data_4RIL # _entry.id 4RIL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 4RIL pdb_00004ril 10.2210/pdb4ril/pdb RCSB RCSB087390 ? ? WWPDB D_1000087390 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.db_id EMD-3028 _pdbx_database_related.details . _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.entry_id 4RIL _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-10-06 _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 _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Rodriguez, J.A.' 1 'Ivanova, M.' 2 'Sawaya, M.R.' 3 'Cascio, D.' 4 'Reyes, F.' 5 'Shi, D.' 6 'Johnson, L.' 7 'Guenther, E.' 8 'Sangwan, S.' 9 'Hattne, J.' 10 'Nannenga, B.' 11 'Brewster, A.S.' 12 'Messerschmidt, M.' 13 'Boutet, S.' 14 'Sauter, N.K.' 15 'Gonen, T.' 16 'Eisenberg, D.S.' 17 # _citation.id primary _citation.title 'Structure of the toxic core of alpha-synuclein from invisible crystals.' _citation.journal_abbrev Nature _citation.journal_volume 525 _citation.page_first 486 _citation.page_last 490 _citation.year 2015 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 26352473 _citation.pdbx_database_id_DOI 10.1038/nature15368 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Rodriguez, J.A.' 1 ? primary 'Ivanova, M.I.' 2 ? primary 'Sawaya, M.R.' 3 ? primary 'Cascio, D.' 4 ? primary 'Reyes, F.E.' 5 ? primary 'Shi, D.' 6 ? primary 'Sangwan, S.' 7 ? primary 'Guenther, E.L.' 8 ? primary 'Johnson, L.M.' 9 ? primary 'Zhang, M.' 10 ? primary 'Jiang, L.' 11 ? primary 'Arbing, M.A.' 12 ? primary 'Nannenga, B.L.' 13 ? primary 'Hattne, J.' 14 ? primary 'Whitelegge, J.' 15 ? primary 'Brewster, A.S.' 16 ? primary 'Messerschmidt, M.' 17 ? primary 'Boutet, S.' 18 ? primary 'Sauter, N.K.' 19 ? primary 'Gonen, T.' 20 ? primary 'Eisenberg, D.S.' 21 ? # _cell.entry_id 4RIL _cell.length_a 70.810 _cell.length_b 4.820 _cell.length_c 16.790 _cell.angle_alpha 90.00 _cell.angle_beta 105.68 _cell.angle_gamma 90.00 _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 4RIL _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _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 syn Alpha-synuclein 944.083 1 ? ? ? ? 2 water nat water 18.015 2 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Non-A beta component of AD amyloid, Non-A4 component of amyloid precursor, NACP' # _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 GAVVTGVTAVA _entity_poly.pdbx_seq_one_letter_code_can GAVVTGVTAVA _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 ALA n 1 3 VAL n 1 4 VAL n 1 5 THR n 1 6 GLY n 1 7 VAL n 1 8 THR n 1 9 ALA n 1 10 VAL n 1 11 ALA n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details 'Synthetic peptide GAVVTGVTAVA corresponding to segment 68-78 of human alpha-synuclein' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SYUA_HUMAN _struct_ref.pdbx_db_accession P37840 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GAVVTGVTAVA _struct_ref.pdbx_align_begin 68 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4RIL _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 11 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P37840 _struct_ref_seq.db_align_beg 68 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 78 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 68 _struct_ref_seq.pdbx_auth_seq_align_end 78 # 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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 4 _exptl.entry_id 4RIL _exptl.method 'ELECTRON CRYSTALLOGRAPHY' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.46 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 15.81 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'batch crystallization' _exptl_crystal_grow.pH 4.0 _exptl_crystal_grow.temp 310 _exptl_crystal_grow.pdbx_details ;1 mg of synthetic peptide GAVVTGVTAVA was dissolved in 1 ml of sterile water and shaken overnight in an orbital mixing plate, pH 4.0, batch crystallization, temperature 310K ; _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.pdbx_serial_crystal_experiment ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CMOS _diffrn_detector.type 'TVIPS F416 CMOS CAMERA' _diffrn_detector.pdbx_collection_date 2014-08-28 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type electron # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.0251 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ELECTRON MICROSCOPE' _diffrn_source.type 'TECNAI F20 TEM' _diffrn_source.pdbx_wavelength_list 0.0251 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.d_resolution_high 1.430 _reflns.d_resolution_low 16.430 _reflns.number_obs 1073 _reflns.pdbx_Rmerge_I_obs 0.175 _reflns.pdbx_netI_over_sigmaI 5.500 _reflns.pdbx_redundancy 4.400 _reflns.percent_possible_obs 89.900 _reflns.B_iso_Wilson_estimate 10.330 _reflns.entry_id 4RIL _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all 1073 _reflns.pdbx_Rsym_value ? _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 # 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_ordinal _reflns_shell.pdbx_diffrn_id 1.430 1.600 ? 1245 ? 0.565 2.500 ? ? 4.400 ? 286 82.500 1 1 3.200 16.430 ? 478 ? 0.080 13.000 ? ? 3.800 ? 126 94.000 2 1 # _refine.entry_id 4RIL _refine.ls_d_res_high 1.4300 _refine.ls_d_res_low 16.4300 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 87.8800 _refine.ls_number_reflns_obs 1073 _refine.ls_number_reflns_all 1073 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ? _refine.ls_R_factor_all 0.2512 _refine.ls_R_factor_obs 0.2512 _refine.ls_R_factor_R_work 0.2483 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2750 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 11.8400 _refine.ls_number_reflns_R_free 127 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 12.7500 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -3.9876 _refine.aniso_B[2][2] 3.4908 _refine.aniso_B[3][3] 0.4968 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -1.5509 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9126 _refine.correlation_coeff_Fo_to_Fc_free 0.9002 _refine.overall_SU_R_Cruickshank_DPI 0.1080 _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.solvent_model_details ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 4RIK _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 74.500 _refine.B_iso_min 3.000 _refine.pdbx_overall_phase_error ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 4RIL _refine_analyze.Luzzati_coordinate_error_obs 0.305 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' # _refine_hist.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 66 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 68 _refine_hist.d_res_high 1.4300 _refine_hist.d_res_low 16.4300 # 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_restraint_function _refine_ls_restr.pdbx_refine_id t_dihedral_angle_d 16 ? ? 2.000 SINUSOIDAL 'ELECTRON CRYSTALLOGRAPHY' t_trig_c_planes 1 ? ? 2.000 HARMONIC 'ELECTRON CRYSTALLOGRAPHY' t_gen_planes 10 ? ? 5.000 HARMONIC 'ELECTRON CRYSTALLOGRAPHY' t_it 65 ? ? 20.000 HARMONIC 'ELECTRON CRYSTALLOGRAPHY' t_nbd ? ? ? ? ? 'ELECTRON CRYSTALLOGRAPHY' t_improper_torsion ? ? ? ? ? 'ELECTRON CRYSTALLOGRAPHY' t_pseud_angle ? ? ? ? ? 'ELECTRON CRYSTALLOGRAPHY' t_chiral_improper_torsion 11 ? ? 5.000 SEMIHARMONIC 'ELECTRON CRYSTALLOGRAPHY' t_sum_occupancies ? ? ? ? ? 'ELECTRON CRYSTALLOGRAPHY' t_utility_distance ? ? ? ? ? 'ELECTRON CRYSTALLOGRAPHY' t_utility_angle ? ? ? ? ? 'ELECTRON CRYSTALLOGRAPHY' t_utility_torsion ? ? ? ? ? 'ELECTRON CRYSTALLOGRAPHY' t_ideal_dist_contact 76 ? ? 4.000 SEMIHARMONIC 'ELECTRON CRYSTALLOGRAPHY' t_bond_d 65 0.010 ? 2.000 HARMONIC 'ELECTRON CRYSTALLOGRAPHY' t_angle_deg 90 1.650 ? 2.000 HARMONIC 'ELECTRON CRYSTALLOGRAPHY' t_omega_torsion ? 4.080 ? ? ? 'ELECTRON CRYSTALLOGRAPHY' t_other_torsion ? 6.490 ? ? ? 'ELECTRON CRYSTALLOGRAPHY' # _refine_ls_shell.d_res_high 1.4300 _refine_ls_shell.d_res_low 1.6000 _refine_ls_shell.pdbx_total_number_of_bins_used 5 _refine_ls_shell.percent_reflns_obs 87.8800 _refine_ls_shell.number_reflns_R_work 245 _refine_ls_shell.R_factor_all 0.2642 _refine_ls_shell.R_factor_R_work 0.2532 _refine_ls_shell.R_factor_R_free 0.3310 _refine_ls_shell.percent_reflns_R_free 14.3400 _refine_ls_shell.number_reflns_R_free 41 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 286 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' # _struct.entry_id 4RIL _struct.title ;Structure of the amyloid forming segment, GAVVTGVTAVA, from the NAC domain of Parkinson's disease protein alpha-synuclein, residues 68-78, determined by electron diffraction ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4RIL _struct_keywords.text ;Amyloid, alpha-synuclein, Parkinson's Disease, Toxic Core, NACore, Lipid Binding Protein ; _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 ;The biological unit is a pair of beta-sheets. One sheet is composed of chain A and unit cell translations along the b dimension. The other sheet is composed of the symmetry mate -x+1/2,y+1/2,-z, and unit cell translations along b. ; # _atom_sites.entry_id 4RIL _atom_sites.fract_transf_matrix[1][1] 0.014122 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.003964 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.207469 _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] 0.061861 _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 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 68 1 GLY GLY A . n A 1 2 ALA 2 69 2 ALA ALA A . n A 1 3 VAL 3 70 3 VAL VAL A . n A 1 4 VAL 4 71 4 VAL VAL A . n A 1 5 THR 5 72 5 THR THR A . n A 1 6 GLY 6 73 6 GLY GLY A . n A 1 7 VAL 7 74 7 VAL VAL A . n A 1 8 THR 8 75 8 THR THR A . n A 1 9 ALA 9 76 9 ALA ALA A . n A 1 10 VAL 10 77 10 VAL VAL A . n A 1 11 ALA 11 78 11 ALA ALA 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 1 101 13 HOH HOH A . B 2 HOH 2 102 14 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 decameric _pdbx_struct_assembly.oligomeric_count 10 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10 _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' 1_535 x,y-2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -9.6400000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_545 x,y-1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -4.8200000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 1_565 x,y+1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4.8200000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 5 'crystal symmetry operation' 1_575 x,y+2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 9.6400000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 6 'crystal symmetry operation' 4_535 -x+1/2,y-3/2,-z -1.0000000000 0.0000000000 0.0000000000 35.4050000000 0.0000000000 1.0000000000 0.0000000000 -7.2300000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 7 'crystal symmetry operation' 4_545 -x+1/2,y-1/2,-z -1.0000000000 0.0000000000 0.0000000000 35.4050000000 0.0000000000 1.0000000000 0.0000000000 -2.4100000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 8 'crystal symmetry operation' 4_555 -x+1/2,y+1/2,-z -1.0000000000 0.0000000000 0.0000000000 35.4050000000 0.0000000000 1.0000000000 0.0000000000 2.4100000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 9 'crystal symmetry operation' 4_565 -x+1/2,y+3/2,-z -1.0000000000 0.0000000000 0.0000000000 35.4050000000 0.0000000000 1.0000000000 0.0000000000 7.2300000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 10 'crystal symmetry operation' 4_575 -x+1/2,y+5/2,-z -1.0000000000 0.0000000000 0.0000000000 35.4050000000 0.0000000000 1.0000000000 0.0000000000 12.0500000000 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 2015-08-26 2 'Structure model' 1 1 2015-09-09 3 'Structure model' 1 2 2015-09-23 4 'Structure model' 1 3 2015-10-07 5 'Structure model' 1 4 2018-04-25 6 'Structure model' 1 5 2021-06-30 7 'Structure model' 1 6 2023-09-20 # _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' 'Database references' 4 5 'Structure model' 'Author supporting evidence' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Data processing' 7 6 'Structure model' 'Data collection' 8 7 'Structure model' 'Data collection' 9 7 'Structure model' 'Database references' 10 7 'Structure model' 'Refinement description' # 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 5 'Structure model' diffrn_source 2 5 'Structure model' em_3d_reconstruction 3 5 'Structure model' em_image_scans 4 5 'Structure model' em_single_particle_entity 5 6 'Structure model' diffrn_detector 6 7 'Structure model' chem_comp_atom 7 7 'Structure model' chem_comp_bond 8 7 'Structure model' database_2 9 7 'Structure model' pdbx_initial_refinement_model # 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 5 'Structure model' '_diffrn_source.source' 2 6 'Structure model' '_diffrn_detector.detector' 3 7 'Structure model' '_database_2.pdbx_DOI' 4 7 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_phasing_MR.entry_id 4RIL _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor ? _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation ? _pdbx_phasing_MR.d_res_low_rotation ? _pdbx_phasing_MR.d_res_high_translation ? _pdbx_phasing_MR.d_res_low_translation ? _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 Aimless 0.3.11 19/08/14 program 'Phil Evans' ? 'data scaling' http://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.html ? ? 2 PHASER 2.5.6 'Tue May 20 11:52:06 2014' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 3 BUSTER-TNT 'BUSTER 2.10.0' ? program 'Gerard Bricogne' buster-develop@GlobalPhasing.com refinement http://www.globalphasing.com/buster/ ? ? 4 PDB_EXTRACT 3.15 'July. 29, 2014' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 XDS . ? ? ? ? 'data reduction' ? ? ? 6 XSCALE . ? ? ? ? 'data scaling' ? ? ? 7 BUSTER . ? ? ? ? refinement ? ? ? # _em_entity_assembly.id 1 _em_entity_assembly.name 'amyloid forming segment GAVVTGVTAVA from the NAC domain of alpha-synuclein' _em_entity_assembly.parent_id 0 _em_entity_assembly.source . _em_entity_assembly.type COMPLEX _em_entity_assembly.details ? _em_entity_assembly.entity_id_list ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.entry_id 4RIL _em_imaging.id 1 _em_imaging.specimen_id 1 _em_imaging.accelerating_voltage 200 _em_imaging.electron_source . _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode DIFFRACTION _em_imaging.microscope_model 'FEI TECNAI F20' _em_imaging.calibrated_defocus_max ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen ? _em_imaging.details ? _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max ? _em_imaging.nominal_defocus_min ? _em_imaging.nominal_magnification ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model 'GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER' _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_vitrification.entry_id 4RIL _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity ? _em_vitrification.chamber_temperature ? _em_vitrification.details ? _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 4RIL _em_experiment.id 1 _em_experiment.entity_assembly_id 1 _em_experiment.reconstruction_method CRYSTALLOGRAPHY _em_experiment.aggregation_state '3D ARRAY' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 GLY N N N N 14 GLY CA C N N 15 GLY C C N N 16 GLY O O N N 17 GLY OXT O N N 18 GLY H H N N 19 GLY H2 H N N 20 GLY HA2 H N N 21 GLY HA3 H N N 22 GLY HXT H N N 23 HOH O O N N 24 HOH H1 H N N 25 HOH H2 H N N 26 THR N N N N 27 THR CA C N S 28 THR C C N N 29 THR O O N N 30 THR CB C N R 31 THR OG1 O N N 32 THR CG2 C N N 33 THR OXT O N N 34 THR H H N N 35 THR H2 H N N 36 THR HA H N N 37 THR HB H N N 38 THR HG1 H N N 39 THR HG21 H N N 40 THR HG22 H N N 41 THR HG23 H N N 42 THR HXT H N N 43 VAL N N N N 44 VAL CA C N S 45 VAL C C N N 46 VAL O O N N 47 VAL CB C N N 48 VAL CG1 C N N 49 VAL CG2 C N N 50 VAL OXT O N N 51 VAL H H N N 52 VAL H2 H N N 53 VAL HA H N N 54 VAL HB H N N 55 VAL HG11 H N N 56 VAL HG12 H N N 57 VAL HG13 H N N 58 VAL HG21 H N N 59 VAL HG22 H N N 60 VAL HG23 H N N 61 VAL HXT H N N 62 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 GLY N CA sing N N 13 GLY N H sing N N 14 GLY N H2 sing N N 15 GLY CA C sing N N 16 GLY CA HA2 sing N N 17 GLY CA HA3 sing N N 18 GLY C O doub N N 19 GLY C OXT sing N N 20 GLY OXT HXT sing N N 21 HOH O H1 sing N N 22 HOH O H2 sing N N 23 THR N CA sing N N 24 THR N H sing N N 25 THR N H2 sing N N 26 THR CA C sing N N 27 THR CA CB sing N N 28 THR CA HA sing N N 29 THR C O doub N N 30 THR C OXT sing N N 31 THR CB OG1 sing N N 32 THR CB CG2 sing N N 33 THR CB HB sing N N 34 THR OG1 HG1 sing N N 35 THR CG2 HG21 sing N N 36 THR CG2 HG22 sing N N 37 THR CG2 HG23 sing N N 38 THR OXT HXT sing N N 39 VAL N CA sing N N 40 VAL N H sing N N 41 VAL N H2 sing N N 42 VAL CA C sing N N 43 VAL CA CB sing N N 44 VAL CA HA sing N N 45 VAL C O doub N N 46 VAL C OXT sing N N 47 VAL CB CG1 sing N N 48 VAL CB CG2 sing N N 49 VAL CB HB sing N N 50 VAL CG1 HG11 sing N N 51 VAL CG1 HG12 sing N N 52 VAL CG1 HG13 sing N N 53 VAL CG2 HG21 sing N N 54 VAL CG2 HG22 sing N N 55 VAL CG2 HG23 sing N N 56 VAL OXT HXT sing N N 57 # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.film_or_detector_model 'TVIPS TEMCAM-F416 (4k x 4k)' _em_image_recording.avg_electron_dose_per_image .35 _em_image_recording.average_exposure_time 3.5 _em_image_recording.details ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_diffraction_images ? _em_image_recording.num_real_images ? _em_image_recording.detector_mode ? # _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.concentration . _em_specimen.vitrification_applied YES _em_specimen.staining_applied NO _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.details . # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 4RIK _pdbx_initial_refinement_model.details ? #