data_3OVJ # _entry.id 3OVJ # _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 3OVJ pdb_00003ovj 10.2210/pdb3ovj/pdb RCSB RCSB061626 ? ? WWPDB D_1000061626 ? ? # 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 2011-07-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3OVJ _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 2010-09-16 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3OW9 _pdbx_database_related.details 'Structure of an amyloid forming peptide KLVFFA from amyloid beta, alternate polymorph II' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Landau, M.' 1 'Eisenberg, D.' 2 # _citation.id primary _citation.title 'Towards a pharmacophore for amyloid.' _citation.journal_abbrev 'Plos Biol.' _citation.journal_volume 9 _citation.page_first e1001080 _citation.page_last e1001080 _citation.year 2011 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1544-9173 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21695112 _citation.pdbx_database_id_DOI 10.1371/journal.pbio.1001080 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Landau, M.' 1 ? primary 'Sawaya, M.R.' 2 ? primary 'Faull, K.F.' 3 ? primary 'Laganowsky, A.' 4 ? primary 'Jiang, L.' 5 ? primary 'Sievers, S.A.' 6 ? primary 'Liu, J.' 7 ? primary 'Barrio, J.R.' 8 ? primary 'Eisenberg, D.' 9 ? # 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 'KLVFFA hexapeptide segment from Amyloid beta' 724.909 4 ? ? 'KLVFFA (UNP residues 687-692)' ? 2 non-polymer syn '7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid' 408.406 2 ? ? ? ? 3 water nat water 18.015 11 ? ? ? ? # _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 KLVFFA _entity_poly.pdbx_seq_one_letter_code_can KLVFFA _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid' ORA 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LYS n 1 2 LEU n 1 3 VAL n 1 4 PHE n 1 5 PHE n 1 6 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 ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details 'KLVFFA (residues 16-21) from Amyloid beta, synthesized' # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 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 ORA non-polymer . '7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid' 'Orange G' 'C16 H12 N2 O7 S2' 408.406 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 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 LYS 1 1 1 LYS LYS A . n A 1 2 LEU 2 2 2 LEU LEU A . n A 1 3 VAL 3 3 3 VAL VAL A . n A 1 4 PHE 4 4 4 PHE PHE A . n A 1 5 PHE 5 5 5 PHE PHE A . n A 1 6 ALA 6 6 6 ALA ALA A . n B 1 1 LYS 1 1 1 LYS LYS B . n B 1 2 LEU 2 2 2 LEU LEU B . n B 1 3 VAL 3 3 3 VAL VAL B . n B 1 4 PHE 4 4 4 PHE PHE B . n B 1 5 PHE 5 5 5 PHE PHE B . n B 1 6 ALA 6 6 6 ALA ALA B . n C 1 1 LYS 1 1 1 LYS LYS C . n C 1 2 LEU 2 2 2 LEU LEU C . n C 1 3 VAL 3 3 3 VAL VAL C . n C 1 4 PHE 4 4 4 PHE PHE C . n C 1 5 PHE 5 5 5 PHE PHE C . n C 1 6 ALA 6 6 6 ALA ALA C . n D 1 1 LYS 1 1 1 LYS LYS D . n D 1 2 LEU 2 2 2 LEU LEU D . n D 1 3 VAL 3 3 3 VAL VAL D . n D 1 4 PHE 4 4 4 PHE PHE D . n D 1 5 PHE 5 5 5 PHE PHE D . n D 1 6 ALA 6 6 6 ALA ALA 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 ORA 1 49 49 ORA ORA B . F 2 ORA 1 50 50 ORA ORA D . G 3 HOH 1 7 1 HOH HOH A . H 3 HOH 1 7 7 HOH HOH B . H 3 HOH 2 8 8 HOH HOH B . H 3 HOH 3 9 9 HOH HOH B . H 3 HOH 4 10 3 HOH HOH B . H 3 HOH 5 11 11 HOH HOH B . H 3 HOH 6 12 4 HOH HOH B . H 3 HOH 7 13 5 HOH HOH B . H 3 HOH 8 14 6 HOH HOH B . I 3 HOH 1 10 10 HOH HOH C . J 3 HOH 1 7 2 HOH HOH D . # 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 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 PHASER 2.1.4 'Wed Jun 24 14:00:05 2009' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 3 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 ADSC Quantum ? ? ? ? 'data collection' ? ? ? 6 DENZO . ? ? ? ? 'data reduction' ? ? ? # _cell.length_a 9.536 _cell.length_b 26.008 _cell.length_c 25.803 _cell.angle_alpha 62.280 _cell.angle_beta 88.590 _cell.angle_gamma 88.450 _cell.entry_id 3OVJ _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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 'P 1' _symmetry.entry_id 3OVJ _symmetry.Int_Tables_number 1 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 2 _exptl.entry_id 3OVJ _exptl.method 'X-RAY DIFFRACTION' # loop_ _exptl_crystal.id _exptl_crystal.density_Matthews _exptl_crystal.density_meas _exptl_crystal.density_percent_sol _exptl_crystal.description _exptl_crystal.F_000 _exptl_crystal.preparation 1 1.95 ? 37.01 ? ? ? 2 ? ? ? ? ? ? # loop_ _exptl_crystal_grow.crystal_id _exptl_crystal_grow.method _exptl_crystal_grow.pH _exptl_crystal_grow.temp _exptl_crystal_grow.pdbx_details _exptl_crystal_grow.temp_details _exptl_crystal_grow.pdbx_pH_range 1 'VAPOR DIFFUSION, HANGING DROP' ? 291 'reservoir contained 30% w/v Polyethylene glycol 1,500, 20% v/v Glycerol, vapor diffusion, hanging drop, temperature 291K' ? ? 2 'VAPOR DIFFUSION, HANGING DROP' ? 291 'reservoir contained 10% w/v Polyethylene glycol 1,500, 30% v/v Glycerol, vapor diffusion, hanging drop, temperature 291K' ? ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 2 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'ADSC QUANTUM 315' 2008-11-16 ? 2 CCD 'ADSC QUANTUM 315' 2009-11-13 ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.monochromator _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.pdbx_scattering_type 1 'SINGLE WAVELENGTH' ? 1 M x-ray 2 'SINGLE WAVELENGTH' ? 1 M x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9792 _diffrn_radiation_wavelength.wt 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_wavelength_list _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline 1 SYNCHROTRON 'APS BEAMLINE 24-ID-E' 0.9792 ? APS 24-ID-E 2 SYNCHROTRON 'APS BEAMLINE 24-ID-E' 0.9792 ? APS 24-ID-E # _reflns.entry_id 3OVJ _reflns.d_resolution_high 1.800 _reflns.d_resolution_low 90.000 _reflns.number_obs 1870 _reflns.pdbx_Rmerge_I_obs 0.189 _reflns.pdbx_netI_over_sigmaI 8.200 _reflns.pdbx_chi_squared 1.054 _reflns.pdbx_redundancy 3.800 _reflns.percent_possible_obs 91.500 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3 _reflns.number_all 1870 _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate 22.6 _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_ordinal 1 _reflns.pdbx_diffrn_id 1,2 # 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 1.800 1.940 ? ? ? 0.414 ? ? 1.030 1.700 ? 304 71.700 1 1,2 1.940 2.130 ? ? ? 0.365 ? ? 1.034 2.100 ? 367 92.700 2 1,2 2.130 2.440 ? ? ? 0.387 ? ? 1.048 4.100 ? 402 96.200 3 1,2 2.440 3.080 ? ? ? 0.307 ? ? 1.069 5.000 ? 403 99.800 4 1,2 3.080 90.000 ? ? ? 0.163 ? ? 1.053 5.400 ? 394 98.000 5 1,2 # _refine.entry_id 3OVJ _refine.ls_d_res_high 1.8000 _refine.ls_d_res_low 23.0200 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 91.8700 _refine.ls_number_reflns_obs 1864 _refine.ls_number_reflns_all 1864 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _refine.ls_R_factor_all 0.2067 _refine.ls_R_factor_obs 0.2067 _refine.ls_R_factor_R_work 0.2054 _refine.ls_wR_factor_R_work 0.2255 _refine.ls_R_factor_R_free 0.2195 _refine.ls_wR_factor_R_free 0.2335 _refine.ls_percent_reflns_R_free 9.2000 _refine.ls_number_reflns_R_free 172 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 16.4603 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.3000 _refine.aniso_B[2][2] -0.1000 _refine.aniso_B[3][3] 0.5200 _refine.aniso_B[1][2] -0.0700 _refine.aniso_B[1][3] 0.0300 _refine.aniso_B[2][3] -0.1100 _refine.correlation_coeff_Fo_to_Fc 0.9520 _refine.correlation_coeff_Fo_to_Fc_free 0.9320 _refine.overall_SU_R_Cruickshank_DPI 0.2654 _refine.overall_SU_R_free 0.1689 _refine.pdbx_overall_ESU_R_Free 0.1690 _refine.overall_SU_ML 0.1280 _refine.overall_SU_B 4.5280 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.8240 _refine.B_iso_max 39.530 _refine.B_iso_min 4.630 _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1,2 _refine.pdbx_overall_ESU_R ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 208 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 54 _refine_hist.number_atoms_solvent 11 _refine_hist.number_atoms_total 273 _refine_hist.d_res_high 1.8000 _refine_hist.d_res_low 23.0200 # 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 270 0.011 0.023 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 166 0.005 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 368 1.690 2.229 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 392 0.690 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 20 6.107 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 8 37.050 20.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 36 17.862 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 36 0.091 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 262 0.007 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 78 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 120 1.214 1.500 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 44 0.260 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 188 2.110 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 150 3.191 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 180 5.097 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.8030 _refine_ls_shell.d_res_low 2.0150 _refine_ls_shell.pdbx_total_number_of_bins_used 5 _refine_ls_shell.percent_reflns_obs 79.8600 _refine_ls_shell.number_reflns_R_work 434 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2890 _refine_ls_shell.R_factor_R_free 0.3660 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 26 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 460 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3OVJ _struct.title 'Structure of an amyloid forming peptide KLVFFA from amyloid beta in complex with orange G' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3OVJ _struct_keywords.text 'amyloid-like protofibril, 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 3 ? H N N 3 ? I N N 3 ? J N N 3 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A4_HUMAN _struct_ref.pdbx_db_accession P05067 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code KLVFFA _struct_ref.pdbx_align_begin 687 _struct_ref.pdbx_db_isoform ? # 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 3OVJ A 1 ? 6 ? P05067 687 ? 692 ? 1 6 2 1 3OVJ B 1 ? 6 ? P05067 687 ? 692 ? 1 6 3 1 3OVJ C 1 ? 6 ? P05067 687 ? 692 ? 1 6 4 1 3OVJ D 1 ? 6 ? P05067 687 ? 692 ? 1 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ;The biological unit is a pair of beta sheets with orange G interrelating between the sheets. The fiber is constructed from unit cell translations along the a direction (i.e. X+1,Y,Z; X+2,Y,Z; X+3,Y,Z, etc.). ; # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 2 ? B ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel B 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 LEU A 2 ? PHE A 5 ? LEU A 2 PHE A 5 A 2 LEU B 2 ? PHE B 5 ? LEU B 2 PHE B 5 B 1 LEU C 2 ? PHE C 5 ? LEU C 2 PHE C 5 B 2 LEU D 2 ? PHE D 5 ? LEU D 2 PHE D 5 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N LEU A 2 ? N LEU A 2 O PHE B 5 ? O PHE B 5 B 1 2 N LEU C 2 ? N LEU C 2 O PHE D 5 ? O PHE D 5 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B ORA 49 ? 12 'BINDING SITE FOR RESIDUE ORA B 49' AC2 Software D ORA 50 ? 11 'BINDING SITE FOR RESIDUE ORA D 50' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 12 LYS A 1 ? LYS A 1 . ? 1_565 ? 2 AC1 12 PHE A 4 ? PHE A 4 . ? 1_455 ? 3 AC1 12 PHE A 4 ? PHE A 4 . ? 1_555 ? 4 AC1 12 LYS B 1 ? LYS B 1 . ? 1_555 ? 5 AC1 12 LYS B 1 ? LYS B 1 . ? 1_655 ? 6 AC1 12 VAL B 3 ? VAL B 3 . ? 1_555 ? 7 AC1 12 LYS C 1 ? LYS C 1 . ? 1_555 ? 8 AC1 12 LYS C 1 ? LYS C 1 . ? 1_655 ? 9 AC1 12 VAL C 3 ? VAL C 3 . ? 1_555 ? 10 AC1 12 HOH I . ? HOH C 10 . ? 1_556 ? 11 AC1 12 LYS D 1 ? LYS D 1 . ? 1_556 ? 12 AC1 12 PHE D 4 ? PHE D 4 . ? 1_555 ? 13 AC2 11 LYS A 1 ? LYS A 1 . ? 1_464 ? 14 AC2 11 LYS A 1 ? LYS A 1 . ? 1_564 ? 15 AC2 11 VAL A 3 ? VAL A 3 . ? 1_564 ? 16 AC2 11 PHE B 4 ? PHE B 4 . ? 1_564 ? 17 AC2 11 LYS C 1 ? LYS C 1 . ? 1_554 ? 18 AC2 11 PHE C 4 ? PHE C 4 . ? 1_555 ? 19 AC2 11 PHE C 4 ? PHE C 4 . ? 1_655 ? 20 AC2 11 HOH I . ? HOH C 10 . ? 1_455 ? 21 AC2 11 LYS D 1 ? LYS D 1 . ? 1_455 ? 22 AC2 11 LYS D 1 ? LYS D 1 . ? 1_555 ? 23 AC2 11 VAL D 3 ? VAL D 3 . ? 1_555 ? # _pdbx_phasing_MR.entry_id 3OVJ _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 1.900 _pdbx_phasing_MR.d_res_low_rotation 23.040 _pdbx_phasing_MR.d_res_high_translation 1.900 _pdbx_phasing_MR.d_res_low_translation 23.040 _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_ _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 HOH O O N N 14 HOH H1 H N N 15 HOH H2 H N N 16 LEU N N N N 17 LEU CA C N S 18 LEU C C N N 19 LEU O O N N 20 LEU CB C N N 21 LEU CG C N N 22 LEU CD1 C N N 23 LEU CD2 C N N 24 LEU OXT O N N 25 LEU H H N N 26 LEU H2 H N N 27 LEU HA H N N 28 LEU HB2 H N N 29 LEU HB3 H N N 30 LEU HG H N N 31 LEU HD11 H N N 32 LEU HD12 H N N 33 LEU HD13 H N N 34 LEU HD21 H N N 35 LEU HD22 H N N 36 LEU HD23 H N N 37 LEU HXT H N N 38 LYS N N N N 39 LYS CA C N S 40 LYS C C N N 41 LYS O O N N 42 LYS CB C N N 43 LYS CG C N N 44 LYS CD C N N 45 LYS CE C N N 46 LYS NZ N N N 47 LYS OXT O N N 48 LYS H H N N 49 LYS H2 H N N 50 LYS HA H N N 51 LYS HB2 H N N 52 LYS HB3 H N N 53 LYS HG2 H N N 54 LYS HG3 H N N 55 LYS HD2 H N N 56 LYS HD3 H N N 57 LYS HE2 H N N 58 LYS HE3 H N N 59 LYS HZ1 H N N 60 LYS HZ2 H N N 61 LYS HZ3 H N N 62 LYS HXT H N N 63 ORA C1 C Y N 64 ORA N1 N N N 65 ORA O1 O N N 66 ORA S1 S N N 67 ORA C2 C Y N 68 ORA N2 N N N 69 ORA O2 O N N 70 ORA S2 S N N 71 ORA C3 C Y N 72 ORA O3 O N N 73 ORA C4 C Y N 74 ORA O4 O N N 75 ORA C5 C Y N 76 ORA O5 O N N 77 ORA C6 C Y N 78 ORA O6 O N N 79 ORA C7 C Y N 80 ORA O7 O N N 81 ORA C8 C Y N 82 ORA C9 C Y N 83 ORA C10 C Y N 84 ORA C11 C Y N 85 ORA C12 C Y N 86 ORA C13 C Y N 87 ORA C14 C Y N 88 ORA C15 C Y N 89 ORA C16 C Y N 90 ORA H1 H N N 91 ORA H2 H N N 92 ORA H3 H N N 93 ORA H4 H N N 94 ORA H5 H N N 95 ORA H6 H N N 96 ORA H7 H N N 97 ORA HO7 H N N 98 ORA H8 H N N 99 ORA H9 H N N 100 ORA H11 H N N 101 ORA H12 H N N 102 PHE N N N N 103 PHE CA C N S 104 PHE C C N N 105 PHE O O N N 106 PHE CB C N N 107 PHE CG C Y N 108 PHE CD1 C Y N 109 PHE CD2 C Y N 110 PHE CE1 C Y N 111 PHE CE2 C Y N 112 PHE CZ C Y N 113 PHE OXT O N N 114 PHE H H N N 115 PHE H2 H N N 116 PHE HA H N N 117 PHE HB2 H N N 118 PHE HB3 H N N 119 PHE HD1 H N N 120 PHE HD2 H N N 121 PHE HE1 H N N 122 PHE HE2 H N N 123 PHE HZ H N N 124 PHE HXT H N N 125 VAL N N N N 126 VAL CA C N S 127 VAL C C N N 128 VAL O O N N 129 VAL CB C N N 130 VAL CG1 C N N 131 VAL CG2 C N N 132 VAL OXT O N N 133 VAL H H N N 134 VAL H2 H N N 135 VAL HA H N N 136 VAL HB H N N 137 VAL HG11 H N N 138 VAL HG12 H N N 139 VAL HG13 H N N 140 VAL HG21 H N N 141 VAL HG22 H N N 142 VAL HG23 H N N 143 VAL HXT H N N 144 # 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 HOH O H1 sing N N 13 HOH O H2 sing N N 14 LEU N CA sing N N 15 LEU N H sing N N 16 LEU N H2 sing N N 17 LEU CA C sing N N 18 LEU CA CB sing N N 19 LEU CA HA sing N N 20 LEU C O doub N N 21 LEU C OXT sing N N 22 LEU CB CG sing N N 23 LEU CB HB2 sing N N 24 LEU CB HB3 sing N N 25 LEU CG CD1 sing N N 26 LEU CG CD2 sing N N 27 LEU CG HG sing N N 28 LEU CD1 HD11 sing N N 29 LEU CD1 HD12 sing N N 30 LEU CD1 HD13 sing N N 31 LEU CD2 HD21 sing N N 32 LEU CD2 HD22 sing N N 33 LEU CD2 HD23 sing N N 34 LEU OXT HXT sing N N 35 LYS N CA sing N N 36 LYS N H sing N N 37 LYS N H2 sing N N 38 LYS CA C sing N N 39 LYS CA CB sing N N 40 LYS CA HA sing N N 41 LYS C O doub N N 42 LYS C OXT sing N N 43 LYS CB CG sing N N 44 LYS CB HB2 sing N N 45 LYS CB HB3 sing N N 46 LYS CG CD sing N N 47 LYS CG HG2 sing N N 48 LYS CG HG3 sing N N 49 LYS CD CE sing N N 50 LYS CD HD2 sing N N 51 LYS CD HD3 sing N N 52 LYS CE NZ sing N N 53 LYS CE HE2 sing N N 54 LYS CE HE3 sing N N 55 LYS NZ HZ1 sing N N 56 LYS NZ HZ2 sing N N 57 LYS NZ HZ3 sing N N 58 LYS OXT HXT sing N N 59 ORA C1 C2 doub Y N 60 ORA C1 C3 sing Y N 61 ORA C1 H1 sing N N 62 ORA N1 N2 doub N N 63 ORA N1 C12 sing N N 64 ORA O1 S1 sing N N 65 ORA S1 O3 doub N N 66 ORA S1 O4 doub N N 67 ORA S1 C15 sing N N 68 ORA C2 C5 sing Y N 69 ORA C2 H2 sing N N 70 ORA N2 C13 sing N N 71 ORA O2 S2 sing N N 72 ORA S2 O5 doub N N 73 ORA S2 O6 doub N N 74 ORA S2 C16 sing N N 75 ORA C3 C6 doub Y N 76 ORA C3 H3 sing N N 77 ORA C4 C7 doub Y N 78 ORA C4 C10 sing Y N 79 ORA C4 H4 sing N N 80 ORA C5 C12 doub Y N 81 ORA C5 H5 sing N N 82 ORA C6 C12 sing Y N 83 ORA C6 H6 sing N N 84 ORA C7 C14 sing Y N 85 ORA C7 H7 sing N N 86 ORA O7 C14 sing N N 87 ORA O7 HO7 sing N N 88 ORA C8 C10 doub Y N 89 ORA C8 C15 sing Y N 90 ORA C8 H8 sing N N 91 ORA C9 C15 doub Y N 92 ORA C9 C16 sing Y N 93 ORA C9 H9 sing N N 94 ORA C10 C11 sing Y N 95 ORA C11 C13 sing Y N 96 ORA C11 C16 doub Y N 97 ORA C13 C14 doub Y N 98 ORA O1 H11 sing N N 99 ORA O2 H12 sing N N 100 PHE N CA sing N N 101 PHE N H sing N N 102 PHE N H2 sing N N 103 PHE CA C sing N N 104 PHE CA CB sing N N 105 PHE CA HA sing N N 106 PHE C O doub N N 107 PHE C OXT sing N N 108 PHE CB CG sing N N 109 PHE CB HB2 sing N N 110 PHE CB HB3 sing N N 111 PHE CG CD1 doub Y N 112 PHE CG CD2 sing Y N 113 PHE CD1 CE1 sing Y N 114 PHE CD1 HD1 sing N N 115 PHE CD2 CE2 doub Y N 116 PHE CD2 HD2 sing N N 117 PHE CE1 CZ doub Y N 118 PHE CE1 HE1 sing N N 119 PHE CE2 CZ sing Y N 120 PHE CE2 HE2 sing N N 121 PHE CZ HZ sing N N 122 PHE OXT HXT sing N N 123 VAL N CA sing N N 124 VAL N H sing N N 125 VAL N H2 sing N N 126 VAL CA C sing N N 127 VAL CA CB sing N N 128 VAL CA HA sing N N 129 VAL C O doub N N 130 VAL C OXT sing N N 131 VAL CB CG1 sing N N 132 VAL CB CG2 sing N N 133 VAL CB HB sing N N 134 VAL CG1 HG11 sing N N 135 VAL CG1 HG12 sing N N 136 VAL CG1 HG13 sing N N 137 VAL CG2 HG21 sing N N 138 VAL CG2 HG22 sing N N 139 VAL CG2 HG23 sing N N 140 VAL OXT HXT sing N N 141 # _atom_sites.entry_id 3OVJ _atom_sites.fract_transf_matrix[1][1] 0.104866 _atom_sites.fract_transf_matrix[1][2] -0.002843 _atom_sites.fract_transf_matrix[1][3] -0.001414 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.038464 _atom_sites.fract_transf_matrix[2][3] -0.020193 _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] 0.043785 _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 N O S # loop_