data_4DDJ # _entry.id 4DDJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.321 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4DDJ RCSB RCSB070193 WWPDB D_1000070193 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2DOB _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 4DDJ _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-01-18 _pdbx_database_status.status_code REL _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Popovic, K.' 1 'Prive, G.G.' 2 # _citation.id primary _citation.title 'Structure of saposin A lipoprotein discs.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 109 _citation.page_first 2908 _citation.page_last 2912 _citation.year 2012 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22308394 _citation.pdbx_database_id_DOI 10.1073/pnas.1115743109 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Popovic, K.' 1 ? primary 'Holyoake, J.' 2 ? primary 'Pomes, R.' 3 ? primary 'Prive, G.G.' 4 ? # _cell.entry_id 4DDJ _cell.length_a 39.794 _cell.length_b 39.794 _cell.length_c 247.284 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4DDJ _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _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 Saposin-A 9061.495 1 ? ? 'UNP residues 60-140' ? 2 non-polymer syn 'LAURYL DIMETHYLAMINE-N-OXIDE' 229.402 20 ? ? ? ? 3 water nat water 18.015 65 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Protein 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 ;MGSLPCDICKDVVTAAGDMLKDNATEEEILVYLEKTCDWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNL CES ; _entity_poly.pdbx_seq_one_letter_code_can ;MGSLPCDICKDVVTAAGDMLKDNATEEEILVYLEKTCDWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNL CES ; _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 MET n 1 2 GLY n 1 3 SER n 1 4 LEU n 1 5 PRO n 1 6 CYS n 1 7 ASP n 1 8 ILE n 1 9 CYS n 1 10 LYS n 1 11 ASP n 1 12 VAL n 1 13 VAL n 1 14 THR n 1 15 ALA n 1 16 ALA n 1 17 GLY n 1 18 ASP n 1 19 MET n 1 20 LEU n 1 21 LYS n 1 22 ASP n 1 23 ASN n 1 24 ALA n 1 25 THR n 1 26 GLU n 1 27 GLU n 1 28 GLU n 1 29 ILE n 1 30 LEU n 1 31 VAL n 1 32 TYR n 1 33 LEU n 1 34 GLU n 1 35 LYS n 1 36 THR n 1 37 CYS n 1 38 ASP n 1 39 TRP n 1 40 LEU n 1 41 PRO n 1 42 LYS n 1 43 PRO n 1 44 ASN n 1 45 MET n 1 46 SER n 1 47 ALA n 1 48 SER n 1 49 CYS n 1 50 LYS n 1 51 GLU n 1 52 ILE n 1 53 VAL n 1 54 ASP n 1 55 SER n 1 56 TYR n 1 57 LEU n 1 58 PRO n 1 59 VAL n 1 60 ILE n 1 61 LEU n 1 62 ASP n 1 63 ILE n 1 64 ILE n 1 65 LYS n 1 66 GLY n 1 67 GLU n 1 68 MET n 1 69 SER n 1 70 ARG n 1 71 PRO n 1 72 GLY n 1 73 GLU n 1 74 VAL n 1 75 CYS n 1 76 SER n 1 77 ALA n 1 78 LEU n 1 79 ASN n 1 80 LEU n 1 81 CYS n 1 82 GLU n 1 83 SER n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'PSAP, GLBA, SAP1' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SAP_HUMAN _struct_ref.pdbx_db_accession P07602 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;SLPCDICKDVVTAAGDMLKDNATEEEILVYLEKTCDWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNLCE S ; _struct_ref.pdbx_align_begin 60 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4DDJ _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 83 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P07602 _struct_ref_seq.db_align_beg 60 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 140 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 81 # 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 4DDJ MET A 1 ? UNP P07602 ? ? 'expression tag' -1 1 1 4DDJ GLY A 2 ? UNP P07602 ? ? 'expression tag' 0 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LDA non-polymer . 'LAURYL DIMETHYLAMINE-N-OXIDE' ? 'C14 H31 N O' 229.402 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 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 4DDJ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.12 _exptl_crystal.density_percent_sol 60.56 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 300 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '1.6 M trisodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 300K' # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'ADSC QUANTUM 315' 2009-07-25 ? 2 'IMAGE PLATE' 'RIGAKU RAXIS IV++' 2009-10-10 ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M 'SAGITALLY FOCUSED Si(111)' 'SINGLE WAVELENGTH' x-ray 2 1 M 'VariMax Cr' 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.009 1.0 2 2.292 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'APS BEAMLINE 19-ID' APS 19-ID ? 1.009 2 'ROTATING ANODE' 'RIGAKU FR-E+ SUPERBRIGHT' ? ? ? 2.292 # _reflns.pdbx_diffrn_id 1,2 _reflns.pdbx_ordinal 1 _reflns.entry_id 4DDJ _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 34.5 _reflns.d_resolution_high 1.90 _reflns.number_obs 9934 _reflns.number_all 10065 _reflns.percent_possible_obs 98.7 _reflns.pdbx_Rmerge_I_obs 0.051 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 44.9 _reflns.B_iso_Wilson_estimate 31.30 _reflns.pdbx_redundancy 9.1 _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_shell.pdbx_diffrn_id 1,2 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.9 _reflns_shell.d_res_low 1.93 _reflns_shell.percent_possible_all 98.1 _reflns_shell.Rmerge_I_obs 0.443 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.2 _reflns_shell.pdbx_redundancy 5.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4DDJ _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 9889 _refine.ls_number_reflns_all 9889 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.00 _refine.ls_d_res_high 1.90 _refine.ls_percent_reflns_obs 99.3 _refine.ls_R_factor_obs 0.232 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.230 _refine.ls_R_factor_R_free 0.280 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.800 _refine.ls_number_reflns_R_free 478 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min 0.500 _refine.occupancy_max 1.000 _refine.correlation_coeff_Fo_to_Fc 0.939 _refine.correlation_coeff_Fo_to_Fc_free 0.913 _refine.B_iso_mean 41.21 _refine.aniso_B[1][1] 1.05000 _refine.aniso_B[2][2] 1.05000 _refine.aniso_B[3][3] -1.57000 _refine.aniso_B[1][2] 0.52000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _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 U VALUES: RESIDUAL ONLY' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _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 ? _refine.pdbx_overall_ESU_R_Free 0.176 _refine.overall_SU_ML 0.118 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 8.515 _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.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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 606 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 320 _refine_hist.number_atoms_solvent 65 _refine_hist.number_atoms_total 991 _refine_hist.d_res_high 1.90 _refine_hist.d_res_low 10.00 # 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 0.017 0.021 ? 917 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.900 2.301 ? 1179 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 4.576 5.000 ? 79 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 40.434 27.727 ? 22 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 14.674 15.000 ? 116 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 10.914 15.000 ? 1 'X-RAY DIFFRACTION' ? r_chiral_restr 0.112 0.200 ? 101 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.021 ? 439 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? '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 1.196 1.500 ? 401 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 2.190 2.000 ? 653 'X-RAY DIFFRACTION' ? r_scbond_it 2.825 3.000 ? 516 'X-RAY DIFFRACTION' ? r_scangle_it 4.550 4.500 ? 526 '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 1.90 _refine_ls_shell.d_res_low 1.95 _refine_ls_shell.number_reflns_R_work 630 _refine_ls_shell.R_factor_R_work 0.2080 _refine_ls_shell.percent_reflns_obs 98.66 _refine_ls_shell.R_factor_R_free 0.2740 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 32 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 4DDJ _struct.title 'Crystal structure of saposin A in complex with lauryldimethylamine-N-oxide (LDAO)' _struct.pdbx_descriptor Saposin-A _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4DDJ _struct_keywords.pdbx_keywords 'LIPID BINDING PROTEIN' _struct_keywords.text ;saposin fold, sphingolipid activator protein, galactosylceramide, lauryldimethylamine-N-oxide, lipid, detergent, lysosome, LIPID 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 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 2 ? L N N 2 ? M N N 2 ? N N N 2 ? O N N 2 ? P N N 2 ? Q N N 2 ? R N N 2 ? S N N 2 ? T N N 2 ? U N N 2 ? V N N 3 ? # 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 3 ? ASP A 22 ? SER A 1 ASP A 20 1 ? 20 HELX_P HELX_P2 2 ALA A 24 ? ASP A 38 ? ALA A 22 ASP A 36 1 ? 15 HELX_P HELX_P3 3 PRO A 43 ? SER A 69 ? PRO A 41 SER A 67 1 ? 27 HELX_P HELX_P4 4 ARG A 70 ? LEU A 78 ? ARG A 68 LEU A 76 1 ? 9 # _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 disulf1 disulf ? ? A CYS 6 SG ? ? ? 1_555 A CYS 81 SG ? ? A CYS 4 A CYS 79 1_555 ? ? ? ? ? ? ? 2.037 ? disulf2 disulf ? ? A CYS 9 SG ? ? ? 1_555 A CYS 75 SG ? ? A CYS 7 A CYS 73 1_555 ? ? ? ? ? ? ? 2.008 ? disulf3 disulf ? ? A CYS 37 SG ? ? ? 1_555 A CYS 49 SG ? ? A CYS 35 A CYS 47 1_555 ? ? ? ? ? ? ? 2.113 ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id LYS _struct_mon_prot_cis.label_seq_id 42 _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 LYS _struct_mon_prot_cis.auth_seq_id 40 _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 43 _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 41 _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 2.55 # 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 LDA A 101' AC2 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE LDA A 102' AC3 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE LDA A 103' AC4 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE LDA A 104' AC5 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE LDA A 105' AC6 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE LDA A 106' AC7 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE LDA A 107' AC8 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE LDA A 108' AC9 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE LDA A 109' BC1 Software ? ? ? ? 2 'BINDING SITE FOR RESIDUE LDA A 110' BC2 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE LDA A 111' BC3 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE LDA A 112' BC4 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE LDA A 113' BC5 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE LDA A 114' BC6 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE LDA A 115' BC7 Software ? ? ? ? 2 'BINDING SITE FOR RESIDUE LDA A 116' BC8 Software ? ? ? ? 8 'BINDING SITE FOR RESIDUE LDA A 117' BC9 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE LDA A 118' CC1 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE LDA A 119' CC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE LDA A 120' # 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 TYR A 32 ? TYR A 30 . ? 1_555 ? 2 AC1 3 THR A 36 ? THR A 34 . ? 1_555 ? 3 AC1 3 TRP A 39 ? TRP A 37 . ? 1_555 ? 4 AC2 5 ASP A 22 ? ASP A 20 . ? 1_555 ? 5 AC2 5 THR A 25 ? THR A 23 . ? 1_555 ? 6 AC2 5 GLU A 28 ? GLU A 26 . ? 1_555 ? 7 AC2 5 LDA D . ? LDA A 103 . ? 1_555 ? 8 AC2 5 LDA J . ? LDA A 109 . ? 1_555 ? 9 AC3 4 GLU A 28 ? GLU A 26 . ? 1_555 ? 10 AC3 4 TYR A 32 ? TYR A 30 . ? 1_555 ? 11 AC3 4 LDA C . ? LDA A 102 . ? 1_555 ? 12 AC3 4 LDA J . ? LDA A 109 . ? 1_555 ? 13 AC4 5 LEU A 78 ? LEU A 76 . ? 1_555 ? 14 AC4 5 ASN A 79 ? ASN A 77 . ? 1_555 ? 15 AC4 5 LDA G . ? LDA A 106 . ? 1_555 ? 16 AC4 5 LDA O . ? LDA A 114 . ? 1_555 ? 17 AC4 5 LDA R . ? LDA A 117 . ? 8_555 ? 18 AC5 6 TYR A 56 ? TYR A 54 . ? 8_555 ? 19 AC5 6 ALA A 77 ? ALA A 75 . ? 1_555 ? 20 AC5 6 ASN A 79 ? ASN A 77 . ? 1_555 ? 21 AC5 6 LDA K . ? LDA A 110 . ? 1_555 ? 22 AC5 6 LDA R . ? LDA A 117 . ? 8_555 ? 23 AC5 6 LDA S . ? LDA A 118 . ? 8_555 ? 24 AC6 4 VAL A 12 ? VAL A 10 . ? 1_555 ? 25 AC6 4 LDA E . ? LDA A 104 . ? 1_555 ? 26 AC6 4 LDA P . ? LDA A 115 . ? 1_555 ? 27 AC6 4 HOH V . ? HOH A 232 . ? 1_555 ? 28 AC7 4 TYR A 32 ? TYR A 30 . ? 1_555 ? 29 AC7 4 LDA I . ? LDA A 108 . ? 1_555 ? 30 AC7 4 LDA J . ? LDA A 109 . ? 1_555 ? 31 AC7 4 HOH V . ? HOH A 252 . ? 1_555 ? 32 AC8 3 LDA H . ? LDA A 107 . ? 1_555 ? 33 AC8 3 LDA O . ? LDA A 114 . ? 8_555 ? 34 AC8 3 LDA T . ? LDA A 119 . ? 8_555 ? 35 AC9 4 LDA C . ? LDA A 102 . ? 1_555 ? 36 AC9 4 LDA D . ? LDA A 103 . ? 1_555 ? 37 AC9 4 LDA H . ? LDA A 107 . ? 1_555 ? 38 AC9 4 LDA T . ? LDA A 119 . ? 1_555 ? 39 BC1 2 ALA A 77 ? ALA A 75 . ? 1_555 ? 40 BC1 2 LDA F . ? LDA A 105 . ? 1_555 ? 41 BC2 6 GLU A 67 ? GLU A 65 . ? 1_555 ? 42 BC2 6 GLU A 73 ? GLU A 71 . ? 1_555 ? 43 BC2 6 LDA M . ? LDA A 112 . ? 1_555 ? 44 BC2 6 LDA N . ? LDA A 113 . ? 1_555 ? 45 BC2 6 LDA Q . ? LDA A 116 . ? 1_555 ? 46 BC2 6 HOH V . ? HOH A 253 . ? 8_655 ? 47 BC3 3 LDA L . ? LDA A 111 . ? 1_555 ? 48 BC3 3 LDA Q . ? LDA A 116 . ? 1_555 ? 49 BC3 3 LDA T . ? LDA A 119 . ? 1_555 ? 50 BC4 5 VAL A 12 ? VAL A 10 . ? 1_555 ? 51 BC4 5 MET A 68 ? MET A 66 . ? 1_555 ? 52 BC4 5 LDA L . ? LDA A 111 . ? 1_555 ? 53 BC4 5 LDA P . ? LDA A 115 . ? 1_555 ? 54 BC4 5 LDA T . ? LDA A 119 . ? 1_555 ? 55 BC5 4 TRP A 39 ? TRP A 37 . ? 8_555 ? 56 BC5 4 LDA E . ? LDA A 104 . ? 1_555 ? 57 BC5 4 LDA I . ? LDA A 108 . ? 8_555 ? 58 BC5 4 LDA R . ? LDA A 117 . ? 8_555 ? 59 BC6 7 LEU A 40 ? LEU A 38 . ? 8_555 ? 60 BC6 7 MET A 45 ? MET A 43 . ? 8_555 ? 61 BC6 7 LDA G . ? LDA A 106 . ? 1_555 ? 62 BC6 7 LDA N . ? LDA A 113 . ? 1_555 ? 63 BC6 7 LDA R . ? LDA A 117 . ? 8_555 ? 64 BC6 7 LDA U . ? LDA A 120 . ? 5_554 ? 65 BC6 7 LDA U . ? LDA A 120 . ? 8_555 ? 66 BC7 2 LDA L . ? LDA A 111 . ? 1_555 ? 67 BC7 2 LDA M . ? LDA A 112 . ? 1_555 ? 68 BC8 8 THR A 36 ? THR A 34 . ? 1_555 ? 69 BC8 8 TRP A 39 ? TRP A 37 . ? 1_555 ? 70 BC8 8 CYS A 49 ? CYS A 47 . ? 1_555 ? 71 BC8 8 VAL A 53 ? VAL A 51 . ? 1_555 ? 72 BC8 8 LDA E . ? LDA A 104 . ? 8_555 ? 73 BC8 8 LDA F . ? LDA A 105 . ? 8_555 ? 74 BC8 8 LDA O . ? LDA A 114 . ? 8_555 ? 75 BC8 8 LDA P . ? LDA A 115 . ? 8_555 ? 76 BC9 6 GLU A 27 ? GLU A 25 . ? 8_665 ? 77 BC9 6 LEU A 30 ? LEU A 28 . ? 8_665 ? 78 BC9 6 GLU A 34 ? GLU A 32 . ? 8_665 ? 79 BC9 6 TYR A 56 ? TYR A 54 . ? 1_555 ? 80 BC9 6 ILE A 63 ? ILE A 61 . ? 1_555 ? 81 BC9 6 LDA F . ? LDA A 105 . ? 8_555 ? 82 CC1 6 MET A 19 ? MET A 17 . ? 1_555 ? 83 CC1 6 LEU A 20 ? LEU A 18 . ? 1_555 ? 84 CC1 6 LDA I . ? LDA A 108 . ? 8_555 ? 85 CC1 6 LDA J . ? LDA A 109 . ? 1_555 ? 86 CC1 6 LDA M . ? LDA A 112 . ? 1_555 ? 87 CC1 6 LDA N . ? LDA A 113 . ? 1_555 ? 88 CC2 3 ASP A 11 ? ASP A 9 . ? 8_555 ? 89 CC2 3 LDA P . ? LDA A 115 . ? 6_555 ? 90 CC2 3 LDA P . ? LDA A 115 . ? 8_555 ? # _atom_sites.entry_id 4DDJ _atom_sites.fract_transf_matrix[1][1] 0.025129 _atom_sites.fract_transf_matrix[1][2] 0.014508 _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] 0.029017 _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] 0.004044 _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 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 MET 1 -1 ? ? ? A . n A 1 2 GLY 2 0 ? ? ? A . n A 1 3 SER 3 1 1 SER SER A . n A 1 4 LEU 4 2 2 LEU LEU A . n A 1 5 PRO 5 3 3 PRO PRO A . n A 1 6 CYS 6 4 4 CYS CYS A . n A 1 7 ASP 7 5 5 ASP ASP A . n A 1 8 ILE 8 6 6 ILE ILE A . n A 1 9 CYS 9 7 7 CYS CYS A . n A 1 10 LYS 10 8 8 LYS LYS A . n A 1 11 ASP 11 9 9 ASP ASP A . n A 1 12 VAL 12 10 10 VAL VAL A . n A 1 13 VAL 13 11 11 VAL VAL A . n A 1 14 THR 14 12 12 THR THR A . n A 1 15 ALA 15 13 13 ALA ALA A . n A 1 16 ALA 16 14 14 ALA ALA A . n A 1 17 GLY 17 15 15 GLY GLY A . n A 1 18 ASP 18 16 16 ASP ASP A . n A 1 19 MET 19 17 17 MET MET A . n A 1 20 LEU 20 18 18 LEU LEU A . n A 1 21 LYS 21 19 19 LYS LYS A . n A 1 22 ASP 22 20 20 ASP ASP A . n A 1 23 ASN 23 21 21 ASN ASN A . n A 1 24 ALA 24 22 22 ALA ALA A . n A 1 25 THR 25 23 23 THR THR A . n A 1 26 GLU 26 24 24 GLU GLU A . n A 1 27 GLU 27 25 25 GLU GLU A . n A 1 28 GLU 28 26 26 GLU GLU A . n A 1 29 ILE 29 27 27 ILE ILE A . n A 1 30 LEU 30 28 28 LEU LEU A . n A 1 31 VAL 31 29 29 VAL VAL A . n A 1 32 TYR 32 30 30 TYR TYR A . n A 1 33 LEU 33 31 31 LEU LEU A . n A 1 34 GLU 34 32 32 GLU GLU A . n A 1 35 LYS 35 33 33 LYS LYS A . n A 1 36 THR 36 34 34 THR THR A . n A 1 37 CYS 37 35 35 CYS CYS A . n A 1 38 ASP 38 36 36 ASP ASP A . n A 1 39 TRP 39 37 37 TRP TRP A . n A 1 40 LEU 40 38 38 LEU LEU A . n A 1 41 PRO 41 39 39 PRO PRO A . n A 1 42 LYS 42 40 40 LYS LYS A . n A 1 43 PRO 43 41 41 PRO PRO A . n A 1 44 ASN 44 42 42 ASN ASN A . n A 1 45 MET 45 43 43 MET MET A . n A 1 46 SER 46 44 44 SER SER A . n A 1 47 ALA 47 45 45 ALA ALA A . n A 1 48 SER 48 46 46 SER SER A . n A 1 49 CYS 49 47 47 CYS CYS A . n A 1 50 LYS 50 48 48 LYS LYS A . n A 1 51 GLU 51 49 49 GLU GLU A . n A 1 52 ILE 52 50 50 ILE ILE A . n A 1 53 VAL 53 51 51 VAL VAL A . n A 1 54 ASP 54 52 52 ASP ASP A . n A 1 55 SER 55 53 53 SER SER A . n A 1 56 TYR 56 54 54 TYR TYR A . n A 1 57 LEU 57 55 55 LEU LEU A . n A 1 58 PRO 58 56 56 PRO PRO A . n A 1 59 VAL 59 57 57 VAL VAL A . n A 1 60 ILE 60 58 58 ILE ILE A . n A 1 61 LEU 61 59 59 LEU LEU A . n A 1 62 ASP 62 60 60 ASP ASP A . n A 1 63 ILE 63 61 61 ILE ILE A . n A 1 64 ILE 64 62 62 ILE ILE A . n A 1 65 LYS 65 63 63 LYS LYS A . n A 1 66 GLY 66 64 64 GLY GLY A . n A 1 67 GLU 67 65 65 GLU GLU A . n A 1 68 MET 68 66 66 MET MET A . n A 1 69 SER 69 67 67 SER SER A . n A 1 70 ARG 70 68 68 ARG ARG A . n A 1 71 PRO 71 69 69 PRO PRO A . n A 1 72 GLY 72 70 70 GLY GLY A . n A 1 73 GLU 73 71 71 GLU GLU A . n A 1 74 VAL 74 72 72 VAL VAL A . n A 1 75 CYS 75 73 73 CYS CYS A . n A 1 76 SER 76 74 74 SER SER A . n A 1 77 ALA 77 75 75 ALA ALA A . n A 1 78 LEU 78 76 76 LEU LEU A . n A 1 79 ASN 79 77 77 ASN ASN A . n A 1 80 LEU 80 78 78 LEU LEU A . n A 1 81 CYS 81 79 79 CYS CYS A . n A 1 82 GLU 82 80 80 GLU GLU A . n A 1 83 SER 83 81 ? ? ? 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 LDA 1 101 101 LDA LDA A . C 2 LDA 1 102 102 LDA LDA A . D 2 LDA 1 103 103 LDA LDA A . E 2 LDA 1 104 104 LDA LDA A . F 2 LDA 1 105 105 LDA LDA A . G 2 LDA 1 106 106 LDA LDA A . H 2 LDA 1 107 107 LDA LDA A . I 2 LDA 1 108 108 LDA LDA A . J 2 LDA 1 109 109 LDA LDA A . K 2 LDA 1 110 110 LDA LDA A . L 2 LDA 1 111 111 LDA LDA A . M 2 LDA 1 112 112 LDA LDA A . N 2 LDA 1 113 113 LDA LDA A . O 2 LDA 1 114 114 LDA LDA A . P 2 LDA 1 115 115 LDA LDA A . Q 2 LDA 1 116 116 LDA LDA A . R 2 LDA 1 117 117 LDA LDA A . S 2 LDA 1 118 118 LDA LDA A . T 2 LDA 1 119 119 LDA LDA A . U 2 LDA 1 120 120 LDA LDA A . V 3 HOH 1 201 201 HOH HOH A . V 3 HOH 2 202 202 HOH HOH A . V 3 HOH 3 203 203 HOH HOH A . V 3 HOH 4 204 204 HOH HOH A . V 3 HOH 5 205 205 HOH HOH A . V 3 HOH 6 206 206 HOH HOH A . V 3 HOH 7 207 207 HOH HOH A . V 3 HOH 8 208 208 HOH HOH A . V 3 HOH 9 209 209 HOH HOH A . V 3 HOH 10 210 210 HOH HOH A . V 3 HOH 11 211 211 HOH HOH A . V 3 HOH 12 212 212 HOH HOH A . V 3 HOH 13 213 213 HOH HOH A . V 3 HOH 14 214 214 HOH HOH A . V 3 HOH 15 215 215 HOH HOH A . V 3 HOH 16 216 216 HOH HOH A . V 3 HOH 17 217 217 HOH HOH A . V 3 HOH 18 218 218 HOH HOH A . V 3 HOH 19 219 219 HOH HOH A . V 3 HOH 20 220 220 HOH HOH A . V 3 HOH 21 221 221 HOH HOH A . V 3 HOH 22 222 222 HOH HOH A . V 3 HOH 23 223 223 HOH HOH A . V 3 HOH 24 224 224 HOH HOH A . V 3 HOH 25 225 225 HOH HOH A . V 3 HOH 26 226 226 HOH HOH A . V 3 HOH 27 227 227 HOH HOH A . V 3 HOH 28 228 228 HOH HOH A . V 3 HOH 29 229 229 HOH HOH A . V 3 HOH 30 230 230 HOH HOH A . V 3 HOH 31 231 231 HOH HOH A . V 3 HOH 32 232 232 HOH HOH A . V 3 HOH 33 233 233 HOH HOH A . V 3 HOH 34 234 234 HOH HOH A . V 3 HOH 35 235 235 HOH HOH A . V 3 HOH 36 236 236 HOH HOH A . V 3 HOH 37 237 237 HOH HOH A . V 3 HOH 38 238 238 HOH HOH A . V 3 HOH 39 239 239 HOH HOH A . V 3 HOH 40 240 240 HOH HOH A . V 3 HOH 41 241 241 HOH HOH A . V 3 HOH 42 242 242 HOH HOH A . V 3 HOH 43 243 243 HOH HOH A . V 3 HOH 44 244 244 HOH HOH A . V 3 HOH 45 245 245 HOH HOH A . V 3 HOH 46 246 246 HOH HOH A . V 3 HOH 47 247 247 HOH HOH A . V 3 HOH 48 248 248 HOH HOH A . V 3 HOH 49 249 249 HOH HOH A . V 3 HOH 50 250 250 HOH HOH A . V 3 HOH 51 251 251 HOH HOH A . V 3 HOH 52 252 252 HOH HOH A . V 3 HOH 53 253 253 HOH HOH A . V 3 HOH 54 254 254 HOH HOH A . V 3 HOH 55 255 255 HOH HOH A . V 3 HOH 56 256 256 HOH HOH A . V 3 HOH 57 257 257 HOH HOH A . V 3 HOH 58 258 258 HOH HOH A . V 3 HOH 59 259 259 HOH HOH A . V 3 HOH 60 260 260 HOH HOH A . V 3 HOH 61 261 261 HOH HOH A . V 3 HOH 62 262 262 HOH HOH A . V 3 HOH 63 263 263 HOH HOH A . V 3 HOH 64 264 264 HOH HOH A . V 3 HOH 65 265 265 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 8_555 x-y,-y,-z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # 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 2012-02-15 2 'Structure model' 1 1 2012-02-22 3 'Structure model' 1 2 2012-03-14 4 'Structure model' 1 3 2020-01-29 # _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 3 'Structure model' 'Database references' 3 4 'Structure model' Advisory 4 4 'Structure model' 'Database references' 5 4 '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 4 'Structure model' pdbx_distant_solvent_atoms 2 4 'Structure model' pdbx_struct_assembly 3 4 'Structure model' pdbx_struct_assembly_gen 4 4 'Structure model' struct_ref_seq_dif # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 4 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_struct_ref_seq_dif.details' # 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 29.558 -4.286 -16.280 0.0322 0.0918 0.0751 -0.0092 0.0042 -0.0480 1.1858 3.4612 1.3810 -0.2517 -0.1908 0.8737 0.0239 0.0514 0.0521 0.0016 0.1416 -0.4036 0.0070 0.0121 -0.1656 'X-RAY DIFFRACTION' 2 ? refined 20.227 13.500 0.310 0.0279 0.1063 0.0511 -0.0311 -0.0010 -0.0328 0.5204 1.1137 3.3582 0.3499 1.3122 1.0582 0.0852 -0.0733 -0.0298 0.0086 -0.0142 -0.0046 0.1719 -0.1482 -0.0710 'X-RAY DIFFRACTION' 3 ? refined 22.584 -0.148 -4.168 0.2401 0.1346 0.1099 0.0466 0.0261 0.0083 0.8933 1.2505 2.4564 0.4957 0.8833 1.2001 -0.1062 -0.2654 -0.0230 -0.0576 -0.1162 0.3045 0.3517 -0.1002 0.2224 # 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 1 ? ? A 17 ? ? ? ? 'X-RAY DIFFRACTION' 2 1 A 68 ? ? A 80 ? ? ? ? 'X-RAY DIFFRACTION' 3 2 A 18 ? ? A 67 ? ? ? ? 'X-RAY DIFFRACTION' 4 3 A 101 ? ? A 101 ? ? ? ? 'X-RAY DIFFRACTION' 5 3 A 102 ? ? A 102 ? ? ? ? 'X-RAY DIFFRACTION' 6 3 A 103 ? ? A 103 ? ? ? ? 'X-RAY DIFFRACTION' 7 3 A 104 ? ? A 104 ? ? ? ? 'X-RAY DIFFRACTION' 8 3 A 105 ? ? A 105 ? ? ? ? 'X-RAY DIFFRACTION' 9 3 A 106 ? ? A 106 ? ? ? ? 'X-RAY DIFFRACTION' 10 3 A 107 ? ? A 107 ? ? ? ? 'X-RAY DIFFRACTION' 11 3 A 108 ? ? A 108 ? ? ? ? 'X-RAY DIFFRACTION' 12 3 A 109 ? ? A 109 ? ? ? ? 'X-RAY DIFFRACTION' 13 3 A 110 ? ? A 110 ? ? ? ? 'X-RAY DIFFRACTION' 14 3 A 111 ? ? A 111 ? ? ? ? 'X-RAY DIFFRACTION' 15 3 A 112 ? ? A 112 ? ? ? ? 'X-RAY DIFFRACTION' 16 3 A 113 ? ? A 113 ? ? ? ? 'X-RAY DIFFRACTION' 17 3 A 114 ? ? A 114 ? ? ? ? 'X-RAY DIFFRACTION' 18 3 A 115 ? ? A 115 ? ? ? ? 'X-RAY DIFFRACTION' 19 3 A 116 ? ? A 116 ? ? ? ? 'X-RAY DIFFRACTION' 20 3 A 117 ? ? A 117 ? ? ? ? 'X-RAY DIFFRACTION' 21 3 A 118 ? ? A 118 ? ? ? ? 'X-RAY DIFFRACTION' 22 3 A 119 ? ? A 119 ? ? ? ? 'X-RAY DIFFRACTION' 23 3 A 120 ? ? A 120 ? ? ? ? # 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 REFMAC 5.5.0102 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 2 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 HKL-3000 . ? ? ? ? 'data collection' ? ? ? 4 HKL-3000 . ? ? ? ? 'data reduction' ? ? ? 5 HKL-3000 . ? ? ? ? 'data scaling' ? ? ? 6 SHELXS . ? ? ? ? phasing ? ? ? # _pdbx_entry_details.entry_id 4DDJ _pdbx_entry_details.nonpolymer_details ;ALTHOUGH THE REAL SPACE R VALUE FOR SOME OF THE LDA RESIDUES ARE HIGH, THESE LDAO DETERGENT MOLECULES (RESIDUE NAME IS LDA) ARE PART OF A MICELLE-TYPE STRUCTURE, AND THE OBSERVED DENSITY FOR THESE LIGANDS IS COMPLETELY CONSISTENT WITH THE PACKING REQUIREMENTS OF THE NEIGHBORING LDA MOLECULES. ; _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 261 ? ? 1_555 O A HOH 263 ? ? 8_565 1.86 2 1 O A HOH 232 ? ? 1_555 O A HOH 233 ? ? 10_554 1.91 3 1 OD2 A ASP 60 ? ? 1_555 O A HOH 242 ? ? 8_665 2.10 # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 235 ? 5.84 . 2 1 O ? A HOH 237 ? 8.66 . 3 1 O ? A HOH 246 ? 7.57 . 4 1 O ? A HOH 250 ? . 8.41 5 1 O ? A HOH 253 ? . 9.04 # 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 MET -1 ? A MET 1 2 1 Y 1 A GLY 0 ? A GLY 2 3 1 Y 1 A SER 81 ? A SER 83 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'LAURYL DIMETHYLAMINE-N-OXIDE' LDA 3 water HOH #