data_4E1I # _entry.id 4E1I # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4E1I RCSB RCSB071050 WWPDB D_1000071050 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 4E1H _pdbx_database_related.details 'Fragment of human prion protein from helices 2 and 3, with iron-citrate cluster' _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 4E1I _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-03-06 _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 # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Apostol, M.I.' 1 'Surewicz, W.K.' 2 # _citation.id primary _citation.title 'Crystal structure of a human prion protein fragment reveals a motif for oligomer formation.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 135 _citation.page_first 10202 _citation.page_last 10205 _citation.year 2013 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23808589 _citation.pdbx_database_id_DOI 10.1021/ja403001q # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Apostol, M.I.' 1 primary 'Perry, K.' 2 primary 'Surewicz, W.K.' 3 # _cell.length_a 35.338 _cell.length_b 41.217 _cell.length_c 46.600 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 4E1I _cell.pdbx_unique_axis ? _cell.Z_PDB 24 _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 21 21 21' _symmetry.entry_id 4E1I _symmetry.Int_Tables_number 19 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # 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 'Major prion protein' 700.784 6 ? ? 'UNP residues 177-182' ? 2 polymer syn 'Major prion protein' 723.858 6 ? ? 'UNP residues 211-216' ? 3 water nat water 18.015 67 ? ? ? ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 'PrP, ASCR, PrP27-30, PrP33-35C' 2 'PrP, ASCR, PrP27-30, PrP33-35C' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no HDCVNI HDCVNI A,C,E,G,I,K ? 2 'polypeptide(L)' no no EQMCIT EQMCIT B,D,F,H,J,L ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 HIS n 1 2 ASP n 1 3 CYS n 1 4 VAL n 1 5 ASN n 1 6 ILE n 2 1 GLU n 2 2 GLN n 2 3 MET n 2 4 CYS n 2 5 ILE n 2 6 THR n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? 'Homo sapiens' human 9606 ? 2 1 sample ? ? 'Homo sapiens' human 9606 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP PRIO_HUMAN P04156 1 HDCVNI 177 ? 2 UNP PRIO_HUMAN P04156 2 EQMCIT 211 ? # 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 4E1I A 1 ? 6 ? P04156 177 ? 182 ? 177 182 2 2 4E1I B 1 ? 6 ? P04156 211 ? 216 ? 211 216 3 1 4E1I C 1 ? 6 ? P04156 177 ? 182 ? 177 182 4 2 4E1I D 1 ? 6 ? P04156 211 ? 216 ? 211 216 5 1 4E1I E 1 ? 6 ? P04156 177 ? 182 ? 177 182 6 2 4E1I F 1 ? 6 ? P04156 211 ? 216 ? 211 216 7 1 4E1I G 1 ? 6 ? P04156 177 ? 182 ? 177 182 8 2 4E1I H 1 ? 6 ? P04156 211 ? 216 ? 211 216 9 1 4E1I I 1 ? 6 ? P04156 177 ? 182 ? 177 182 10 2 4E1I J 1 ? 6 ? P04156 211 ? 216 ? 211 216 11 1 4E1I K 1 ? 6 ? P04156 177 ? 182 ? 177 182 12 2 4E1I L 1 ? 6 ? P04156 211 ? 216 ? 211 216 # 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 4E1I _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.99 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 38.04 _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 5.5 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '100mM Bis Tris pH 5.5, 25% PEG 3350, vapor diffusion, hanging drop, temperature 298K' _exptl_crystal_grow.temp_details ? _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 'RIGAKU SATURN 944+' _diffrn_detector.pdbx_collection_date 2010-10-13 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU MICROMAX-007 HF' _diffrn_source.pdbx_wavelength_list 1.5418 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.entry_id 4E1I _reflns.d_resolution_high 2.028 _reflns.d_resolution_low 30.873 _reflns.number_all 4685 _reflns.number_obs 4685 _reflns.pdbx_netI_over_sigmaI 20.100 _reflns.pdbx_Rsym_value 0.064 _reflns.pdbx_redundancy 5.700 _reflns.percent_possible_obs 98.600 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.B_iso_Wilson_estimate ? _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_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.028 2.140 ? 2312 ? 0.196 3.900 0.196 ? 3.800 ? 605 90.700 1 1 2.140 2.270 ? 3806 ? 0.174 4.400 0.174 ? 6.000 ? 637 99.900 2 1 2.270 2.420 ? 3669 ? 0.140 5.500 0.140 ? 6.100 ? 606 100.000 3 1 2.420 2.620 ? 3469 ? 0.106 7.200 0.106 ? 6.200 ? 564 100.000 4 1 2.620 2.870 ? 3208 ? 0.093 7.900 0.093 ? 6.100 ? 522 100.000 5 1 2.870 3.210 ? 2925 ? 0.058 12.500 0.058 ? 6.100 ? 480 100.000 6 1 3.210 3.700 ? 2586 ? 0.044 15.400 0.044 ? 6.100 ? 426 100.000 7 1 3.700 4.530 ? 2185 ? 0.038 17.400 0.038 ? 5.900 ? 372 99.900 8 1 4.530 6.410 ? 1652 ? 0.037 15.300 0.037 ? 5.700 ? 289 99.800 9 1 6.410 41.217 ? 914 ? 0.038 16.100 0.038 ? 5.000 ? 184 98.400 10 1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4E1I _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 4649 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 23.30 _refine.ls_d_res_high 2.03 _refine.ls_percent_reflns_obs 98.3 _refine.ls_R_factor_obs 0.190 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.187 _refine.ls_R_factor_R_free 0.253 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.600 _refine.ls_number_reflns_R_free 212 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.944 _refine.correlation_coeff_Fo_to_Fc_free 0.905 _refine.B_iso_mean 18.35 _refine.aniso_B[1][1] 0.39000 _refine.aniso_B[2][2] 0.07000 _refine.aniso_B[3][3] -0.45000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _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 U VALUES: WITH TLS ADDED' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _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 0.234 _refine.pdbx_overall_ESU_R_Free 0.202 _refine.overall_SU_ML 0.131 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 5.172 _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.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 576 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 67 _refine_hist.number_atoms_total 643 _refine_hist.d_res_high 2.03 _refine_hist.d_res_low 23.30 # 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 0.012 0.021 ? 594 'X-RAY DIFFRACTION' ? r_bond_other_d 0.000 0.020 ? 334 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.225 1.945 ? 800 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.649 3.000 ? 849 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 10.208 5.000 ? 63 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 42.904 27.813 ? 32 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 17.085 15.000 ? 111 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.081 0.200 ? 98 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.010 0.020 ? 624 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.003 0.020 ? 76 '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 1.534 1.500 ? 368 'X-RAY DIFFRACTION' ? r_mcbond_other 0.412 1.500 ? 134 'X-RAY DIFFRACTION' ? r_mcangle_it 2.607 2.000 ? 602 'X-RAY DIFFRACTION' ? r_scbond_it 4.282 3.000 ? 226 'X-RAY DIFFRACTION' ? r_scangle_it 6.290 4.500 ? 197 '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 2.03 _refine_ls_shell.d_res_low 2.08 _refine_ls_shell.number_reflns_R_work 275 _refine_ls_shell.R_factor_R_work 0.2050 _refine_ls_shell.percent_reflns_obs 81.18 _refine_ls_shell.R_factor_R_free 0.3500 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 14 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 4E1I _struct.title 'Fragment of human prion protein' _struct.pdbx_descriptor 'Major prion protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4E1I _struct_keywords.text 'beta prism, amyloid-related oligomer, PROTEIN FIBRIL, cell cycle' _struct_keywords.pdbx_keywords 'CELL CYCLE' # 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 ? C N N 1 ? D N N 2 ? E N N 1 ? F N N 2 ? G N N 1 ? H N N 2 ? I N N 1 ? J N N 2 ? K N N 1 ? L N N 2 ? M N N 3 ? N N N 3 ? O N N 3 ? P N N 3 ? Q N N 3 ? R N N 3 ? S N N 3 ? T N N 3 ? U N N 3 ? V N N 3 ? W N N 3 ? X N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf1 disulf ? ? A CYS 3 SG ? ? ? 1_555 B CYS 4 SG ? ? A CYS 179 B CYS 214 1_555 ? ? ? ? ? ? ? 2.021 ? disulf2 disulf ? ? C CYS 3 SG ? ? ? 1_555 D CYS 4 SG ? ? C CYS 179 D CYS 214 1_555 ? ? ? ? ? ? ? 2.034 ? disulf3 disulf ? ? E CYS 3 SG ? ? ? 1_555 F CYS 4 SG ? ? E CYS 179 F CYS 214 1_555 ? ? ? ? ? ? ? 2.074 ? disulf4 disulf ? ? G CYS 3 SG ? ? ? 1_555 H CYS 4 SG ? ? G CYS 179 H CYS 214 1_555 ? ? ? ? ? ? ? 2.003 ? disulf5 disulf ? ? I CYS 3 SG ? ? ? 1_555 J CYS 4 SG ? ? I CYS 179 J CYS 214 1_555 ? ? ? ? ? ? ? 2.029 ? disulf6 disulf ? ? K CYS 3 SG ? ? ? 1_555 L CYS 4 SG ? ? K CYS 179 L CYS 214 1_555 ? ? ? ? ? ? ? 2.042 ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 4 ? C ? 4 ? # 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 A 2 3 ? anti-parallel A 3 4 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel C 3 4 ? 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 ASP A 2 ? ASN A 5 ? ASP A 178 ASN A 181 A 2 GLN B 2 ? ILE B 5 ? GLN B 212 ILE B 215 A 3 GLN D 2 ? ILE D 5 ? GLN D 212 ILE D 215 A 4 ASP C 2 ? ASN C 5 ? ASP C 178 ASN C 181 B 1 CYS E 3 ? ASN E 5 ? CYS E 179 ASN E 181 B 2 GLN F 2 ? THR F 6 ? GLN F 212 THR F 216 B 3 GLN H 2 ? ILE H 5 ? GLN H 212 ILE H 215 B 4 CYS G 3 ? ASN G 5 ? CYS G 179 ASN G 181 C 1 CYS I 3 ? ASN I 5 ? CYS I 179 ASN I 181 C 2 GLN J 2 ? THR J 6 ? GLN J 212 THR J 216 C 3 GLN L 2 ? ILE L 5 ? GLN L 212 ILE L 215 C 4 CYS K 3 ? ASN K 5 ? CYS K 179 ASN K 181 # 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 ASP A 2 ? N ASP A 178 O ILE B 5 ? O ILE B 215 A 2 3 N CYS B 4 ? N CYS B 214 O CYS D 4 ? O CYS D 214 A 3 4 O ILE D 5 ? O ILE D 215 N ASP C 2 ? N ASP C 178 B 1 2 N VAL E 4 ? N VAL E 180 O MET F 3 ? O MET F 213 B 2 3 N CYS F 4 ? N CYS F 214 O CYS H 4 ? O CYS H 214 B 3 4 O MET H 3 ? O MET H 213 N VAL G 4 ? N VAL G 180 C 1 2 N VAL I 4 ? N VAL I 180 O MET J 3 ? O MET J 213 C 2 3 N CYS J 4 ? N CYS J 214 O CYS L 4 ? O CYS L 214 C 3 4 O MET L 3 ? O MET L 213 N VAL K 4 ? N VAL K 180 # _atom_sites.entry_id 4E1I _atom_sites.fract_transf_matrix[1][1] 0.028298 _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] 0.024262 _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] 0.021459 _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_ _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 HIS 1 177 177 HIS HIS A . n A 1 2 ASP 2 178 178 ASP ASP A . n A 1 3 CYS 3 179 179 CYS CYS A . n A 1 4 VAL 4 180 180 VAL VAL A . n A 1 5 ASN 5 181 181 ASN ASN A . n A 1 6 ILE 6 182 182 ILE ILE A . n B 2 1 GLU 1 211 211 GLU GLU B . n B 2 2 GLN 2 212 212 GLN GLN B . n B 2 3 MET 3 213 213 MET MET B . n B 2 4 CYS 4 214 214 CYS CYS B . n B 2 5 ILE 5 215 215 ILE ILE B . n B 2 6 THR 6 216 216 THR THR B . n C 1 1 HIS 1 177 177 HIS HIS C . n C 1 2 ASP 2 178 178 ASP ASP C . n C 1 3 CYS 3 179 179 CYS CYS C . n C 1 4 VAL 4 180 180 VAL VAL C . n C 1 5 ASN 5 181 181 ASN ASN C . n C 1 6 ILE 6 182 182 ILE ILE C . n D 2 1 GLU 1 211 211 GLU GLU D . n D 2 2 GLN 2 212 212 GLN GLN D . n D 2 3 MET 3 213 213 MET MET D . n D 2 4 CYS 4 214 214 CYS CYS D . n D 2 5 ILE 5 215 215 ILE ILE D . n D 2 6 THR 6 216 216 THR THR D . n E 1 1 HIS 1 177 177 HIS HIS E . n E 1 2 ASP 2 178 178 ASP ASP E . n E 1 3 CYS 3 179 179 CYS CYS E . n E 1 4 VAL 4 180 180 VAL VAL E . n E 1 5 ASN 5 181 181 ASN ASN E . n E 1 6 ILE 6 182 182 ILE ILE E . n F 2 1 GLU 1 211 211 GLU GLU F . n F 2 2 GLN 2 212 212 GLN GLN F . n F 2 3 MET 3 213 213 MET MET F . n F 2 4 CYS 4 214 214 CYS CYS F . n F 2 5 ILE 5 215 215 ILE ILE F . n F 2 6 THR 6 216 216 THR THR F . n G 1 1 HIS 1 177 177 HIS HIS G . n G 1 2 ASP 2 178 178 ASP ASP G . n G 1 3 CYS 3 179 179 CYS CYS G . n G 1 4 VAL 4 180 180 VAL VAL G . n G 1 5 ASN 5 181 181 ASN ASN G . n G 1 6 ILE 6 182 182 ILE ILE G . n H 2 1 GLU 1 211 211 GLU GLU H . n H 2 2 GLN 2 212 212 GLN GLN H . n H 2 3 MET 3 213 213 MET MET H . n H 2 4 CYS 4 214 214 CYS CYS H . n H 2 5 ILE 5 215 215 ILE ILE H . n H 2 6 THR 6 216 216 THR THR H . n I 1 1 HIS 1 177 177 HIS HIS I . n I 1 2 ASP 2 178 178 ASP ASP I . n I 1 3 CYS 3 179 179 CYS CYS I . n I 1 4 VAL 4 180 180 VAL VAL I . n I 1 5 ASN 5 181 181 ASN ASN I . n I 1 6 ILE 6 182 182 ILE ILE I . n J 2 1 GLU 1 211 211 GLU GLU J . n J 2 2 GLN 2 212 212 GLN GLN J . n J 2 3 MET 3 213 213 MET MET J . n J 2 4 CYS 4 214 214 CYS CYS J . n J 2 5 ILE 5 215 215 ILE ILE J . n J 2 6 THR 6 216 216 THR THR J . n K 1 1 HIS 1 177 177 HIS HIS K . n K 1 2 ASP 2 178 178 ASP ASP K . n K 1 3 CYS 3 179 179 CYS CYS K . n K 1 4 VAL 4 180 180 VAL VAL K . n K 1 5 ASN 5 181 181 ASN ASN K . n K 1 6 ILE 6 182 182 ILE ILE K . n L 2 1 GLU 1 211 211 GLU GLU L . n L 2 2 GLN 2 212 212 GLN GLN L . n L 2 3 MET 3 213 213 MET MET L . n L 2 4 CYS 4 214 214 CYS CYS L . n L 2 5 ILE 5 215 215 ILE ILE L . n L 2 6 THR 6 216 216 THR THR L . n # _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 dodecameric _pdbx_struct_assembly.oligomeric_count 12 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X # 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)' 7340 ? 1 MORE -57 ? 1 'SSA (A^2)' 4520 ? # _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 # 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 2013-03-06 2 'Structure model' 1 1 2013-11-27 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x -12.5408 _pdbx_refine_tls.origin_y 1.9013 _pdbx_refine_tls.origin_z 8.8177 _pdbx_refine_tls.T[1][1] 0.0730 _pdbx_refine_tls.T[2][2] 0.0573 _pdbx_refine_tls.T[3][3] 0.0245 _pdbx_refine_tls.T[1][2] 0.0483 _pdbx_refine_tls.T[1][3] 0.0413 _pdbx_refine_tls.T[2][3] 0.0150 _pdbx_refine_tls.L[1][1] 3.9660 _pdbx_refine_tls.L[2][2] 2.7367 _pdbx_refine_tls.L[3][3] 5.5905 _pdbx_refine_tls.L[1][2] 1.2601 _pdbx_refine_tls.L[1][3] 3.8912 _pdbx_refine_tls.L[2][3] 0.9050 _pdbx_refine_tls.S[1][1] 0.0837 _pdbx_refine_tls.S[1][2] -0.0710 _pdbx_refine_tls.S[1][3] -0.0777 _pdbx_refine_tls.S[2][1] 0.1232 _pdbx_refine_tls.S[2][2] 0.2043 _pdbx_refine_tls.S[2][3] -0.0380 _pdbx_refine_tls.S[3][1] -0.2999 _pdbx_refine_tls.S[3][2] -0.3194 _pdbx_refine_tls.S[3][3] -0.2880 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 177 _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 182 _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ? # _pdbx_phasing_MR.entry_id 4E1I _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor ? _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation 2.030 _pdbx_phasing_MR.d_res_low_rotation 26.830 _pdbx_phasing_MR.d_res_high_translation 2.030 _pdbx_phasing_MR.d_res_low_translation 26.830 _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALA 3.3.16 2010/01/06 other 'Phil R. Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/scala.html Fortran_77 ? 2 PHASER 2.1.4 'Wed Jun 24 14:00:05 2009' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 3 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 XSCALE . ? ? ? ? 'data scaling' ? ? ? # _pdbx_entry_details.entry_id 4E1I _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details 'FRAGMENT OF HUMAN PRION PROTEIN FROM HELIX 2 AND 3' _pdbx_entry_details.source_details ;SEGMENTS CORRESPONDING TO RESIDUES 177-182 AND 211-216 OF HUMAN PRION WAS LINKED BY DISULFIDE BOND BETWEEN 179 AND 214 DURING SYNTHESIS ; # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OE2 _pdbx_validate_close_contact.auth_asym_id_1 D _pdbx_validate_close_contact.auth_comp_id_1 GLU _pdbx_validate_close_contact.auth_seq_id_1 211 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 K _pdbx_validate_close_contact.auth_comp_id_2 ILE _pdbx_validate_close_contact.auth_seq_id_2 182 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.16 # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # 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 M 3 HOH 1 201 201 HOH HOH A . M 3 HOH 2 202 202 HOH HOH A . M 3 HOH 3 203 203 HOH HOH A . M 3 HOH 4 204 204 HOH HOH A . N 3 HOH 1 301 301 HOH HOH B . N 3 HOH 2 302 302 HOH HOH B . N 3 HOH 3 303 303 HOH HOH B . N 3 HOH 4 304 304 HOH HOH B . N 3 HOH 5 305 305 HOH HOH B . O 3 HOH 1 201 201 HOH HOH C . O 3 HOH 2 202 202 HOH HOH C . O 3 HOH 3 203 203 HOH HOH C . O 3 HOH 4 204 204 HOH HOH C . O 3 HOH 5 205 205 HOH HOH C . P 3 HOH 1 301 301 HOH HOH D . Q 3 HOH 1 201 201 HOH HOH E . Q 3 HOH 2 202 202 HOH HOH E . Q 3 HOH 3 203 203 HOH HOH E . Q 3 HOH 4 204 204 HOH HOH E . Q 3 HOH 5 205 205 HOH HOH E . R 3 HOH 1 301 301 HOH HOH F . R 3 HOH 2 302 302 HOH HOH F . R 3 HOH 3 303 303 HOH HOH F . R 3 HOH 4 304 304 HOH HOH F . R 3 HOH 5 305 305 HOH HOH F . R 3 HOH 6 306 306 HOH HOH F . R 3 HOH 7 307 307 HOH HOH F . R 3 HOH 8 308 308 HOH HOH F . S 3 HOH 1 201 201 HOH HOH G . S 3 HOH 2 202 202 HOH HOH G . S 3 HOH 3 203 203 HOH HOH G . S 3 HOH 4 204 204 HOH HOH G . S 3 HOH 5 205 205 HOH HOH G . S 3 HOH 6 206 206 HOH HOH G . S 3 HOH 7 207 207 HOH HOH G . T 3 HOH 1 301 301 HOH HOH H . T 3 HOH 2 302 302 HOH HOH H . T 3 HOH 3 303 303 HOH HOH H . T 3 HOH 4 304 304 HOH HOH H . T 3 HOH 5 305 305 HOH HOH H . U 3 HOH 1 201 201 HOH HOH I . U 3 HOH 2 202 202 HOH HOH I . U 3 HOH 3 203 203 HOH HOH I . U 3 HOH 4 204 204 HOH HOH I . U 3 HOH 5 205 205 HOH HOH I . U 3 HOH 6 206 206 HOH HOH I . U 3 HOH 7 207 207 HOH HOH I . U 3 HOH 8 208 208 HOH HOH I . U 3 HOH 9 209 209 HOH HOH I . V 3 HOH 1 301 301 HOH HOH J . V 3 HOH 2 302 302 HOH HOH J . V 3 HOH 3 303 303 HOH HOH J . V 3 HOH 4 304 304 HOH HOH J . V 3 HOH 5 305 305 HOH HOH J . V 3 HOH 6 306 306 HOH HOH J . V 3 HOH 7 307 307 HOH HOH J . V 3 HOH 8 308 308 HOH HOH J . W 3 HOH 1 201 201 HOH HOH K . W 3 HOH 2 202 202 HOH HOH K . W 3 HOH 3 203 203 HOH HOH K . W 3 HOH 4 204 204 HOH HOH K . W 3 HOH 5 205 205 HOH HOH K . W 3 HOH 6 206 206 HOH HOH K . X 3 HOH 1 301 301 HOH HOH L . X 3 HOH 2 302 302 HOH HOH L . X 3 HOH 3 303 303 HOH HOH L . X 3 HOH 4 304 304 HOH HOH L . #