data_4NP9 # _entry.id 4NP9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.360 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4NP9 pdb_00004np9 10.2210/pdb4np9/pdb RCSB RCSB083484 ? ? WWPDB D_1000083484 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4NS0 . unspecified PDB 2CHD 'CRYSTAL STRUCTURE OF THE C2A DOMAIN OF RABPHILIN-3A' unspecified PDB 2K3H 'STRUCTURAL DETERMINANTS FOR CA2+ AND PIP2 BINDING BY THE C2A DOMAIN OF RABPHILIN-3A' unspecified PDB 2CM5 'CRYSTAL STRUCTURE OF THE C2B DOMAIN OF RABPHILIN' unspecified PDB 2CM6 'CRYSTAL STRUCTURE OF THE C2B DOMAIN OF RABPHILIN 3A' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4NP9 _pdbx_database_status.recvd_initial_deposition_date 2013-11-21 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Guillen, J.' 1 'Ferrer-Orta, C.' 2 'Buxaderas, M.' 3 'Perez-Sanchez, D.' 4 'Guerrero-Valero, M.' 5 'Luengo-Gil, G.' 6 'Pous, J.' 7 'Guerra, P.' 8 'Gomez-Fernandez, J.C.' 9 'Verdaguer, N.' 10 'Corbalan-Garcia, S.' 11 # _citation.id primary _citation.title 'Structural insights into the Ca2+ and PI(4,5)P2 binding modes of the C2 domains of rabphilin 3A and synaptotagmin 1.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 110 _citation.page_first 20503 _citation.page_last 20508 _citation.year 2013 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 1091-6490 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24302762 _citation.pdbx_database_id_DOI 10.1073/pnas.1316179110 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Guillen, J.' 1 ? primary 'Ferrer-Orta, C.' 2 ? primary 'Buxaderas, M.' 3 ? primary 'Perez-Sanchez, D.' 4 ? primary 'Guerrero-Valero, M.' 5 ? primary 'Luengo-Gil, G.' 6 ? primary 'Pous, J.' 7 ? primary 'Guerra, P.' 8 ? primary 'Gomez-Fernandez, J.C.' 9 ? primary 'Verdaguer, N.' 10 ? primary 'Corbalan-Garcia, S.' 11 ? # _cell.entry_id 4NP9 _cell.length_a 38.27 _cell.length_b 39.47 _cell.length_c 89.26 _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4NP9 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 Rabphilin-3A 15305.478 1 ? ? 'C2 domain, UNP RESIDUES 378-510' ? 2 non-polymer syn D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE 420.096 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 4 water nat water 18.015 139 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name Exophilin-1 # _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 ;DQATTLGALEFSLLYDQDNSNLQCTIIRAKGLKPMDSNGLADPYVKLHLLPGASKSNKLRTKTLRNTRNPVWNETLQYHG ITEEDMQRKTLRISVCDEDKFGHNEFIGETRFSLKKLKANQRKNFNICLERVI ; _entity_poly.pdbx_seq_one_letter_code_can ;DQATTLGALEFSLLYDQDNSNLQCTIIRAKGLKPMDSNGLADPYVKLHLLPGASKSNKLRTKTLRNTRNPVWNETLQYHG ITEEDMQRKTLRISVCDEDKFGHNEFIGETRFSLKKLKANQRKNFNICLERVI ; _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 ASP n 1 2 GLN n 1 3 ALA n 1 4 THR n 1 5 THR n 1 6 LEU n 1 7 GLY n 1 8 ALA n 1 9 LEU n 1 10 GLU n 1 11 PHE n 1 12 SER n 1 13 LEU n 1 14 LEU n 1 15 TYR n 1 16 ASP n 1 17 GLN n 1 18 ASP n 1 19 ASN n 1 20 SER n 1 21 ASN n 1 22 LEU n 1 23 GLN n 1 24 CYS n 1 25 THR n 1 26 ILE n 1 27 ILE n 1 28 ARG n 1 29 ALA n 1 30 LYS n 1 31 GLY n 1 32 LEU n 1 33 LYS n 1 34 PRO n 1 35 MET n 1 36 ASP n 1 37 SER n 1 38 ASN n 1 39 GLY n 1 40 LEU n 1 41 ALA n 1 42 ASP n 1 43 PRO n 1 44 TYR n 1 45 VAL n 1 46 LYS n 1 47 LEU n 1 48 HIS n 1 49 LEU n 1 50 LEU n 1 51 PRO n 1 52 GLY n 1 53 ALA n 1 54 SER n 1 55 LYS n 1 56 SER n 1 57 ASN n 1 58 LYS n 1 59 LEU n 1 60 ARG n 1 61 THR n 1 62 LYS n 1 63 THR n 1 64 LEU n 1 65 ARG n 1 66 ASN n 1 67 THR n 1 68 ARG n 1 69 ASN n 1 70 PRO n 1 71 VAL n 1 72 TRP n 1 73 ASN n 1 74 GLU n 1 75 THR n 1 76 LEU n 1 77 GLN n 1 78 TYR n 1 79 HIS n 1 80 GLY n 1 81 ILE n 1 82 THR n 1 83 GLU n 1 84 GLU n 1 85 ASP n 1 86 MET n 1 87 GLN n 1 88 ARG n 1 89 LYS n 1 90 THR n 1 91 LEU n 1 92 ARG n 1 93 ILE n 1 94 SER n 1 95 VAL n 1 96 CYS n 1 97 ASP n 1 98 GLU n 1 99 ASP n 1 100 LYS n 1 101 PHE n 1 102 GLY n 1 103 HIS n 1 104 ASN n 1 105 GLU n 1 106 PHE n 1 107 ILE n 1 108 GLY n 1 109 GLU n 1 110 THR n 1 111 ARG n 1 112 PHE n 1 113 SER n 1 114 LEU n 1 115 LYS n 1 116 LYS n 1 117 LEU n 1 118 LYS n 1 119 ALA n 1 120 ASN n 1 121 GLN n 1 122 ARG n 1 123 LYS n 1 124 ASN n 1 125 PHE n 1 126 ASN n 1 127 ILE n 1 128 CYS n 1 129 LEU n 1 130 GLU n 1 131 ARG n 1 132 VAL n 1 133 ILE 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 'brown rat,rat,rats' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene Rph3a _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 pET28a _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code RP3A_RAT _struct_ref.pdbx_db_accession P47709 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;DQATTLGALEFSLLYDQDNSNLQCTIIRAKGLKPMDSNGLADPYVKLHLLPGASKSNKLRTKTLRNTRNPVWNETLQYHG ITEEDMQRKTLRISVCDEDKFGHNEFIGETRFSLKKLKANQRKNFNICLERVI ; _struct_ref.pdbx_align_begin 378 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4NP9 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 133 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P47709 _struct_ref_seq.db_align_beg 378 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 510 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 378 _struct_ref_seq.pdbx_auth_seq_align_end 510 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 I3P non-polymer . D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE ? 'C6 H15 O15 P3' 420.096 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 4NP9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.20 _exptl_crystal.density_percent_sol 44.15 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.4 _exptl_crystal_grow.pdbx_details '25-28% PEG 4K, 10-20mM Ammonium sulfate, 100mM HEPES pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 77 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'PSI PILATUS 6M' _diffrn_detector.pdbx_collection_date 2012-03-18 _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 'Monochromator Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.980110 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SOLEIL BEAMLINE PROXIMA 1' _diffrn_source.pdbx_synchrotron_site SOLEIL _diffrn_source.pdbx_synchrotron_beamline 'PROXIMA 1' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.980110 # _reflns.entry_id 4NP9 _reflns.observed_criterion_sigma_I 3.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 44.93 _reflns.d_resolution_high 1.92 _reflns.number_obs 10862 _reflns.number_all 11230 _reflns.percent_possible_obs 98.7 _reflns.pdbx_Rmerge_I_obs 0.087 _reflns.pdbx_Rsym_value 0.088 _reflns.pdbx_netI_over_sigmaI 13.19 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 9.5 _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.92 _reflns_shell.d_res_low 2.041 _reflns_shell.percent_possible_all 95.0 _reflns_shell.Rmerge_I_obs 0.30 _reflns_shell.pdbx_Rsym_value 0.35 _reflns_shell.meanI_over_sigI_obs 4.2 _reflns_shell.pdbx_redundancy 50.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1687 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4NP9 _refine.ls_number_reflns_obs 10754 _refine.ls_number_reflns_all 10862 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.02 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.566 _refine.ls_d_res_high 1.920 _refine.ls_percent_reflns_obs 99.03 _refine.ls_R_factor_obs 0.2108 _refine.ls_R_factor_all 0.2501 _refine.ls_R_factor_R_work 0.2089 _refine.ls_R_factor_R_free 0.2501 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.84 _refine.ls_number_reflns_R_free 520 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.26 _refine.pdbx_overall_phase_error 25.27 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1036 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 29 _refine_hist.number_atoms_solvent 139 _refine_hist.number_atoms_total 1204 _refine_hist.d_res_high 1.920 _refine_hist.d_res_low 29.566 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.004 ? ? 1080 ? 'X-RAY DIFFRACTION' f_angle_d 0.903 ? ? 1459 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 15.171 ? ? 418 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.034 ? ? 163 ? 'X-RAY DIFFRACTION' f_plane_restr 0.003 ? ? 184 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs 'X-RAY DIFFRACTION' 4 1.9200 2.1132 2499 0.2209 98.00 0.2928 . . 124 . . . . 'X-RAY DIFFRACTION' 4 2.1132 2.4188 2463 0.2178 98.00 0.2638 . . 138 . . . . 'X-RAY DIFFRACTION' 4 2.4188 3.0470 2576 0.2019 100.00 0.2522 . . 136 . . . . 'X-RAY DIFFRACTION' 4 3.0470 29.5698 2696 0.2068 100.00 0.2323 . . 122 . . . . # _struct.entry_id 4NP9 _struct.title 'Structure of Rabphilin C2A domain bound to IP3' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4NP9 _struct_keywords.pdbx_keywords 'PROTEIN TRANSPORT' _struct_keywords.text 'RABPHILIN-3A, C2 DOMAIN, C2A, CALCIUM BINDING, SYNAPTIC EXOCYTOSIS METAL-BINDING, PROTEIN TRANSPORT, C-2 domain fold, EXOPHILIN-1' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLN A 17 ? ASN A 19 ? GLN A 394 ASN A 396 5 ? 3 HELX_P HELX_P2 2 SER A 54 ? SER A 56 ? SER A 431 SER A 433 5 ? 3 HELX_P HELX_P3 3 THR A 82 ? LYS A 89 ? THR A 459 LYS A 466 1 ? 8 HELX_P HELX_P4 4 LYS A 115 ? LEU A 117 ? LYS A 492 LEU A 494 5 ? 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id LEU _struct_mon_prot_cis.label_seq_id 50 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id LEU _struct_mon_prot_cis.auth_seq_id 427 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 51 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 428 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -4.62 # 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 71 ? HIS A 79 ? VAL A 448 HIS A 456 A 2 ASN A 21 ? LYS A 30 ? ASN A 398 LYS A 407 A 3 ALA A 8 ? ASP A 16 ? ALA A 385 ASP A 393 A 4 LYS A 123 ? CYS A 128 ? LYS A 500 CYS A 505 B 1 LYS A 58 ? ARG A 60 ? LYS A 435 ARG A 437 B 2 PRO A 43 ? LEU A 50 ? PRO A 420 LEU A 427 B 3 THR A 90 ? GLU A 98 ? THR A 467 GLU A 475 B 4 ASN A 104 ? SER A 113 ? ASN A 481 SER A 490 # 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 LEU A 76 ? O LEU A 453 N CYS A 24 ? N CYS A 401 A 2 3 O ARG A 28 ? O ARG A 405 N GLU A 10 ? N GLU A 387 A 3 4 N PHE A 11 ? N PHE A 388 O PHE A 125 ? O PHE A 502 B 1 2 O LEU A 59 ? O LEU A 436 N LEU A 47 ? N LEU A 424 B 2 3 N LEU A 50 ? N LEU A 427 O THR A 90 ? O THR A 467 B 3 4 N VAL A 95 ? N VAL A 472 O GLY A 108 ? O GLY A 485 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A I3P 601 ? 14 'BINDING SITE FOR RESIDUE I3P A 601' AC2 Software A SO4 602 ? 6 'BINDING SITE FOR RESIDUE SO4 A 602' # 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 14 LYS A 33 ? LYS A 410 . ? 4_556 ? 2 AC1 14 PRO A 34 ? PRO A 411 . ? 4_556 ? 3 AC1 14 MET A 35 ? MET A 412 . ? 4_556 ? 4 AC1 14 TYR A 44 ? TYR A 421 . ? 1_555 ? 5 AC1 14 LYS A 46 ? LYS A 423 . ? 1_555 ? 6 AC1 14 HIS A 48 ? HIS A 425 . ? 1_555 ? 7 AC1 14 LYS A 58 ? LYS A 435 . ? 1_555 ? 8 AC1 14 ARG A 60 ? ARG A 437 . ? 1_555 ? 9 AC1 14 ASN A 104 ? ASN A 481 . ? 1_555 ? 10 AC1 14 SO4 C . ? SO4 A 602 . ? 1_555 ? 11 AC1 14 HOH D . ? HOH A 702 . ? 4_556 ? 12 AC1 14 HOH D . ? HOH A 763 . ? 1_555 ? 13 AC1 14 HOH D . ? HOH A 764 . ? 1_555 ? 14 AC1 14 HOH D . ? HOH A 803 . ? 1_555 ? 15 AC2 6 LYS A 46 ? LYS A 423 . ? 1_555 ? 16 AC2 6 ARG A 65 ? ARG A 442 . ? 4_456 ? 17 AC2 6 ARG A 92 ? ARG A 469 . ? 1_555 ? 18 AC2 6 SER A 94 ? SER A 471 . ? 1_555 ? 19 AC2 6 PHE A 106 ? PHE A 483 . ? 1_555 ? 20 AC2 6 I3P B . ? I3P A 601 . ? 1_555 ? # _database_PDB_matrix.entry_id 4NP9 _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 4NP9 _atom_sites.fract_transf_matrix[1][1] 0.026130 _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] 0.025336 _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] 0.011203 _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 N O P 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 ASP 1 378 ? ? ? A . n A 1 2 GLN 2 379 ? ? ? A . n A 1 3 ALA 3 380 ? ? ? A . n A 1 4 THR 4 381 ? ? ? A . n A 1 5 THR 5 382 382 THR THR A . n A 1 6 LEU 6 383 383 LEU LEU A . n A 1 7 GLY 7 384 384 GLY GLY A . n A 1 8 ALA 8 385 385 ALA ALA A . n A 1 9 LEU 9 386 386 LEU LEU A . n A 1 10 GLU 10 387 387 GLU GLU A . n A 1 11 PHE 11 388 388 PHE PHE A . n A 1 12 SER 12 389 389 SER SER A . n A 1 13 LEU 13 390 390 LEU LEU A . n A 1 14 LEU 14 391 391 LEU LEU A . n A 1 15 TYR 15 392 392 TYR TYR A . n A 1 16 ASP 16 393 393 ASP ASP A . n A 1 17 GLN 17 394 394 GLN GLN A . n A 1 18 ASP 18 395 395 ASP ASP A . n A 1 19 ASN 19 396 396 ASN ASN A . n A 1 20 SER 20 397 397 SER SER A . n A 1 21 ASN 21 398 398 ASN ASN A . n A 1 22 LEU 22 399 399 LEU LEU A . n A 1 23 GLN 23 400 400 GLN GLN A . n A 1 24 CYS 24 401 401 CYS CYS A . n A 1 25 THR 25 402 402 THR THR A . n A 1 26 ILE 26 403 403 ILE ILE A . n A 1 27 ILE 27 404 404 ILE ILE A . n A 1 28 ARG 28 405 405 ARG ARG A . n A 1 29 ALA 29 406 406 ALA ALA A . n A 1 30 LYS 30 407 407 LYS LYS A . n A 1 31 GLY 31 408 408 GLY GLY A . n A 1 32 LEU 32 409 409 LEU LEU A . n A 1 33 LYS 33 410 410 LYS LYS A . n A 1 34 PRO 34 411 411 PRO PRO A . n A 1 35 MET 35 412 412 MET MET A . n A 1 36 ASP 36 413 413 ASP ASP A . n A 1 37 SER 37 414 414 SER SER A . n A 1 38 ASN 38 415 415 ASN ASN A . n A 1 39 GLY 39 416 416 GLY GLY A . n A 1 40 LEU 40 417 417 LEU LEU A . n A 1 41 ALA 41 418 418 ALA ALA A . n A 1 42 ASP 42 419 419 ASP ASP A . n A 1 43 PRO 43 420 420 PRO PRO A . n A 1 44 TYR 44 421 421 TYR TYR A . n A 1 45 VAL 45 422 422 VAL VAL A . n A 1 46 LYS 46 423 423 LYS LYS A . n A 1 47 LEU 47 424 424 LEU LEU A . n A 1 48 HIS 48 425 425 HIS HIS A . n A 1 49 LEU 49 426 426 LEU LEU A . n A 1 50 LEU 50 427 427 LEU LEU A . n A 1 51 PRO 51 428 428 PRO PRO A . n A 1 52 GLY 52 429 429 GLY GLY A . n A 1 53 ALA 53 430 430 ALA ALA A . n A 1 54 SER 54 431 431 SER SER A . n A 1 55 LYS 55 432 432 LYS LYS A . n A 1 56 SER 56 433 433 SER SER A . n A 1 57 ASN 57 434 434 ASN ASN A . n A 1 58 LYS 58 435 435 LYS LYS A . n A 1 59 LEU 59 436 436 LEU LEU A . n A 1 60 ARG 60 437 437 ARG ARG A . n A 1 61 THR 61 438 438 THR THR A . n A 1 62 LYS 62 439 439 LYS LYS A . n A 1 63 THR 63 440 440 THR THR A . n A 1 64 LEU 64 441 441 LEU LEU A . n A 1 65 ARG 65 442 442 ARG ARG A . n A 1 66 ASN 66 443 443 ASN ASN A . n A 1 67 THR 67 444 444 THR THR A . n A 1 68 ARG 68 445 445 ARG ARG A . n A 1 69 ASN 69 446 446 ASN ASN A . n A 1 70 PRO 70 447 447 PRO PRO A . n A 1 71 VAL 71 448 448 VAL VAL A . n A 1 72 TRP 72 449 449 TRP TRP A . n A 1 73 ASN 73 450 450 ASN ASN A . n A 1 74 GLU 74 451 451 GLU GLU A . n A 1 75 THR 75 452 452 THR THR A . n A 1 76 LEU 76 453 453 LEU LEU A . n A 1 77 GLN 77 454 454 GLN GLN A . n A 1 78 TYR 78 455 455 TYR TYR A . n A 1 79 HIS 79 456 456 HIS HIS A . n A 1 80 GLY 80 457 457 GLY GLY A . n A 1 81 ILE 81 458 458 ILE ILE A . n A 1 82 THR 82 459 459 THR THR A . n A 1 83 GLU 83 460 460 GLU GLU A . n A 1 84 GLU 84 461 461 GLU GLU A . n A 1 85 ASP 85 462 462 ASP ASP A . n A 1 86 MET 86 463 463 MET MET A . n A 1 87 GLN 87 464 464 GLN GLN A . n A 1 88 ARG 88 465 465 ARG ARG A . n A 1 89 LYS 89 466 466 LYS LYS A . n A 1 90 THR 90 467 467 THR THR A . n A 1 91 LEU 91 468 468 LEU LEU A . n A 1 92 ARG 92 469 469 ARG ARG A . n A 1 93 ILE 93 470 470 ILE ILE A . n A 1 94 SER 94 471 471 SER SER A . n A 1 95 VAL 95 472 472 VAL VAL A . n A 1 96 CYS 96 473 473 CYS CYS A . n A 1 97 ASP 97 474 474 ASP ASP A . n A 1 98 GLU 98 475 475 GLU GLU A . n A 1 99 ASP 99 476 476 ASP ASP A . n A 1 100 LYS 100 477 477 LYS LYS A . n A 1 101 PHE 101 478 478 PHE PHE A . n A 1 102 GLY 102 479 479 GLY GLY A . n A 1 103 HIS 103 480 480 HIS HIS A . n A 1 104 ASN 104 481 481 ASN ASN A . n A 1 105 GLU 105 482 482 GLU GLU A . n A 1 106 PHE 106 483 483 PHE PHE A . n A 1 107 ILE 107 484 484 ILE ILE A . n A 1 108 GLY 108 485 485 GLY GLY A . n A 1 109 GLU 109 486 486 GLU GLU A . n A 1 110 THR 110 487 487 THR THR A . n A 1 111 ARG 111 488 488 ARG ARG A . n A 1 112 PHE 112 489 489 PHE PHE A . n A 1 113 SER 113 490 490 SER SER A . n A 1 114 LEU 114 491 491 LEU LEU A . n A 1 115 LYS 115 492 492 LYS LYS A . n A 1 116 LYS 116 493 493 LYS LYS A . n A 1 117 LEU 117 494 494 LEU LEU A . n A 1 118 LYS 118 495 495 LYS LYS A . n A 1 119 ALA 119 496 496 ALA ALA A . n A 1 120 ASN 120 497 497 ASN ASN A . n A 1 121 GLN 121 498 498 GLN GLN A . n A 1 122 ARG 122 499 499 ARG ARG A . n A 1 123 LYS 123 500 500 LYS LYS A . n A 1 124 ASN 124 501 501 ASN ASN A . n A 1 125 PHE 125 502 502 PHE PHE A . n A 1 126 ASN 126 503 503 ASN ASN A . n A 1 127 ILE 127 504 504 ILE ILE A . n A 1 128 CYS 128 505 505 CYS CYS A . n A 1 129 LEU 129 506 506 LEU LEU A . n A 1 130 GLU 130 507 507 GLU GLU A . n A 1 131 ARG 131 508 508 ARG ARG A . n A 1 132 VAL 132 509 509 VAL VAL A . n A 1 133 ILE 133 510 510 ILE ILE 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 I3P 1 601 1 I3P I3P A . C 3 SO4 1 602 1 SO4 SO4 A . D 4 HOH 1 701 1 HOH HOH A . D 4 HOH 2 702 2 HOH HOH A . D 4 HOH 3 703 3 HOH HOH A . D 4 HOH 4 704 4 HOH HOH A . D 4 HOH 5 705 5 HOH HOH A . D 4 HOH 6 706 6 HOH HOH A . D 4 HOH 7 707 7 HOH HOH A . D 4 HOH 8 708 8 HOH HOH A . D 4 HOH 9 709 9 HOH HOH A . D 4 HOH 10 710 10 HOH HOH A . D 4 HOH 11 711 11 HOH HOH A . D 4 HOH 12 712 12 HOH HOH A . D 4 HOH 13 713 13 HOH HOH A . D 4 HOH 14 714 14 HOH HOH A . D 4 HOH 15 715 15 HOH HOH A . D 4 HOH 16 716 16 HOH HOH A . D 4 HOH 17 717 17 HOH HOH A . D 4 HOH 18 718 18 HOH HOH A . D 4 HOH 19 719 19 HOH HOH A . D 4 HOH 20 720 20 HOH HOH A . D 4 HOH 21 721 21 HOH HOH A . D 4 HOH 22 722 22 HOH HOH A . D 4 HOH 23 723 23 HOH HOH A . D 4 HOH 24 724 24 HOH HOH A . D 4 HOH 25 725 25 HOH HOH A . D 4 HOH 26 726 26 HOH HOH A . D 4 HOH 27 727 27 HOH HOH A . D 4 HOH 28 728 28 HOH HOH A . D 4 HOH 29 729 29 HOH HOH A . D 4 HOH 30 730 30 HOH HOH A . D 4 HOH 31 731 31 HOH HOH A . D 4 HOH 32 732 32 HOH HOH A . D 4 HOH 33 733 33 HOH HOH A . D 4 HOH 34 734 34 HOH HOH A . D 4 HOH 35 735 35 HOH HOH A . D 4 HOH 36 736 36 HOH HOH A . D 4 HOH 37 737 37 HOH HOH A . D 4 HOH 38 738 38 HOH HOH A . D 4 HOH 39 739 39 HOH HOH A . D 4 HOH 40 740 40 HOH HOH A . D 4 HOH 41 741 41 HOH HOH A . D 4 HOH 42 742 42 HOH HOH A . D 4 HOH 43 743 43 HOH HOH A . D 4 HOH 44 744 44 HOH HOH A . D 4 HOH 45 745 45 HOH HOH A . D 4 HOH 46 746 46 HOH HOH A . D 4 HOH 47 747 47 HOH HOH A . D 4 HOH 48 748 48 HOH HOH A . D 4 HOH 49 749 49 HOH HOH A . D 4 HOH 50 750 50 HOH HOH A . D 4 HOH 51 751 51 HOH HOH A . D 4 HOH 52 752 52 HOH HOH A . D 4 HOH 53 753 53 HOH HOH A . D 4 HOH 54 754 54 HOH HOH A . D 4 HOH 55 755 55 HOH HOH A . D 4 HOH 56 756 56 HOH HOH A . D 4 HOH 57 757 57 HOH HOH A . D 4 HOH 58 758 58 HOH HOH A . D 4 HOH 59 759 59 HOH HOH A . D 4 HOH 60 760 60 HOH HOH A . D 4 HOH 61 761 61 HOH HOH A . D 4 HOH 62 762 62 HOH HOH A . D 4 HOH 63 763 63 HOH HOH A . D 4 HOH 64 764 64 HOH HOH A . D 4 HOH 65 765 65 HOH HOH A . D 4 HOH 66 766 66 HOH HOH A . D 4 HOH 67 767 67 HOH HOH A . D 4 HOH 68 768 68 HOH HOH A . D 4 HOH 69 769 69 HOH HOH A . D 4 HOH 70 770 70 HOH HOH A . D 4 HOH 71 771 71 HOH HOH A . D 4 HOH 72 772 72 HOH HOH A . D 4 HOH 73 773 73 HOH HOH A . D 4 HOH 74 774 74 HOH HOH A . D 4 HOH 75 775 75 HOH HOH A . D 4 HOH 76 776 76 HOH HOH A . D 4 HOH 77 777 77 HOH HOH A . D 4 HOH 78 778 78 HOH HOH A . D 4 HOH 79 779 79 HOH HOH A . D 4 HOH 80 780 80 HOH HOH A . D 4 HOH 81 781 81 HOH HOH A . D 4 HOH 82 782 82 HOH HOH A . D 4 HOH 83 783 83 HOH HOH A . D 4 HOH 84 784 84 HOH HOH A . D 4 HOH 85 785 85 HOH HOH A . D 4 HOH 86 786 86 HOH HOH A . D 4 HOH 87 787 87 HOH HOH A . D 4 HOH 88 788 88 HOH HOH A . D 4 HOH 89 789 89 HOH HOH A . D 4 HOH 90 790 90 HOH HOH A . D 4 HOH 91 791 91 HOH HOH A . D 4 HOH 92 792 92 HOH HOH A . D 4 HOH 93 793 93 HOH HOH A . D 4 HOH 94 794 94 HOH HOH A . D 4 HOH 95 795 95 HOH HOH A . D 4 HOH 96 796 96 HOH HOH A . D 4 HOH 97 797 97 HOH HOH A . D 4 HOH 98 798 98 HOH HOH A . D 4 HOH 99 799 99 HOH HOH A . D 4 HOH 100 800 100 HOH HOH A . D 4 HOH 101 801 101 HOH HOH A . D 4 HOH 102 802 102 HOH HOH A . D 4 HOH 103 803 103 HOH HOH A . D 4 HOH 104 804 104 HOH HOH A . D 4 HOH 105 805 105 HOH HOH A . D 4 HOH 106 806 106 HOH HOH A . D 4 HOH 107 807 107 HOH HOH A . D 4 HOH 108 808 108 HOH HOH A . D 4 HOH 109 809 109 HOH HOH A . D 4 HOH 110 810 110 HOH HOH A . D 4 HOH 111 811 111 HOH HOH A . D 4 HOH 112 812 112 HOH HOH A . D 4 HOH 113 813 113 HOH HOH A . D 4 HOH 114 814 114 HOH HOH A . D 4 HOH 115 815 115 HOH HOH A . D 4 HOH 116 816 116 HOH HOH A . D 4 HOH 117 817 117 HOH HOH A . D 4 HOH 118 818 118 HOH HOH A . D 4 HOH 119 819 119 HOH HOH A . D 4 HOH 120 820 120 HOH HOH A . D 4 HOH 121 821 121 HOH HOH A . D 4 HOH 122 822 122 HOH HOH A . D 4 HOH 123 823 123 HOH HOH A . D 4 HOH 124 824 124 HOH HOH A . D 4 HOH 125 825 125 HOH HOH A . D 4 HOH 126 826 126 HOH HOH A . D 4 HOH 127 827 127 HOH HOH A . D 4 HOH 128 828 128 HOH HOH A . D 4 HOH 129 829 129 HOH HOH A . D 4 HOH 130 830 130 HOH HOH A . D 4 HOH 131 831 131 HOH HOH A . D 4 HOH 132 832 132 HOH HOH A . D 4 HOH 133 833 133 HOH HOH A . D 4 HOH 134 834 134 HOH HOH A . D 4 HOH 135 835 135 HOH HOH A . D 4 HOH 136 836 136 HOH HOH A . D 4 HOH 137 837 137 HOH HOH A . D 4 HOH 138 838 138 HOH HOH A . D 4 HOH 139 839 139 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 # _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 2013-12-25 2 'Structure model' 1 1 2022-08-24 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 2 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' database_2 3 2 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_database_2.pdbx_DOI' 5 2 'Structure model' '_database_2.pdbx_database_accession' 6 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 7 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 8 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DNA 'data collection' . ? 1 REFMAC refinement . ? 2 PHENIX refinement '(phenix.refine: 1.8.4_1496)' ? 3 XDS 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 REFMAC phasing . ? 6 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 801 ? ? O A HOH 812 ? ? 1.86 2 1 O A HOH 822 ? ? O A HOH 825 ? ? 1.87 3 1 O A HOH 792 ? ? O A HOH 831 ? ? 1.91 4 1 O A HOH 820 ? ? O A HOH 827 ? ? 1.98 5 1 O A LEU 494 ? ? O A HOH 805 ? ? 2.07 6 1 OG1 A THR 382 ? ? O A HOH 766 ? ? 2.08 7 1 O A HOH 810 ? ? O A HOH 834 ? ? 2.11 8 1 O A HOH 759 ? ? O A HOH 813 ? ? 2.13 9 1 O A HOH 773 ? ? O A HOH 788 ? ? 2.13 10 1 O A HOH 732 ? ? O A HOH 790 ? ? 2.15 11 1 O A HOH 823 ? ? O A HOH 836 ? ? 2.17 12 1 O A HOH 770 ? ? O A HOH 805 ? ? 2.17 # 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 ILE A 404 ? ? -91.91 -70.08 2 1 MET A 412 ? ? -119.86 -112.63 3 1 ASP A 419 ? ? -115.95 77.81 4 1 ALA A 430 ? ? -77.16 30.56 5 1 SER A 431 ? ? 57.34 -177.73 6 1 LYS A 432 ? ? 55.05 -84.20 7 1 HIS A 480 ? ? -77.57 -167.48 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ILE 510 ? CA ? A ILE 133 CA 2 1 Y 1 A ILE 510 ? C ? A ILE 133 C 3 1 Y 1 A ILE 510 ? O ? A ILE 133 O 4 1 Y 1 A ILE 510 ? CB ? A ILE 133 CB 5 1 Y 1 A ILE 510 ? CG1 ? A ILE 133 CG1 6 1 Y 1 A ILE 510 ? CG2 ? A ILE 133 CG2 7 1 Y 1 A ILE 510 ? CD1 ? A ILE 133 CD1 # 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 ASP 378 ? A ASP 1 2 1 Y 1 A GLN 379 ? A GLN 2 3 1 Y 1 A ALA 380 ? A ALA 3 4 1 Y 1 A THR 381 ? A THR 4 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE I3P 3 'SULFATE ION' SO4 4 water HOH #