data_2ONX # _entry.id 2ONX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 2ONX pdb_00002onx 10.2210/pdb2onx/pdb RCSB RCSB041369 ? ? WWPDB D_1000041369 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1YJP . unspecified PDB 1YJO . unspecified PDB 2OKZ . unspecified PDB 2OLX . unspecified # _pdbx_database_status.entry_id 2ONX _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-01-24 _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sawaya, M.R.' 1 'Sambashivan, S.' 2 'Nelson, R.' 3 'Ivanova, M.' 4 'Sievers, S.A.' 5 'Apostol, M.I.' 6 'Thompson, M.J.' 7 'Balbirnie, M.' 8 'Wiltzius, J.J.' 9 'McFarlane, H.' 10 'Madsen, A.O.' 11 'Riekel, C.' 12 'Eisenberg, D.' 13 # _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 ? # _cell.length_a 4.854 _cell.length_b 16.014 _cell.length_c 15.546 _cell.angle_alpha 90.000 _cell.angle_beta 96.910 _cell.angle_gamma 90.000 _cell.entry_id 2ONX _cell.pdbx_unique_axis ? _cell.Z_PDB 2 _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 21 1' _symmetry.entry_id 2ONX _symmetry.Int_Tables_number 4 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'peptide corresponding to residues 8-11 of yeast prion sup35' _entity.formula_weight 502.478 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'residues 8-11' _entity.details ? # _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 NNQQ _entity_poly.pdbx_seq_one_letter_code_can NNQQ _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASN n 1 2 ASN n 1 3 GLN n 1 4 GLN n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2ONX _struct_ref.pdbx_db_accession 2ONX _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2ONX _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 4 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2ONX _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 4 _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 4 # 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 # _exptl.crystals_number 1 _exptl.entry_id 2ONX _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 5.6 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;30-50 mg/mL peptide disolved in water and mixed with an equal volume of reservoir solution consisting of 100 mM trisodium citrate, 20% polyethylene glycol 4000 and 20% isopropanol, pH 5.6, 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 2005-07-16 _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 0.94660 _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 0.94660 _diffrn_source.pdbx_wavelength_list ? _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID13 # _reflns.entry_id 2ONX _reflns.d_resolution_high 1.500 _reflns.d_resolution_low 90.000 _reflns.number_obs 259 _reflns.pdbx_Rmerge_I_obs 0.152 _reflns.pdbx_netI_over_sigmaI 10.100 _reflns.pdbx_chi_squared 1.150 _reflns.pdbx_redundancy 1.500 _reflns.percent_possible_obs 63.800 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I 0 _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate 20.4 _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 # 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_diffrn_id _reflns_shell.pdbx_ordinal 1.50 1.62 ? ? ? 0.299 ? ? 0.949 1.20 ? 23 26.10 ? 1 1.62 1.78 ? ? ? 0.277 ? ? 1.011 1.10 ? 29 42.60 ? 2 1.78 2.04 ? ? ? 0.322 ? ? 1.279 1.30 ? 63 79.70 ? 3 2.04 2.56 ? ? ? 0.173 ? ? 1.072 1.40 ? 74 85.10 ? 4 2.56 90.00 ? ? ? 0.101 ? ? 1.169 1.90 ? 70 83.30 ? 5 # _refine.entry_id 2ONX _refine.ls_d_res_high 1.520 _refine.ls_d_res_low 15.430 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 66.050 _refine.ls_number_reflns_obs 251 _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 0.175 _refine.ls_R_factor_R_work 0.172 _refine.ls_R_factor_R_free 0.202 _refine.ls_percent_reflns_R_free 11.200 _refine.ls_number_reflns_R_free 28 _refine.B_iso_mean 12.236 _refine.aniso_B[1][1] -1.650 _refine.aniso_B[2][2] 0.160 _refine.aniso_B[3][3] 1.590 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.390 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.968 _refine.correlation_coeff_Fo_to_Fc_free 0.962 _refine.pdbx_overall_ESU_R 0.203 _refine.pdbx_overall_ESU_R_Free 0.146 _refine.overall_SU_ML 0.072 _refine.overall_SU_B 2.275 _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 'pdb entry 1yjp' _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.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 35 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 35 _refine_hist.d_res_high 1.520 _refine_hist.d_res_low 15.430 # 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 34 0.013 0.021 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 19 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 45 1.314 1.851 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 48 0.926 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 3 6.443 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 4 49.819 30.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 6 12.152 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 4 0.148 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 41 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 3 0.000 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 1 0.201 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 16 0.165 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 12 0.158 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 21 0.066 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 9 0.178 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 3 0.170 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 26 4.914 2.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 7 1.240 2.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 31 8.154 3.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 16 5.002 2.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 14 7.297 3.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.520 _refine_ls_shell.d_res_low 1.563 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 33.330 _refine_ls_shell.number_reflns_R_work 9 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.556 _refine_ls_shell.R_factor_R_free 0.487 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 2 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs 11 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2ONX _struct.title 'NNQQ peptide corresponding to residues 8-11 of yeast prion sup35 (alternate crystal form)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2ONX _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' _struct_keywords.text 'steric zipper, beta sheets, PROTEIN FIBRIL' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.details ;One sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the "a" unit cell dimension. The second sheet of the steric zipper can be generated by application of the crystallographic operator -X,1/2+Y,1-Z, and repeated unit cell translations of this strand along the "a" unit cell dimension. ; _struct_biol.pdbx_parent_biol_id ? # _database_PDB_matrix.entry_id 2ONX _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 2ONX _atom_sites.fract_transf_matrix[1][1] 0.206016 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.024967 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.062445 _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] 0.064796 _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_ _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 ASN 1 1 1 ASN ASN A . n A 1 2 ASN 2 2 2 ASN ASN A . n A 1 3 GLN 3 3 3 GLN GLN A . n A 1 4 GLN 4 4 4 GLN GLN A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 _pdbx_struct_assembly_gen.asym_id_list A # 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_655 x+1,y,z 1.0000000000 0.0000000000 0.0000000000 4.8540000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 2_556 -x,y+1/2,-z+1 -1.0000000000 0.0000000000 0.0000000000 -1.8703409055 0.0000000000 1.0000000000 0.0000000000 8.0070000000 0.0000000000 0.0000000000 -1.0000000000 15.4330794366 4 'crystal symmetry operation' 2_656 -x+1,y+1/2,-z+1 -1.0000000000 0.0000000000 0.0000000000 2.9836590945 0.0000000000 1.0000000000 0.0000000000 8.0070000000 0.0000000000 0.0000000000 -1.0000000000 15.4330794366 # 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 2007-02-06 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 2023-08-30 # _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' # 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' 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' # 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 # 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 GLN N N N N 18 GLN CA C N S 19 GLN C C N N 20 GLN O O N N 21 GLN CB C N N 22 GLN CG C N N 23 GLN CD C N N 24 GLN OE1 O N N 25 GLN NE2 N N N 26 GLN OXT O N N 27 GLN H H N N 28 GLN H2 H N N 29 GLN HA H N N 30 GLN HB2 H N N 31 GLN HB3 H N N 32 GLN HG2 H N N 33 GLN HG3 H N N 34 GLN HE21 H N N 35 GLN HE22 H N N 36 GLN HXT H N N 37 # 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 GLN N CA sing N N 17 GLN N H sing N N 18 GLN N H2 sing N N 19 GLN CA C sing N N 20 GLN CA CB sing N N 21 GLN CA HA sing N N 22 GLN C O doub N N 23 GLN C OXT sing N N 24 GLN CB CG sing N N 25 GLN CB HB2 sing N N 26 GLN CB HB3 sing N N 27 GLN CG CD sing N N 28 GLN CG HG2 sing N N 29 GLN CG HG3 sing N N 30 GLN CD OE1 doub N N 31 GLN CD NE2 sing N N 32 GLN NE2 HE21 sing N N 33 GLN NE2 HE22 sing N N 34 GLN OXT HXT sing N N 35 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1YJP _pdbx_initial_refinement_model.details 'pdb entry 1yjp' #