data_2Y29 # _entry.id 2Y29 # _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 2Y29 pdb_00002y29 10.2210/pdb2y29/pdb PDBE EBI-46721 ? ? WWPDB D_1290046721 ? ? # 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 2011-10-26 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 2Y29 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2010-12-14 _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 2Y3J unspecified 'STRUCTURE OF SEGMENT AIIGLM FROM THE AMYLOID-BETA PEPTIDE (AB, RESIDUES 30-35)' PDB 1TKN unspecified 'SOLUTION STRUCTURE OF CAPPD*, AN INDEPENDENTLY FOLDEDEXTRACELLULAR DOMAIN OF HUMAN AMYLOID-BETA PRECURSORPROTEIN' PDB 1QCM unspecified 'AMYLOID BETA PEPTIDE (25-35), NMR, 20 STRUCTURES' 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 1UO8 unspecified 'AFTER 2NS' PDB 1BRC unspecified . 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 1AAP unspecified . PDB 2WK3 unspecified 'CRYSTAL STRUCTURE OF HUMAN INSULIN-DEGRADING ENZYME IN COMPLEX WITH AMYLOID-BETA (1-42)' 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 2BP4 unspecified ;ZINC-BINDING DOMAIN OF ALZHEIMER'S DISEASE AMYLOID BETA-PEPTIDE IN TFE-WATER (80-20) SOLUTION ; PDB 1ZJD unspecified ;CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH KUNITZ PROTEASE INHIBITOR DOMAINOF PROTEASE NEXIN II ; 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 1HZ3 unspecified ;ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10- 35) ; # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Colletier, J.' 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' 724.909 1 ? ? 'SEGMENT KLVFFA, RESIDUES 687-692' ? 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 KLVFFA _entity_poly.pdbx_seq_one_letter_code_can KLVFFA _entity_poly.pdbx_strand_id A _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 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 '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 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 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 2 2 LYS LYS A . n A 1 2 LEU 2 3 3 LEU LEU A . n A 1 3 VAL 3 4 4 VAL VAL A . n A 1 4 PHE 4 5 5 PHE PHE A . n A 1 5 PHE 5 6 6 PHE PHE A . n A 1 6 ALA 6 7 7 ALA ALA A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 2001 2001 HOH HOH A . B 2 HOH 2 2002 2002 HOH HOH A . # 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 2Y29 _cell.length_a 9.590 _cell.length_b 12.070 _cell.length_c 42.210 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Y29 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # _exptl.entry_id 2Y29 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 3 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.73 _exptl_crystal.density_percent_sol 29 _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 8.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;AB16-21 FORM III CRYSTALS WERE OBTAINED AFTER THE SEGMENT WAS DISSOLVED IN WATER AT 5 MG/ML AND MIXED WITH 0.2M AMMONIUM ACETATE, 0.1 M TRIS BUFFER PH 8.5 AND 30% ISOPROPANOL. ; # _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 2Y29 _reflns.observed_criterion_sigma_I 3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.00 _reflns.d_resolution_high 2.30 _reflns.number_obs 266 _reflns.number_all ? _reflns.percent_possible_obs 94.3 _reflns.pdbx_Rmerge_I_obs 0.19 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 5.90 _reflns.B_iso_Wilson_estimate 34.134 _reflns.pdbx_redundancy 3.9 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.30 _reflns_shell.d_res_low 2.40 _reflns_shell.percent_possible_all 89.5 _reflns_shell.Rmerge_I_obs 0.52 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.19 _reflns_shell.pdbx_redundancy 3.1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2Y29 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 251 _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 20.00 _refine.ls_d_res_high 2.30 _refine.ls_percent_reflns_obs 94.31 _refine.ls_R_factor_obs 0.22609 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.22410 _refine.ls_R_factor_R_free 0.26003 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.3 _refine.ls_number_reflns_R_free 14 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.930 _refine.correlation_coeff_Fo_to_Fc_free 0.958 _refine.B_iso_mean 22.654 _refine.aniso_B[1][1] -11.45 _refine.aniso_B[2][2] 11.80 _refine.aniso_B[3][3] -0.34 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _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 0.141 _refine.pdbx_overall_ESU_R_Free 0.061 _refine.overall_SU_ML 0.080 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 3.543 _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 52 _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 54 _refine_hist.d_res_high 2.30 _refine_hist.d_res_low 20.00 # 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 0.023 0.023 ? 53 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.519 1.987 ? 70 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.136 5.000 ? 5 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 14.728 20.000 ? 2 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 19.219 15.000 ? 9 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.127 0.200 ? 8 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 38 '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 2.301 _refine_ls_shell.d_res_low 2.360 _refine_ls_shell.number_reflns_R_work 26 _refine_ls_shell.R_factor_R_work 0.276 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.683 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 1 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 2Y29 _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 2Y29 _struct.title 'Structure of segment KLVFFA from the amyloid-beta peptide (Ab, residues 16-21), alternate polymorph III' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2Y29 _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 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 ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2Y29 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P05067 _struct_ref_seq.db_align_beg 687 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 692 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 7 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 # _pdbx_entry_details.entry_id 2Y29 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;IN VIVO AMYLOID BETA PEPTIDE (AB) IS A PROTEOLYTIC PRODUCT OF THE AMYLOID PRECURSOR PROTEIN (APP). AB SEGMENT 16-KLVFFA-21 CORRESPONDS TO RESIDUES 687-692 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 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 PHE N N N N 64 PHE CA C N S 65 PHE C C N N 66 PHE O O N N 67 PHE CB C N N 68 PHE CG C Y N 69 PHE CD1 C Y N 70 PHE CD2 C Y N 71 PHE CE1 C Y N 72 PHE CE2 C Y N 73 PHE CZ C Y N 74 PHE OXT O N N 75 PHE H H N N 76 PHE H2 H N N 77 PHE HA H N N 78 PHE HB2 H N N 79 PHE HB3 H N N 80 PHE HD1 H N N 81 PHE HD2 H N N 82 PHE HE1 H N N 83 PHE HE2 H N N 84 PHE HZ H N N 85 PHE HXT H N N 86 VAL N N N N 87 VAL CA C N S 88 VAL C C N N 89 VAL O O N N 90 VAL CB C N N 91 VAL CG1 C N N 92 VAL CG2 C N N 93 VAL OXT O N N 94 VAL H H N N 95 VAL H2 H N N 96 VAL HA H N N 97 VAL HB H N N 98 VAL HG11 H N N 99 VAL HG12 H N N 100 VAL HG13 H N N 101 VAL HG21 H N N 102 VAL HG22 H N N 103 VAL HG23 H N N 104 VAL HXT H N N 105 # 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 PHE N CA sing N N 60 PHE N H sing N N 61 PHE N H2 sing N N 62 PHE CA C sing N N 63 PHE CA CB sing N N 64 PHE CA HA sing N N 65 PHE C O doub N N 66 PHE C OXT sing N N 67 PHE CB CG sing N N 68 PHE CB HB2 sing N N 69 PHE CB HB3 sing N N 70 PHE CG CD1 doub Y N 71 PHE CG CD2 sing Y N 72 PHE CD1 CE1 sing Y N 73 PHE CD1 HD1 sing N N 74 PHE CD2 CE2 doub Y N 75 PHE CD2 HD2 sing N N 76 PHE CE1 CZ doub Y N 77 PHE CE1 HE1 sing N N 78 PHE CE2 CZ sing Y N 79 PHE CE2 HE2 sing N N 80 PHE CZ HZ sing N N 81 PHE OXT HXT sing N N 82 VAL N CA sing N N 83 VAL N H sing N N 84 VAL N H2 sing N N 85 VAL CA C sing N N 86 VAL CA CB sing N N 87 VAL CA HA sing N N 88 VAL C O doub N N 89 VAL C OXT sing N N 90 VAL CB CG1 sing N N 91 VAL CB CG2 sing N N 92 VAL CB HB sing N N 93 VAL CG1 HG11 sing N N 94 VAL CG1 HG12 sing N N 95 VAL CG1 HG13 sing N N 96 VAL CG2 HG21 sing N N 97 VAL CG2 HG22 sing N N 98 VAL CG2 HG23 sing N N 99 VAL OXT HXT sing N N 100 # _atom_sites.entry_id 2Y29 _atom_sites.fract_transf_matrix[1][1] 0.104275 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.082850 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.023691 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . LYS A 1 1 ? -3.367 5.703 7.940 1.00 24.11 ? 2 LYS A N 1 ATOM 2 C CA . LYS A 1 1 ? -3.973 6.815 7.193 1.00 25.75 ? 2 LYS A CA 1 ATOM 3 C C . LYS A 1 1 ? -4.182 6.420 5.718 1.00 22.45 ? 2 LYS A C 1 ATOM 4 O O . LYS A 1 1 ? -5.254 5.972 5.404 1.00 22.63 ? 2 LYS A O 1 ATOM 5 C CB . LYS A 1 1 ? -3.204 8.133 7.368 1.00 36.28 ? 2 LYS A CB 1 ATOM 6 C CG . LYS A 1 1 ? -3.553 8.966 8.663 1.00 37.36 ? 2 LYS A CG 1 ATOM 7 C CD . LYS A 1 1 ? -4.568 10.129 8.386 1.00 43.82 ? 2 LYS A CD 1 ATOM 8 C CE . LYS A 1 1 ? -4.592 11.222 9.509 1.00 38.18 ? 2 LYS A CE 1 ATOM 9 N NZ . LYS A 1 1 ? -5.860 12.074 9.514 1.00 37.31 ? 2 LYS A NZ 1 ATOM 10 N N . LEU A 1 2 ? -3.178 6.516 4.843 1.00 20.46 ? 3 LEU A N 1 ATOM 11 C CA . LEU A 1 2 ? -3.378 6.265 3.417 1.00 16.76 ? 3 LEU A CA 1 ATOM 12 C C . LEU A 1 2 ? -2.869 4.947 2.927 1.00 15.82 ? 3 LEU A C 1 ATOM 13 O O . LEU A 1 2 ? -1.662 4.690 3.015 1.00 14.04 ? 3 LEU A O 1 ATOM 14 C CB . LEU A 1 2 ? -2.742 7.362 2.566 1.00 18.25 ? 3 LEU A CB 1 ATOM 15 C CG . LEU A 1 2 ? -2.870 7.162 1.045 1.00 20.82 ? 3 LEU A CG 1 ATOM 16 C CD1 . LEU A 1 2 ? -4.316 7.370 0.513 1.00 18.21 ? 3 LEU A CD1 1 ATOM 17 C CD2 . LEU A 1 2 ? -1.880 8.040 0.272 1.00 23.81 ? 3 LEU A CD2 1 ATOM 18 N N . VAL A 1 3 ? -3.775 4.132 2.356 1.00 14.07 ? 4 VAL A N 1 ATOM 19 C CA . VAL A 1 3 ? -3.374 2.906 1.669 1.00 14.54 ? 4 VAL A CA 1 ATOM 20 C C . VAL A 1 3 ? -3.942 2.715 0.301 1.00 16.12 ? 4 VAL A C 1 ATOM 21 O O . VAL A 1 3 ? -5.144 2.489 0.125 1.00 18.28 ? 4 VAL A O 1 ATOM 22 C CB . VAL A 1 3 ? -3.682 1.660 2.471 1.00 14.30 ? 4 VAL A CB 1 ATOM 23 C CG1 . VAL A 1 3 ? -3.181 0.420 1.697 1.00 14.29 ? 4 VAL A CG1 1 ATOM 24 C CG2 . VAL A 1 3 ? -3.007 1.755 3.808 1.00 13.11 ? 4 VAL A CG2 1 ATOM 25 N N . PHE A 1 4 ? -3.053 2.791 -0.676 1.00 19.17 ? 5 PHE A N 1 ATOM 26 C CA . PHE A 1 4 ? -3.405 2.635 -2.083 1.00 18.86 ? 5 PHE A CA 1 ATOM 27 C C . PHE A 1 4 ? -2.753 1.390 -2.696 1.00 18.52 ? 5 PHE A C 1 ATOM 28 O O . PHE A 1 4 ? -1.542 1.185 -2.546 1.00 19.22 ? 5 PHE A O 1 ATOM 29 C CB . PHE A 1 4 ? -2.989 3.886 -2.863 1.00 19.73 ? 5 PHE A CB 1 ATOM 30 C CG . PHE A 1 4 ? -3.228 3.777 -4.344 1.00 19.23 ? 5 PHE A CG 1 ATOM 31 C CD1 . PHE A 1 4 ? -2.407 2.992 -5.140 1.00 19.50 ? 5 PHE A CD1 1 ATOM 32 C CD2 . PHE A 1 4 ? -4.274 4.472 -4.940 1.00 19.79 ? 5 PHE A CD2 1 ATOM 33 C CE1 . PHE A 1 4 ? -2.646 2.881 -6.512 1.00 20.32 ? 5 PHE A CE1 1 ATOM 34 C CE2 . PHE A 1 4 ? -4.511 4.367 -6.279 1.00 19.74 ? 5 PHE A CE2 1 ATOM 35 C CZ . PHE A 1 4 ? -3.696 3.559 -7.072 1.00 19.06 ? 5 PHE A CZ 1 ATOM 36 N N . PHE A 1 5 ? -3.559 0.594 -3.396 1.00 18.19 ? 6 PHE A N 1 ATOM 37 C CA . PHE A 1 5 ? -3.115 -0.607 -4.121 1.00 21.35 ? 6 PHE A CA 1 ATOM 38 C C . PHE A 1 5 ? -3.888 -0.800 -5.415 1.00 24.27 ? 6 PHE A C 1 ATOM 39 O O . PHE A 1 5 ? -5.062 -1.252 -5.404 1.00 21.75 ? 6 PHE A O 1 ATOM 40 C CB . PHE A 1 5 ? -3.208 -1.925 -3.274 1.00 21.59 ? 6 PHE A CB 1 ATOM 41 C CG . PHE A 1 5 ? -2.330 -3.029 -3.805 1.00 23.29 ? 6 PHE A CG 1 ATOM 42 C CD1 . PHE A 1 5 ? -0.920 -2.975 -3.642 1.00 24.72 ? 6 PHE A CD1 1 ATOM 43 C CD2 . PHE A 1 5 ? -2.870 -4.096 -4.537 1.00 22.64 ? 6 PHE A CD2 1 ATOM 44 C CE1 . PHE A 1 5 ? -0.091 -3.994 -4.191 1.00 24.66 ? 6 PHE A CE1 1 ATOM 45 C CE2 . PHE A 1 5 ? -2.037 -5.101 -5.091 1.00 19.71 ? 6 PHE A CE2 1 ATOM 46 C CZ . PHE A 1 5 ? -0.672 -5.068 -4.920 1.00 19.51 ? 6 PHE A CZ 1 ATOM 47 N N . ALA A 1 6 ? -3.223 -0.505 -6.532 1.00 24.61 ? 7 ALA A N 1 ATOM 48 C CA . ALA A 1 6 ? -3.827 -0.715 -7.821 1.00 26.63 ? 7 ALA A CA 1 ATOM 49 C C . ALA A 1 6 ? -3.187 -1.922 -8.487 1.00 31.16 ? 7 ALA A C 1 ATOM 50 O O . ALA A 1 6 ? -1.980 -1.962 -8.645 1.00 29.56 ? 7 ALA A O 1 ATOM 51 C CB . ALA A 1 6 ? -3.694 0.510 -8.669 1.00 29.69 ? 7 ALA A CB 1 ATOM 52 O OXT . ALA A 1 6 ? -3.840 -2.909 -8.854 1.00 38.24 ? 7 ALA A OXT 1 HETATM 53 O O . HOH B 2 . ? -5.967 -2.380 -10.310 1.00 17.97 ? 2001 HOH A O 1 HETATM 54 O O . HOH B 2 . ? -6.843 -4.832 -7.024 1.00 29.82 ? 2002 HOH A O 1 #