data_2Y3J # _entry.id 2Y3J # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 2Y3J pdb_00002y3j 10.2210/pdb2y3j/pdb PDBE EBI-46727 ? ? WWPDB D_1290046727 ? ? # 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 2011-11-02 2 'Structure model' 1 1 2024-05-08 # _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 2 'Structure model' Other # 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' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' pdbx_database_status # 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' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_sf' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2Y3J _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2010-12-21 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1UOA unspecified 'AFTER 3NS' PDB 1TAW unspecified 'BOVINE TRYPSIN COMPLEXED TO APPI' PDB 1QCM unspecified 'AMYLOID BETA PEPTIDE (25-35), NMR, 20 STRUCTURES' PDB 1TKN unspecified 'SOLUTION STRUCTURE OF CAPPD*, AN INDEPENDENTLY FOLDEDEXTRACELLULAR DOMAIN OF HUMAN AMYLOID-BETA PRECURSORPROTEIN' PDB 1BA6 unspecified ;SOLUTION STRUCTURE OF THE METHIONINE-OXIDIZED AMYLOID BETA-PEPTIDE (1-40). DOES OXIDATION AFFECT CONFORMATIONAL SWITCHING? NMR, 10 STRUCTURES ; PDB 1QYT unspecified 'SOLUTION STRUCTURE OF FRAGMENT (25-35) OF BETA AMYLOIDPEPTIDE IN SDS MICELLAR SOLUTION' PDB 1BJB unspecified 'SOLUTION NMR STRUCTURE OF AMYLOID BETA[E16], RESIDUES 1-28, 14 STRUCTURES' PDB 2Y3L unspecified 'STRUCTURE OF SEGMENT MVGGVVIA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 35-42), ALTERNATE POLYMORPH 2' PDB 2Y2A unspecified 'STRUCTURE OF SEGMENT KLVFFA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 16-21), ALTERNATE POLYMORPH I' PDB 2Y3K unspecified 'STRUCTURE OF SEGMENT MVGGVVIA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 35-42), ALTERNATE POLYMORPH 1' PDB 1CA0 unspecified 'BOVINE CHYMOTRYPSIN COMPLEXED TO APPI' PDB 1BRC unspecified . PDB 1UO8 unspecified 'AFTER 2NS' PDB 1BA4 unspecified ;THE SOLUTION STRUCTURE OF AMYLOID BETA-PEPTIDE (1-40 ) IN A WATER-MICELLE ENVIRONMENT. IS THE MEMBRANE- SPANNING DOMAIN WHERE WE THINK IT IS? NMR, 10 STRUCTURES ; PDB 2WK3 unspecified 'CRYSTAL STRUCTURE OF HUMAN INSULIN-DEGRADING ENZYME IN COMPLEX WITH AMYLOID-BETA (1-42)' PDB 1AAP unspecified . PDB 1QWP unspecified 'NMR ANALYSIS OF 25-35 FRAGMENT OF BETA AMYLOID PEPTIDE' PDB 1X11 unspecified 'X11 PTB DOMAIN' PDB 1ZE9 unspecified ;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE COMPLEXED WITH A ZINC (II) CATION ; PDB 1QXC unspecified 'NMR STRUCTURE OF THE FRAGMENT 25-35 OF BETA AMYLOID PEPTIDEIN 20/80 V:V HEXAFLUOROISOPROPANOL/WATER MIXTURE' PDB 1IYT unspecified ;SOLUTION STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (1-42) ; PDB 1ZE7 unspecified ;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE IN WATER SOLUTION AT PH 6.5 ; PDB 2BEG unspecified ;3D STRUCTURE OF ALZHEIMER'S ABETA(1-42) FIBRILS ; PDB 1UOI unspecified 'AFTER 4NS' PDB 1AMB unspecified ;ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (RESIDUES 1 - 28) (NMR, MINIMIZED AVERAGE STRUCTURE) ; PDB 1RW6 unspecified 'HUMAN APP CORE DOMAIN' PDB 1UO7 unspecified 'MOLECULAR DYNAMICS SIMULATION OF AMYLOID BETA 1-42 ( PDB: 1IYT) IN WATER' PDB 1OWT unspecified ;STRUCTURE OF THE ALZHEIMER'S DISEASE AMYLOID PRECURSORPROTEIN COPPER BINDING DOMAIN ; PDB 1AML unspecified ;THE ALZHEIMER'S DISEASE AMYLOID A4 PEPTIDE (RESIDUES 1 -40) ; PDB 1AMC unspecified ;ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE (RESIDUES 1 - 28) (NMR, 5 STRUCTURES) ; PDB 1ZJD unspecified ;CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH KUNITZ PROTEASE INHIBITOR DOMAINOF PROTEASE NEXIN II ; PDB 2BP4 unspecified ;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE IN TFE-WATER (80-20) SOLUTION ; PDB 2BOM unspecified ;MODEL OF ALZHEIMER'S DISEASE AMYLOID-SS PEPTIDE BASED ON A RNA BINDING PROTEIN ; PDB 1BJC unspecified 'SOLUTION NMR STRUCTURE OF AMYLOID BETA[F16], RESIDUES 1-28, 15 STRUCTURES' PDB 1MWP unspecified 'N-TERMINAL DOMAIN OF THE AMYLOID PRECURSOR PROTEIN' PDB 2Y29 unspecified 'STRUCTURE OF SEGMENT KLVFFA FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 16-21), ALTERNATE POLYMORPH III' PDB 1HZ3 unspecified ;ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10- 35) ; # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Colletier, J.P.' 1 'Laganowsky, A.' 2 'Sawaya, M.R.' 3 'Eisenberg, D.' 4 # _citation.id primary _citation.title 'Molecular Basis for Amyloid-{Beta} Polymorphism.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 108 _citation.page_first 16938 _citation.page_last ? _citation.year 2011 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21949245 _citation.pdbx_database_id_DOI 10.1073/PNAS.1112600108 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Colletier, J.' 1 ? primary 'Laganowsky, A.' 2 ? primary 'Landau, M.' 3 ? primary 'Zhao, M.' 4 ? primary 'Soriaga, A.B.' 5 ? primary 'Goldschmidt, L.' 6 ? primary 'Flot, D.' 7 ? primary 'Cascio, D.' 8 ? primary 'Sawaya, M.R.' 9 ? primary 'Eisenberg, D.' 10 ? # 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 'AMYLOID BETA A4 PROTEIN' 616.814 8 ? ? 'RESIDUES 701-706' ? 2 water nat water 18.015 2 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;AMYLOID BETA PEPTIDE, ABPP, APPI, APP, ALZHEIMER DISEASE AMYLOID PROTEIN, CEREBRAL VASCULAR AMYLOID PEPTIDE, CVAP, PREA4, PROTEASE NEXIN-II, PN-II ; # _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 AIIGLM _entity_poly.pdbx_seq_one_letter_code_can AIIGLM _entity_poly.pdbx_strand_id A,B,C,D,E,F,G,H _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 ALA n 1 2 ILE n 1 3 ILE n 1 4 GLY n 1 5 LEU n 1 6 MET 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 ? # 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 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ALA 1 1 1 ALA ALA A . n A 1 2 ILE 2 2 2 ILE ILE A . n A 1 3 ILE 3 3 3 ILE ILE A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 MET 6 6 6 MET MET A . n B 1 1 ALA 1 1 1 ALA ALA B . n B 1 2 ILE 2 2 2 ILE ILE B . n B 1 3 ILE 3 3 3 ILE ILE B . n B 1 4 GLY 4 4 4 GLY GLY B . n B 1 5 LEU 5 5 5 LEU LEU B . n B 1 6 MET 6 6 6 MET MET B . n C 1 1 ALA 1 1 1 ALA ALA C . n C 1 2 ILE 2 2 2 ILE ILE C . n C 1 3 ILE 3 3 3 ILE ILE C . n C 1 4 GLY 4 4 4 GLY GLY C . n C 1 5 LEU 5 5 5 LEU LEU C . n C 1 6 MET 6 6 6 MET MET C . n D 1 1 ALA 1 1 1 ALA ALA D . n D 1 2 ILE 2 2 2 ILE ILE D . n D 1 3 ILE 3 3 3 ILE ILE D . n D 1 4 GLY 4 4 4 GLY GLY D . n D 1 5 LEU 5 5 5 LEU LEU D . n D 1 6 MET 6 6 6 MET MET D . n E 1 1 ALA 1 1 1 ALA ALA E . n E 1 2 ILE 2 2 2 ILE ILE E . n E 1 3 ILE 3 3 3 ILE ILE E . n E 1 4 GLY 4 4 4 GLY GLY E . n E 1 5 LEU 5 5 5 LEU LEU E . n E 1 6 MET 6 6 6 MET MET E . n F 1 1 ALA 1 1 1 ALA ALA F . n F 1 2 ILE 2 2 2 ILE ILE F . n F 1 3 ILE 3 3 3 ILE ILE F . n F 1 4 GLY 4 4 4 GLY GLY F . n F 1 5 LEU 5 5 5 LEU LEU F . n F 1 6 MET 6 6 6 MET MET F . n G 1 1 ALA 1 1 1 ALA ALA G . n G 1 2 ILE 2 2 2 ILE ILE G . n G 1 3 ILE 3 3 3 ILE ILE G . n G 1 4 GLY 4 4 4 GLY GLY G . n G 1 5 LEU 5 5 5 LEU LEU G . n G 1 6 MET 6 6 6 MET MET G . n H 1 1 ALA 1 1 1 ALA ALA H . n H 1 2 ILE 2 2 2 ILE ILE H . n H 1 3 ILE 3 3 3 ILE ILE H . n H 1 4 GLY 4 4 4 GLY GLY H . n H 1 5 LEU 5 5 5 LEU LEU H . n H 1 6 MET 6 6 6 MET MET H . 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 I 2 HOH 1 2001 2001 HOH HOH B . J 2 HOH 1 2001 2001 HOH HOH E . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.6.0081 ? 1 XDS 'data reduction' . ? 2 XSCALE 'data scaling' . ? 3 PHASER phasing . ? 4 # _cell.entry_id 2Y3J _cell.length_a 9.560 _cell.length_b 15.640 _cell.length_c 45.230 _cell.angle_alpha 89.87 _cell.angle_beta 90.02 _cell.angle_gamma 89.91 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Y3J _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 2Y3J _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.41 _exptl_crystal.density_percent_sol 13.04 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'AB3035 WAS DISSOLVED IN WATER AT 1MG/ML AND MIXED WITH 2 M SODIUM CHLORIDE, pH 7' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.87260 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID23-2' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID23-2 _diffrn_source.pdbx_wavelength 0.87260 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2Y3J _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 45.23 _reflns.d_resolution_high 2.00 _reflns.number_obs 1679 _reflns.number_all ? _reflns.percent_possible_obs 97.5 _reflns.pdbx_Rmerge_I_obs 0.10 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 4.91 _reflns.B_iso_Wilson_estimate 14.79 _reflns.pdbx_redundancy 1.73 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.00 _reflns_shell.d_res_low 2.05 _reflns_shell.percent_possible_all 88.5 _reflns_shell.Rmerge_I_obs 0.19 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.11 _reflns_shell.pdbx_redundancy 1.63 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2Y3J _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 1679 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 45.23 _refine.ls_d_res_high 1.99 _refine.ls_percent_reflns_obs 97.54 _refine.ls_R_factor_obs 0.22462 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.22194 _refine.ls_R_factor_R_free 0.26710 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 3.6 _refine.ls_number_reflns_R_free 62 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.935 _refine.correlation_coeff_Fo_to_Fc_free 0.950 _refine.B_iso_mean 23.107 _refine.aniso_B[1][1] 13.20 _refine.aniso_B[2][2] -0.79 _refine.aniso_B[3][3] -12.41 _refine.aniso_B[1][2] -2.81 _refine.aniso_B[1][3] -3.49 _refine.aniso_B[2][3] -2.71 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.098 _refine.pdbx_overall_ESU_R_Free 0.052 _refine.overall_SU_ML 0.047 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.600 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 336 _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 338 _refine_hist.d_res_high 1.99 _refine_hist.d_res_low 45.23 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.019 0.023 ? 328 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.710 2.135 ? 432 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 9.574 5.000 ? 40 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 28.434 15.000 ? 72 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.182 0.200 ? 64 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.020 ? 192 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.995 _refine_ls_shell.d_res_low 2.047 _refine_ls_shell.number_reflns_R_work 132 _refine_ls_shell.R_factor_R_work 0.137 _refine_ls_shell.percent_reflns_obs 88.59 _refine_ls_shell.R_factor_R_free 0.000 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 0 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 2Y3J _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 2Y3J _struct.title 'Structure of segment AIIGLM from the amyloid-beta peptide (Ab, residues 30-35)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2Y3J _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' _struct_keywords.text 'PROTEIN FIBRIL, ALZHEIMER DISEASE' # 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 1 ? F N N 1 ? G N N 1 ? H N N 1 ? I N N 2 ? J N N 2 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A4_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P05067 _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 2Y3J A 1 ? 6 ? P05067 701 ? 706 ? 1 6 2 1 2Y3J B 1 ? 6 ? P05067 701 ? 706 ? 1 6 3 1 2Y3J C 1 ? 6 ? P05067 701 ? 706 ? 1 6 4 1 2Y3J D 1 ? 6 ? P05067 701 ? 706 ? 1 6 5 1 2Y3J E 1 ? 6 ? P05067 701 ? 706 ? 1 6 6 1 2Y3J F 1 ? 6 ? P05067 701 ? 706 ? 1 6 7 1 2Y3J G 1 ? 6 ? P05067 701 ? 706 ? 1 6 8 1 2Y3J H 1 ? 6 ? P05067 701 ? 706 ? 1 6 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA tetrameric 4 2 author_and_software_defined_assembly PISA tetrameric 4 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1910 ? 1 MORE -18.8 ? 1 'SSA (A^2)' 2410 ? 2 'ABSA (A^2)' 1970 ? 2 MORE -18.8 ? 2 'SSA (A^2)' 2390 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D,I 2 1 E,F,G,H,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 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 2 ? BA ? 2 ? EA ? 2 ? FA ? 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 AA 1 2 ? parallel BA 1 2 ? parallel EA 1 2 ? parallel FA 1 2 ? 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 AA 1 ILE A 2 ? LEU A 5 ? ILE A 2 LEU A 5 AA 2 ILE C 2 ? LEU C 5 ? ILE C 2 LEU C 5 BA 1 ILE B 2 ? LEU B 5 ? ILE B 2 LEU B 5 BA 2 ILE D 2 ? LEU D 5 ? ILE D 2 LEU D 5 EA 1 ILE E 2 ? LEU E 5 ? ILE E 2 LEU E 5 EA 2 ILE G 2 ? LEU G 5 ? ILE G 2 LEU G 5 FA 1 ILE F 2 ? LEU F 5 ? ILE F 2 LEU F 5 FA 2 ILE H 2 ? LEU H 5 ? ILE H 2 LEU H 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 AA 1 2 N GLY A 4 ? N GLY A 4 O ILE C 3 ? O ILE C 3 BA 1 2 N ILE B 3 ? N ILE B 3 O ILE D 2 ? O ILE D 2 EA 1 2 N GLY E 4 ? N GLY E 4 O ILE G 3 ? O ILE G 3 FA 1 2 N ILE F 3 ? N ILE F 3 O ILE H 2 ? O ILE H 2 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CA D LEU 5 ? ? CB D LEU 5 ? ? CG D LEU 5 ? ? 131.43 115.30 16.13 2.30 N 2 1 CG1 F ILE 2 ? ? CB F ILE 2 ? ? CG2 F ILE 2 ? ? 97.32 111.40 -14.08 2.20 N 3 1 CA H LEU 5 ? ? CB H LEU 5 ? ? CG H LEU 5 ? ? 130.02 115.30 14.72 2.30 N # _pdbx_entry_details.entry_id 2Y3J _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;AMYLOID BETA PEPTIDE (AB) IS A PROTEOLYTIC PRODUCT OF THE AMYLOID PRECURSOR PROTEIN (APP). AB SEGMENT 30-AIIGLM-35 CORRESPONDS TO RESIDUES 701-706 OF APP ; _pdbx_entry_details.has_ligand_of_interest ? # 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 ILE N N N N 27 ILE CA C N S 28 ILE C C N N 29 ILE O O N N 30 ILE CB C N S 31 ILE CG1 C N N 32 ILE CG2 C N N 33 ILE CD1 C N N 34 ILE OXT O N N 35 ILE H H N N 36 ILE H2 H N N 37 ILE HA H N N 38 ILE HB H N N 39 ILE HG12 H N N 40 ILE HG13 H N N 41 ILE HG21 H N N 42 ILE HG22 H N N 43 ILE HG23 H N N 44 ILE HD11 H N N 45 ILE HD12 H N N 46 ILE HD13 H N N 47 ILE HXT H N N 48 LEU N N N N 49 LEU CA C N S 50 LEU C C N N 51 LEU O O N N 52 LEU CB C N N 53 LEU CG C N N 54 LEU CD1 C N N 55 LEU CD2 C N N 56 LEU OXT O N N 57 LEU H H N N 58 LEU H2 H N N 59 LEU HA H N N 60 LEU HB2 H N N 61 LEU HB3 H N N 62 LEU HG H N N 63 LEU HD11 H N N 64 LEU HD12 H N N 65 LEU HD13 H N N 66 LEU HD21 H N N 67 LEU HD22 H N N 68 LEU HD23 H N N 69 LEU HXT H N N 70 MET N N N N 71 MET CA C N S 72 MET C C N N 73 MET O O N N 74 MET CB C N N 75 MET CG C N N 76 MET SD S N N 77 MET CE C N N 78 MET OXT O N N 79 MET H H N N 80 MET H2 H N N 81 MET HA H N N 82 MET HB2 H N N 83 MET HB3 H N N 84 MET HG2 H N N 85 MET HG3 H N N 86 MET HE1 H N N 87 MET HE2 H N N 88 MET HE3 H N N 89 MET HXT H N N 90 # 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 ILE N CA sing N N 24 ILE N H sing N N 25 ILE N H2 sing N N 26 ILE CA C sing N N 27 ILE CA CB sing N N 28 ILE CA HA sing N N 29 ILE C O doub N N 30 ILE C OXT sing N N 31 ILE CB CG1 sing N N 32 ILE CB CG2 sing N N 33 ILE CB HB sing N N 34 ILE CG1 CD1 sing N N 35 ILE CG1 HG12 sing N N 36 ILE CG1 HG13 sing N N 37 ILE CG2 HG21 sing N N 38 ILE CG2 HG22 sing N N 39 ILE CG2 HG23 sing N N 40 ILE CD1 HD11 sing N N 41 ILE CD1 HD12 sing N N 42 ILE CD1 HD13 sing N N 43 ILE OXT HXT sing N N 44 LEU N CA sing N N 45 LEU N H sing N N 46 LEU N H2 sing N N 47 LEU CA C sing N N 48 LEU CA CB sing N N 49 LEU CA HA sing N N 50 LEU C O doub N N 51 LEU C OXT sing N N 52 LEU CB CG sing N N 53 LEU CB HB2 sing N N 54 LEU CB HB3 sing N N 55 LEU CG CD1 sing N N 56 LEU CG CD2 sing N N 57 LEU CG HG sing N N 58 LEU CD1 HD11 sing N N 59 LEU CD1 HD12 sing N N 60 LEU CD1 HD13 sing N N 61 LEU CD2 HD21 sing N N 62 LEU CD2 HD22 sing N N 63 LEU CD2 HD23 sing N N 64 LEU OXT HXT sing N N 65 MET N CA sing N N 66 MET N H sing N N 67 MET N H2 sing N N 68 MET CA C sing N N 69 MET CA CB sing N N 70 MET CA HA sing N N 71 MET C O doub N N 72 MET C OXT sing N N 73 MET CB CG sing N N 74 MET CB HB2 sing N N 75 MET CB HB3 sing N N 76 MET CG SD sing N N 77 MET CG HG2 sing N N 78 MET CG HG3 sing N N 79 MET SD CE sing N N 80 MET CE HE1 sing N N 81 MET CE HE2 sing N N 82 MET CE HE3 sing N N 83 MET OXT HXT sing N N 84 # loop_ _pdbx_reflns_twin.domain_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.type _pdbx_reflns_twin.operator _pdbx_reflns_twin.fraction 1 1 1 ? 'H, K, L' 0.875 2 1 1 ? h,-k,-l 0.012 3 1 1 ? -h,-k,l 0.051 4 1 1 ? '-H, K, -L' 0.062 # _atom_sites.entry_id 2Y3J _atom_sites.fract_transf_matrix[1][1] 0.104603 _atom_sites.fract_transf_matrix[1][2] -0.000164 _atom_sites.fract_transf_matrix[1][3] 0.000037 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.063939 _atom_sites.fract_transf_matrix[2][3] -0.000145 _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] 0.022109 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # loop_