data_3DG1 # _entry.id 3DG1 # _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 3DG1 pdb_00003dg1 10.2210/pdb3dg1/pdb RCSB RCSB047992 ? ? WWPDB D_1000047992 ? ? # 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 2008-07-01 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2015-06-03 4 'Structure model' 1 3 2017-10-25 5 'Structure model' 1 4 2024-02-21 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' 'Derived calculations' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 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 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' # _pdbx_database_status.entry_id 3DG1 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-06-12 _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.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1YJO . unspecified PDB 2OMM . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Wiltzius, J.J.' 1 'Sievers, S.A.' 2 'Sawaya, M.R.' 3 'Cascio, D.' 4 'Eisenberg, D.' 5 # _citation.id primary _citation.title 'Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin).' _citation.journal_abbrev 'Protein Sci.' _citation.journal_volume 17 _citation.page_first 1467 _citation.page_last 1474 _citation.year 2008 _citation.journal_id_ASTM PRCIEI _citation.country US _citation.journal_id_ISSN 0961-8368 _citation.journal_id_CSD 0795 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18556473 _citation.pdbx_database_id_DOI 10.1110/ps.036509.108 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wiltzius, J.J.' 1 ? primary 'Sievers, S.A.' 2 ? primary 'Sawaya, M.R.' 3 ? primary 'Cascio, D.' 4 ? primary 'Popov, D.' 5 ? primary 'Riekel, C.' 6 ? primary 'Eisenberg, D.' 7 ? # 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 'SSTNVG from Islet Amyloid Polypeptide' 563.560 1 ? ? ? ? 2 water nat water 18.015 2 ? ? ? ? # _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 SSTNVG _entity_poly.pdbx_seq_one_letter_code_can SSTNVG _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 SER n 1 2 SER n 1 3 THR n 1 4 ASN n 1 5 VAL n 1 6 GLY 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 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 SER 1 1 1 SER SER A . n A 1 2 SER 2 2 2 SER SER A . n A 1 3 THR 3 3 3 THR THR A . n A 1 4 ASN 4 4 4 ASN ASN A . n A 1 5 VAL 5 5 5 VAL VAL A . n A 1 6 GLY 6 6 6 GLY GLY 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 7 1 HOH HOH A . B 2 HOH 2 8 2 HOH HOH A . # 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' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 PHASER . ? 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 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 # _cell.length_a 41.400 _cell.length_b 4.785 _cell.length_c 18.594 _cell.angle_alpha 90.000 _cell.angle_beta 115.880 _cell.angle_gamma 90.000 _cell.entry_id 3DG1 _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 'C 1 2 1' _symmetry.entry_id 3DG1 _symmetry.Int_Tables_number 5 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3DG1 _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 ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details '30% MPD, no buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _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 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2007-07-21 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'Si(111) 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 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X06SA' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X06SA # _reflns.entry_id 3DG1 _reflns.d_resolution_high 1.650 _reflns.d_resolution_low 90.000 _reflns.number_obs 460 _reflns.pdbx_Rmerge_I_obs 0.170 _reflns.pdbx_netI_over_sigmaI 5.500 _reflns.pdbx_chi_squared 1.472 _reflns.pdbx_redundancy 2.800 _reflns.percent_possible_obs 97.900 _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.number_all 460 _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate 30.7 _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 # _reflns_shell.d_res_high 1.65 _reflns_shell.d_res_low 1.71 _reflns_shell.number_measured_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_unique_obs ? _reflns_shell.Rmerge_I_obs .524 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 1.426 _reflns_shell.pdbx_redundancy 3.10 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 37 _reflns_shell.percent_possible_all 97.40 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3DG1 _refine.ls_d_res_high 1.660 _refine.ls_d_res_low 18.620 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 95.620 _refine.ls_number_reflns_obs 459 _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 0.207 _refine.ls_R_factor_R_free 0.244 _refine.ls_percent_reflns_R_free 9.800 _refine.ls_number_reflns_R_free 45 _refine.B_iso_mean 19.277 _refine.aniso_B[1][1] 0.050 _refine.aniso_B[2][2] -0.920 _refine.aniso_B[3][3] 0.730 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] -0.170 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.967 _refine.correlation_coeff_Fo_to_Fc_free 0.960 _refine.pdbx_overall_ESU_R 0.146 _refine.pdbx_overall_ESU_R_Free 0.134 _refine.overall_SU_ML 0.077 _refine.overall_SU_B 2.359 _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_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.overall_FOM_work_R_set 0.826 _refine.B_iso_max 37.16 _refine.B_iso_min 14.55 _refine.occupancy_max 1.00 _refine.occupancy_min 0.50 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 459 _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_starting_model 'poly-alanine beta strand' _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _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 39 _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 41 _refine_hist.d_res_high 1.660 _refine_hist.d_res_low 18.620 # 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 38 0.006 0.021 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 20 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 51 1.011 1.967 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 51 0.455 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5 4.208 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 1 75.296 30.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 5 2.845 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 7 0.057 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 43 0.003 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 5 0.000 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 1 0.016 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 11 0.217 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 17 0.156 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 25 0.082 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 4 0.076 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 7 0.286 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 3 0.114 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 38 1.634 2.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 12 0.361 2.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 46 2.248 3.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 9 1.451 2.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 5 1.458 3.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.66 _refine_ls_shell.d_res_low 1.699 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 69.440 _refine_ls_shell.number_reflns_R_work 25 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.379 _refine_ls_shell.R_factor_R_free ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3DG1 _struct.title 'Segment SSTNVG derived from IAPP' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3DG1 _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' _struct_keywords.text 'steric zipper, IAPP, SSTNVG, Amyloid, 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 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3DG1 _struct_ref.pdbx_db_accession 3DG1 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3DG1 _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 3DG1 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 6 # _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 _pdbx_struct_assembly_gen.asym_id_list A,B # 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 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4.7850000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_575 x,y+2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 9.5700000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 4_556 -x+1/2,y+1/2,-z+1 -1.0000000000 0.0000000000 0.0000000000 12.5839466489 0.0000000000 1.0000000000 0.0000000000 2.3925000000 0.0000000000 0.0000000000 -1.0000000000 16.7292113981 5 'crystal symmetry operation' 4_566 -x+1/2,y+3/2,-z+1 -1.0000000000 0.0000000000 0.0000000000 12.5839466489 0.0000000000 1.0000000000 0.0000000000 7.1775000000 0.0000000000 0.0000000000 -1.0000000000 16.7292113981 6 'crystal symmetry operation' 4_576 -x+1/2,y+5/2,-z+1 -1.0000000000 0.0000000000 0.0000000000 12.5839466489 0.0000000000 1.0000000000 0.0000000000 11.9625000000 0.0000000000 0.0000000000 -1.0000000000 16.7292113981 # _struct_biol.id 1 _struct_biol.details ;The biologic assembly is an amyloid-like fiber that can be generated by multiple application of the symmetry operators X, Y+n, Z and 1/2-X,n+(1/2)+Y,-Z+1, where n is an integer. ; # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 7 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_phasing_MR.entry_id 3DG1 _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details ? _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 ? _pdbx_phasing_MR.d_res_low_rotation ? _pdbx_phasing_MR.d_res_high_translation ? _pdbx_phasing_MR.d_res_low_translation ? _pdbx_phasing_MR.packing 0.000 _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 ASN N N N N 1 ASN CA C N S 2 ASN C C N N 3 ASN O O N N 4 ASN CB C N N 5 ASN CG C N N 6 ASN OD1 O N N 7 ASN ND2 N N N 8 ASN OXT O N N 9 ASN H H N N 10 ASN H2 H N N 11 ASN HA H N N 12 ASN HB2 H N N 13 ASN HB3 H N N 14 ASN HD21 H N N 15 ASN HD22 H N N 16 ASN HXT H N N 17 GLY N N N N 18 GLY CA C N N 19 GLY C C N N 20 GLY O O N N 21 GLY OXT O N N 22 GLY H H N N 23 GLY H2 H N N 24 GLY HA2 H N N 25 GLY HA3 H N N 26 GLY HXT H N N 27 HOH O O N N 28 HOH H1 H N N 29 HOH H2 H N N 30 SER N N N N 31 SER CA C N S 32 SER C C N N 33 SER O O N N 34 SER CB C N N 35 SER OG O N N 36 SER OXT O N N 37 SER H H N N 38 SER H2 H N N 39 SER HA H N N 40 SER HB2 H N N 41 SER HB3 H N N 42 SER HG H N N 43 SER HXT H N N 44 THR N N N N 45 THR CA C N S 46 THR C C N N 47 THR O O N N 48 THR CB C N R 49 THR OG1 O N N 50 THR CG2 C N N 51 THR OXT O N N 52 THR H H N N 53 THR H2 H N N 54 THR HA H N N 55 THR HB H N N 56 THR HG1 H N N 57 THR HG21 H N N 58 THR HG22 H N N 59 THR HG23 H N N 60 THR HXT H N N 61 VAL N N N N 62 VAL CA C N S 63 VAL C C N N 64 VAL O O N N 65 VAL CB C N N 66 VAL CG1 C N N 67 VAL CG2 C N N 68 VAL OXT O N N 69 VAL H H N N 70 VAL H2 H N N 71 VAL HA H N N 72 VAL HB H N N 73 VAL HG11 H N N 74 VAL HG12 H N N 75 VAL HG13 H N N 76 VAL HG21 H N N 77 VAL HG22 H N N 78 VAL HG23 H N N 79 VAL HXT H N N 80 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ASN N CA sing N N 1 ASN N H sing N N 2 ASN N H2 sing N N 3 ASN CA C sing N N 4 ASN CA CB sing N N 5 ASN CA HA sing N N 6 ASN C O doub N N 7 ASN C OXT sing N N 8 ASN CB CG sing N N 9 ASN CB HB2 sing N N 10 ASN CB HB3 sing N N 11 ASN CG OD1 doub N N 12 ASN CG ND2 sing N N 13 ASN ND2 HD21 sing N N 14 ASN ND2 HD22 sing N N 15 ASN OXT HXT sing N N 16 GLY N CA sing N N 17 GLY N H sing N N 18 GLY N H2 sing N N 19 GLY CA C sing N N 20 GLY CA HA2 sing N N 21 GLY CA HA3 sing N N 22 GLY C O doub N N 23 GLY C OXT sing N N 24 GLY OXT HXT sing N N 25 HOH O H1 sing N N 26 HOH O H2 sing N N 27 SER N CA sing N N 28 SER N H sing N N 29 SER N H2 sing N N 30 SER CA C sing N N 31 SER CA CB sing N N 32 SER CA HA sing N N 33 SER C O doub N N 34 SER C OXT sing N N 35 SER CB OG sing N N 36 SER CB HB2 sing N N 37 SER CB HB3 sing N N 38 SER OG HG sing N N 39 SER OXT HXT sing N N 40 THR N CA sing N N 41 THR N H sing N N 42 THR N H2 sing N N 43 THR CA C sing N N 44 THR CA CB sing N N 45 THR CA HA sing N N 46 THR C O doub N N 47 THR C OXT sing N N 48 THR CB OG1 sing N N 49 THR CB CG2 sing N N 50 THR CB HB sing N N 51 THR OG1 HG1 sing N N 52 THR CG2 HG21 sing N N 53 THR CG2 HG22 sing N N 54 THR CG2 HG23 sing N N 55 THR OXT HXT sing N N 56 VAL N CA sing N N 57 VAL N H sing N N 58 VAL N H2 sing N N 59 VAL CA C sing N N 60 VAL CA CB sing N N 61 VAL CA HA sing N N 62 VAL C O doub N N 63 VAL C OXT sing N N 64 VAL CB CG1 sing N N 65 VAL CB CG2 sing N N 66 VAL CB HB sing N N 67 VAL CG1 HG11 sing N N 68 VAL CG1 HG12 sing N N 69 VAL CG1 HG13 sing N N 70 VAL CG2 HG21 sing N N 71 VAL CG2 HG22 sing N N 72 VAL CG2 HG23 sing N N 73 VAL OXT HXT sing N N 74 # _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 'poly-alanine beta strand' # _atom_sites.entry_id 3DG1 _atom_sites.fract_transf_matrix[1][1] 0.024155 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.011719 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.208986 _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] 0.059777 _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 # loop_