data_2R1Q # _entry.id 2R1Q # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2R1Q RCSB RCSB044316 WWPDB D_1000044316 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2Z9A . unspecified PDB 2QYP . unspecified PDB 2R0R . unspecified PDB 2RB3 . unspecified # _pdbx_database_status.entry_id 2R1Q _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-08-23 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Maier, T.' 1 'Rossman, M.' 2 'Saenger, W.' 3 # _citation.id primary _citation.title 'Crystal structures of human saposins C and d: implications for lipid recognition and membrane interactions.' _citation.journal_abbrev Structure _citation.journal_volume 16 _citation.page_first 809 _citation.page_last 817 _citation.year 2008 _citation.journal_id_ASTM STRUE6 _citation.country UK _citation.journal_id_ISSN 0969-2126 _citation.journal_id_CSD 2005 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18462685 _citation.pdbx_database_id_DOI 10.1016/j.str.2008.02.016 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Rossmann, M.' 1 primary 'Schultz-Heienbrok, R.' 2 primary 'Behlke, J.' 3 primary 'Remmel, N.' 4 primary 'Alings, C.' 5 primary 'Sandhoff, K.' 6 primary 'Saenger, W.' 7 primary 'Maier, T.' 8 # _cell.length_a 40.465 _cell.length_b 74.879 _cell.length_c 66.791 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 2R1Q _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.entry_id 2R1Q _symmetry.Int_Tables_number 20 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Proactivator polypeptide' 9780.049 1 ? ? ? ? 2 water nat water 18.015 6 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;AGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAE(IYR)EPVLIEILVEVMDPSFVCLKIGA CPSHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;AGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACPSH HHHHH ; _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 ALA n 1 2 GLY n 1 3 PHE n 1 4 CYS n 1 5 GLU n 1 6 VAL n 1 7 CYS n 1 8 LYS n 1 9 LYS n 1 10 LEU n 1 11 VAL n 1 12 GLY n 1 13 TYR n 1 14 LEU n 1 15 ASP n 1 16 ARG n 1 17 ASN n 1 18 LEU n 1 19 GLU n 1 20 LYS n 1 21 ASN n 1 22 SER n 1 23 THR n 1 24 LYS n 1 25 GLN n 1 26 GLU n 1 27 ILE n 1 28 LEU n 1 29 ALA n 1 30 ALA n 1 31 LEU n 1 32 GLU n 1 33 LYS n 1 34 GLY n 1 35 CYS n 1 36 SER n 1 37 PHE n 1 38 LEU n 1 39 PRO n 1 40 ASP n 1 41 PRO n 1 42 TYR n 1 43 GLN n 1 44 LYS n 1 45 GLN n 1 46 CYS n 1 47 ASP n 1 48 GLN n 1 49 PHE n 1 50 VAL n 1 51 ALA n 1 52 GLU n 1 53 IYR n 1 54 GLU n 1 55 PRO n 1 56 VAL n 1 57 LEU n 1 58 ILE n 1 59 GLU n 1 60 ILE n 1 61 LEU n 1 62 VAL n 1 63 GLU n 1 64 VAL n 1 65 MET n 1 66 ASP n 1 67 PRO n 1 68 SER n 1 69 PHE n 1 70 VAL n 1 71 CYS n 1 72 LEU n 1 73 LYS n 1 74 ILE n 1 75 GLY n 1 76 ALA n 1 77 CYS n 1 78 PRO n 1 79 SER n 1 80 HIS n 1 81 HIS n 1 82 HIS n 1 83 HIS n 1 84 HIS n 1 85 HIS 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 Homo _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 'Pichia pastoris' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 4922 _entity_src_gen.host_org_genus Pichia _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 GS115 _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 pPIC9K _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 GFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACPS _struct_ref.pdbx_align_begin 407 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2R1Q _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 79 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P07602 _struct_ref_seq.db_align_beg 407 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 484 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 3 _struct_ref_seq.pdbx_auth_seq_align_end 80 # 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 2R1Q ALA A 1 ? UNP P07602 ? ? 'EXPRESSION TAG' 2 1 1 2R1Q HIS A 80 ? UNP P07602 ? ? 'EXPRESSION TAG' 81 2 1 2R1Q HIS A 81 ? UNP P07602 ? ? 'EXPRESSION TAG' 82 3 1 2R1Q HIS A 82 ? UNP P07602 ? ? 'EXPRESSION TAG' 83 4 1 2R1Q HIS A 83 ? UNP P07602 ? ? 'EXPRESSION TAG' 84 5 1 2R1Q HIS A 84 ? UNP P07602 ? ? 'EXPRESSION TAG' 85 6 1 2R1Q HIS A 85 ? UNP P07602 ? ? 'EXPRESSION TAG' 86 7 # 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 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 IYR 'L-peptide linking' n 3-IODO-TYROSINE ? 'C9 H10 I N O3' 307.085 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 2R1Q _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.59 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 52.45 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 5.9 _exptl_crystal_grow.temp 291 _exptl_crystal_grow.pdbx_details '100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, vapor diffusion, hanging drop, temperature 291K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2004-04-23 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator GRAPHITE _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.12714 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'BESSY BEAMLINE 14.1' _diffrn_source.pdbx_wavelength_list 1.12714 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site BESSY _diffrn_source.pdbx_synchrotron_beamline 14.1 # _reflns.entry_id 2R1Q _reflns.d_resolution_high 2.500 _reflns.d_resolution_low 20.000 _reflns.number_obs 3670 _reflns.pdbx_Rmerge_I_obs 0.104 _reflns.pdbx_netI_over_sigmaI 12.300 _reflns.pdbx_chi_squared 1.034 _reflns.percent_possible_obs 98.700 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 2.50 2.59 ? ? ? 0.546 ? ? 0.858 ? ? 342 97.70 ? 1 2.59 2.69 ? ? ? 0.419 ? ? 1.069 ? ? 363 98.10 ? 2 2.69 2.81 ? ? ? 0.322 ? ? 1.078 ? ? 352 97.50 ? 3 2.81 2.96 ? ? ? 0.244 ? ? 1.030 ? ? 351 97.80 ? 4 2.96 3.15 ? ? ? 0.184 ? ? 1.077 ? ? 364 98.10 ? 5 3.15 3.39 ? ? ? 0.143 ? ? 1.062 ? ? 368 99.50 ? 6 3.39 3.73 ? ? ? 0.113 ? ? 1.079 ? ? 372 100.00 ? 7 3.73 4.26 ? ? ? 0.091 ? ? 1.032 ? ? 373 99.70 ? 8 4.26 5.35 ? ? ? 0.077 ? ? 1.017 ? ? 380 99.20 ? 9 5.35 20.00 ? ? ? 0.093 ? ? 1.026 ? ? 405 99.30 ? 10 # _refine.entry_id 2R1Q _refine.ls_d_res_high 2.500 _refine.ls_d_res_low 19.350 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 98.700 _refine.ls_number_reflns_obs 3657 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_R_factor_obs 0.250 _refine.ls_R_factor_R_work 0.248 _refine.ls_R_factor_R_free 0.278 _refine.ls_percent_reflns_R_free 4.400 _refine.ls_number_reflns_R_free 162 _refine.B_iso_mean 50.440 _refine.aniso_B[1][1] 0.260 _refine.aniso_B[2][2] -0.260 _refine.aniso_B[3][3] 0.000 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.932 _refine.correlation_coeff_Fo_to_Fc_free 0.909 _refine.pdbx_overall_ESU_R 0.491 _refine.pdbx_overall_ESU_R_Free 0.298 _refine.overall_SU_ML 0.252 _refine.overall_SU_B 12.191 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.400 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 609 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 8 _refine_hist.number_atoms_total 617 _refine_hist.d_res_high 2.500 _refine_hist.d_res_low 19.350 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 623 0.011 0.022 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 844 1.389 2.027 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 77 5.373 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 25 44.037 26.800 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 113 19.006 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 1 39.701 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 95 0.100 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 458 0.004 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 286 0.243 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 435 0.313 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 22 0.122 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 24 0.257 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 1 0.306 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 396 0.447 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 631 0.860 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 253 1.446 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 213 2.138 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.500 _refine_ls_shell.d_res_low 2.564 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 98.820 _refine_ls_shell.number_reflns_R_work 239 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.354 _refine_ls_shell.R_factor_R_free 0.277 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 12 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 251 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2R1Q _struct.title 'Crystal Structure of Iodinated Human Saposin D in Space Group C2221' _struct.pdbx_descriptor 'Proactivator polypeptide' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2R1Q _struct_keywords.text ;lipid binding protein, saposin, activator protein, sap, Alternative splicing, Disease mutation, Gaucher disease, Glycoprotein, GM2-gangliosidosis, Lipid metabolism, Lysosome, Metachromatic leukodystrophy, Sphingolipid metabolism ; _struct_keywords.pdbx_keywords '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 ? # _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 PHE A 3 ? LEU A 18 ? PHE A 4 LEU A 19 1 ? 16 HELX_P HELX_P2 2 THR A 23 ? CYS A 35 ? THR A 24 CYS A 36 1 ? 13 HELX_P HELX_P3 3 SER A 36 ? LEU A 38 ? SER A 37 LEU A 39 5 ? 3 HELX_P HELX_P4 4 PRO A 39 ? PRO A 41 ? PRO A 40 PRO A 42 5 ? 3 HELX_P HELX_P5 5 TYR A 42 ? VAL A 62 ? TYR A 43 VAL A 63 1 ? 21 HELX_P HELX_P6 6 ASP A 66 ? ILE A 74 ? ASP A 67 ILE A 75 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 4 SG ? ? ? 1_555 A CYS 77 SG ? ? A CYS 5 A CYS 78 1_555 ? ? ? ? ? ? ? 2.053 ? disulf2 disulf ? ? A CYS 7 SG ? ? ? 1_555 A CYS 71 SG ? ? A CYS 8 A CYS 72 1_555 ? ? ? ? ? ? ? 2.015 ? disulf3 disulf ? ? A CYS 35 SG ? ? ? 1_555 A CYS 46 SG ? ? A CYS 36 A CYS 47 1_555 ? ? ? ? ? ? ? 2.030 ? covale1 covale ? ? A GLU 52 C ? ? ? 1_555 A IYR 53 N ? ? A GLU 53 A IYR 54 1_555 ? ? ? ? ? ? ? 1.323 ? covale2 covale ? ? A IYR 53 C ? ? ? 1_555 A GLU 54 N ? ? A IYR 54 A GLU 55 1_555 ? ? ? ? ? ? ? 1.326 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # _atom_sites.entry_id 2R1Q _atom_sites.fract_transf_matrix[1][1] 0.024713 _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] 0.013355 _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] 0.014972 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C I 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 ALA 1 2 2 ALA ALA A . n A 1 2 GLY 2 3 3 GLY GLY A . n A 1 3 PHE 3 4 4 PHE PHE A . n A 1 4 CYS 4 5 5 CYS CYS A . n A 1 5 GLU 5 6 6 GLU GLU A . n A 1 6 VAL 6 7 7 VAL VAL A . n A 1 7 CYS 7 8 8 CYS CYS A . n A 1 8 LYS 8 9 9 LYS LYS A . n A 1 9 LYS 9 10 10 LYS LYS A . n A 1 10 LEU 10 11 11 LEU LEU A . n A 1 11 VAL 11 12 12 VAL VAL A . n A 1 12 GLY 12 13 13 GLY GLY A . n A 1 13 TYR 13 14 14 TYR TYR A . n A 1 14 LEU 14 15 15 LEU LEU A . n A 1 15 ASP 15 16 16 ASP ASP A . n A 1 16 ARG 16 17 17 ARG ARG A . n A 1 17 ASN 17 18 18 ASN ASN A . n A 1 18 LEU 18 19 19 LEU LEU A . n A 1 19 GLU 19 20 20 GLU GLU A . n A 1 20 LYS 20 21 21 LYS LYS A . n A 1 21 ASN 21 22 22 ASN ASN A . n A 1 22 SER 22 23 23 SER SER A . n A 1 23 THR 23 24 24 THR THR A . n A 1 24 LYS 24 25 25 LYS LYS A . n A 1 25 GLN 25 26 26 GLN GLN A . n A 1 26 GLU 26 27 27 GLU GLU A . n A 1 27 ILE 27 28 28 ILE ILE A . n A 1 28 LEU 28 29 29 LEU LEU A . n A 1 29 ALA 29 30 30 ALA ALA A . n A 1 30 ALA 30 31 31 ALA ALA A . n A 1 31 LEU 31 32 32 LEU LEU A . n A 1 32 GLU 32 33 33 GLU GLU A . n A 1 33 LYS 33 34 34 LYS LYS A . n A 1 34 GLY 34 35 35 GLY GLY A . n A 1 35 CYS 35 36 36 CYS CYS A . n A 1 36 SER 36 37 37 SER SER A . n A 1 37 PHE 37 38 38 PHE PHE A . n A 1 38 LEU 38 39 39 LEU LEU A . n A 1 39 PRO 39 40 40 PRO PRO A . n A 1 40 ASP 40 41 41 ASP ASP A . n A 1 41 PRO 41 42 42 PRO PRO A . n A 1 42 TYR 42 43 43 TYR TYR A . n A 1 43 GLN 43 44 44 GLN GLN A . n A 1 44 LYS 44 45 45 LYS LYS A . n A 1 45 GLN 45 46 46 GLN GLN A . n A 1 46 CYS 46 47 47 CYS CYS A . n A 1 47 ASP 47 48 48 ASP ASP A . n A 1 48 GLN 48 49 49 GLN GLN A . n A 1 49 PHE 49 50 50 PHE PHE A . n A 1 50 VAL 50 51 51 VAL VAL A . n A 1 51 ALA 51 52 52 ALA ALA A . n A 1 52 GLU 52 53 53 GLU GLU A . n A 1 53 IYR 53 54 54 IYR IYR A . n A 1 54 GLU 54 55 55 GLU GLU A . n A 1 55 PRO 55 56 56 PRO PRO A . n A 1 56 VAL 56 57 57 VAL VAL A . n A 1 57 LEU 57 58 58 LEU LEU A . n A 1 58 ILE 58 59 59 ILE ILE A . n A 1 59 GLU 59 60 60 GLU GLU A . n A 1 60 ILE 60 61 61 ILE ILE A . n A 1 61 LEU 61 62 62 LEU LEU A . n A 1 62 VAL 62 63 63 VAL VAL A . n A 1 63 GLU 63 64 64 GLU GLU A . n A 1 64 VAL 64 65 65 VAL VAL A . n A 1 65 MET 65 66 66 MET MET A . n A 1 66 ASP 66 67 67 ASP ASP A . n A 1 67 PRO 67 68 68 PRO PRO A . n A 1 68 SER 68 69 69 SER SER A . n A 1 69 PHE 69 70 70 PHE PHE A . n A 1 70 VAL 70 71 71 VAL VAL A . n A 1 71 CYS 71 72 72 CYS CYS A . n A 1 72 LEU 72 73 73 LEU LEU A . n A 1 73 LYS 73 74 74 LYS LYS A . n A 1 74 ILE 74 75 75 ILE ILE A . n A 1 75 GLY 75 76 76 GLY GLY A . n A 1 76 ALA 76 77 77 ALA ALA A . n A 1 77 CYS 77 78 78 CYS CYS A . n A 1 78 PRO 78 79 79 PRO PRO A . n A 1 79 SER 79 80 ? ? ? A . n A 1 80 HIS 80 81 ? ? ? A . n A 1 81 HIS 81 82 ? ? ? A . n A 1 82 HIS 82 83 ? ? ? A . n A 1 83 HIS 83 84 ? ? ? A . n A 1 84 HIS 84 85 ? ? ? A . n A 1 85 HIS 85 86 ? ? ? 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 HOH 1 87 1 HOH HOH A . B 2 HOH 2 88 2 HOH HOH A . B 2 HOH 3 89 4 HOH HOH A . B 2 HOH 4 90 5 HOH HOH A . B 2 HOH 5 91 6 HOH HOH A . B 2 HOH 6 92 7 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id IYR _pdbx_struct_mod_residue.label_seq_id 53 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id IYR _pdbx_struct_mod_residue.auth_seq_id 54 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id TYR _pdbx_struct_mod_residue.details 3-IODO-TYROSINE # _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 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 # 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' 3_655 -x+1,y,-z+1/2 -1.0000000000 0.0000000000 0.0000000000 40.4650000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 33.3955000000 # 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 2008-04-29 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 3 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal DENZO . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data reduction' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 2 REFMAC . ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 3 PDB_EXTRACT 3.000 'July 2, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 4 MAR345dtb . ? ? ? ? 'data collection' ? ? ? 5 AMoRE . ? ? ? ? phasing ? ? ? 6 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 LYS A 21 ? ? -62.35 8.29 2 1 PRO A 40 ? ? -47.41 151.91 # 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 SER 80 ? A SER 79 2 1 Y 1 A HIS 81 ? A HIS 80 3 1 Y 1 A HIS 82 ? A HIS 81 4 1 Y 1 A HIS 83 ? A HIS 82 5 1 Y 1 A HIS 84 ? A HIS 83 6 1 Y 1 A HIS 85 ? A HIS 84 7 1 Y 1 A HIS 86 ? A HIS 85 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #