B 31 ? GLU B 37 ? LYS B 23 GLU B 29 5 ? 7 HELX_P HELX_P4 4 PRO B 56 ? TYR B 67 ? PRO B 48 TYR B 59 1 ? 12 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A SER 8 C ? ? ? 1_555 A MSE 9 N ? ? A SER 0 A MSE 1 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale2 covale both ? A MSE 9 C ? ? ? 1_555 A LYS 10 N ? ? A MSE 1 A LYS 2 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale3 covale both ? A PRO 56 C ? ? ? 1_555 A MSE 57 N ? ? A PRO 48 A MSE 49 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale4 covale both ? A MSE 57 C ? ? ? 1_555 A TRP 58 N ? ? A MSE 49 A TRP 50 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale5 covale both ? A TRP 58 C ? ? ? 1_555 A MSE 59 N ? ? A TRP 50 A MSE 51 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale6 covale both ? A MSE 59 C ? ? ? 1_555 A HIS 60 N ? ? A MSE 51 A HIS 52 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale7 covale both ? B SER 8 C ? ? ? 1_555 B MSE 9 N ? ? B SER 0 B MSE 1 1_555 ? ? ? ? ? ? ? 1.320 ? ? covale8 covale both ? B MSE 9 C ? ? ? 1_555 B LYS 10 N ? ? B MSE 1 B LYS 2 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale9 covale both ? B PRO 56 C ? ? ? 1_555 B MSE 57 N ? ? B PRO 48 B MSE 49 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale10 covale both ? B MSE 57 C ? ? ? 1_555 B TRP 58 N ? ? B MSE 49 B TRP 50 1_555 ? ? ? ? ? ? ? 1.316 ? ? covale11 covale both ? B TRP 58 C ? ? ? 1_555 B MSE 59 N ? ? B TRP 50 B MSE 51 1_555 ? ? ? ? ? ? ? 1.313 ? ? covale12 covale both ? B MSE 59 C ? ? ? 1_555 B HIS 60 N ? ? B MSE 51 B HIS 52 1_555 ? ? ? ? ? ? ? 1.330 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 6 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? parallel A 3 4 ? parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? parallel B 3 4 ? parallel B 4 5 ? anti-parallel B 5 6 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 MSE A 9 ? ARG A 16 ? MSE A 1 ARG A 8 A 2 PHE A 19 ? ILE A 26 ? PHE A 11 ILE A 18 A 3 GLY A 48 ? SER A 52 ? GLY A 40 SER A 44 A 4 VAL A 73 ? ASP A 77 ? VAL A 65 ASP A 69 A 5 GLY A 81 ? GLN A 86 ? GLY A 73 GLN A 78 A 6 VAL A 96 ? ILE A 97 ? VAL A 88 ILE A 89 B 1 MSE B 9 ? ARG B 16 ? MSE B 1 ARG B 8 B 2 PHE B 19 ? ILE B 26 ? PHE B 11 ILE B 18 B 3 VAL B 49 ? SER B 52 ? VAL B 41 SER B 44 B 4 VAL B 73 ? ASP B 77 ? VAL B 65 ASP B 69 B 5 GLY B 81 ? GLN B 86 ? GLY B 73 GLN B 78 B 6 VAL B 96 ? ILE B 97 ? VAL B 88 ILE B 89 # 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 ILE A 14 ? N ILE A 6 O LEU A 21 ? O LEU A 13 A 2 3 N ILE A 22 ? N ILE A 14 O VAL A 50 ? O VAL A 42 A 3 4 N ILE A 51 ? N ILE A 43 O TYR A 76 ? O TYR A 68 A 4 5 N VAL A 75 ? N VAL A 67 O VAL A 83 ? O VAL A 75 A 5 6 N ALA A 82 ? N ALA A 74 O ILE A 97 ? O ILE A 89 B 1 2 N ILE B 14 ? N ILE B 6 O LEU B 21 ? O LEU B 13 B 2 3 N ILE B 22 ? N ILE B 14 O VAL B 50 ? O VAL B 42 B 3 4 N ILE B 51 ? N ILE B 43 O TYR B 76 ? O TYR B 68 B 4 5 N VAL B 75 ? N VAL B 67 O VAL B 83 ? O VAL B 75 B 5 6 N ALA B 82 ? N ALA B 74 O ILE B 97 ? O ILE B 89 # 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 MN 201 ? 3 'BINDING SITE FOR RESIDUE MN A 201' AC2 Software A MN 202 ? 1 'BINDING SITE FOR RESIDUE MN A 202' AC3 Software B MN 201 ? 1 'BINDING SITE FOR RESIDUE MN B 201' AC4 Software B MN 202 ? 1 'BINDING SITE FOR RESIDUE MN B 202' AC5 Software B MN 203 ? 1 'BINDING SITE FOR RESIDUE MN B 203' # 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 3 HIS A 65 ? HIS A 57 . ? 1_555 ? 2 AC1 3 LYS A 66 ? LYS A 58 . ? 1_555 ? 3 AC1 3 GLU B 93 ? GLU B 85 . ? 1_555 ? 4 AC2 1 HIS A 88 ? HIS A 80 . ? 1_555 ? 5 AC3 1 ARG B 92 ? ARG B 84 . ? 1_555 ? 6 AC4 1 LYS B 66 ? LYS B 58 . ? 1_555 ? 7 AC5 1 HIS B 88 ? HIS B 80 . ? 1_555 ? # _database_PDB_matrix.entry_id 3WZH _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 3WZH _atom_sites.fract_transf_matrix[1][1] 0.011531 _atom_sites.fract_transf_matrix[1][2] 0.006657 _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] 0.013314 _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] 0.008887 _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 MN N O S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 -7 ? ? ? A . n A 1 2 SER 2 -6 ? ? ? A . n A 1 3 HIS 3 -5 ? ? ? A . n A 1 4 MSE 4 -4 ? ? ? A . n A 1 5 ALA 5 -3 ? ? ? A . n A 1 6 SER 6 -2 ? ? ? A . n A 1 7 ALA 7 -1 -1 ALA ALA A . n A 1 8 SER 8 0 0 SER SER A . n A 1 9 MSE 9 1 1 MSE MSE A . n A 1 10 LYS 10 2 2 LYS LYS A . n A 1 11 PHE 11 3 3 PHE PHE A . n A 1 12 ALA 12 4 4 ALA ALA A . n A 1 13 VAL 13 5 5 VAL VAL A . n A 1 14 ILE 14 6 6 ILE ILE A . n A 1 15 ASP 15 7 7 ASP ASP A . n A 1 16 ARG 16 8 8 ARG ARG A . n A 1 17 LYS 17 9 9 LYS LYS A . n A 1 18 ASN 18 10 10 ASN ASN A . n A 1 19 PHE 19 11 11 PHE PHE A . n A 1 20 THR 20 12 12 THR THR A . n A 1 21 LEU 21 13 13 LEU LEU A . n A 1 22 ILE 22 14 14 ILE ILE A . n A 1 23 HIS 23 15 15 HIS HIS A . n A 1 24 PHE 24 16 16 PHE PHE A . n A 1 25 GLU 25 17 17 GLU GLU A . n A 1 26 ILE 26 18 18 ILE ILE A . n A 1 27 GLU 27 19 19 GLU GLU A . n A 1 28 LYS 28 20 20 LYS LYS A . n A 1 29 PRO 29 21 21 PRO PRO A . n A 1 30 ILE 30 22 22 ILE ILE A . n A 1 31 LYS 31 23 23 LYS LYS A . n A 1 32 PRO 32 24 24 PRO PRO A . n A 1 33 GLU 33 25 25 GLU GLU A . n A 1 34 ILE 34 26 26 ILE ILE A . n A 1 35 LEU 35 27 27 LEU LEU A . n A 1 36 LYS 36 28 28 LYS LYS A . n A 1 37 GLU 37 29 29 GLU GLU A . n A 1 38 ILE 38 30 30 ILE ILE A . n A 1 39 GLU 39 31 31 GLU GLU A . n A 1 40 ILE 40 32 32 ILE ILE A . n A 1 41 PRO 41 33 33 PRO PRO A . n A 1 42 SER 42 34 34 SER SER A . n A 1 43 VAL 43 35 35 VAL VAL A . n A 1 44 ASP 44 36 36 ASP ASP A . n A 1 45 THR 45 37 37 THR THR A . n A 1 46 ARG 46 38 38 ARG ARG A . n A 1 47 LYS 47 39 39 LYS LYS A . n A 1 48 GLY 48 40 40 GLY GLY A . n A 1 49 VAL 49 41 41 VAL VAL A . n A 1 50 VAL 50 42 42 VAL VAL A . n A 1 51 ILE 51 43 43 ILE ILE A . n A 1 52 SER 52 44 44 SER SER A . n A 1 53 GLY 53 45 45 GLY GLY A . n A 1 54 ARG 54 46 46 ARG ARG A . n A 1 55 GLY 55 47 47 GLY GLY A . n A 1 56 PRO 56 48 48 PRO PRO A . n A 1 57 MSE 57 49 49 MSE MSE A . n A 1 58 TRP 58 50 50 TRP TRP A . n A 1 59 MSE 59 51 51 MSE MSE A . n A 1 60 HIS 60 52 52 HIS HIS A . n A 1 61 CYS 61 53 53 CYS CYS A . n A 1 62 PHE 62 54 54 PHE PHE A . n A 1 63 LEU 63 55 55 LEU LEU A . n A 1 64 ALA 64 56 56 ALA ALA A . n A 1 65 HIS 65 57 57 HIS HIS A . n A 1 66 LYS 66 58 58 LYS LYS A . n A 1 67 TYR 67 59 59 TYR TYR A . n A 1 68 HIS 68 60 60 HIS HIS A . n A 1 69 HIS 69 61 61 HIS HIS A . n A 1 70 THR 70 62 62 THR THR A . n A 1 71 PRO 71 63 63 PRO PRO A . n A 1 72 PHE 72 64 64 PHE PHE A . n A 1 73 VAL 73 65 65 VAL VAL A . n A 1 74 ALA 74 66 66 ALA ALA A . n A 1 75 VAL 75 67 67 VAL VAL A . n A 1 76 TYR 76 68 68 TYR TYR A . n A 1 77 ASP 77 69 69 ASP ASP A . n A 1 78 PRO 78 70 70 PRO PRO A . n A 1 79 ARG 79 71 71 ARG ARG A . n A 1 80 LEU 80 72 72 LEU LEU A . n A 1 81 GLY 81 73 73 GLY GLY A . n A 1 82 ALA 82 74 74 ALA ALA A . n A 1 83 VAL 83 75 75 VAL VAL A . n A 1 84 VAL 84 76 76 VAL VAL A . n A 1 85 VAL 85 77 77 VAL VAL A . n A 1 86 GLN 86 78 78 GLN GLN A . n A 1 87 SER 87 79 79 SER SER A . n A 1 88 HIS 88 80 80 HIS HIS A . n A 1 89 SER 89 81 81 SER SER A . n A 1 90 GLU 90 82 82 GLU GLU A . n A 1 91 LEU 91 83 83 LEU LEU A . n A 1 92 ARG 92 84 84 ARG ARG A . n A 1 93 GLU 93 85 85 GLU GLU A . n A 1 94 GLY 94 86 86 GLY GLY A . n A 1 95 ASP 95 87 87 ASP ASP A . n A 1 96 VAL 96 88 88 VAL VAL A . n A 1 97 ILE 97 89 89 ILE ILE A . n A 1 98 ASP 98 90 90 ASP ASP A . n A 1 99 VAL 99 91 91 VAL VAL A . n A 1 100 VAL 100 92 92 VAL VAL A . n A 1 101 VAL 101 93 93 VAL VAL A . n A 1 102 GLU 102 94 94 GLU GLU A . n A 1 103 GLU 103 95 95 GLU GLU A . n A 1 104 ILE 104 96 96 ILE ILE A . n A 1 105 LEU 105 97 ? ? ? A . n A 1 106 LYS 106 98 ? ? ? A . n A 1 107 GLY 107 99 ? ? ? A . n A 1 108 GLY 108 100 ? ? ? A . n A 1 109 VAL 109 101 ? ? ? A . n A 1 110 ARG 110 102 ? ? ? A . n A 1 111 HIS 111 103 ? ? ? A . n A 1 112 VAL 112 104 ? ? ? A . n B 1 1 GLY 1 -7 ? ? ? B . n B 1 2 SER 2 -6 ? ? ? B . n B 1 3 HIS 3 -5 ? ? ? B . n B 1 4 MSE 4 -4 ? ? ? B . n B 1 5 ALA 5 -3 ? ? ? B . n B 1 6 SER 6 -2 ? ? ? B . n B 1 7 ALA 7 -1 -1 ALA ALA B . n B 1 8 SER 8 0 0 SER SER B . n B 1 9 MSE 9 1 1 MSE MSE B . n B 1 10 LYS 10 2 2 LYS LYS B . n B 1 11 PHE 11 3 3 PHE PHE B . n B 1 12 ALA 12 4 4 ALA ALA B . n B 1 13 VAL 13 5 5 VAL VAL B . n B 1 14 ILE 14 6 6 ILE ILE B . n B 1 15 ASP 15 7 7 ASP ASP B . n B 1 16 ARG 16 8 8 ARG ARG B . n B 1 17 LYS 17 9 9 LYS LYS B . n B 1 18 ASN 18 10 10 ASN ASN B . n B 1 19 PHE 19 11 11 PHE PHE B . n B 1 20 THR 20 12 12 THR THR B . n B 1 21 LEU 21 13 13 LEU LEU B . n B 1 22 ILE 22 14 14 ILE ILE B . n B 1 23 HIS 23 15 15 HIS HIS B . n B 1 24 PHE 24 16 16 PHE PHE B . n B 1 25 GLU 25 17 17 GLU GLU B . n B 1 26 ILE 26 18 18 ILE ILE B . n B 1 27 GLU 27 19 19 GLU GLU B . n B 1 28 LYS 28 20 20 LYS LYS B . n B 1 29 PRO 29 21 21 PRO PRO B . n B 1 30 ILE 30 22 22 ILE ILE B . n B 1 31 LYS 31 23 23 LYS LYS B . n B 1 32 PRO 32 24 24 PRO PRO B . n B 1 33 GLU 33 25 25 GLU GLU B . n B 1 34 ILE 34 26 26 ILE ILE B . n B 1 35 LEU 35 27 27 LEU LEU B . n B 1 36 LYS 36 28 28 LYS LYS B . n B 1 37 GLU 37 29 29 GLU GLU B . n B 1 38 ILE 38 30 30 ILE ILE B . n B 1 39 GLU 39 31 31 GLU GLU B . n B 1 40 ILE 40 32 32 ILE ILE B . n B 1 41 PRO 41 33 33 PRO PRO B . n B 1 42 SER 42 34 34 SER SER B . n B 1 43 VAL 43 35 35 VAL VAL B . n B 1 44 ASP 44 36 36 ASP ASP B . n B 1 45 THR 45 37 37 THR THR B . n B 1 46 ARG 46 38 38 ARG ARG B . n B 1 47 LYS 47 39 39 LYS LYS B . n B 1 48 GLY 48 40 40 GLY GLY B . n B 1 49 VAL 49 41 41 VAL VAL B . n B 1 50 VAL 50 42 42 VAL VAL B . n B 1 51 ILE 51 43 43 ILE ILE B . n B 1 52 SER 52 44 44 SER SER B . n B 1 53 GLY 53 45 45 GLY GLY B . n B 1 54 ARG 54 46 46 ARG ARG B . n B 1 55 GLY 55 47 47 GLY GLY B . n B 1 56 PRO 56 48 48 PRO PRO B . n B 1 57 MSE 57 49 49 MSE MSE B . n B 1 58 TRP 58 50 50 TRP TRP B . n B 1 59 MSE 59 51 51 MSE MSE B . n B 1 60 HIS 60 52 52 HIS HIS B . n B 1 61 CYS 61 53 53 CYS CYS B . n B 1 62 PHE 62 54 54 PHE PHE B . n B 1 63 LEU 63 55 55 LEU LEU B . n B 1 64 ALA 64 56 56 ALA ALA B . n B 1 65 HIS 65 57 57 HIS HIS B . n B 1 66 LYS 66 58 58 LYS LYS B . n B 1 67 TYR 67 59 59 TYR TYR B . n B 1 68 HIS 68 60 60 HIS HIS B . n B 1 69 HIS 69 61 61 HIS HIS B . n B 1 70 THR 70 62 62 THR THR B . n B 1 71 PRO 71 63 63 PRO PRO B . n B 1 72 PHE 72 64 64 PHE PHE B . n B 1 73 VAL 73 65 65 VAL VAL B . n B 1 74 ALA 74 66 66 ALA ALA B . n B 1 75 VAL 75 67 67 VAL VAL B . n B 1 76 TYR 76 68 68 TYR TYR B . n B 1 77 ASP 77 69 69 ASP ASP B . n B 1 78 PRO 78 70 70 PRO PRO B . n B 1 79 ARG 79 71 71 ARG ARG B . n B 1 80 LEU 80 72 72 LEU LEU B . n B 1 81 GLY 81 73 73 GLY GLY B . n B 1 82 ALA 82 74 74 ALA ALA B . n B 1 83 VAL 83 75 75 VAL VAL B . n B 1 84 VAL 84 76 76 VAL VAL B . n B 1 85 VAL 85 77 77 VAL VAL B . n B 1 86 GLN 86 78 78 GLN GLN B . n B 1 87 SER 87 79 79 SER SER B . n B 1 88 HIS 88 80 80 HIS HIS B . n B 1 89 SER 89 81 81 SER SER B . n B 1 90 GLU 90 82 82 GLU GLU B . n B 1 91 LEU 91 83 83 LEU LEU B . n B 1 92 ARG 92 84 84 ARG ARG B . n B 1 93 GLU 93 85 85 GLU GLU B . n B 1 94 GLY 94 86 86 GLY GLY B . n B 1 95 ASP 95 87 87 ASP ASP B . n B 1 96 VAL 96 88 88 VAL VAL B . n B 1 97 ILE 97 89 89 ILE ILE B . n B 1 98 ASP 98 90 90 ASP ASP B . n B 1 99 VAL 99 91 91 VAL VAL B . n B 1 100 VAL 100 92 92 VAL VAL B . n B 1 101 VAL 101 93 93 VAL VAL B . n B 1 102 GLU 102 94 94 GLU GLU B . n B 1 103 GLU 103 95 95 GLU GLU B . n B 1 104 ILE 104 96 96 ILE ILE B . n B 1 105 LEU 105 97 97 LEU LEU B . n B 1 106 LYS 106 98 98 LYS LYS B . n B 1 107 GLY 107 99 ? ? ? B . n B 1 108 GLY 108 100 ? ? ? B . n B 1 109 VAL 109 101 ? ? ? B . n B 1 110 ARG 110 102 ? ? ? B . n B 1 111 HIS 111 103 ? ? ? B . n B 1 112 VAL 112 104 ? ? ? 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 2 MN 1 201 1 MN MN A . D 2 MN 1 202 4 MN MN A . E 2 MN 1 201 2 MN MN B . F 2 MN 1 202 3 MN MN B . G 2 MN 1 203 5 MN MN B . H 3 HOH 1 301 3 HOH HOH A . H 3 HOH 2 302 6 HOH HOH A . H 3 HOH 3 303 8 HOH HOH A . H 3 HOH 4 304 9 HOH HOH A . H 3 HOH 5 305 10 HOH HOH A . H 3 HOH 6 306 13 HOH HOH A . H 3 HOH 7 307 16 HOH HOH A . H 3 HOH 8 308 20 HOH HOH A . I 3 HOH 1 301 1 HOH HOH B . I 3 HOH 2 302 2 HOH HOH B . I 3 HOH 3 303 4 HOH HOH B . I 3 HOH 4 304 5 HOH HOH B . I 3 HOH 5 305 7 HOH HOH B . I 3 HOH 6 306 11 HOH HOH B . I 3 HOH 7 307 12 HOH HOH B . I 3 HOH 8 308 14 HOH HOH B . I 3 HOH 9 309 15 HOH HOH B . I 3 HOH 10 310 17 HOH HOH B . I 3 HOH 11 311 18 HOH HOH B . I 3 HOH 12 312 19 HOH HOH B . I 3 HOH 13 313 21 HOH HOH B . I 3 HOH 14 314 22 HOH HOH B . I 3 HOH 15 315 23 HOH HOH B . I 3 HOH 16 316 24 HOH HOH B . I 3 HOH 17 317 25 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 9 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 57 A MSE 49 ? MET SELENOMETHIONINE 3 A MSE 59 A MSE 51 ? MET SELENOMETHIONINE 4 B MSE 9 B MSE 1 ? MET SELENOMETHIONINE 5 B MSE 57 B MSE 49 ? MET SELENOMETHIONINE 6 B MSE 59 B MSE 51 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 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,F,G,H,I # 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)' 2870 ? 1 MORE -41 ? 1 'SSA (A^2)' 11220 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2015-07-15 2 'Structure model' 1 1 2022-08-24 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 2 '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 2 'Structure model' citation 2 2 'Structure model' database_2 3 2 'Structure model' struct_conn 4 2 'Structure model' struct_ref_seq_dif 5 2 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 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' 5 2 'Structure model' '_database_2.pdbx_DOI' 6 2 'Structure model' '_database_2.pdbx_database_accession' 7 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 2 'Structure model' '_struct_ref_seq_dif.details' 9 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 10 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 11 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 39.5784 -13.7428 7.4804 0.1490 0.1636 0.0110 -0.0333 0.0186 0.0081 3.0778 7.0931 3.8530 2.1305 1.3551 1.7151 -0.1776 0.3264 -0.1488 0.1796 -0.1008 -0.0416 -0.2099 0.0448 0.0678 'X-RAY DIFFRACTION' 2 ? refined 38.3408 -19.2591 26.0046 0.1983 0.0698 0.0981 0.0311 0.0312 0.0441 4.7129 4.7328 4.5820 2.2891 1.4723 0.5419 0.0194 0.3122 -0.3316 0.0780 -0.5181 -0.0407 0.1477 0.5980 -0.2419 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A -1 A 96 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 B -1 B 98 ? . . . . ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 SHARP phasing . ? 2 REFMAC refinement 5.7.0029 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A LEU 27 ? ? 1_555 NH2 B ARG 84 ? ? 5_555 1.93 2 1 OE2 A GLU 31 ? ? 1_555 OD2 B ASP 87 ? ? 5_555 2.17 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 N _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 MSE _pdbx_validate_rmsd_angle.auth_seq_id_1 49 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CA _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 MSE _pdbx_validate_rmsd_angle.auth_seq_id_2 49 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 CB _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 MSE _pdbx_validate_rmsd_angle.auth_seq_id_3 49 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 122.40 _pdbx_validate_rmsd_angle.angle_target_value 110.60 _pdbx_validate_rmsd_angle.angle_deviation 11.80 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.80 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLU A 19 ? ? -107.25 -64.79 2 1 PRO A 63 ? ? -47.59 -19.17 3 1 PHE A 64 ? ? 179.42 162.99 4 1 PRO A 70 ? ? -35.07 -38.78 5 1 GLU A 95 ? ? -108.46 72.60 6 1 PHE B 64 ? ? 179.44 161.93 7 1 PRO B 70 ? ? -39.66 -34.38 # 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 -7 ? A GLY 1 2 1 Y 1 A SER -6 ? A SER 2 3 1 Y 1 A HIS -5 ? A HIS 3 4 1 Y 1 A MSE -4 ? A MSE 4 5 1 Y 1 A ALA -3 ? A ALA 5 6 1 Y 1 A SER -2 ? A SER 6 7 1 Y 1 A LEU 97 ? A LEU 105 8 1 Y 1 A LYS 98 ? A LYS 106 9 1 Y 1 A GLY 99 ? A GLY 107 10 1 Y 1 A GLY 100 ? A GLY 108 11 1 Y 1 A VAL 101 ? A VAL 109 12 1 Y 1 A ARG 102 ? A ARG 110 13 1 Y 1 A HIS 103 ? A HIS 111 14 1 Y 1 A VAL 104 ? A VAL 112 15 1 Y 1 B GLY -7 ? B GLY 1 16 1 Y 1 B SER -6 ? B SER 2 17 1 Y 1 B HIS -5 ? B HIS 3 18 1 Y 1 B MSE -4 ? B MSE 4 19 1 Y 1 B ALA -3 ? B ALA 5 20 1 Y 1 B SER -2 ? B SER 6 21 1 Y 1 B GLY 99 ? B GLY 107 22 1 Y 1 B GLY 100 ? B GLY 108 23 1 Y 1 B VAL 101 ? B VAL 109 24 1 Y 1 B ARG 102 ? B ARG 110 25 1 Y 1 B HIS 103 ? B HIS 111 26 1 Y 1 B VAL 104 ? B VAL 112 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MANGANESE (II) ION' MN 3 water HOH #