data_2ONA # _entry.id 2ONA # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 2ONA pdb_00002ona 10.2210/pdb2ona/pdb RCSB RCSB041347 ? ? WWPDB D_1000041347 ? ? # 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 2007-01-30 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2023-12-27 6 'Structure model' 1 5 2024-04-03 # _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' 'Version format compliance' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Refinement description' 7 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' struct_ncs_dom_lim 6 6 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_struct_ncs_dom_lim.beg_auth_comp_id' 4 5 'Structure model' '_struct_ncs_dom_lim.end_auth_comp_id' # _pdbx_database_status.entry_id 2ONA _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-01-23 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2OKZ _pdbx_database_related.details 'same peptide sequence in a different crystal packing' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sambashivan, S.' 1 'Sawaya, M.R.' 2 'Eisenberg, D.' 3 # _citation.id primary _citation.title 'Atomic structures of amyloid cross-beta spines reveal varied steric zippers.' _citation.journal_abbrev Nature _citation.journal_volume 447 _citation.page_first 453 _citation.page_last 457 _citation.year 2007 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17468747 _citation.pdbx_database_id_DOI 10.1038/nature05695 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sawaya, M.R.' 1 ? primary 'Sambashivan, S.' 2 ? primary 'Nelson, R.' 3 ? primary 'Ivanova, M.I.' 4 ? primary 'Sievers, S.A.' 5 ? primary 'Apostol, M.I.' 6 ? primary 'Thompson, M.J.' 7 ? primary 'Balbirnie, M.' 8 ? primary 'Wiltzius, J.J.' 9 ? primary 'McFarlane, H.T.' 10 ? primary 'Madsen, A.O.' 11 ? primary 'Riekel, C.' 12 ? primary 'Eisenberg, D.' 13 ? # 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 ;MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40 ; 560.707 4 ? ? 'residues 35-40' ? 2 water nat water 18.015 6 ? ? ? ? # _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 MVGGVV _entity_poly.pdbx_seq_one_letter_code_can MVGGVV _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 VAL n 1 3 GLY n 1 4 GLY n 1 5 VAL n 1 6 VAL n # 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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 MET 1 1 1 MET MET A . n A 1 2 VAL 2 2 2 VAL VAL A . n A 1 3 GLY 3 3 3 GLY GLY A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 VAL 5 5 5 VAL VAL A . n A 1 6 VAL 6 6 6 VAL VAL A . n B 1 1 MET 1 1 1 MET MET B . n B 1 2 VAL 2 2 2 VAL VAL B . n B 1 3 GLY 3 3 3 GLY GLY B . n B 1 4 GLY 4 4 4 GLY GLY B . n B 1 5 VAL 5 5 5 VAL VAL B . n B 1 6 VAL 6 6 6 VAL VAL B . n C 1 1 MET 1 1 1 MET MET C . n C 1 2 VAL 2 2 2 VAL VAL C . n C 1 3 GLY 3 3 3 GLY GLY C . n C 1 4 GLY 4 4 4 GLY GLY C . n C 1 5 VAL 5 5 5 VAL VAL C . n C 1 6 VAL 6 6 6 VAL VAL C . n D 1 1 MET 1 1 1 MET MET D . n D 1 2 VAL 2 2 2 VAL VAL D . n D 1 3 GLY 3 3 3 GLY GLY D . n D 1 4 GLY 4 4 4 GLY GLY D . n D 1 5 VAL 5 5 5 VAL VAL D . n D 1 6 VAL 6 6 6 VAL VAL D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 HOH 1 7 1 HOH HOH A . E 2 HOH 2 8 2 HOH HOH A . E 2 HOH 3 9 3 HOH HOH A . F 2 HOH 1 7 4 HOH HOH B . F 2 HOH 2 8 5 HOH HOH B . G 2 HOH 1 7 6 HOH HOH D . # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal DENZO . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data reduction' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 2 PHASER . ? other 'R. J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 3 REFMAC . ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 4 PDB_EXTRACT 2.000 'April. 3, 2006' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 5 # _cell.length_a 25.862 _cell.length_b 9.699 _cell.length_c 15.851 _cell.angle_alpha 77.180 _cell.angle_beta 74.690 _cell.angle_gamma 86.930 _cell.entry_id 2ONA _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 2ONA _symmetry.Int_Tables_number 1 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 2ONA _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews ? _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;30 mg/mL peptide in water mixed 1:1 with reservoir containing 0.02 M CaCl2, 30% MPD, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K ; _exptl_crystal_grow.pdbx_pH_range . # _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 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2005-12-18 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9466 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID13' _diffrn_source.pdbx_wavelength 0.9466 _diffrn_source.pdbx_wavelength_list ? _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID13 # _reflns.entry_id 2ONA _reflns.d_resolution_high 2.000 _reflns.d_resolution_low 90.000 _reflns.number_obs 409 _reflns.pdbx_Rmerge_I_obs 0.16 _reflns.pdbx_netI_over_sigmaI 10.200 _reflns.pdbx_chi_squared 1.068 _reflns.pdbx_redundancy 1.600 _reflns.percent_possible_obs 90.200 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3.0 _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate 25.4 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.00 _reflns_shell.d_res_low 2.15 _reflns_shell.number_measured_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_unique_obs ? _reflns_shell.Rmerge_I_obs 0.222 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 1.124 _reflns_shell.pdbx_redundancy 1.60 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 163 _reflns_shell.percent_possible_all 94.20 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2ONA _refine.ls_d_res_high 2.030 _refine.ls_d_res_low 24.940 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs ? _refine.ls_number_reflns_obs 409 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_R_factor_obs 0.211 _refine.ls_R_factor_R_work 0.202 _refine.ls_R_factor_R_free 0.264 _refine.ls_percent_reflns_R_free 10.800 _refine.ls_number_reflns_R_free 44 _refine.B_iso_mean 10.788 _refine.aniso_B[1][1] -0.100 _refine.aniso_B[2][2] 0.100 _refine.aniso_B[3][3] -0.080 _refine.aniso_B[1][2] -0.280 _refine.aniso_B[1][3] 0.260 _refine.aniso_B[2][3] -0.070 _refine.correlation_coeff_Fo_to_Fc 0.951 _refine.correlation_coeff_Fo_to_Fc_free 0.945 _refine.pdbx_overall_ESU_R_Free 0.481 _refine.overall_SU_ML 0.118 _refine.overall_SU_B 4.305 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.400 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'polyalanine idealized beta strand' _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 152 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 6 _refine_hist.number_atoms_total 158 _refine_hist.d_res_high 2.030 _refine_hist.d_res_low 24.940 # 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 148 0.009 0.023 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 80 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 196 1.254 2.057 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 204 0.669 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 20 2.560 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 24 18.457 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 28 0.084 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 156 0.003 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 20 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 19 0.159 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 62 0.180 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 66 0.140 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 99 0.085 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 5 0.145 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 12 0.230 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 16 0.177 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 2 0.096 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 137 1.732 2.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 52 0.456 2.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 176 1.821 3.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 37 2.080 2.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 20 2.628 3.000 ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_restr_ncs.dom_id _refine_ls_restr_ncs.pdbx_type _refine_ls_restr_ncs.pdbx_auth_asym_id _refine_ls_restr_ncs.pdbx_number _refine_ls_restr_ncs.rms_dev_position _refine_ls_restr_ncs.weight_position _refine_ls_restr_ncs.pdbx_ens_id _refine_ls_restr_ncs.pdbx_refine_id _refine_ls_restr_ncs.pdbx_ordinal _refine_ls_restr_ncs.ncs_model_details _refine_ls_restr_ncs.rms_dev_B_iso _refine_ls_restr_ncs.weight_B_iso _refine_ls_restr_ncs.pdbx_asym_id _refine_ls_restr_ncs.pdbx_rms _refine_ls_restr_ncs.pdbx_weight 1 'MEDIUM POSITIONAL' A 33 0.490 0.500 1 'X-RAY DIFFRACTION' 1 ? ? ? ? ? ? 2 'MEDIUM POSITIONAL' B 33 0.550 0.500 1 'X-RAY DIFFRACTION' 2 ? ? ? ? ? ? 3 'MEDIUM POSITIONAL' C 33 0.140 0.500 1 'X-RAY DIFFRACTION' 3 ? ? ? ? ? ? 4 'MEDIUM POSITIONAL' D 33 0.170 0.500 1 'X-RAY DIFFRACTION' 4 ? ? ? ? ? ? 1 'LOOSE POSITIONAL' A 25 0.800 5.000 1 'X-RAY DIFFRACTION' 5 ? ? ? ? ? ? 2 'LOOSE POSITIONAL' B 25 1.030 5.000 1 'X-RAY DIFFRACTION' 6 ? ? ? ? ? ? 3 'LOOSE POSITIONAL' C 25 0.600 5.000 1 'X-RAY DIFFRACTION' 7 ? ? ? ? ? ? 4 'LOOSE POSITIONAL' D 25 0.500 5.000 1 'X-RAY DIFFRACTION' 8 ? ? ? ? ? ? 1 'MEDIUM THERMAL' A 33 0.460 2.000 1 'X-RAY DIFFRACTION' 9 ? ? ? ? ? ? 2 'MEDIUM THERMAL' B 33 0.490 2.000 1 'X-RAY DIFFRACTION' 10 ? ? ? ? ? ? 3 'MEDIUM THERMAL' C 33 0.540 2.000 1 'X-RAY DIFFRACTION' 11 ? ? ? ? ? ? 4 'MEDIUM THERMAL' D 33 0.690 2.000 1 'X-RAY DIFFRACTION' 12 ? ? ? ? ? ? 1 'LOOSE THERMAL' A 25 1.570 10.000 1 'X-RAY DIFFRACTION' 13 ? ? ? ? ? ? 2 'LOOSE THERMAL' B 25 1.410 10.000 1 'X-RAY DIFFRACTION' 14 ? ? ? ? ? ? 3 'LOOSE THERMAL' C 25 1.030 10.000 1 'X-RAY DIFFRACTION' 15 ? ? ? ? ? ? 4 'LOOSE THERMAL' D 25 2.090 10.000 1 'X-RAY DIFFRACTION' 16 ? ? ? ? ? ? # _refine_ls_shell.d_res_high 2.030 _refine_ls_shell.d_res_low 2.085 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 37.310 _refine_ls_shell.number_reflns_R_work 24 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.208 _refine_ls_shell.R_factor_R_free 0.408 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 1 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs 25 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _struct_ncs_dom.pdbx_ens_id _struct_ncs_dom.id _struct_ncs_dom.details 1 1 A 1 2 B 1 3 C 1 4 D # loop_ _struct_ncs_dom_lim.pdbx_ens_id _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.pdbx_component_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.beg_auth_asym_id _struct_ncs_dom_lim.beg_auth_comp_id _struct_ncs_dom_lim.beg_auth_seq_id _struct_ncs_dom_lim.end_auth_asym_id _struct_ncs_dom_lim.end_auth_comp_id _struct_ncs_dom_lim.end_auth_seq_id _struct_ncs_dom_lim.pdbx_refine_code _struct_ncs_dom_lim.selection_details 1 1 1 A MET 1 . A VAL 6 . A MET 1 A VAL 6 5 ? 1 2 1 B MET 1 . B VAL 6 . B MET 1 B VAL 6 5 ? 1 3 1 C MET 1 . C VAL 6 . C MET 1 C VAL 6 5 ? 1 4 1 D MET 1 . D VAL 6 . D MET 1 D VAL 6 5 ? # _struct_ncs_ens.id 1 _struct_ncs_ens.details ? # _struct.entry_id 2ONA _struct.title ;MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40 ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2ONA _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' _struct_keywords.text 'steric zipper, beta sheet, PROTEIN FIBRIL' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2ONA _struct_ref.pdbx_db_accession 2ONA _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 2ONA A 1 ? 6 ? 2ONA 1 ? 6 ? 1 6 2 1 2ONA B 1 ? 6 ? 2ONA 1 ? 6 ? 1 6 3 1 2ONA C 1 ? 6 ? 2ONA 1 ? 6 ? 1 6 4 1 2ONA D 1 ? 6 ? 2ONA 1 ? 6 ? 1 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 1_565 x,y+1,z 1.0000000000 0.0000000000 0.0000000000 0.5194393823 0.0000000000 1.0000000000 0.0000000000 9.6850804709 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details 'The steric zipper can be generated by repeated application of the crystallographic unit cell translation along the b axis.' _struct_biol.pdbx_parent_biol_id ? # 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 VAL A 2 ? VAL A 5 ? VAL A 2 VAL A 5 A 2 VAL B 2 ? VAL B 5 ? VAL B 2 VAL B 5 B 1 VAL C 2 ? VAL C 5 ? VAL C 2 VAL C 5 B 2 VAL D 2 ? VAL D 5 ? VAL D 2 VAL 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 VAL A 5 ? N VAL A 5 O VAL B 2 ? O VAL B 2 B 1 2 N GLY C 3 ? N GLY C 3 O GLY D 4 ? O GLY D 4 # 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 GLY N N N N 1 GLY CA C N N 2 GLY C C N N 3 GLY O O N N 4 GLY OXT O N N 5 GLY H H N N 6 GLY H2 H N N 7 GLY HA2 H N N 8 GLY HA3 H N N 9 GLY HXT H N N 10 HOH O O N N 11 HOH H1 H N N 12 HOH H2 H N N 13 MET N N N N 14 MET CA C N S 15 MET C C N N 16 MET O O N N 17 MET CB C N N 18 MET CG C N N 19 MET SD S N N 20 MET CE C N N 21 MET OXT O N N 22 MET H H N N 23 MET H2 H N N 24 MET HA H N N 25 MET HB2 H N N 26 MET HB3 H N N 27 MET HG2 H N N 28 MET HG3 H N N 29 MET HE1 H N N 30 MET HE2 H N N 31 MET HE3 H N N 32 MET HXT H N N 33 VAL N N N N 34 VAL CA C N S 35 VAL C C N N 36 VAL O O N N 37 VAL CB C N N 38 VAL CG1 C N N 39 VAL CG2 C N N 40 VAL OXT O N N 41 VAL H H N N 42 VAL H2 H N N 43 VAL HA H N N 44 VAL HB H N N 45 VAL HG11 H N N 46 VAL HG12 H N N 47 VAL HG13 H N N 48 VAL HG21 H N N 49 VAL HG22 H N N 50 VAL HG23 H N N 51 VAL HXT H N N 52 # 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 GLY N CA sing N N 1 GLY N H sing N N 2 GLY N H2 sing N N 3 GLY CA C sing N N 4 GLY CA HA2 sing N N 5 GLY CA HA3 sing N N 6 GLY C O doub N N 7 GLY C OXT sing N N 8 GLY OXT HXT sing N N 9 HOH O H1 sing N N 10 HOH O H2 sing N N 11 MET N CA sing N N 12 MET N H sing N N 13 MET N H2 sing N N 14 MET CA C sing N N 15 MET CA CB sing N N 16 MET CA HA sing N N 17 MET C O doub N N 18 MET C OXT sing N N 19 MET CB CG sing N N 20 MET CB HB2 sing N N 21 MET CB HB3 sing N N 22 MET CG SD sing N N 23 MET CG HG2 sing N N 24 MET CG HG3 sing N N 25 MET SD CE sing N N 26 MET CE HE1 sing N N 27 MET CE HE2 sing N N 28 MET CE HE3 sing N N 29 MET OXT HXT sing N N 30 VAL N CA sing N N 31 VAL N H sing N N 32 VAL N H2 sing N N 33 VAL CA C sing N N 34 VAL CA CB sing N N 35 VAL CA HA sing N N 36 VAL C O doub N N 37 VAL C OXT sing N N 38 VAL CB CG1 sing N N 39 VAL CB CG2 sing N N 40 VAL CB HB sing N N 41 VAL CG1 HG11 sing N N 42 VAL CG1 HG12 sing N N 43 VAL CG1 HG13 sing N N 44 VAL CG2 HG21 sing N N 45 VAL CG2 HG22 sing N N 46 VAL CG2 HG23 sing N N 47 VAL OXT HXT sing N N 48 # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'polyalanine idealized beta strand' # _atom_sites.entry_id 2ONA _atom_sites.fract_transf_matrix[1][1] 0.038667 _atom_sites.fract_transf_matrix[1][2] -0.002074 _atom_sites.fract_transf_matrix[1][3] -0.010382 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.103252 _atom_sites.fract_transf_matrix[2][3] -0.022808 _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] 0.066986 _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_