data_1W16 # _entry.id 1W16 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.308 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1W16 PDBE EBI-15608 WWPDB D_1290015608 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1W15 _pdbx_database_related.content_type unspecified _pdbx_database_related.details 'RAT SYNAPTOTAGMIN 4 C2B DOMAIN IN THE PRESENCE OF CALCIUM' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1W16 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2004-06-16 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Dai, H.' 1 'Shin, O.-H.' 2 'Machius, M.' 3 'Tomchick, D.R.' 4 'Sudhof, T.C.' 5 'Rizo, J.' 6 # _citation.id primary _citation.title 'Structural Basis for the Evolutionary Inactivation of Ca2+ Binding to Synaptotagmin 4' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 11 _citation.page_first 844 _citation.page_last ? _citation.year 2004 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9993 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15311271 _citation.pdbx_database_id_DOI 10.1038/NSMB817 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dai, H.' 1 ? primary 'Shin, O.-H.' 2 ? primary 'Machius, M.' 3 ? primary 'Tomchick, D.R.' 4 ? primary 'Sudhof, T.C.' 5 ? primary 'Rizo, J.' 6 ? # _cell.entry_id 1W16 _cell.length_a 91.061 _cell.length_b 91.061 _cell.length_c 122.860 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1W16 _symmetry.space_group_name_H-M 'P 63 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 # 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 'SYNAPTOTAGMIN IV' 16620.102 1 ? ? 'C2B DOMAIN, RESIDUES 288-425' ? 2 non-polymer syn 'SODIUM ION' 22.990 2 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 7 ? ? ? ? 4 water nat water 18.015 53 ? ? ? ? # _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 ;GSPGISGGGGGIPSGRGELLVSLCYQSTTNTLTVVVLKARHLPKSDVSGLSDPYVKVNLYHAKKRISKKKTHVKKCTPNA VFNELFVFDIPCESLEEISVEFLVLDSERGSRNEVIGRLVLGATAEGSGGGHWKEICDFPRRQIAKWHMLCDG ; _entity_poly.pdbx_seq_one_letter_code_can ;GSPGISGGGGGIPSGRGELLVSLCYQSTTNTLTVVVLKARHLPKSDVSGLSDPYVKVNLYHAKKRISKKKTHVKKCTPNA VFNELFVFDIPCESLEEISVEFLVLDSERGSRNEVIGRLVLGATAEGSGGGHWKEICDFPRRQIAKWHMLCDG ; _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 GLY n 1 2 SER n 1 3 PRO n 1 4 GLY n 1 5 ILE n 1 6 SER n 1 7 GLY n 1 8 GLY n 1 9 GLY n 1 10 GLY n 1 11 GLY n 1 12 ILE n 1 13 PRO n 1 14 SER n 1 15 GLY n 1 16 ARG n 1 17 GLY n 1 18 GLU n 1 19 LEU n 1 20 LEU n 1 21 VAL n 1 22 SER n 1 23 LEU n 1 24 CYS n 1 25 TYR n 1 26 GLN n 1 27 SER n 1 28 THR n 1 29 THR n 1 30 ASN n 1 31 THR n 1 32 LEU n 1 33 THR n 1 34 VAL n 1 35 VAL n 1 36 VAL n 1 37 LEU n 1 38 LYS n 1 39 ALA n 1 40 ARG n 1 41 HIS n 1 42 LEU n 1 43 PRO n 1 44 LYS n 1 45 SER n 1 46 ASP n 1 47 VAL n 1 48 SER n 1 49 GLY n 1 50 LEU n 1 51 SER n 1 52 ASP n 1 53 PRO n 1 54 TYR n 1 55 VAL n 1 56 LYS n 1 57 VAL n 1 58 ASN n 1 59 LEU n 1 60 TYR n 1 61 HIS n 1 62 ALA n 1 63 LYS n 1 64 LYS n 1 65 ARG n 1 66 ILE n 1 67 SER n 1 68 LYS n 1 69 LYS n 1 70 LYS n 1 71 THR n 1 72 HIS n 1 73 VAL n 1 74 LYS n 1 75 LYS n 1 76 CYS n 1 77 THR n 1 78 PRO n 1 79 ASN n 1 80 ALA n 1 81 VAL n 1 82 PHE n 1 83 ASN n 1 84 GLU n 1 85 LEU n 1 86 PHE n 1 87 VAL n 1 88 PHE n 1 89 ASP n 1 90 ILE n 1 91 PRO n 1 92 CYS n 1 93 GLU n 1 94 SER n 1 95 LEU n 1 96 GLU n 1 97 GLU n 1 98 ILE n 1 99 SER n 1 100 VAL n 1 101 GLU n 1 102 PHE n 1 103 LEU n 1 104 VAL n 1 105 LEU n 1 106 ASP n 1 107 SER n 1 108 GLU n 1 109 ARG n 1 110 GLY n 1 111 SER n 1 112 ARG n 1 113 ASN n 1 114 GLU n 1 115 VAL n 1 116 ILE n 1 117 GLY n 1 118 ARG n 1 119 LEU n 1 120 VAL n 1 121 LEU n 1 122 GLY n 1 123 ALA n 1 124 THR n 1 125 ALA n 1 126 GLU n 1 127 GLY n 1 128 SER n 1 129 GLY n 1 130 GLY n 1 131 GLY n 1 132 HIS n 1 133 TRP n 1 134 LYS n 1 135 GLU n 1 136 ILE n 1 137 CYS n 1 138 ASP n 1 139 PHE n 1 140 PRO n 1 141 ARG n 1 142 ARG n 1 143 GLN n 1 144 ILE n 1 145 ALA n 1 146 LYS n 1 147 TRP n 1 148 HIS n 1 149 MET n 1 150 LEU n 1 151 CYS n 1 152 ASP n 1 153 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 RAT _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _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 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _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-KG _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 1W16 1 ? ? 1W16 ? 2 UNP SYT4_RAT 1 ? ? P50232 ? # 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 1W16 A 1 ? 15 ? 1W16 273 ? 287 ? 273 287 2 2 1W16 A 16 ? 153 ? P50232 288 ? 425 ? 288 425 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 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 1W16 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.4 _exptl_crystal.density_percent_sol 72.0 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.50 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;THE RAT SYNAPTOTAGMIN IV C2B DOMAIN WAS CRYSTALLIZED BY THE VAPOR DIFFUSION METHOD (HANGING DROP) BY MIXING 1 MICROLITER PROTEIN (IN 20 MM MES, 150 MM NACL AND 1 MM EDTA, PH 6.32) WITH 1 MICROLITER RESERVOIR SOLUTION (2.5M NACL, 0.1M CACL2, 0.1M HEPES, PH 7.5) SUSPENDED OVER 500 MICROLITERS RESERVOIR SOLUTION. HEXAGONAL CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF 0.1 X 0.1 X 0.2 MM WITHIN TWO DAYS. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO CRYSTALLIZATION SOLUTION CONTAINING 4.25 M NACL, 0.1 M HEPES PH 7.5 AND 5%(V/V) ETHYLENE GLYCOL AND THEN COOLED IN LIQUID PROPANE. ; # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type CUSTOM _diffrn_detector.pdbx_collection_date 2003-11-29 _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 0.9876 _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_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-BM _diffrn_source.pdbx_wavelength 0.9876 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 1W16 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 29.810 _reflns.d_resolution_high 2.300 _reflns.number_obs 13974 _reflns.number_all ? _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs 0.05300 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 45.8000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.400 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.30 _reflns_shell.d_res_low 2.34 _reflns_shell.percent_possible_all 95.2 _reflns_shell.Rmerge_I_obs 0.72500 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.800 _reflns_shell.pdbx_redundancy 4.70 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 1W16 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.ls_number_reflns_obs 12558 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30.00 _refine.ls_d_res_high 2.30 _refine.ls_percent_reflns_obs 99.6 _refine.ls_R_factor_obs 0.217 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.213 _refine.ls_R_factor_R_free 0.257 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.000 _refine.ls_number_reflns_R_free 1392 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.944 _refine.correlation_coeff_Fo_to_Fc_free 0.921 _refine.B_iso_mean 55.09 _refine.aniso_B[1][1] 1.02000 _refine.aniso_B[2][2] 1.02000 _refine.aniso_B[3][3] -1.53000 _refine.aniso_B[1][2] 0.51000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details 'BABINET MODEL WITH 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 'PDB ENTRY 1K5W' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.183 _refine.pdbx_overall_ESU_R_Free 0.178 _refine.overall_SU_ML 0.125 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 7.453 _refine.overall_SU_R_Cruickshank_DPI ? _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 992 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 9 _refine_hist.number_atoms_solvent 53 _refine_hist.number_atoms_total 1054 _refine_hist.d_res_high 2.30 _refine_hist.d_res_low 30.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.020 0.021 ? 1027 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.851 1.949 ? 1388 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 7.423 5.000 ? 126 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 36.557 22.955 ? 44 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 18.583 15.000 ? 186 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 15.413 15.000 ? 8 'X-RAY DIFFRACTION' ? r_chiral_restr 0.115 0.200 ? 159 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 757 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.205 0.200 ? 410 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.312 0.200 ? 662 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.158 0.200 ? 59 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.053 0.200 ? 2 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.246 0.200 ? 30 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.229 0.200 ? 7 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 1.216 1.500 ? 630 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 2.247 2.000 ? 1021 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 3.114 3.000 ? 410 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 4.815 4.500 ? 367 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.30 _refine_ls_shell.d_res_low 2.36 _refine_ls_shell.number_reflns_R_work 850 _refine_ls_shell.R_factor_R_work 0.3200 _refine_ls_shell.percent_reflns_obs 94.93 _refine_ls_shell.R_factor_R_free 0.3900 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 105 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1W16 _struct.title 'rat synaptotagmin 4 C2B domain in the absence of calcium' _struct.pdbx_descriptor 'SYNAPTOTAGMIN IV' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1W16 _struct_keywords.pdbx_keywords 'METAL BINDING PROTEIN' _struct_keywords.text 'METAL BINDING PROTEIN, SYNAPTOTAGMIN, ENDOCYTOSIS/EXOCYTOSIS, NEUROTRANSMITTER RELEASE, TRANSMEMBRANE' # 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 3 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 3 ? K N N 4 ? # _struct_biol.id 1 # 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 SER A 27 ? THR A 29 ? SER A 299 THR A 301 5 ? 3 HELX_P HELX_P2 2 GLY A 127 ? PHE A 139 ? GLY A 399 PHE A 411 1 ? 13 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc1 metalc ? ? C NA . NA ? ? ? 1_555 A SER 111 O ? ? A NA 1002 A SER 383 1_555 ? ? ? ? ? ? ? 2.366 ? metalc2 metalc ? ? C NA . NA ? ? ? 1_555 A GLU 108 O ? ? A NA 1002 A GLU 380 1_555 ? ? ? ? ? ? ? 2.348 ? metalc3 metalc ? ? C NA . NA ? ? ? 1_555 A ASN 113 OD1 ? ? A NA 1002 A ASN 385 1_555 ? ? ? ? ? ? ? 2.464 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 4 ? AB ? 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 AA 1 2 ? anti-parallel AA 2 3 ? anti-parallel AA 3 4 ? anti-parallel AB 1 2 ? anti-parallel AB 2 3 ? anti-parallel AB 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 AA 1 VAL A 81 ? ASP A 89 ? VAL A 353 ASP A 361 AA 2 THR A 31 ? ARG A 40 ? THR A 303 ARG A 312 AA 3 GLU A 18 ? GLN A 26 ? GLU A 290 GLN A 298 AA 4 GLN A 143 ? MET A 149 ? GLN A 415 MET A 421 AB 1 LYS A 64 ? LYS A 70 ? LYS A 336 LYS A 342 AB 2 PRO A 53 ? HIS A 61 ? PRO A 325 HIS A 333 AB 3 ILE A 98 ? ASP A 106 ? ILE A 370 ASP A 378 AB 4 GLU A 114 ? GLY A 122 ? GLU A 386 GLY A 394 # 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 AA 1 2 N PHE A 88 ? N PHE A 360 O LEU A 32 ? O LEU A 304 AA 2 3 N ARG A 40 ? N ARG A 312 O GLU A 18 ? O GLU A 290 AA 3 4 N LEU A 23 ? N LEU A 295 O ILE A 144 ? O ILE A 416 AB 1 2 N LYS A 69 ? N LYS A 341 O VAL A 57 ? O VAL A 329 AB 2 3 N TYR A 60 ? N TYR A 332 O SER A 99 ? O SER A 371 AB 3 4 N ASP A 106 ? N ASP A 378 O GLU A 114 ? O GLU A 386 # 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 ? ? ? ? 3 'BINDING SITE FOR RESIDUE NA A1001' AC2 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE NA A1002' AC3 Software ? ? ? ? 1 'BINDING SITE FOR RESIDUE CL A3001' AC4 Software ? ? ? ? 1 'BINDING SITE FOR RESIDUE CL A3002' AC5 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE CL A3003' AC6 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE CL A3004' AC7 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE CL A3005' AC8 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE CL A3006' AC9 Software ? ? ? ? 2 'BINDING SITE FOR RESIDUE CL A3007' # 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 SER A 67 ? SER A 339 . ? 1_555 ? 2 AC1 3 PHE A 88 ? PHE A 360 . ? 1_555 ? 3 AC1 3 ASP A 89 ? ASP A 361 . ? 1_555 ? 4 AC2 5 GLU A 108 ? GLU A 380 . ? 1_555 ? 5 AC2 5 SER A 111 ? SER A 383 . ? 1_555 ? 6 AC2 5 ASN A 113 ? ASN A 385 . ? 1_555 ? 7 AC2 5 HOH K . ? HOH A 2033 . ? 1_555 ? 8 AC2 5 HOH K . ? HOH A 2035 . ? 1_555 ? 9 AC3 1 ASN A 83 ? ASN A 355 . ? 1_555 ? 10 AC4 1 TRP A 147 ? TRP A 419 . ? 1_555 ? 11 AC5 3 TYR A 54 ? TYR A 326 . ? 1_555 ? 12 AC5 3 LYS A 56 ? LYS A 328 . ? 1_555 ? 13 AC5 3 ARG A 112 ? ARG A 384 . ? 1_555 ? 14 AC6 4 LYS A 69 ? LYS A 341 . ? 1_555 ? 15 AC6 4 PHE A 86 ? PHE A 358 . ? 1_555 ? 16 AC6 4 VAL A 87 ? VAL A 359 . ? 1_555 ? 17 AC6 4 TRP A 147 ? TRP A 419 . ? 1_555 ? 18 AC7 5 LYS A 56 ? LYS A 328 . ? 1_555 ? 19 AC7 5 ASN A 58 ? ASN A 330 . ? 1_555 ? 20 AC7 5 ARG A 65 ? ARG A 337 . ? 1_555 ? 21 AC7 5 ARG A 112 ? ARG A 384 . ? 1_555 ? 22 AC7 5 HOH K . ? HOH A 2051 . ? 1_555 ? 23 AC8 3 LYS A 56 ? LYS A 328 . ? 1_555 ? 24 AC8 3 ARG A 65 ? ARG A 337 . ? 1_555 ? 25 AC8 3 LYS A 68 ? LYS A 340 . ? 1_555 ? 26 AC9 2 ARG A 40 ? ARG A 312 . ? 1_555 ? 27 AC9 2 HIS A 41 ? HIS A 313 . ? 1_555 ? # _database_PDB_matrix.entry_id 1W16 _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 1W16 _atom_sites.fract_transf_matrix[1][1] 0.010982 _atom_sites.fract_transf_matrix[1][2] 0.006340 _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] 0.012680 _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] 0.008139 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CL N NA 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 GLY 1 273 ? ? ? A . n A 1 2 SER 2 274 ? ? ? A . n A 1 3 PRO 3 275 ? ? ? A . n A 1 4 GLY 4 276 ? ? ? A . n A 1 5 ILE 5 277 ? ? ? A . n A 1 6 SER 6 278 ? ? ? A . n A 1 7 GLY 7 279 ? ? ? A . n A 1 8 GLY 8 280 ? ? ? A . n A 1 9 GLY 9 281 ? ? ? A . n A 1 10 GLY 10 282 ? ? ? A . n A 1 11 GLY 11 283 ? ? ? A . n A 1 12 ILE 12 284 ? ? ? A . n A 1 13 PRO 13 285 ? ? ? A . n A 1 14 SER 14 286 ? ? ? A . n A 1 15 GLY 15 287 ? ? ? A . n A 1 16 ARG 16 288 288 ARG ARG A . n A 1 17 GLY 17 289 289 GLY GLY A . n A 1 18 GLU 18 290 290 GLU GLU A . n A 1 19 LEU 19 291 291 LEU LEU A . n A 1 20 LEU 20 292 292 LEU LEU A . n A 1 21 VAL 21 293 293 VAL VAL A . n A 1 22 SER 22 294 294 SER SER A . n A 1 23 LEU 23 295 295 LEU LEU A . n A 1 24 CYS 24 296 296 CYS CYS A . n A 1 25 TYR 25 297 297 TYR TYR A . n A 1 26 GLN 26 298 298 GLN GLN A . n A 1 27 SER 27 299 299 SER SER A . n A 1 28 THR 28 300 300 THR THR A . n A 1 29 THR 29 301 301 THR THR A . n A 1 30 ASN 30 302 302 ASN ASN A . n A 1 31 THR 31 303 303 THR THR A . n A 1 32 LEU 32 304 304 LEU LEU A . n A 1 33 THR 33 305 305 THR THR A . n A 1 34 VAL 34 306 306 VAL VAL A . n A 1 35 VAL 35 307 307 VAL VAL A . n A 1 36 VAL 36 308 308 VAL VAL A . n A 1 37 LEU 37 309 309 LEU LEU A . n A 1 38 LYS 38 310 310 LYS LYS A . n A 1 39 ALA 39 311 311 ALA ALA A . n A 1 40 ARG 40 312 312 ARG ARG A . n A 1 41 HIS 41 313 313 HIS HIS A . n A 1 42 LEU 42 314 314 LEU LEU A . n A 1 43 PRO 43 315 315 PRO PRO A . n A 1 44 LYS 44 316 ? ? ? A . n A 1 45 SER 45 317 ? ? ? A . n A 1 46 ASP 46 318 ? ? ? A . n A 1 47 VAL 47 319 ? ? ? A . n A 1 48 SER 48 320 ? ? ? A . n A 1 49 GLY 49 321 ? ? ? A . n A 1 50 LEU 50 322 ? ? ? A . n A 1 51 SER 51 323 323 SER SER A . n A 1 52 ASP 52 324 324 ASP ASP A . n A 1 53 PRO 53 325 325 PRO PRO A . n A 1 54 TYR 54 326 326 TYR TYR A . n A 1 55 VAL 55 327 327 VAL VAL A . n A 1 56 LYS 56 328 328 LYS LYS A . n A 1 57 VAL 57 329 329 VAL VAL A . n A 1 58 ASN 58 330 330 ASN ASN A . n A 1 59 LEU 59 331 331 LEU LEU A . n A 1 60 TYR 60 332 332 TYR TYR A . n A 1 61 HIS 61 333 333 HIS HIS A . n A 1 62 ALA 62 334 334 ALA ALA A . n A 1 63 LYS 63 335 335 LYS LYS A . n A 1 64 LYS 64 336 336 LYS LYS A . n A 1 65 ARG 65 337 337 ARG ARG A . n A 1 66 ILE 66 338 338 ILE ILE A . n A 1 67 SER 67 339 339 SER SER A . n A 1 68 LYS 68 340 340 LYS LYS A . n A 1 69 LYS 69 341 341 LYS LYS A . n A 1 70 LYS 70 342 342 LYS LYS A . n A 1 71 THR 71 343 343 THR THR A . n A 1 72 HIS 72 344 344 HIS HIS A . n A 1 73 VAL 73 345 345 VAL VAL A . n A 1 74 LYS 74 346 ? ? ? A . n A 1 75 LYS 75 347 ? ? ? A . n A 1 76 CYS 76 348 ? ? ? A . n A 1 77 THR 77 349 ? ? ? A . n A 1 78 PRO 78 350 ? ? ? A . n A 1 79 ASN 79 351 ? ? ? A . n A 1 80 ALA 80 352 352 ALA ALA A . n A 1 81 VAL 81 353 353 VAL VAL A . n A 1 82 PHE 82 354 354 PHE PHE A . n A 1 83 ASN 83 355 355 ASN ASN A . n A 1 84 GLU 84 356 356 GLU GLU A . n A 1 85 LEU 85 357 357 LEU LEU A . n A 1 86 PHE 86 358 358 PHE PHE A . n A 1 87 VAL 87 359 359 VAL VAL A . n A 1 88 PHE 88 360 360 PHE PHE A . n A 1 89 ASP 89 361 361 ASP ASP A . n A 1 90 ILE 90 362 362 ILE ILE A . n A 1 91 PRO 91 363 363 PRO PRO A . n A 1 92 CYS 92 364 364 CYS CYS A . n A 1 93 GLU 93 365 365 GLU GLU A . n A 1 94 SER 94 366 366 SER SER A . n A 1 95 LEU 95 367 367 LEU LEU A . n A 1 96 GLU 96 368 368 GLU GLU A . n A 1 97 GLU 97 369 369 GLU GLU A . n A 1 98 ILE 98 370 370 ILE ILE A . n A 1 99 SER 99 371 371 SER SER A . n A 1 100 VAL 100 372 372 VAL VAL A . n A 1 101 GLU 101 373 373 GLU GLU A . n A 1 102 PHE 102 374 374 PHE PHE A . n A 1 103 LEU 103 375 375 LEU LEU A . n A 1 104 VAL 104 376 376 VAL VAL A . n A 1 105 LEU 105 377 377 LEU LEU A . n A 1 106 ASP 106 378 378 ASP ASP A . n A 1 107 SER 107 379 379 SER SER A . n A 1 108 GLU 108 380 380 GLU GLU A . n A 1 109 ARG 109 381 381 ARG ARG A . n A 1 110 GLY 110 382 382 GLY GLY A . n A 1 111 SER 111 383 383 SER SER A . n A 1 112 ARG 112 384 384 ARG ARG A . n A 1 113 ASN 113 385 385 ASN ASN A . n A 1 114 GLU 114 386 386 GLU GLU A . n A 1 115 VAL 115 387 387 VAL VAL A . n A 1 116 ILE 116 388 388 ILE ILE A . n A 1 117 GLY 117 389 389 GLY GLY A . n A 1 118 ARG 118 390 390 ARG ARG A . n A 1 119 LEU 119 391 391 LEU LEU A . n A 1 120 VAL 120 392 392 VAL VAL A . n A 1 121 LEU 121 393 393 LEU LEU A . n A 1 122 GLY 122 394 394 GLY GLY A . n A 1 123 ALA 123 395 395 ALA ALA A . n A 1 124 THR 124 396 396 THR THR A . n A 1 125 ALA 125 397 397 ALA ALA A . n A 1 126 GLU 126 398 398 GLU GLU A . n A 1 127 GLY 127 399 399 GLY GLY A . n A 1 128 SER 128 400 400 SER SER A . n A 1 129 GLY 129 401 401 GLY GLY A . n A 1 130 GLY 130 402 402 GLY GLY A . n A 1 131 GLY 131 403 403 GLY GLY A . n A 1 132 HIS 132 404 404 HIS HIS A . n A 1 133 TRP 133 405 405 TRP TRP A . n A 1 134 LYS 134 406 406 LYS LYS A . n A 1 135 GLU 135 407 407 GLU GLU A . n A 1 136 ILE 136 408 408 ILE ILE A . n A 1 137 CYS 137 409 409 CYS CYS A . n A 1 138 ASP 138 410 410 ASP ASP A . n A 1 139 PHE 139 411 411 PHE PHE A . n A 1 140 PRO 140 412 412 PRO PRO A . n A 1 141 ARG 141 413 413 ARG ARG A . n A 1 142 ARG 142 414 414 ARG ARG A . n A 1 143 GLN 143 415 415 GLN GLN A . n A 1 144 ILE 144 416 416 ILE ILE A . n A 1 145 ALA 145 417 417 ALA ALA A . n A 1 146 LYS 146 418 418 LYS LYS A . n A 1 147 TRP 147 419 419 TRP TRP A . n A 1 148 HIS 148 420 420 HIS HIS A . n A 1 149 MET 149 421 421 MET MET A . n A 1 150 LEU 150 422 422 LEU LEU A . n A 1 151 CYS 151 423 423 CYS CYS A . n A 1 152 ASP 152 424 424 ASP ASP A . n A 1 153 GLY 153 425 425 GLY GLY 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 NA 1 1001 1001 NA NA A . C 2 NA 1 1002 1002 NA NA A . D 3 CL 1 3001 3001 CL CL A . E 3 CL 1 3002 3002 CL CL A . F 3 CL 1 3003 3003 CL CL A . G 3 CL 1 3004 3004 CL CL A . H 3 CL 1 3005 3005 CL CL A . I 3 CL 1 3006 3006 CL CL A . J 3 CL 1 3007 3007 CL CL A . K 4 HOH 1 2001 2001 HOH HOH A . K 4 HOH 2 2002 2002 HOH HOH A . K 4 HOH 3 2003 2003 HOH HOH A . K 4 HOH 4 2004 2004 HOH HOH A . K 4 HOH 5 2005 2005 HOH HOH A . K 4 HOH 6 2006 2006 HOH HOH A . K 4 HOH 7 2007 2007 HOH HOH A . K 4 HOH 8 2008 2008 HOH HOH A . K 4 HOH 9 2009 2009 HOH HOH A . K 4 HOH 10 2010 2010 HOH HOH A . K 4 HOH 11 2011 2011 HOH HOH A . K 4 HOH 12 2012 2012 HOH HOH A . K 4 HOH 13 2013 2013 HOH HOH A . K 4 HOH 14 2014 2014 HOH HOH A . K 4 HOH 15 2015 2015 HOH HOH A . K 4 HOH 16 2016 2016 HOH HOH A . K 4 HOH 17 2017 2017 HOH HOH A . K 4 HOH 18 2018 2018 HOH HOH A . K 4 HOH 19 2019 2019 HOH HOH A . K 4 HOH 20 2020 2020 HOH HOH A . K 4 HOH 21 2021 2021 HOH HOH A . K 4 HOH 22 2022 2022 HOH HOH A . K 4 HOH 23 2023 2023 HOH HOH A . K 4 HOH 24 2024 2024 HOH HOH A . K 4 HOH 25 2025 2025 HOH HOH A . K 4 HOH 26 2026 2026 HOH HOH A . K 4 HOH 27 2027 2027 HOH HOH A . K 4 HOH 28 2028 2028 HOH HOH A . K 4 HOH 29 2029 2029 HOH HOH A . K 4 HOH 30 2030 2030 HOH HOH A . K 4 HOH 31 2031 2031 HOH HOH A . K 4 HOH 32 2032 2032 HOH HOH A . K 4 HOH 33 2033 2033 HOH HOH A . K 4 HOH 34 2034 2034 HOH HOH A . K 4 HOH 35 2035 2035 HOH HOH A . K 4 HOH 36 2036 2036 HOH HOH A . K 4 HOH 37 2037 2037 HOH HOH A . K 4 HOH 38 2038 2038 HOH HOH A . K 4 HOH 39 2039 2039 HOH HOH A . K 4 HOH 40 2040 2040 HOH HOH A . K 4 HOH 41 2041 2041 HOH HOH A . K 4 HOH 42 2042 2042 HOH HOH A . K 4 HOH 43 2043 2043 HOH HOH A . K 4 HOH 44 2044 2044 HOH HOH A . K 4 HOH 45 2045 2045 HOH HOH A . K 4 HOH 46 2046 2046 HOH HOH A . K 4 HOH 47 2047 2047 HOH HOH A . K 4 HOH 48 2048 2048 HOH HOH A . K 4 HOH 49 2049 2049 HOH HOH A . K 4 HOH 50 2050 2050 HOH HOH A . K 4 HOH 51 2051 2051 HOH HOH A . K 4 HOH 52 2052 2052 HOH HOH A . K 4 HOH 53 2053 2053 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PQS _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,F,G,H,I,J,K # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id CL _pdbx_struct_special_symmetry.auth_seq_id 3001 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id CL _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? A SER 111 ? A SER 383 ? 1_555 NA ? C NA . ? A NA 1002 ? 1_555 O ? A GLU 108 ? A GLU 380 ? 1_555 87.4 ? 2 O ? A SER 111 ? A SER 383 ? 1_555 NA ? C NA . ? A NA 1002 ? 1_555 OD1 ? A ASN 113 ? A ASN 385 ? 1_555 98.6 ? 3 O ? A GLU 108 ? A GLU 380 ? 1_555 NA ? C NA . ? A NA 1002 ? 1_555 OD1 ? A ASN 113 ? A ASN 385 ? 1_555 86.1 ? # 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 2004-08-13 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2019-05-08 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Experimental preparation' 5 3 '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' database_PDB_rev 2 3 'Structure model' database_PDB_rev_record 3 3 'Structure model' exptl_crystal_grow 4 3 'Structure model' pdbx_database_proc 5 3 '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 3 'Structure model' '_exptl_crystal_grow.method' 2 3 'Structure model' '_pdbx_database_status.recvd_author_approval' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 41.2690 15.5249 46.4235 -.0240 -.1300 -.0425 -.0319 -.0061 .0285 5.7711 6.1312 12.2066 -1.1001 -5.4013 -3.2046 -.5855 .1261 -.3530 -.2010 .1407 -.0826 .9879 .0256 .4448 'X-RAY DIFFRACTION' 2 ? refined 38.6085 13.4452 58.2845 .0177 -.1211 -.0690 -.0023 .0296 .0764 4.2746 6.4880 7.1930 -1.7174 -2.4223 .7724 -.1873 -.3415 .1887 .9367 .3391 .2176 .2883 -.2718 -.1518 'X-RAY DIFFRACTION' 3 ? refined 43.3825 9.0114 50.8988 .0355 -.1787 -.0930 -.0040 -.0022 .0182 1.9244 3.5619 4.8817 .1112 -.7095 -3.2631 -.1459 .0800 -.1169 .0498 .0735 -.0200 .5197 -.0244 .0724 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 A 273 ? ? A 300 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 308 ? ? A 331 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 336 ? ? A 409 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0003 ? 1 HKL-2000 'data reduction' . ? 2 HKL-2000 'data scaling' . ? 3 AMoRE phasing . ? 4 # _pdbx_entry_details.entry_id 1W16 _pdbx_entry_details.compound_details ;MAY BE INVOLVED IN CA(2+)-DEPENDENT EXOCYTOSIS OF SECRETORY VESICLES THROUGH CA(2+) ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # 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 ASP 324 ? ? CG A ASP 324 ? ? OD2 A ASP 324 ? ? 125.29 118.30 6.99 0.90 N 2 1 CB A ASP 361 ? ? CG A ASP 361 ? ? OD2 A ASP 361 ? ? 123.88 118.30 5.58 0.90 N 3 1 NE A ARG 384 ? ? CZ A ARG 384 ? ? NH1 A ARG 384 ? ? 123.57 120.30 3.27 0.50 N 4 1 NE A ARG 384 ? ? CZ A ARG 384 ? ? NH2 A ARG 384 ? ? 114.90 120.30 -5.40 0.50 N 5 1 NE A ARG 413 ? ? CZ A ARG 413 ? ? NH1 A ARG 413 ? ? 123.52 120.30 3.22 0.50 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 ASP A 324 ? ? -116.60 71.19 2 1 ALA A 334 ? ? 50.87 -111.39 3 1 ASN A 355 ? ? 35.11 61.13 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 GLY _pdbx_validate_peptide_omega.auth_asym_id_1 A _pdbx_validate_peptide_omega.auth_seq_id_1 401 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 ? _pdbx_validate_peptide_omega.auth_comp_id_2 GLY _pdbx_validate_peptide_omega.auth_asym_id_2 A _pdbx_validate_peptide_omega.auth_seq_id_2 402 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega 149.16 # 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 273 ? A GLY 1 2 1 Y 1 A SER 274 ? A SER 2 3 1 Y 1 A PRO 275 ? A PRO 3 4 1 Y 1 A GLY 276 ? A GLY 4 5 1 Y 1 A ILE 277 ? A ILE 5 6 1 Y 1 A SER 278 ? A SER 6 7 1 Y 1 A GLY 279 ? A GLY 7 8 1 Y 1 A GLY 280 ? A GLY 8 9 1 Y 1 A GLY 281 ? A GLY 9 10 1 Y 1 A GLY 282 ? A GLY 10 11 1 Y 1 A GLY 283 ? A GLY 11 12 1 Y 1 A ILE 284 ? A ILE 12 13 1 Y 1 A PRO 285 ? A PRO 13 14 1 Y 1 A SER 286 ? A SER 14 15 1 Y 1 A GLY 287 ? A GLY 15 16 1 Y 1 A LYS 316 ? A LYS 44 17 1 Y 1 A SER 317 ? A SER 45 18 1 Y 1 A ASP 318 ? A ASP 46 19 1 Y 1 A VAL 319 ? A VAL 47 20 1 Y 1 A SER 320 ? A SER 48 21 1 Y 1 A GLY 321 ? A GLY 49 22 1 Y 1 A LEU 322 ? A LEU 50 23 1 Y 1 A LYS 346 ? A LYS 74 24 1 Y 1 A LYS 347 ? A LYS 75 25 1 Y 1 A CYS 348 ? A CYS 76 26 1 Y 1 A THR 349 ? A THR 77 27 1 Y 1 A PRO 350 ? A PRO 78 28 1 Y 1 A ASN 351 ? A ASN 79 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SODIUM ION' NA 3 'CHLORIDE ION' CL 4 water HOH #