data_6DIX # _entry.id 6DIX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 6DIX pdb_00006dix 10.2210/pdb6dix/pdb WWPDB D_1000234726 ? ? # 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 2018-10-31 2 'Structure model' 1 1 2018-11-07 3 'Structure model' 1 2 2019-01-02 4 'Structure model' 1 3 2019-12-18 5 'Structure model' 1 4 2020-01-15 6 'Structure model' 1 5 2024-03-13 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 4 'Structure model' 'Author supporting evidence' 6 5 'Structure model' 'Data collection' 7 6 'Structure model' 'Data collection' 8 6 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' citation 4 4 'Structure model' pdbx_audit_support 5 5 'Structure model' reflns_shell 6 6 'Structure model' chem_comp_atom 7 6 'Structure model' chem_comp_bond 8 6 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_abbrev' 2 2 'Structure model' '_citation.pdbx_database_id_DOI' 3 2 'Structure model' '_citation.pdbx_database_id_PubMed' 4 2 'Structure model' '_citation.title' 5 3 'Structure model' '_citation.journal_volume' 6 3 'Structure model' '_citation.page_first' 7 3 'Structure model' '_citation.page_last' 8 3 'Structure model' '_citation.title' 9 4 'Structure model' '_pdbx_audit_support.funding_organization' 10 5 'Structure model' '_reflns_shell.percent_possible_all' 11 6 'Structure model' '_database_2.pdbx_DOI' 12 6 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6DIX _pdbx_database_status.recvd_initial_deposition_date 2018-05-23 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 _audit_author.identifier_ORCID 'Brumshtein, B.' 1 ? 'Esswein, S.R.' 2 ? 'Sawaya, M.R.' 3 ? 'Eisenberg, D.S.' 4 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'J. Biol. Chem.' _citation.journal_id_ASTM JBCHA3 _citation.journal_id_CSD 0071 _citation.journal_id_ISSN 1083-351X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 293 _citation.language ? _citation.page_first 19659 _citation.page_last 19671 _citation.title ;Identification of two principal amyloid-driving segments in variable domains of Ig light chains in systemic light-chain amyloidosis. ; _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1074/jbc.RA118.004142 _citation.pdbx_database_id_PubMed 30355736 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Brumshtein, B.' 1 ? primary 'Esswein, S.R.' 2 0000-0002-5142-0190 primary 'Sawaya, M.R.' 3 ? primary 'Rosenberg, G.' 4 ? primary 'Ly, A.T.' 5 ? primary 'Landau, M.' 6 ? primary 'Eisenberg, D.S.' 7 0000-0003-2432-5419 # 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 'NFVFGT Immunoglobulin Light-Chain Variable Domain' 683.752 4 ? ? ? ? 2 water nat water 18.015 18 ? ? ? ? # _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 NFVFGT _entity_poly.pdbx_seq_one_letter_code_can NFVFGT _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASN n 1 2 PHE n 1 3 VAL n 1 4 PHE n 1 5 GLY n 1 6 THR 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 6 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # 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 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # 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 ASN 1 98 98 ASN ASN A . n A 1 2 PHE 2 99 99 PHE PHE A . n A 1 3 VAL 3 100 100 VAL VAL A . n A 1 4 PHE 4 101 101 PHE PHE A . n A 1 5 GLY 5 102 102 GLY GLY A . n A 1 6 THR 6 103 103 THR THR A . n B 1 1 ASN 1 98 98 ASN ASN B . n B 1 2 PHE 2 99 99 PHE PHE B . n B 1 3 VAL 3 100 100 VAL VAL B . n B 1 4 PHE 4 101 101 PHE PHE B . n B 1 5 GLY 5 102 102 GLY GLY B . n B 1 6 THR 6 103 103 THR THR B . n C 1 1 ASN 1 98 98 ASN ASN C . n C 1 2 PHE 2 99 99 PHE PHE C . n C 1 3 VAL 3 100 100 VAL VAL C . n C 1 4 PHE 4 101 101 PHE PHE C . n C 1 5 GLY 5 102 102 GLY GLY C . n C 1 6 THR 6 103 103 THR THR C . n D 1 1 ASN 1 98 98 ASN ASN D . n D 1 2 PHE 2 99 99 PHE PHE D . n D 1 3 VAL 3 100 100 VAL VAL D . n D 1 4 PHE 4 101 101 PHE PHE D . n D 1 5 GLY 5 102 102 GLY GLY D . n D 1 6 THR 6 103 103 THR THR D . 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 E 2 HOH 1 201 4 HOH HOH A . E 2 HOH 2 202 2 HOH HOH A . E 2 HOH 3 203 18 HOH HOH A . E 2 HOH 4 204 12 HOH HOH A . E 2 HOH 5 205 13 HOH HOH A . F 2 HOH 1 201 6 HOH HOH B . F 2 HOH 2 202 7 HOH HOH B . F 2 HOH 3 203 3 HOH HOH B . F 2 HOH 4 204 8 HOH HOH B . F 2 HOH 5 205 17 HOH HOH B . F 2 HOH 6 206 14 HOH HOH B . G 2 HOH 1 201 9 HOH HOH C . G 2 HOH 2 202 5 HOH HOH C . H 2 HOH 1 201 10 HOH HOH D . H 2 HOH 2 202 11 HOH HOH D . H 2 HOH 3 203 1 HOH HOH D . H 2 HOH 4 204 15 HOH HOH D . H 2 HOH 5 205 16 HOH HOH D . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? . 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.24 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXD ? ? ? . 5 # _cell.angle_alpha 90.890 _cell.angle_alpha_esd ? _cell.angle_beta 103.230 _cell.angle_beta_esd ? _cell.angle_gamma 90.260 _cell.angle_gamma_esd ? _cell.entry_id 6DIX _cell.details ? _cell.formula_units_Z ? _cell.length_a 16.030 _cell.length_a_esd ? _cell.length_b 11.660 _cell.length_b_esd ? _cell.length_c 21.940 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DIX _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 6DIX _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.46 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 15.72 _exptl_crystal.description rod _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 8.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.1 M Imidazole, 20% PEG 3000, 0.2 M Zinc Acetate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 6M-F' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-03-06 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Cryo-cooled-double crystal' _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9717 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 24-ID-C' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9717 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 24-ID-C _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 8.571 _reflns.entry_id 6DIX _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.000 _reflns.d_resolution_low 21.350 _reflns.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.number_all ? _reflns.number_obs 6835 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 81.800 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.424 _reflns.pdbx_Rmerge_I_obs 0.066 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 12.830 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.025 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.077 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.997 _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 1.000 1.070 ? 6.730 ? ? ? ? 926 60.400 ? ? ? ? 0.124 ? ? ? ? ? ? ? ? 3.177 ? ? ? ? 0.148 ? ? 1 1 0.982 ? 1.070 2.300 ? 13.090 ? ? ? ? 5295 86.200 ? ? ? ? 0.068 ? ? ? ? ? ? ? ? 3.446 ? ? ? ? 0.080 ? ? 2 1 0.996 ? 2.300 3.000 ? 19.810 ? ? ? ? 337 91.300 ? ? ? ? 0.059 ? ? ? ? ? ? ? ? 3.611 ? ? ? ? 0.069 ? ? 3 1 0.997 ? 3.000 5.000 ? 19.800 ? ? ? ? 211 86.100 ? ? ? ? 0.065 ? ? ? ? ? ? ? ? 3.588 ? ? ? ? 0.076 ? ? 4 1 0.996 ? 5.000 8.000 ? 20.220 ? ? ? ? 52 100.000 ? ? ? ? 0.048 ? ? ? ? ? ? ? ? 3.673 ? ? ? ? 0.057 ? ? 5 1 0.999 ? 8.000 10.000 ? 19.200 ? ? ? ? 6 75.000 ? ? ? ? 0.111 ? ? ? ? ? ? ? ? 3.333 ? ? ? ? 0.129 ? ? 6 1 0.964 ? 10.000 21.350 ? 20.230 ? ? ? ? 8 100.000 ? ? ? ? 0.043 ? ? ? ? ? ? ? ? 3.500 ? ? ? ? 0.050 ? ? 7 1 0.998 ? # _refine.aniso_B[1][1] -0.3800 _refine.aniso_B[1][2] -0.2400 _refine.aniso_B[1][3] -0.1800 _refine.aniso_B[2][2] -0.0300 _refine.aniso_B[2][3] -0.0200 _refine.aniso_B[3][3] 0.4500 _refine.B_iso_max 35.600 _refine.B_iso_mean 7.4880 _refine.B_iso_min 2.830 _refine.correlation_coeff_Fo_to_Fc 0.9820 _refine.correlation_coeff_Fo_to_Fc_free 0.9710 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 6DIX _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.0000 _refine.ls_d_res_low 21.3500 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 6154 _refine.ls_number_reflns_R_free 684 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 81.8300 _refine.ls_percent_reflns_R_free 10.0000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1048 _refine.ls_R_factor_R_free 0.1247 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1025 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _refine.pdbx_starting_model 'NO Starting model, We used DIRECT METHODS' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.0260 _refine.pdbx_overall_ESU_R_Free 0.0260 _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI 0.0262 _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.0000 _refine_hist.d_res_low 21.3500 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 18 _refine_hist.number_atoms_total 214 _refine_hist.pdbx_number_residues_total 24 _refine_hist.pdbx_B_iso_mean_solvent 21.32 _refine_hist.pdbx_number_atoms_protein 196 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.009 0.013 210 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.000 0.018 184 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.589 1.688 286 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 1.477 1.685 418 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? 8.046 5.000 24 ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? 39.969 23.333 12 ? r_dihedral_angle_2_deg ? ? 'X-RAY DIFFRACTION' ? 12.470 15.000 22 ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? 0.086 0.200 26 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.009 0.020 242 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.010 0.020 62 ? r_gen_planes_other ? ? 'X-RAY DIFFRACTION' ? 20.279 3.000 394 ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? 17.741 5.000 9 ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? 6.447 5.000 397 ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.0000 _refine_ls_shell.d_res_low 1.0260 _refine_ls_shell.number_reflns_all 277 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 28 _refine_ls_shell.number_reflns_R_work 249 _refine_ls_shell.percent_reflns_obs 46.7100 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.1230 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.1450 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 6DIX _struct.title 'NFVFGT segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 98-103, assembled as an amyloid fibril' _struct.pdbx_model_details 'NFVFGT segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 98-103, assembled as an amyloid fibril' _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6DIX _struct_keywords.text 'amyloid fibril, PROTEIN FIBRIL' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # 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 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6DIX _struct_ref.pdbx_db_accession 6DIX _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 6DIX A 1 ? 6 ? 6DIX 98 ? 103 ? 98 103 2 1 6DIX B 1 ? 6 ? 6DIX 98 ? 103 ? 98 103 3 1 6DIX C 1 ? 6 ? 6DIX 98 ? 103 ? 98 103 4 1 6DIX D 1 ? 6 ? 6DIX 98 ? 103 ? 98 103 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # 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_445 x-1,y-1,z 1.0000000000 0.0000000000 0.0000000000 -15.9770887800 0.0000000000 1.0000000000 0.0000000000 -11.6598799480 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_565 x,y+1,z 1.0000000000 0.0000000000 0.0000000000 -0.0529112200 0.0000000000 1.0000000000 0.0000000000 11.6598799480 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 1_455 x-1,y,z 1.0000000000 0.0000000000 0.0000000000 -16.0300000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 4 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 VAL B 3 ? GLY B 5 ? VAL B 100 GLY B 102 AA1 2 PHE A 2 ? GLY A 5 ? PHE A 99 GLY A 102 AA1 3 PHE D 2 ? GLY D 5 ? PHE D 99 GLY D 102 AA1 4 VAL C 3 ? GLY C 5 ? VAL C 100 GLY C 102 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 O PHE B 4 ? O PHE B 101 N PHE A 4 ? N PHE A 101 AA1 2 3 N GLY A 5 ? N GLY A 102 O PHE D 2 ? O PHE D 99 AA1 3 4 O VAL D 3 ? O VAL D 100 N GLY C 5 ? N GLY C 102 # 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 ASN N N N N 1 ASN CA C N S 2 ASN C C N N 3 ASN O O N N 4 ASN CB C N N 5 ASN CG C N N 6 ASN OD1 O N N 7 ASN ND2 N N N 8 ASN OXT O N N 9 ASN H H N N 10 ASN H2 H N N 11 ASN HA H N N 12 ASN HB2 H N N 13 ASN HB3 H N N 14 ASN HD21 H N N 15 ASN HD22 H N N 16 ASN HXT H N N 17 GLY N N N N 18 GLY CA C N N 19 GLY C C N N 20 GLY O O N N 21 GLY OXT O N N 22 GLY H H N N 23 GLY H2 H N N 24 GLY HA2 H N N 25 GLY HA3 H N N 26 GLY HXT H N N 27 HOH O O N N 28 HOH H1 H N N 29 HOH H2 H N N 30 PHE N N N N 31 PHE CA C N S 32 PHE C C N N 33 PHE O O N N 34 PHE CB C N N 35 PHE CG C Y N 36 PHE CD1 C Y N 37 PHE CD2 C Y N 38 PHE CE1 C Y N 39 PHE CE2 C Y N 40 PHE CZ C Y N 41 PHE OXT O N N 42 PHE H H N N 43 PHE H2 H N N 44 PHE HA H N N 45 PHE HB2 H N N 46 PHE HB3 H N N 47 PHE HD1 H N N 48 PHE HD2 H N N 49 PHE HE1 H N N 50 PHE HE2 H N N 51 PHE HZ H N N 52 PHE HXT H N N 53 THR N N N N 54 THR CA C N S 55 THR C C N N 56 THR O O N N 57 THR CB C N R 58 THR OG1 O N N 59 THR CG2 C N N 60 THR OXT O N N 61 THR H H N N 62 THR H2 H N N 63 THR HA H N N 64 THR HB H N N 65 THR HG1 H N N 66 THR HG21 H N N 67 THR HG22 H N N 68 THR HG23 H N N 69 THR HXT H N N 70 VAL N N N N 71 VAL CA C N S 72 VAL C C N N 73 VAL O O N N 74 VAL CB C N N 75 VAL CG1 C N N 76 VAL CG2 C N N 77 VAL OXT O N N 78 VAL H H N N 79 VAL H2 H N N 80 VAL HA H N N 81 VAL HB H N N 82 VAL HG11 H N N 83 VAL HG12 H N N 84 VAL HG13 H N N 85 VAL HG21 H N N 86 VAL HG22 H N N 87 VAL HG23 H N N 88 VAL HXT H N N 89 # 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 ASN N CA sing N N 1 ASN N H sing N N 2 ASN N H2 sing N N 3 ASN CA C sing N N 4 ASN CA CB sing N N 5 ASN CA HA sing N N 6 ASN C O doub N N 7 ASN C OXT sing N N 8 ASN CB CG sing N N 9 ASN CB HB2 sing N N 10 ASN CB HB3 sing N N 11 ASN CG OD1 doub N N 12 ASN CG ND2 sing N N 13 ASN ND2 HD21 sing N N 14 ASN ND2 HD22 sing N N 15 ASN OXT HXT sing N N 16 GLY N CA sing N N 17 GLY N H sing N N 18 GLY N H2 sing N N 19 GLY CA C sing N N 20 GLY CA HA2 sing N N 21 GLY CA HA3 sing N N 22 GLY C O doub N N 23 GLY C OXT sing N N 24 GLY OXT HXT sing N N 25 HOH O H1 sing N N 26 HOH O H2 sing N N 27 PHE N CA sing N N 28 PHE N H sing N N 29 PHE N H2 sing N N 30 PHE CA C sing N N 31 PHE CA CB sing N N 32 PHE CA HA sing N N 33 PHE C O doub N N 34 PHE C OXT sing N N 35 PHE CB CG sing N N 36 PHE CB HB2 sing N N 37 PHE CB HB3 sing N N 38 PHE CG CD1 doub Y N 39 PHE CG CD2 sing Y N 40 PHE CD1 CE1 sing Y N 41 PHE CD1 HD1 sing N N 42 PHE CD2 CE2 doub Y N 43 PHE CD2 HD2 sing N N 44 PHE CE1 CZ doub Y N 45 PHE CE1 HE1 sing N N 46 PHE CE2 CZ sing Y N 47 PHE CE2 HE2 sing N N 48 PHE CZ HZ sing N N 49 PHE OXT HXT sing N N 50 THR N CA sing N N 51 THR N H sing N N 52 THR N H2 sing N N 53 THR CA C sing N N 54 THR CA CB sing N N 55 THR CA HA sing N N 56 THR C O doub N N 57 THR C OXT sing N N 58 THR CB OG1 sing N N 59 THR CB CG2 sing N N 60 THR CB HB sing N N 61 THR OG1 HG1 sing N N 62 THR CG2 HG21 sing N N 63 THR CG2 HG22 sing N N 64 THR CG2 HG23 sing N N 65 THR OXT HXT sing N N 66 VAL N CA sing N N 67 VAL N H sing N N 68 VAL N H2 sing N N 69 VAL CA C sing N N 70 VAL CA CB sing N N 71 VAL CA HA sing N N 72 VAL C O doub N N 73 VAL C OXT sing N N 74 VAL CB CG1 sing N N 75 VAL CB CG2 sing N N 76 VAL CB HB sing N N 77 VAL CG1 HG11 sing N N 78 VAL CG1 HG12 sing N N 79 VAL CG1 HG13 sing N N 80 VAL CG2 HG21 sing N N 81 VAL CG2 HG22 sing N N 82 VAL CG2 HG23 sing N N 83 VAL OXT HXT sing N N 84 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute on Aging (NIH/NIA)' 'United States' 1R01AG048120-01 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' 'P41 GM103403' 2 # _atom_sites.entry_id 6DIX _atom_sites.fract_transf_matrix[1][1] 0.062383 _atom_sites.fract_transf_matrix[1][2] 0.000279 _atom_sites.fract_transf_matrix[1][3] 0.014669 _atom_sites.fract_transf_matrix[2][1] -0.000000 _atom_sites.fract_transf_matrix[2][2] 0.085764 _atom_sites.fract_transf_matrix[2][3] 0.001460 _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] 0.046828 _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 H N O # loop_