data_3KAT # _entry.id 3KAT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.312 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3KAT RCSB RCSB055761 WWPDB D_1000055761 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id HR3486E _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 3KAT _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-10-19 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _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 'Forouhar, F.' 1 'Abashidze, M.' 2 'Seetharaman, J.' 3 'Mao, M.' 4 'Xiao, R.' 5 'Ciccosanti, C.' 6 'Shastry, R.' 7 'Everett, J.K.' 8 'Nair, R.' 9 'Acton, T.B.' 10 'Rost, B.' 11 'Montelione, G.T.' 12 'Tong, L.' 13 'Hunt, J.F.' 14 'Northeast Structural Genomics Consortium (NESG)' 15 # _citation.id primary _citation.title 'Northeast Structural Genomics Consortium Target HR3486E' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Forouhar, F.' 1 ? primary 'Abashidze, M.' 2 ? primary 'Seetharaman, J.' 3 ? primary 'Mao, M.' 4 ? primary 'Xiao, R.' 5 ? primary 'Ciccosanti, C.' 6 ? primary 'Shastry, R.' 7 ? primary 'Everett, J.K.' 8 ? primary 'Nair, R.' 9 ? primary 'Acton, T.B.' 10 ? primary 'Rost, B.' 11 ? primary 'Montelione, G.T.' 12 ? primary 'Tong, L.' 13 ? primary 'Hunt, J.F.' 14 ? # _cell.entry_id 3KAT _cell.length_a 40.708 _cell.length_b 40.708 _cell.length_c 160.413 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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 3KAT _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.Int_Tables_number 92 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'NACHT, LRR and PYD domains-containing protein 1' _entity.formula_weight 12733.026 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'CARD domain' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name ;Death effector filament-forming ced-4-like apoptosis protein, Nucleotide-binding domain and caspase recruitment domain, Caspase recruitment domain-containing protein 7 ; # _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 ;(MSE)GHHHHHHSHSPLDAPQLLHFVDQYREQLIARVTSVEVVLDKLHGQVLSQEQYERVLAENTRPSQ(MSE)RKLFSL SQSWDRKCKDGLYQALKETHPHLI(MSE)ELWEKGSKKG ; _entity_poly.pdbx_seq_one_letter_code_can ;MGHHHHHHSHSPLDAPQLLHFVDQYREQLIARVTSVEVVLDKLHGQVLSQEQYERVLAENTRPSQMRKLFSLSQSWDRKC KDGLYQALKETHPHLIMELWEKGSKKG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier HR3486E # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MSE n 1 2 GLY n 1 3 HIS n 1 4 HIS n 1 5 HIS n 1 6 HIS n 1 7 HIS n 1 8 HIS n 1 9 SER n 1 10 HIS n 1 11 SER n 1 12 PRO n 1 13 LEU n 1 14 ASP n 1 15 ALA n 1 16 PRO n 1 17 GLN n 1 18 LEU n 1 19 LEU n 1 20 HIS n 1 21 PHE n 1 22 VAL n 1 23 ASP n 1 24 GLN n 1 25 TYR n 1 26 ARG n 1 27 GLU n 1 28 GLN n 1 29 LEU n 1 30 ILE n 1 31 ALA n 1 32 ARG n 1 33 VAL n 1 34 THR n 1 35 SER n 1 36 VAL n 1 37 GLU n 1 38 VAL n 1 39 VAL n 1 40 LEU n 1 41 ASP n 1 42 LYS n 1 43 LEU n 1 44 HIS n 1 45 GLY n 1 46 GLN n 1 47 VAL n 1 48 LEU n 1 49 SER n 1 50 GLN n 1 51 GLU n 1 52 GLN n 1 53 TYR n 1 54 GLU n 1 55 ARG n 1 56 VAL n 1 57 LEU n 1 58 ALA n 1 59 GLU n 1 60 ASN n 1 61 THR n 1 62 ARG n 1 63 PRO n 1 64 SER n 1 65 GLN n 1 66 MSE n 1 67 ARG n 1 68 LYS n 1 69 LEU n 1 70 PHE n 1 71 SER n 1 72 LEU n 1 73 SER n 1 74 GLN n 1 75 SER n 1 76 TRP n 1 77 ASP n 1 78 ARG n 1 79 LYS n 1 80 CYS n 1 81 LYS n 1 82 ASP n 1 83 GLY n 1 84 LEU n 1 85 TYR n 1 86 GLN n 1 87 ALA n 1 88 LEU n 1 89 LYS n 1 90 GLU n 1 91 THR n 1 92 HIS n 1 93 PRO n 1 94 HIS n 1 95 LEU n 1 96 ILE n 1 97 MSE n 1 98 GLU n 1 99 LEU n 1 100 TRP n 1 101 GLU n 1 102 LYS n 1 103 GLY n 1 104 SER n 1 105 LYS n 1 106 LYS n 1 107 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 'CARD7, DEFCAP, KIAA0926, NAC, NALP1, NLRP1' _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)+ Magic' _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 'pET 14-15C' _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code NALP1_HUMAN _struct_ref.pdbx_db_accession Q9C000 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;SPLDAPQLLHFVDQYREQLIARVTSVEVVLDKLHGQVLSQEQYERVLAENTRPSQMRKLFSLSQSWDRKCKDGLYQALKE THPHLIMELWEKGSKKG ; _struct_ref.pdbx_align_begin 1371 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3KAT _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 11 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 107 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9C000 _struct_ref_seq.db_align_beg 1371 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 1467 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1371 _struct_ref_seq.pdbx_auth_seq_align_end 1467 # 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 3KAT MSE A 1 ? UNP Q9C000 ? ? 'expression tag' 1361 1 1 3KAT GLY A 2 ? UNP Q9C000 ? ? 'expression tag' 1362 2 1 3KAT HIS A 3 ? UNP Q9C000 ? ? 'expression tag' 1363 3 1 3KAT HIS A 4 ? UNP Q9C000 ? ? 'expression tag' 1364 4 1 3KAT HIS A 5 ? UNP Q9C000 ? ? 'expression tag' 1365 5 1 3KAT HIS A 6 ? UNP Q9C000 ? ? 'expression tag' 1366 6 1 3KAT HIS A 7 ? UNP Q9C000 ? ? 'expression tag' 1367 7 1 3KAT HIS A 8 ? UNP Q9C000 ? ? 'expression tag' 1368 8 1 3KAT SER A 9 ? UNP Q9C000 ? ? 'expression tag' 1369 9 1 3KAT HIS A 10 ? UNP Q9C000 ? ? 'expression tag' 1370 10 # 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 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 3KAT _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.61 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 52.87 _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.pH 7.5 _exptl_crystal_grow.temp 291 _exptl_crystal_grow.pdbx_details ;Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 18% PEG3350 and 150 mM sodium formate., VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _exptl_crystal_grow.temp_details ? _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 CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2009-10-15 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'Si 111 CHANNEL' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97882 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X4A' _diffrn_source.pdbx_wavelength_list 0.97882 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X4A # _reflns.entry_id 3KAT _reflns.observed_criterion_sigma_F 1.0 _reflns.observed_criterion_sigma_I 1.0 _reflns.d_resolution_high 3.1 _reflns.d_resolution_low 30 _reflns.number_all 4726 _reflns.number_obs 3795 _reflns.percent_possible_obs 80.3 _reflns.pdbx_Rmerge_I_obs 0.065 _reflns.pdbx_Rsym_value 0.063 _reflns.pdbx_netI_over_sigmaI 18.01 _reflns.B_iso_Wilson_estimate 43.4 _reflns.pdbx_redundancy 5.2 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 3.1 _reflns_shell.d_res_low 3.21 _reflns_shell.percent_possible_obs ? _reflns_shell.percent_possible_all 54.9 _reflns_shell.Rmerge_I_obs 0.157 _reflns_shell.meanI_over_sigI_obs 3.79 _reflns_shell.pdbx_Rsym_value 0.198 _reflns_shell.pdbx_redundancy 2.3 _reflns_shell.number_unique_all 462 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3KAT _refine.ls_d_res_high 3.100 _refine.ls_d_res_low 19.970 _refine.pdbx_ls_sigma_F 2.00 _refine.pdbx_data_cutoff_high_absF 196886.016 _refine.pdbx_data_cutoff_low_absF 0.000 _refine.ls_percent_reflns_obs 80.400 _refine.ls_number_reflns_obs 3749 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.ls_R_factor_R_work 0.202 _refine.ls_R_factor_R_free 0.260 _refine.ls_percent_reflns_R_free 4.700 _refine.ls_number_reflns_R_free 176 _refine.ls_R_factor_R_free_error 0.020 _refine.B_iso_mean 58.800 _refine.solvent_model_param_bsol 33.595 _refine.solvent_model_param_ksol 0.350 _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.aniso_B[1][1] 2.180 _refine.aniso_B[2][2] 2.180 _refine.aniso_B[3][3] -4.360 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.solvent_model_details 'FLAT MODEL' _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_redundancy_reflns_obs ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.occupancy_max ? _refine.occupancy_min ? _refine.details ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _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_diffrn_id 1 _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_analyze.entry_id 3KAT _refine_analyze.Luzzati_coordinate_error_obs 0.350 _refine_analyze.Luzzati_sigma_a_obs 0.590 _refine_analyze.Luzzati_d_res_low_obs 5.000 _refine_analyze.Luzzati_coordinate_error_free 0.430 _refine_analyze.Luzzati_sigma_a_free 0.680 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 707 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 707 _refine_hist.d_res_high 3.100 _refine_hist.d_res_low 19.970 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d ? 0.009 ? ? 'X-RAY DIFFRACTION' ? c_angle_deg ? 1.300 ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d ? 19.500 ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d ? 0.660 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 3.100 _refine_ls_shell.d_res_low 3.210 _refine_ls_shell.pdbx_total_number_of_bins_used 10 _refine_ls_shell.percent_reflns_obs 53.800 _refine_ls_shell.number_reflns_R_work 237 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.331 _refine_ls_shell.R_factor_R_free 0.395 _refine_ls_shell.percent_reflns_R_free 6.000 _refine_ls_shell.number_reflns_R_free 15 _refine_ls_shell.R_factor_R_free_error 0.102 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs 252 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3KAT _struct.title 'Crystal Structure of the CARD domain of the human NLRP1 protein, Northeast Structural Genomics Consortium Target HR3486E' _struct.pdbx_descriptor 'NACHT, LRR and PYD domains-containing protein 1' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3KAT _struct_keywords.text ;Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Alternative splicing, ATP-binding, Cytoplasm, Leucine-rich repeat, Nucleotide-binding, Nucleus, Polymorphism, APOPTOSIS ; _struct_keywords.pdbx_keywords APOPTOSIS # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.details 'light scattering data suggest monomer.' # 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 LEU A 19 ? TYR A 25 ? LEU A 1379 TYR A 1385 1 ? 7 HELX_P HELX_P2 2 TYR A 25 ? ALA A 31 ? TYR A 1385 ALA A 1391 1 ? 7 HELX_P HELX_P3 3 SER A 35 ? HIS A 44 ? SER A 1395 HIS A 1404 1 ? 10 HELX_P HELX_P4 4 SER A 49 ? GLU A 59 ? SER A 1409 GLU A 1419 1 ? 11 HELX_P HELX_P5 5 THR A 61 ? LEU A 72 ? THR A 1421 LEU A 1432 1 ? 12 HELX_P HELX_P6 6 SER A 73 ? TRP A 76 ? SER A 1433 TRP A 1436 5 ? 4 HELX_P HELX_P7 7 LYS A 79 ? HIS A 92 ? LYS A 1439 HIS A 1452 1 ? 14 HELX_P HELX_P8 8 HIS A 92 ? LYS A 102 ? HIS A 1452 LYS A 1462 1 ? 11 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale both ? A GLN 65 C ? ? ? 1_555 A MSE 66 N ? ? A GLN 1425 A MSE 1426 1_555 ? ? ? ? ? ? ? 1.328 ? covale2 covale both ? A MSE 66 C ? ? ? 1_555 A ARG 67 N ? ? A MSE 1426 A ARG 1427 1_555 ? ? ? ? ? ? ? 1.329 ? covale3 covale both ? A ILE 96 C ? ? ? 1_555 A MSE 97 N ? ? A ILE 1456 A MSE 1457 1_555 ? ? ? ? ? ? ? 1.325 ? covale4 covale both ? A MSE 97 C ? ? ? 1_555 A GLU 98 N ? ? A MSE 1457 A GLU 1458 1_555 ? ? ? ? ? ? ? 1.329 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 3KAT _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 3KAT _atom_sites.fract_transf_matrix[1][1] 0.024565 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.024565 _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] 0.006234 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C 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 MSE 1 1361 ? ? ? A . n A 1 2 GLY 2 1362 ? ? ? A . n A 1 3 HIS 3 1363 ? ? ? A . n A 1 4 HIS 4 1364 ? ? ? A . n A 1 5 HIS 5 1365 ? ? ? A . n A 1 6 HIS 6 1366 ? ? ? A . n A 1 7 HIS 7 1367 ? ? ? A . n A 1 8 HIS 8 1368 ? ? ? A . n A 1 9 SER 9 1369 ? ? ? A . n A 1 10 HIS 10 1370 ? ? ? A . n A 1 11 SER 11 1371 ? ? ? A . n A 1 12 PRO 12 1372 ? ? ? A . n A 1 13 LEU 13 1373 ? ? ? A . n A 1 14 ASP 14 1374 ? ? ? A . n A 1 15 ALA 15 1375 ? ? ? A . n A 1 16 PRO 16 1376 ? ? ? A . n A 1 17 GLN 17 1377 ? ? ? A . n A 1 18 LEU 18 1378 ? ? ? A . n A 1 19 LEU 19 1379 1379 LEU LEU A . n A 1 20 HIS 20 1380 1380 HIS HIS A . n A 1 21 PHE 21 1381 1381 PHE PHE A . n A 1 22 VAL 22 1382 1382 VAL VAL A . n A 1 23 ASP 23 1383 1383 ASP ASP A . n A 1 24 GLN 24 1384 1384 GLN GLN A . n A 1 25 TYR 25 1385 1385 TYR TYR A . n A 1 26 ARG 26 1386 1386 ARG ARG A . n A 1 27 GLU 27 1387 1387 GLU GLU A . n A 1 28 GLN 28 1388 1388 GLN GLN A . n A 1 29 LEU 29 1389 1389 LEU LEU A . n A 1 30 ILE 30 1390 1390 ILE ILE A . n A 1 31 ALA 31 1391 1391 ALA ALA A . n A 1 32 ARG 32 1392 1392 ARG ARG A . n A 1 33 VAL 33 1393 1393 VAL VAL A . n A 1 34 THR 34 1394 1394 THR THR A . n A 1 35 SER 35 1395 1395 SER SER A . n A 1 36 VAL 36 1396 1396 VAL VAL A . n A 1 37 GLU 37 1397 1397 GLU GLU A . n A 1 38 VAL 38 1398 1398 VAL VAL A . n A 1 39 VAL 39 1399 1399 VAL VAL A . n A 1 40 LEU 40 1400 1400 LEU LEU A . n A 1 41 ASP 41 1401 1401 ASP ASP A . n A 1 42 LYS 42 1402 1402 LYS LYS A . n A 1 43 LEU 43 1403 1403 LEU LEU A . n A 1 44 HIS 44 1404 1404 HIS HIS A . n A 1 45 GLY 45 1405 1405 GLY GLY A . n A 1 46 GLN 46 1406 1406 GLN GLN A . n A 1 47 VAL 47 1407 1407 VAL VAL A . n A 1 48 LEU 48 1408 1408 LEU LEU A . n A 1 49 SER 49 1409 1409 SER SER A . n A 1 50 GLN 50 1410 1410 GLN GLN A . n A 1 51 GLU 51 1411 1411 GLU GLU A . n A 1 52 GLN 52 1412 1412 GLN GLN A . n A 1 53 TYR 53 1413 1413 TYR TYR A . n A 1 54 GLU 54 1414 1414 GLU GLU A . n A 1 55 ARG 55 1415 1415 ARG ARG A . n A 1 56 VAL 56 1416 1416 VAL VAL A . n A 1 57 LEU 57 1417 1417 LEU LEU A . n A 1 58 ALA 58 1418 1418 ALA ALA A . n A 1 59 GLU 59 1419 1419 GLU GLU A . n A 1 60 ASN 60 1420 1420 ASN ASN A . n A 1 61 THR 61 1421 1421 THR THR A . n A 1 62 ARG 62 1422 1422 ARG ARG A . n A 1 63 PRO 63 1423 1423 PRO PRO A . n A 1 64 SER 64 1424 1424 SER SER A . n A 1 65 GLN 65 1425 1425 GLN GLN A . n A 1 66 MSE 66 1426 1426 MSE MSE A . n A 1 67 ARG 67 1427 1427 ARG ARG A . n A 1 68 LYS 68 1428 1428 LYS LYS A . n A 1 69 LEU 69 1429 1429 LEU LEU A . n A 1 70 PHE 70 1430 1430 PHE PHE A . n A 1 71 SER 71 1431 1431 SER SER A . n A 1 72 LEU 72 1432 1432 LEU LEU A . n A 1 73 SER 73 1433 1433 SER SER A . n A 1 74 GLN 74 1434 1434 GLN GLN A . n A 1 75 SER 75 1435 1435 SER SER A . n A 1 76 TRP 76 1436 1436 TRP TRP A . n A 1 77 ASP 77 1437 1437 ASP ASP A . n A 1 78 ARG 78 1438 1438 ARG ARG A . n A 1 79 LYS 79 1439 1439 LYS LYS A . n A 1 80 CYS 80 1440 1440 CYS CYS A . n A 1 81 LYS 81 1441 1441 LYS LYS A . n A 1 82 ASP 82 1442 1442 ASP ASP A . n A 1 83 GLY 83 1443 1443 GLY GLY A . n A 1 84 LEU 84 1444 1444 LEU LEU A . n A 1 85 TYR 85 1445 1445 TYR TYR A . n A 1 86 GLN 86 1446 1446 GLN GLN A . n A 1 87 ALA 87 1447 1447 ALA ALA A . n A 1 88 LEU 88 1448 1448 LEU LEU A . n A 1 89 LYS 89 1449 1449 LYS LYS A . n A 1 90 GLU 90 1450 1450 GLU GLU A . n A 1 91 THR 91 1451 1451 THR THR A . n A 1 92 HIS 92 1452 1452 HIS HIS A . n A 1 93 PRO 93 1453 1453 PRO PRO A . n A 1 94 HIS 94 1454 1454 HIS HIS A . n A 1 95 LEU 95 1455 1455 LEU LEU A . n A 1 96 ILE 96 1456 1456 ILE ILE A . n A 1 97 MSE 97 1457 1457 MSE MSE A . n A 1 98 GLU 98 1458 1458 GLU GLU A . n A 1 99 LEU 99 1459 1459 LEU LEU A . n A 1 100 TRP 100 1460 1460 TRP TRP A . n A 1 101 GLU 101 1461 1461 GLU GLU A . n A 1 102 LYS 102 1462 1462 LYS LYS A . n A 1 103 GLY 103 1463 ? ? ? A . n A 1 104 SER 104 1464 ? ? ? A . n A 1 105 LYS 105 1465 ? ? ? A . n A 1 106 LYS 106 1466 ? ? ? A . n A 1 107 GLY 107 1467 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Northeast Structural Genomics Consortium' _pdbx_SG_project.initial_of_center NESG # 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 66 A MSE 1426 ? MET SELENOMETHIONINE 2 A MSE 97 A MSE 1457 ? MET SELENOMETHIONINE # 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_defined_assembly ? monomeric 1 2 software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A 2 1,2 A # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 2 'ABSA (A^2)' 690 ? 2 MORE -9 ? 2 'SSA (A^2)' 9310 ? # 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' 7_555 y,x,-z 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 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 2009-10-27 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2019-07-17 # _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' 'Version format compliance' 2 3 'Structure model' 'Author supporting evidence' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Refinement description' # 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_struct_assembly_auth_evidence 2 4 'Structure model' software 3 4 '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 4 'Structure model' '_software.contact_author' 2 4 'Structure model' '_software.contact_author_email' 3 4 'Structure model' '_software.language' 4 4 'Structure model' '_software.location' 5 4 'Structure model' '_software.name' 6 4 'Structure model' '_software.type' 7 4 'Structure model' '_software.version' 8 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal CNS '1.2 & XtalView' ? ? ? ? refinement ? ? ? 1 PDB_EXTRACT 3.00 'March. 27, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 2 ADSC Quantum ? ? ? ? 'data collection' ? ? ? 3 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 4 SCALEPACK . ? ? ? ? 'data scaling' ? ? ? 5 SHELX 'then SOLVE/RESOLVE' ? ? ? ? phasing ? ? ? 6 REFMAC . ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 7 # 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 HIS A 1380 ? ? -55.05 -2.72 2 1 TYR A 1385 ? ? -81.33 34.85 3 1 ARG A 1386 ? ? -56.36 -72.03 4 1 ARG A 1392 ? ? -143.12 -19.35 5 1 GLN A 1406 ? ? -148.84 -44.84 6 1 SER A 1409 ? ? -67.06 -178.29 7 1 ASN A 1420 ? ? -69.62 -73.23 8 1 THR A 1451 ? ? -55.73 -73.90 # 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 MSE 1361 ? A MSE 1 2 1 Y 1 A GLY 1362 ? A GLY 2 3 1 Y 1 A HIS 1363 ? A HIS 3 4 1 Y 1 A HIS 1364 ? A HIS 4 5 1 Y 1 A HIS 1365 ? A HIS 5 6 1 Y 1 A HIS 1366 ? A HIS 6 7 1 Y 1 A HIS 1367 ? A HIS 7 8 1 Y 1 A HIS 1368 ? A HIS 8 9 1 Y 1 A SER 1369 ? A SER 9 10 1 Y 1 A HIS 1370 ? A HIS 10 11 1 Y 1 A SER 1371 ? A SER 11 12 1 Y 1 A PRO 1372 ? A PRO 12 13 1 Y 1 A LEU 1373 ? A LEU 13 14 1 Y 1 A ASP 1374 ? A ASP 14 15 1 Y 1 A ALA 1375 ? A ALA 15 16 1 Y 1 A PRO 1376 ? A PRO 16 17 1 Y 1 A GLN 1377 ? A GLN 17 18 1 Y 1 A LEU 1378 ? A LEU 18 19 1 Y 1 A GLY 1463 ? A GLY 103 20 1 Y 1 A SER 1464 ? A SER 104 21 1 Y 1 A LYS 1465 ? A LYS 105 22 1 Y 1 A LYS 1466 ? A LYS 106 23 1 Y 1 A GLY 1467 ? A GLY 107 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'light scattering' _pdbx_struct_assembly_auth_evidence.details ? #