data_3KWT # _entry.id 3KWT # _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 3KWT RCSB RCSB056545 WWPDB D_1000056545 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2019-02-20 _pdbx_database_PDB_obs_spr.pdb_id 6NYC _pdbx_database_PDB_obs_spr.replace_pdb_id 3KWT _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3KWU _pdbx_database_related.details 'Munc13-1 C2B-domain, calcium bound' _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 3KWT _pdbx_database_status.status_code OBS _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-12-01 _pdbx_database_status.status_code_sf OBS _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 'Tomchick, D.R.' 1 'Rizo, J.' 2 'Machius, M.' 3 'Lu, J.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _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 _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Munc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis.' Nat.Struct.Mol.Biol. 17 280 288 2010 ? US 1545-9993 ? ? 20154707 10.1038/nsmb.1758 1 'Calmodulin and Munc13 form a Ca2+ sensor/effector complex that controls short-term synaptic plasticity.' 'Cell(Cambridge,Mass.)' 118 389 401 2004 CELLB5 US 0092-8674 0998 ? ? ? 2 'Munc-13 is essential for fusion competence of glutamatergic synaptic vesicles.' Nature 400 457 461 1999 NATUAS UK 0028-0836 0006 ? ? ? 3 'Mammalian homologues of C. elegans unc-13 gene define novel family of C2-domain proteins.' J.Biol.Chem. 270 25273 25280 1995 JBCHA3 US 0021-9258 0071 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Shin, O.H.' 1 ? primary 'Lu, J.' 2 ? primary 'Rhee, J.S.' 3 ? primary 'Tomchick, D.R.' 4 ? primary 'Pang, Z.P.' 5 ? primary 'Wojcik, S.M.' 6 ? primary 'Camacho-Perez, M.' 7 ? primary 'Brose, N.' 8 ? primary 'Machius, M.' 9 ? primary 'Rizo, J.' 10 ? primary 'Rosenmund, C.' 11 ? primary 'Sudhof, T.C.' 12 ? 1 'Junge, H.J.' 13 ? 1 'Rhee, J.S.' 14 ? 1 'Jahn, O.' 15 ? 1 'Varoqueaux, F.' 16 ? 1 'Speiss, J.' 17 ? 1 'Waxham, M.N.' 18 ? 1 'Rosenmund, C.' 19 ? 1 'Brose, N.' 20 ? 2 'Augustin, I.' 21 ? 2 'Rosenmund, C.' 22 ? 2 'Sudhof, T.C.' 23 ? 2 'Brose, N.' 24 ? 3 'Brose, N.' 25 ? 3 'Hofmann, K.' 26 ? 3 'Hata, Y.' 27 ? 3 'Sudhof, T.C.' 28 ? # _cell.length_a 42.572 _cell.length_b 101.141 _cell.length_c 68.038 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3KWT _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.space_group_name_H-M 'C 2 2 21' _symmetry.entry_id 3KWT _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 20 _symmetry.cell_setting ? _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 Munc13-1 16864.078 1 ? ? 'C2B domain, residues 675-820' ? 2 non-polymer syn 'CHLORIDE ION' 35.453 2 ? ? ? ? 3 non-polymer syn '2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL' 282.334 1 ? ? ? ? 4 water nat water 18.015 60 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Protein unc-13 homolog A' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;EFAVKQSVLDGTSKWSAKISITVVCAQGLQAKDKTGSSDPYVTVQVGKTKKRTKTIYGNLNPVWEENFHFECHNSSDRIK VRVLDEDDDIKSRVKQRFKRESDDFLGQTIIEVRTLSGEMDVWYNLDKRTDKSAVSGAIRLHISVEIK ; _entity_poly.pdbx_seq_one_letter_code_can ;EFAVKQSVLDGTSKWSAKISITVVCAQGLQAKDKTGSSDPYVTVQVGKTKKRTKTIYGNLNPVWEENFHFECHNSSDRIK VRVLDEDDDIKSRVKQRFKRESDDFLGQTIIEVRTLSGEMDVWYNLDKRTDKSAVSGAIRLHISVEIK ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLU n 1 2 PHE n 1 3 ALA n 1 4 VAL n 1 5 LYS n 1 6 GLN n 1 7 SER n 1 8 VAL n 1 9 LEU n 1 10 ASP n 1 11 GLY n 1 12 THR n 1 13 SER n 1 14 LYS n 1 15 TRP n 1 16 SER n 1 17 ALA n 1 18 LYS n 1 19 ILE n 1 20 SER n 1 21 ILE n 1 22 THR n 1 23 VAL n 1 24 VAL n 1 25 CYS n 1 26 ALA n 1 27 GLN n 1 28 GLY n 1 29 LEU n 1 30 GLN n 1 31 ALA n 1 32 LYS n 1 33 ASP n 1 34 LYS n 1 35 THR n 1 36 GLY n 1 37 SER n 1 38 SER n 1 39 ASP n 1 40 PRO n 1 41 TYR n 1 42 VAL n 1 43 THR n 1 44 VAL n 1 45 GLN n 1 46 VAL n 1 47 GLY n 1 48 LYS n 1 49 THR n 1 50 LYS n 1 51 LYS n 1 52 ARG n 1 53 THR n 1 54 LYS n 1 55 THR n 1 56 ILE n 1 57 TYR n 1 58 GLY n 1 59 ASN n 1 60 LEU n 1 61 ASN n 1 62 PRO n 1 63 VAL n 1 64 TRP n 1 65 GLU n 1 66 GLU n 1 67 ASN n 1 68 PHE n 1 69 HIS n 1 70 PHE n 1 71 GLU n 1 72 CYS n 1 73 HIS n 1 74 ASN n 1 75 SER n 1 76 SER n 1 77 ASP n 1 78 ARG n 1 79 ILE n 1 80 LYS n 1 81 VAL n 1 82 ARG n 1 83 VAL n 1 84 LEU n 1 85 ASP n 1 86 GLU n 1 87 ASP n 1 88 ASP n 1 89 ASP n 1 90 ILE n 1 91 LYS n 1 92 SER n 1 93 ARG n 1 94 VAL n 1 95 LYS n 1 96 GLN n 1 97 ARG n 1 98 PHE n 1 99 LYS n 1 100 ARG n 1 101 GLU n 1 102 SER n 1 103 ASP n 1 104 ASP n 1 105 PHE n 1 106 LEU n 1 107 GLY n 1 108 GLN n 1 109 THR n 1 110 ILE n 1 111 ILE n 1 112 GLU n 1 113 VAL n 1 114 ARG n 1 115 THR n 1 116 LEU n 1 117 SER n 1 118 GLY n 1 119 GLU n 1 120 MET n 1 121 ASP n 1 122 VAL n 1 123 TRP n 1 124 TYR n 1 125 ASN n 1 126 LEU n 1 127 ASP n 1 128 LYS n 1 129 ARG n 1 130 THR n 1 131 ASP n 1 132 LYS n 1 133 SER n 1 134 ALA n 1 135 VAL n 1 136 SER n 1 137 GLY n 1 138 ALA n 1 139 ILE n 1 140 ARG n 1 141 LEU n 1 142 HIS n 1 143 ILE n 1 144 SER n 1 145 VAL n 1 146 GLU n 1 147 ILE n 1 148 LYS n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name rat _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'unc-13, Unc13a, Unc13h1' _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 'Rattus norvegicus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10116 _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 '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 pGEX-KT _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code UN13A_RAT _struct_ref.pdbx_db_accession Q62768 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;AVKQSVLDGTSKWSAKISITVVCAQGLQAKDKTGSSDPYVTVQVGKTKKRTKTIYGNLNPVWEENFHFECHNSSDRIKVR VLDEDDDIKSRVKQRFKRESDDFLGQTIIEVRTLSGEMDVWYNLDKRTDKSAVSGAIRLHISVEIK ; _struct_ref.pdbx_align_begin 675 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3KWT _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 148 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q62768 _struct_ref_seq.db_align_beg 675 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 820 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 675 _struct_ref_seq.pdbx_auth_seq_align_end 820 # 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 3KWT GLU A 1 ? UNP Q62768 ? ? 'EXPRESSION TAG' 673 1 1 3KWT PHE A 2 ? UNP Q62768 ? ? 'EXPRESSION TAG' 674 2 # 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 B3P non-polymer . '2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL' ? 'C11 H26 N2 O6' 282.334 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 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 3KWT _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.17 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 43.36 _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 6.8 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '30% PEG-MME 2000, 0.1 M bis-tris propane pH 6.8, 0.1 M NaCl, 0.5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _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 SBC-3 _diffrn_detector.pdbx_collection_date 2003-11-23 _diffrn_detector.details monochromator # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'SAGITALLY FOCUSED Si(111)' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.98066 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-BM' _diffrn_source.pdbx_wavelength_list 0.98066 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-BM # _reflns.entry_id 3KWT _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 1.89 _reflns.d_resolution_low 26.43 _reflns.number_all 10907 _reflns.number_obs 10907 _reflns.percent_possible_obs 86.5 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 33.1 _reflns.B_iso_Wilson_estimate 31.5 _reflns.pdbx_redundancy 7.5 _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 1.89 _reflns_shell.d_res_low 1.93 _reflns_shell.percent_possible_obs ? _reflns_shell.percent_possible_all 47.5 _reflns_shell.Rmerge_I_obs 0.379 _reflns_shell.meanI_over_sigI_obs 2.4 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_redundancy 3.3 _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3KWT _refine.ls_d_res_high 1.890 _refine.ls_d_res_low 26.000 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 86.310 _refine.ls_number_reflns_obs 10406 _refine.ls_number_reflns_all 10907 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_R_factor_all 0.220 _refine.ls_R_factor_obs 0.220 _refine.ls_R_factor_R_work 0.217 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.282 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.800 _refine.ls_number_reflns_R_free 501 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 44.100 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model 'isotropic plus TLS' _refine.aniso_B[1][1] -1.610 _refine.aniso_B[2][2] -1.990 _refine.aniso_B[3][3] 3.600 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.946 _refine.correlation_coeff_Fo_to_Fc_free 0.907 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.184 _refine.pdbx_overall_ESU_R_Free 0.183 _refine.overall_SU_ML 0.113 _refine.overall_SU_B 7.119 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.400 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 'PDB ENTRY 1RSY' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 114.55 _refine.B_iso_min 20.59 _refine.occupancy_max 1.00 _refine.occupancy_min 0.50 _refine.pdbx_ls_sigma_I 0.00 _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_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 3KWT _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs 0.175 _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _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 928 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 21 _refine_hist.number_atoms_solvent 63 _refine_hist.number_atoms_total 1012 _refine_hist.d_res_high 1.890 _refine_hist.d_res_low 26.000 # 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 r_bond_refined_d 967 0.017 0.022 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1304 1.579 1.951 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 114 7.269 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 46 33.851 24.783 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 173 16.735 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 6 17.881 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 148 0.118 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 703 0.008 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 351 0.211 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 614 0.306 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 68 0.137 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 27 0.169 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 9 0.232 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 594 0.912 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 940 1.429 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 422 1.902 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 364 2.949 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.89 _refine_ls_shell.d_res_low 1.942 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 48.350 _refine_ls_shell.number_reflns_R_work 411 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.263 _refine_ls_shell.R_factor_R_free 0.318 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 13 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 424 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3KWT _struct.title 'Munc13-1 C2B-domain, calcium-free' _struct.pdbx_descriptor 'Rat Munc13-1 C2B domain' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3KWT _struct_keywords.text 'PHOSPHOLIPID BINDING PROTEIN, METAL BINDING PROTEIN' _struct_keywords.pdbx_keywords 'METAL BINDING 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 2 ? D N N 3 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id ARG _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 114 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id LEU _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 116 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ARG _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 786 _struct_conf.end_auth_comp_id LEU _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 788 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 4 ? # 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 ? anti-parallel A 3 4 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? 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 63 ? CYS A 72 ? VAL A 735 CYS A 744 A 2 ALA A 17 ? GLN A 27 ? ALA A 689 GLN A 699 A 3 ALA A 138 ? GLU A 146 ? ALA A 810 GLU A 818 A 4 GLU A 119 ? ASN A 125 ? GLU A 791 ASN A 797 B 1 THR A 49 ? ARG A 52 ? THR A 721 ARG A 724 B 2 PRO A 40 ? VAL A 46 ? PRO A 712 VAL A 718 B 3 ARG A 78 ? ASP A 85 ? ARG A 750 ASP A 757 B 4 ASP A 104 ? GLU A 112 ? ASP A 776 GLU A 784 # 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 O PHE A 68 ? O PHE A 740 N ILE A 21 ? N ILE A 693 A 2 3 N THR A 22 ? N THR A 694 O HIS A 142 ? O HIS A 814 A 3 4 O ILE A 143 ? O ILE A 815 N MET A 120 ? N MET A 792 B 1 2 O LYS A 51 ? O LYS A 723 N VAL A 44 ? N VAL A 716 B 2 3 N GLN A 45 ? N GLN A 717 O LYS A 80 ? O LYS A 752 B 3 4 N VAL A 83 ? N VAL A 755 O LEU A 106 ? O LEU A 778 # 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 CL A 911' AC2 Software ? ? ? ? 1 'BINDING SITE FOR RESIDUE CL A 912' AC3 Software ? ? ? ? 13 'BINDING SITE FOR RESIDUE B3P A 1001' # 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 HOH E . ? HOH A 18 . ? 1_555 ? 2 AC1 4 LYS A 50 ? LYS A 722 . ? 1_555 ? 3 AC1 4 GLY A 58 ? GLY A 730 . ? 8_456 ? 4 AC1 4 ARG A 82 ? ARG A 754 . ? 1_555 ? 5 AC2 1 GLN A 27 ? GLN A 699 . ? 1_555 ? 6 AC3 13 HOH E . ? HOH A 14 . ? 8_456 ? 7 AC3 13 HOH E . ? HOH A 16 . ? 1_555 ? 8 AC3 13 HOH E . ? HOH A 21 . ? 1_555 ? 9 AC3 13 TYR A 41 ? TYR A 713 . ? 1_555 ? 10 AC3 13 LYS A 50 ? LYS A 722 . ? 1_555 ? 11 AC3 13 ARG A 52 ? ARG A 724 . ? 1_555 ? 12 AC3 13 TYR A 57 ? TYR A 729 . ? 8_456 ? 13 AC3 13 GLY A 58 ? GLY A 730 . ? 8_456 ? 14 AC3 13 GLU A 86 ? GLU A 758 . ? 1_555 ? 15 AC3 13 ASP A 87 ? ASP A 759 . ? 1_555 ? 16 AC3 13 GLU A 101 ? GLU A 773 . ? 1_555 ? 17 AC3 13 SER A 102 ? SER A 774 . ? 1_555 ? 18 AC3 13 ASP A 103 ? ASP A 775 . ? 1_555 ? # _atom_sites.entry_id 3KWT _atom_sites.fract_transf_matrix[1][1] 0.023490 _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] 0.009887 _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] 0.014698 _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 CL N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLU 1 673 ? ? ? A . n A 1 2 PHE 2 674 ? ? ? A . n A 1 3 ALA 3 675 ? ? ? A . n A 1 4 VAL 4 676 ? ? ? A . n A 1 5 LYS 5 677 ? ? ? A . n A 1 6 GLN 6 678 ? ? ? A . n A 1 7 SER 7 679 ? ? ? A . n A 1 8 VAL 8 680 ? ? ? A . n A 1 9 LEU 9 681 ? ? ? A . n A 1 10 ASP 10 682 ? ? ? A . n A 1 11 GLY 11 683 ? ? ? A . n A 1 12 THR 12 684 ? ? ? A . n A 1 13 SER 13 685 ? ? ? A . n A 1 14 LYS 14 686 ? ? ? A . n A 1 15 TRP 15 687 ? ? ? A . n A 1 16 SER 16 688 688 SER SER A . n A 1 17 ALA 17 689 689 ALA ALA A . n A 1 18 LYS 18 690 690 LYS LYS A . n A 1 19 ILE 19 691 691 ILE ILE A . n A 1 20 SER 20 692 692 SER SER A . n A 1 21 ILE 21 693 693 ILE ILE A . n A 1 22 THR 22 694 694 THR THR A . n A 1 23 VAL 23 695 695 VAL VAL A . n A 1 24 VAL 24 696 696 VAL VAL A . n A 1 25 CYS 25 697 697 CYS CYS A . n A 1 26 ALA 26 698 698 ALA ALA A . n A 1 27 GLN 27 699 699 GLN GLN A . n A 1 28 GLY 28 700 700 GLY GLY A . n A 1 29 LEU 29 701 701 LEU LEU A . n A 1 30 GLN 30 702 702 GLN GLN A . n A 1 31 ALA 31 703 703 ALA ALA A . n A 1 32 LYS 32 704 704 LYS LYS A . n A 1 33 ASP 33 705 705 ASP ASP A . n A 1 34 LYS 34 706 ? ? ? A . n A 1 35 THR 35 707 ? ? ? A . n A 1 36 GLY 36 708 708 GLY GLY A . n A 1 37 SER 37 709 709 SER SER A . n A 1 38 SER 38 710 710 SER SER A . n A 1 39 ASP 39 711 711 ASP ASP A . n A 1 40 PRO 40 712 712 PRO PRO A . n A 1 41 TYR 41 713 713 TYR TYR A . n A 1 42 VAL 42 714 714 VAL VAL A . n A 1 43 THR 43 715 715 THR THR A . n A 1 44 VAL 44 716 716 VAL VAL A . n A 1 45 GLN 45 717 717 GLN GLN A . n A 1 46 VAL 46 718 718 VAL VAL A . n A 1 47 GLY 47 719 719 GLY GLY A . n A 1 48 LYS 48 720 720 LYS LYS A . n A 1 49 THR 49 721 721 THR THR A . n A 1 50 LYS 50 722 722 LYS LYS A . n A 1 51 LYS 51 723 723 LYS LYS A . n A 1 52 ARG 52 724 724 ARG ARG A . n A 1 53 THR 53 725 725 THR THR A . n A 1 54 LYS 54 726 726 LYS LYS A . n A 1 55 THR 55 727 727 THR THR A . n A 1 56 ILE 56 728 728 ILE ILE A . n A 1 57 TYR 57 729 729 TYR TYR A . n A 1 58 GLY 58 730 730 GLY GLY A . n A 1 59 ASN 59 731 731 ASN ASN A . n A 1 60 LEU 60 732 732 LEU LEU A . n A 1 61 ASN 61 733 733 ASN ASN A . n A 1 62 PRO 62 734 734 PRO PRO A . n A 1 63 VAL 63 735 735 VAL VAL A . n A 1 64 TRP 64 736 736 TRP TRP A . n A 1 65 GLU 65 737 737 GLU GLU A . n A 1 66 GLU 66 738 738 GLU GLU A . n A 1 67 ASN 67 739 739 ASN ASN A . n A 1 68 PHE 68 740 740 PHE PHE A . n A 1 69 HIS 69 741 741 HIS HIS A . n A 1 70 PHE 70 742 742 PHE PHE A . n A 1 71 GLU 71 743 743 GLU GLU A . n A 1 72 CYS 72 744 744 CYS CYS A . n A 1 73 HIS 73 745 745 HIS HIS A . n A 1 74 ASN 74 746 746 ASN ASN A . n A 1 75 SER 75 747 747 SER SER A . n A 1 76 SER 76 748 748 SER SER A . n A 1 77 ASP 77 749 749 ASP ASP A . n A 1 78 ARG 78 750 750 ARG ARG A . n A 1 79 ILE 79 751 751 ILE ILE A . n A 1 80 LYS 80 752 752 LYS LYS A . n A 1 81 VAL 81 753 753 VAL VAL A . n A 1 82 ARG 82 754 754 ARG ARG A . n A 1 83 VAL 83 755 755 VAL VAL A . n A 1 84 LEU 84 756 756 LEU LEU A . n A 1 85 ASP 85 757 757 ASP ASP A . n A 1 86 GLU 86 758 758 GLU GLU A . n A 1 87 ASP 87 759 759 ASP ASP A . n A 1 88 ASP 88 760 760 ASP ASP A . n A 1 89 ASP 89 761 761 ASP ASP A . n A 1 90 ILE 90 762 762 ILE ILE A . n A 1 91 LYS 91 763 763 LYS LYS A . n A 1 92 SER 92 764 ? ? ? A . n A 1 93 ARG 93 765 ? ? ? A . n A 1 94 VAL 94 766 ? ? ? A . n A 1 95 LYS 95 767 ? ? ? A . n A 1 96 GLN 96 768 ? ? ? A . n A 1 97 ARG 97 769 ? ? ? A . n A 1 98 PHE 98 770 ? ? ? A . n A 1 99 LYS 99 771 ? ? ? A . n A 1 100 ARG 100 772 ? ? ? A . n A 1 101 GLU 101 773 773 GLU GLU A . n A 1 102 SER 102 774 774 SER SER A . n A 1 103 ASP 103 775 775 ASP ASP A . n A 1 104 ASP 104 776 776 ASP ASP A . n A 1 105 PHE 105 777 777 PHE PHE A . n A 1 106 LEU 106 778 778 LEU LEU A . n A 1 107 GLY 107 779 779 GLY GLY A . n A 1 108 GLN 108 780 780 GLN GLN A . n A 1 109 THR 109 781 781 THR THR A . n A 1 110 ILE 110 782 782 ILE ILE A . n A 1 111 ILE 111 783 783 ILE ILE A . n A 1 112 GLU 112 784 784 GLU GLU A . n A 1 113 VAL 113 785 785 VAL VAL A . n A 1 114 ARG 114 786 786 ARG ARG A . n A 1 115 THR 115 787 787 THR THR A . n A 1 116 LEU 116 788 788 LEU LEU A . n A 1 117 SER 117 789 789 SER SER A . n A 1 118 GLY 118 790 790 GLY GLY A . n A 1 119 GLU 119 791 791 GLU GLU A . n A 1 120 MET 120 792 792 MET MET A . n A 1 121 ASP 121 793 793 ASP ASP A . n A 1 122 VAL 122 794 794 VAL VAL A . n A 1 123 TRP 123 795 795 TRP TRP A . n A 1 124 TYR 124 796 796 TYR TYR A . n A 1 125 ASN 125 797 797 ASN ASN A . n A 1 126 LEU 126 798 798 LEU LEU A . n A 1 127 ASP 127 799 799 ASP ASP A . n A 1 128 LYS 128 800 800 LYS LYS A . n A 1 129 ARG 129 801 801 ARG ARG A . n A 1 130 THR 130 802 ? ? ? A . n A 1 131 ASP 131 803 ? ? ? A . n A 1 132 LYS 132 804 ? ? ? A . n A 1 133 SER 133 805 ? ? ? A . n A 1 134 ALA 134 806 ? ? ? A . n A 1 135 VAL 135 807 807 VAL VAL A . n A 1 136 SER 136 808 808 SER SER A . n A 1 137 GLY 137 809 809 GLY GLY A . n A 1 138 ALA 138 810 810 ALA ALA A . n A 1 139 ILE 139 811 811 ILE ILE A . n A 1 140 ARG 140 812 812 ARG ARG A . n A 1 141 LEU 141 813 813 LEU LEU A . n A 1 142 HIS 142 814 814 HIS HIS A . n A 1 143 ILE 143 815 815 ILE ILE A . n A 1 144 SER 144 816 816 SER SER A . n A 1 145 VAL 145 817 817 VAL VAL A . n A 1 146 GLU 146 818 818 GLU GLU A . n A 1 147 ILE 147 819 819 ILE ILE A . n A 1 148 LYS 148 820 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CL 1 911 911 CL CL A . C 2 CL 1 912 912 CL CL A . D 3 B3P 1 1001 1001 B3P B3P A . E 4 HOH 1 1 1 HOH HOH A . E 4 HOH 2 2 2 HOH HOH A . E 4 HOH 3 3 3 HOH HOH A . E 4 HOH 4 4 4 HOH HOH A . E 4 HOH 5 5 5 HOH HOH A . E 4 HOH 6 6 6 HOH HOH A . E 4 HOH 7 7 7 HOH HOH A . E 4 HOH 8 8 8 HOH HOH A . E 4 HOH 9 9 9 HOH HOH A . E 4 HOH 10 10 10 HOH HOH A . E 4 HOH 11 11 11 HOH HOH A . E 4 HOH 12 12 12 HOH HOH A . E 4 HOH 13 13 13 HOH HOH A . E 4 HOH 14 14 14 HOH HOH A . E 4 HOH 15 15 15 HOH HOH A . E 4 HOH 16 16 16 HOH HOH A . E 4 HOH 17 17 17 HOH HOH A . E 4 HOH 18 18 18 HOH HOH A . E 4 HOH 19 19 19 HOH HOH A . E 4 HOH 20 20 20 HOH HOH A . E 4 HOH 21 21 21 HOH HOH A . E 4 HOH 22 22 22 HOH HOH A . E 4 HOH 23 23 23 HOH HOH A . E 4 HOH 24 24 24 HOH HOH A . E 4 HOH 25 25 25 HOH HOH A . E 4 HOH 26 26 26 HOH HOH A . E 4 HOH 27 27 27 HOH HOH A . E 4 HOH 28 28 28 HOH HOH A . E 4 HOH 29 29 29 HOH HOH A . E 4 HOH 30 30 30 HOH HOH A . E 4 HOH 31 31 31 HOH HOH A . E 4 HOH 32 32 32 HOH HOH A . E 4 HOH 33 33 33 HOH HOH A . E 4 HOH 34 34 34 HOH HOH A . E 4 HOH 35 35 35 HOH HOH A . E 4 HOH 36 36 36 HOH HOH A . E 4 HOH 37 37 37 HOH HOH A . E 4 HOH 38 38 38 HOH HOH A . E 4 HOH 39 39 39 HOH HOH A . E 4 HOH 40 40 40 HOH HOH A . E 4 HOH 41 41 41 HOH HOH A . E 4 HOH 42 42 42 HOH HOH A . E 4 HOH 43 43 43 HOH HOH A . E 4 HOH 44 44 44 HOH HOH A . E 4 HOH 45 45 45 HOH HOH A . E 4 HOH 46 46 46 HOH HOH A . E 4 HOH 47 47 47 HOH HOH A . E 4 HOH 48 48 48 HOH HOH A . E 4 HOH 49 49 49 HOH HOH A . E 4 HOH 50 50 50 HOH HOH A . E 4 HOH 51 51 51 HOH HOH A . E 4 HOH 52 52 52 HOH HOH A . E 4 HOH 53 53 53 HOH HOH A . E 4 HOH 54 54 54 HOH HOH A . E 4 HOH 55 55 55 HOH HOH A . E 4 HOH 56 56 56 HOH HOH A . E 4 HOH 57 57 57 HOH HOH A . E 4 HOH 58 58 58 HOH HOH A . E 4 HOH 59 59 59 HOH HOH A . E 4 HOH 60 60 60 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _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 2010-02-16 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-01 4 'Structure model' 1 3 2019-02-20 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 4 'Structure model' repository Obsolete ? # 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' 'Refinement description' 3 4 'Structure model' Advisory 4 4 'Structure model' 'Data collection' 5 4 'Structure model' Other # 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' software 2 4 'Structure model' pdbx_database_PDB_obs_spr 3 4 'Structure model' pdbx_database_status # 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' '_pdbx_database_status.status_code' 2 4 'Structure model' '_pdbx_database_status.status_code_sf' # 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 18.3435 33.8707 29.4679 -0.1438 -0.1250 -0.0973 -0.0097 0.0049 -0.0435 3.9289 6.1160 2.1970 -0.3917 -0.0062 -0.3787 -0.0780 0.1176 -0.0396 0.1273 -0.2235 0.0659 -0.1698 -0.0466 -0.1188 'X-RAY DIFFRACTION' 2 ? refined 20.8333 16.0661 30.3524 0.0348 -0.1144 0.2964 -0.1188 0.0143 -0.0831 30.3699 27.8149 13.2077 -24.8809 -6.9023 7.9177 -0.6996 0.0307 0.6689 1.2521 -2.6017 0.6626 0.2584 1.2524 0.1209 'X-RAY DIFFRACTION' 3 ? refined 13.2560 42.4569 32.6842 -0.1348 -0.1019 -0.0240 0.0297 -0.0499 -0.0035 2.6209 8.8250 1.4709 -1.4161 -0.3654 0.3038 0.2187 0.0325 -0.2512 0.0199 0.2285 1.1359 0.1793 -0.3078 -0.1074 'X-RAY DIFFRACTION' 4 ? refined 13.2968 35.1901 41.5981 0.0336 0.0402 -0.2778 0.0222 0.0262 -0.0182 31.9590 19.1457 2.8232 7.5439 -4.6683 4.9958 0.1847 -0.3606 0.1759 -1.7198 0.8679 1.4122 0.8862 0.5194 0.2307 'X-RAY DIFFRACTION' 5 ? refined 18.1274 47.3644 25.6414 0.1516 -0.0615 -0.1720 0.0105 -0.0227 -0.0655 6.6812 11.4147 6.1363 0.2462 -3.3046 -3.3835 0.1300 0.1566 -0.2866 0.8682 -0.0806 -0.0647 -1.1984 -0.5203 -0.3582 # 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 689 A 759 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 A 760 A 775 ? . . . . ? 'X-RAY DIFFRACTION' 3 3 A 776 A 796 ? . . . . ? 'X-RAY DIFFRACTION' 4 4 A 797 A 811 ? . . . . ? 'X-RAY DIFFRACTION' 5 5 A 812 A 819 ? . . . . ? # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 AMoRE . ? program 'Jorge Navaza' ccp4@ccp4.ac.uk phasing http://www.ccp4.ac.uk/ Fortran_77 ? 4 REFMAC 5.2.0019 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 5 PDB_EXTRACT 3.005 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 HKL-2000 . ? ? ? ? 'data collection' ? ? ? 7 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 8 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CB A LEU 756 ? ? CG A LEU 756 ? ? CD1 A LEU 756 ? ? 126.73 111.00 15.73 1.70 N 2 1 CB A LEU 756 ? ? CG A LEU 756 ? ? CD2 A LEU 756 ? ? 126.98 111.00 15.98 1.70 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 LYS A 704 ? ? -20.18 -63.90 2 1 SER A 789 ? ? -78.82 -138.22 # 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 GLU 673 ? A GLU 1 2 1 Y 1 A PHE 674 ? A PHE 2 3 1 Y 1 A ALA 675 ? A ALA 3 4 1 Y 1 A VAL 676 ? A VAL 4 5 1 Y 1 A LYS 677 ? A LYS 5 6 1 Y 1 A GLN 678 ? A GLN 6 7 1 Y 1 A SER 679 ? A SER 7 8 1 Y 1 A VAL 680 ? A VAL 8 9 1 Y 1 A LEU 681 ? A LEU 9 10 1 Y 1 A ASP 682 ? A ASP 10 11 1 Y 1 A GLY 683 ? A GLY 11 12 1 Y 1 A THR 684 ? A THR 12 13 1 Y 1 A SER 685 ? A SER 13 14 1 Y 1 A LYS 686 ? A LYS 14 15 1 Y 1 A TRP 687 ? A TRP 15 16 1 Y 1 A LYS 706 ? A LYS 34 17 1 Y 1 A THR 707 ? A THR 35 18 1 Y 1 A SER 764 ? A SER 92 19 1 Y 1 A ARG 765 ? A ARG 93 20 1 Y 1 A VAL 766 ? A VAL 94 21 1 Y 1 A LYS 767 ? A LYS 95 22 1 Y 1 A GLN 768 ? A GLN 96 23 1 Y 1 A ARG 769 ? A ARG 97 24 1 Y 1 A PHE 770 ? A PHE 98 25 1 Y 1 A LYS 771 ? A LYS 99 26 1 Y 1 A ARG 772 ? A ARG 100 27 1 Y 1 A THR 802 ? A THR 130 28 1 Y 1 A ASP 803 ? A ASP 131 29 1 Y 1 A LYS 804 ? A LYS 132 30 1 Y 1 A SER 805 ? A SER 133 31 1 Y 1 A ALA 806 ? A ALA 134 32 1 Y 1 A LYS 820 ? A LYS 148 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CHLORIDE ION' CL 3 '2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL' B3P 4 water HOH #