data_1NIO # _entry.id 1NIO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1NIO RCSB RCSB017901 WWPDB D_1000017901 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NIO _pdbx_database_status.recvd_initial_deposition_date 2002-12-24 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _audit_author.name 'Wu, S.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of beta-luffin, a ribosome-inactivating protein, at 2.0 A resolution.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 59 _citation.page_first 1366 _citation.page_last 1370 _citation.year 2003 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12876337 _citation.pdbx_database_id_DOI 10.1107/S0907444903011156 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ma, Q.J.' 1 ? primary 'Li, J.H.' 2 ? primary 'Li, H.G.' 3 ? primary 'Wu, S.' 4 ? primary 'Dong, Y.C.' 5 ? # _cell.entry_id 1NIO _cell.length_a 89.902 _cell.length_b 59.823 _cell.length_c 55.184 _cell.angle_alpha 90.00 _cell.angle_beta 120.81 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NIO _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # 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 man b-luffin 27104.002 1 3.2.2.22 ? 'residues 1-247' ? 2 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 3 ? ? ? ? 3 water nat water 18.015 128 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name beta-luffin # _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 ;ANVSFSLSGADSKSYSKFITALRKALPSKEKVSNIPLLLPSASGASRYILMQLSNYDAKAITMAIDVTNVYIMGYLVNST SYFFNESDAKLASQYVFKGSTIVTLPYSGNYERLQNAAGKVREKIPLGFRAFDSAITSLFHYDSTAAAGAFLVIIQTTAE ASRFKYIEGQIIKRIPKNEVPSPAALSLENEWSALSKQIQLAQTNNGAFRTPVVIIDNKGQRVEIKDVNSKVVTNNIKLL LNKQNIA ; _entity_poly.pdbx_seq_one_letter_code_can ;ANVSFSLSGADSKSYSKFITALRKALPSKEKVSNIPLLLPSASGASRYILMQLSNYDAKAITMAIDVTNVYIMGYLVNST SYFFNESDAKLASQYVFKGSTIVTLPYSGNYERLQNAAGKVREKIPLGFRAFDSAITSLFHYDSTAAAGAFLVIIQTTAE ASRFKYIEGQIIKRIPKNEVPSPAALSLENEWSALSKQIQLAQTNNGAFRTPVVIIDNKGQRVEIKDVNSKVVTNNIKLL LNKQNIA ; _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 ALA n 1 2 ASN n 1 3 VAL n 1 4 SER n 1 5 PHE n 1 6 SER n 1 7 LEU n 1 8 SER n 1 9 GLY n 1 10 ALA n 1 11 ASP n 1 12 SER n 1 13 LYS n 1 14 SER n 1 15 TYR n 1 16 SER n 1 17 LYS n 1 18 PHE n 1 19 ILE n 1 20 THR n 1 21 ALA n 1 22 LEU n 1 23 ARG n 1 24 LYS n 1 25 ALA n 1 26 LEU n 1 27 PRO n 1 28 SER n 1 29 LYS n 1 30 GLU n 1 31 LYS n 1 32 VAL n 1 33 SER n 1 34 ASN n 1 35 ILE n 1 36 PRO n 1 37 LEU n 1 38 LEU n 1 39 LEU n 1 40 PRO n 1 41 SER n 1 42 ALA n 1 43 SER n 1 44 GLY n 1 45 ALA n 1 46 SER n 1 47 ARG n 1 48 TYR n 1 49 ILE n 1 50 LEU n 1 51 MET n 1 52 GLN n 1 53 LEU n 1 54 SER n 1 55 ASN n 1 56 TYR n 1 57 ASP n 1 58 ALA n 1 59 LYS n 1 60 ALA n 1 61 ILE n 1 62 THR n 1 63 MET n 1 64 ALA n 1 65 ILE n 1 66 ASP n 1 67 VAL n 1 68 THR n 1 69 ASN n 1 70 VAL n 1 71 TYR n 1 72 ILE n 1 73 MET n 1 74 GLY n 1 75 TYR n 1 76 LEU n 1 77 VAL n 1 78 ASN n 1 79 SER n 1 80 THR n 1 81 SER n 1 82 TYR n 1 83 PHE n 1 84 PHE n 1 85 ASN n 1 86 GLU n 1 87 SER n 1 88 ASP n 1 89 ALA n 1 90 LYS n 1 91 LEU n 1 92 ALA n 1 93 SER n 1 94 GLN n 1 95 TYR n 1 96 VAL n 1 97 PHE n 1 98 LYS n 1 99 GLY n 1 100 SER n 1 101 THR n 1 102 ILE n 1 103 VAL n 1 104 THR n 1 105 LEU n 1 106 PRO n 1 107 TYR n 1 108 SER n 1 109 GLY n 1 110 ASN n 1 111 TYR n 1 112 GLU n 1 113 ARG n 1 114 LEU n 1 115 GLN n 1 116 ASN n 1 117 ALA n 1 118 ALA n 1 119 GLY n 1 120 LYS n 1 121 VAL n 1 122 ARG n 1 123 GLU n 1 124 LYS n 1 125 ILE n 1 126 PRO n 1 127 LEU n 1 128 GLY n 1 129 PHE n 1 130 ARG n 1 131 ALA n 1 132 PHE n 1 133 ASP n 1 134 SER n 1 135 ALA n 1 136 ILE n 1 137 THR n 1 138 SER n 1 139 LEU n 1 140 PHE n 1 141 HIS n 1 142 TYR n 1 143 ASP n 1 144 SER n 1 145 THR n 1 146 ALA n 1 147 ALA n 1 148 ALA n 1 149 GLY n 1 150 ALA n 1 151 PHE n 1 152 LEU n 1 153 VAL n 1 154 ILE n 1 155 ILE n 1 156 GLN n 1 157 THR n 1 158 THR n 1 159 ALA n 1 160 GLU n 1 161 ALA n 1 162 SER n 1 163 ARG n 1 164 PHE n 1 165 LYS n 1 166 TYR n 1 167 ILE n 1 168 GLU n 1 169 GLY n 1 170 GLN n 1 171 ILE n 1 172 ILE n 1 173 LYS n 1 174 ARG n 1 175 ILE n 1 176 PRO n 1 177 LYS n 1 178 ASN n 1 179 GLU n 1 180 VAL n 1 181 PRO n 1 182 SER n 1 183 PRO n 1 184 ALA n 1 185 ALA n 1 186 LEU n 1 187 SER n 1 188 LEU n 1 189 GLU n 1 190 ASN n 1 191 GLU n 1 192 TRP n 1 193 SER n 1 194 ALA n 1 195 LEU n 1 196 SER n 1 197 LYS n 1 198 GLN n 1 199 ILE n 1 200 GLN n 1 201 LEU n 1 202 ALA n 1 203 GLN n 1 204 THR n 1 205 ASN n 1 206 ASN n 1 207 GLY n 1 208 ALA n 1 209 PHE n 1 210 ARG n 1 211 THR n 1 212 PRO n 1 213 VAL n 1 214 VAL n 1 215 ILE n 1 216 ILE n 1 217 ASP n 1 218 ASN n 1 219 LYS n 1 220 GLY n 1 221 GLN n 1 222 ARG n 1 223 VAL n 1 224 GLU n 1 225 ILE n 1 226 LYS n 1 227 ASP n 1 228 VAL n 1 229 ASN n 1 230 SER n 1 231 LYS n 1 232 VAL n 1 233 VAL n 1 234 THR n 1 235 ASN n 1 236 ASN n 1 237 ILE n 1 238 LYS n 1 239 LEU n 1 240 LEU n 1 241 LEU n 1 242 ASN n 1 243 LYS n 1 244 GLN n 1 245 ASN n 1 246 ILE n 1 247 ALA n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name 'smooth loofah' _entity_src_gen.gene_src_genus Luffa _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Luffa aegyptiaca' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 3670 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code RIPB_LUFCY _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ANVSFSLSGADSKSYSKFITALRKALPSKEKVSNIPLLLPSASGASRYILMQLSNYDAKAITMAIDVTNVYIMGYLVNST SYFFNESDAKLASQYVFKGSTIVTLPYSGNYERLQNAAGKVREKIPLGFRAFDSAITSLFHYDSTAAAGAFLVIIQTTAE ASRFKYIEGQIIERIPKNEVPSPAALSLENEWSALSKQIQLAQTNNGAFRTPVVIIDNKGQRVEIKDVNSKVVTNNIKLL LNKQNIA ; _struct_ref.pdbx_align_begin 22 _struct_ref.pdbx_db_accession P22851 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1NIO _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 247 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P22851 _struct_ref_seq.db_align_beg 22 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 268 _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 247 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 1NIO _struct_ref_seq_dif.mon_id LYS _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 173 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code P22851 _struct_ref_seq_dif.db_mon_id GLU _struct_ref_seq_dif.pdbx_seq_db_seq_num 194 _struct_ref_seq_dif.details conflict _struct_ref_seq_dif.pdbx_auth_seq_num 173 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 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 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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ? 'C8 H15 N O6' 221.208 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 1NIO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.19 _exptl_crystal.density_percent_sol 43.33 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_details 'Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 290 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1NIO _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F 1.0 _reflns.d_resolution_low 29.21 _reflns.d_resolution_high 2.0 _reflns.number_obs 60278 _reflns.number_all 60539 _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs 0.111 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 14.0 _reflns.pdbx_redundancy ? _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.0 _reflns_shell.d_res_low 2.07 _reflns_shell.percent_possible_all 96 _reflns_shell.Rmerge_I_obs 0.111 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 17034 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1NIO _refine.ls_number_reflns_obs 16425 _refine.ls_number_reflns_all 60539 _refine.pdbx_ls_sigma_I 2.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 341791.35 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.ls_d_res_low 29.21 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 96.0 _refine.ls_R_factor_obs 0.162 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.162 _refine.ls_R_factor_R_free 0.203 _refine.ls_R_factor_R_free_error 0.005 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 1639 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 21.3 _refine.aniso_B[1][1] 0.50 _refine.aniso_B[2][2] 0.54 _refine.aniso_B[3][3] -1.04 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] -0.15 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.371814 _refine.solvent_model_param_bsol 49.5375 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _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_analyze.entry_id 1NIO _refine_analyze.Luzzati_coordinate_error_obs 0.18 _refine_analyze.Luzzati_sigma_a_obs 0.15 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.23 _refine_analyze.Luzzati_sigma_a_free 0.20 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1911 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 42 _refine_hist.number_atoms_solvent 128 _refine_hist.number_atoms_total 2081 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 29.21 # 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 c_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.3 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 23.0 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.84 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.30 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 1.90 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 3.14 2.50 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 4.54 3.50 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 10 _refine_ls_shell.d_res_high 2.00 _refine_ls_shell.d_res_low 2.07 _refine_ls_shell.number_reflns_R_work 1352 _refine_ls_shell.R_factor_R_work 0.227 _refine_ls_shell.percent_reflns_obs 91.0 _refine_ls_shell.R_factor_R_free 0.272 _refine_ls_shell.R_factor_R_free_error 0.022 _refine_ls_shell.percent_reflns_R_free 10.4 _refine_ls_shell.number_reflns_R_free 157 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 WATER_REP.PARAM WATER.TOP 'X-RAY DIFFRACTION' 3 ION.PARAM ION.TOP 'X-RAY DIFFRACTION' 4 CARBOHYDRATE.PARAM CARBOHYDRATE.TOP 'X-RAY DIFFRACTION' # _struct.entry_id 1NIO _struct.title 'Crystal structure of beta-luffin, a ribosome inactivating protein at 2.0A resolution' _struct.pdbx_descriptor 'b-luffin(E.C.3.2.2.22)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1NIO _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'Ribosome inactivating protein(RIP), beta-luffin, hydrolase' # 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 2 ? D N N 2 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASP A 11 ? LEU A 26 ? ASP A 11 LEU A 26 1 ? 16 HELX_P HELX_P2 2 SER A 43 ? SER A 46 ? SER A 43 SER A 46 5 ? 4 HELX_P HELX_P3 3 GLU A 86 ? SER A 93 ? GLU A 86 SER A 93 1 ? 8 HELX_P HELX_P4 4 ASN A 110 ? GLY A 119 ? ASN A 110 GLY A 119 1 ? 10 HELX_P HELX_P5 5 VAL A 121 ? ILE A 125 ? VAL A 121 ILE A 125 5 ? 5 HELX_P HELX_P6 6 GLY A 128 ? HIS A 141 ? GLY A 128 HIS A 141 1 ? 14 HELX_P HELX_P7 7 ALA A 146 ? THR A 158 ? ALA A 146 THR A 158 1 ? 13 HELX_P HELX_P8 8 THR A 158 ? PHE A 164 ? THR A 158 PHE A 164 1 ? 7 HELX_P HELX_P9 9 PHE A 164 ? ARG A 174 ? PHE A 164 ARG A 174 1 ? 11 HELX_P HELX_P10 10 SER A 182 ? GLN A 203 ? SER A 182 GLN A 203 1 ? 22 HELX_P HELX_P11 11 SER A 230 ? ASN A 235 ? SER A 230 ASN A 235 1 ? 6 HELX_P HELX_P12 12 ASN A 242 ? ILE A 246 ? ASN A 242 ILE A 246 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 _struct_conn.pdbx_role covale1 covale one ? A ASN 2 ND2 ? ? ? 1_555 B NAG . C1 ? ? A ASN 2 A NAG 248 1_555 ? ? ? ? ? ? ? 1.454 ? N-Glycosylation covale2 covale one ? A ASN 78 ND2 ? ? ? 1_555 C NAG . C1 ? ? A ASN 78 A NAG 249 1_555 ? ? ? ? ? ? ? 1.447 ? N-Glycosylation covale3 covale one ? A ASN 85 ND2 ? ? ? 1_555 D NAG . C1 ? ? A ASN 85 A NAG 250 1_555 ? ? ? ? ? ? ? 1.452 ? N-Glycosylation # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 2 ? C ? 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 ? parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? parallel B 1 2 ? anti-parallel C 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 3 ? SER A 6 ? VAL A 3 SER A 6 A 2 TYR A 48 ? SER A 54 ? TYR A 48 SER A 54 A 3 ALA A 60 ? ASP A 66 ? ALA A 60 ASP A 66 A 4 ILE A 72 ? VAL A 77 ? ILE A 72 VAL A 77 A 5 THR A 80 ? PHE A 83 ? THR A 80 PHE A 83 A 6 THR A 101 ? THR A 104 ? THR A 101 THR A 104 B 1 SER A 28 ? VAL A 32 ? SER A 28 VAL A 32 B 2 ILE A 35 ? LEU A 38 ? ILE A 35 LEU A 38 C 1 ALA A 208 ? ILE A 216 ? ALA A 208 ILE A 216 C 2 ARG A 222 ? ASP A 227 ? ARG A 222 ASP A 227 # 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 3 ? N VAL A 3 O GLN A 52 ? O GLN A 52 A 2 3 N MET A 51 ? N MET A 51 O MET A 63 ? O MET A 63 A 3 4 N THR A 62 ? N THR A 62 O LEU A 76 ? O LEU A 76 A 4 5 N TYR A 75 ? N TYR A 75 O TYR A 82 ? O TYR A 82 A 5 6 N SER A 81 ? N SER A 81 O VAL A 103 ? O VAL A 103 B 1 2 N GLU A 30 ? N GLU A 30 O LEU A 37 ? O LEU A 37 C 1 2 N VAL A 213 ? N VAL A 213 O ILE A 225 ? O ILE A 225 # _database_PDB_matrix.entry_id 1NIO _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1NIO _atom_sites.fract_transf_matrix[1][1] 0.011123 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.006634 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.016716 _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] 0.021099 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O 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 ALA 1 1 1 ALA ALA A . n A 1 2 ASN 2 2 2 ASN ASN A . n A 1 3 VAL 3 3 3 VAL VAL A . n A 1 4 SER 4 4 4 SER SER A . n A 1 5 PHE 5 5 5 PHE PHE A . n A 1 6 SER 6 6 6 SER SER A . n A 1 7 LEU 7 7 7 LEU LEU A . n A 1 8 SER 8 8 8 SER SER A . n A 1 9 GLY 9 9 9 GLY GLY A . n A 1 10 ALA 10 10 10 ALA ALA A . n A 1 11 ASP 11 11 11 ASP ASP A . n A 1 12 SER 12 12 12 SER SER A . n A 1 13 LYS 13 13 13 LYS LYS A . n A 1 14 SER 14 14 14 SER SER A . n A 1 15 TYR 15 15 15 TYR TYR A . n A 1 16 SER 16 16 16 SER SER A . n A 1 17 LYS 17 17 17 LYS LYS A . n A 1 18 PHE 18 18 18 PHE PHE A . n A 1 19 ILE 19 19 19 ILE ILE A . n A 1 20 THR 20 20 20 THR THR A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 LEU 22 22 22 LEU LEU A . n A 1 23 ARG 23 23 23 ARG ARG A . n A 1 24 LYS 24 24 24 LYS LYS A . n A 1 25 ALA 25 25 25 ALA ALA A . n A 1 26 LEU 26 26 26 LEU LEU A . n A 1 27 PRO 27 27 27 PRO PRO A . n A 1 28 SER 28 28 28 SER SER A . n A 1 29 LYS 29 29 29 LYS LYS A . n A 1 30 GLU 30 30 30 GLU GLU A . n A 1 31 LYS 31 31 31 LYS LYS A . n A 1 32 VAL 32 32 32 VAL VAL A . n A 1 33 SER 33 33 33 SER SER A . n A 1 34 ASN 34 34 34 ASN ASN A . n A 1 35 ILE 35 35 35 ILE ILE A . n A 1 36 PRO 36 36 36 PRO PRO A . n A 1 37 LEU 37 37 37 LEU LEU A . n A 1 38 LEU 38 38 38 LEU LEU A . n A 1 39 LEU 39 39 39 LEU LEU A . n A 1 40 PRO 40 40 40 PRO PRO A . n A 1 41 SER 41 41 41 SER SER A . n A 1 42 ALA 42 42 42 ALA ALA A . n A 1 43 SER 43 43 43 SER SER A . n A 1 44 GLY 44 44 44 GLY GLY A . n A 1 45 ALA 45 45 45 ALA ALA A . n A 1 46 SER 46 46 46 SER SER A . n A 1 47 ARG 47 47 47 ARG ARG A . n A 1 48 TYR 48 48 48 TYR TYR A . n A 1 49 ILE 49 49 49 ILE ILE A . n A 1 50 LEU 50 50 50 LEU LEU A . n A 1 51 MET 51 51 51 MET MET A . n A 1 52 GLN 52 52 52 GLN GLN A . n A 1 53 LEU 53 53 53 LEU LEU A . n A 1 54 SER 54 54 54 SER SER A . n A 1 55 ASN 55 55 55 ASN ASN A . n A 1 56 TYR 56 56 56 TYR TYR A . n A 1 57 ASP 57 57 57 ASP ASP A . n A 1 58 ALA 58 58 58 ALA ALA A . n A 1 59 LYS 59 59 59 LYS LYS A . n A 1 60 ALA 60 60 60 ALA ALA A . n A 1 61 ILE 61 61 61 ILE ILE A . n A 1 62 THR 62 62 62 THR THR A . n A 1 63 MET 63 63 63 MET MET A . n A 1 64 ALA 64 64 64 ALA ALA A . n A 1 65 ILE 65 65 65 ILE ILE A . n A 1 66 ASP 66 66 66 ASP ASP A . n A 1 67 VAL 67 67 67 VAL VAL A . n A 1 68 THR 68 68 68 THR THR A . n A 1 69 ASN 69 69 69 ASN ASN A . n A 1 70 VAL 70 70 70 VAL VAL A . n A 1 71 TYR 71 71 71 TYR TYR A . n A 1 72 ILE 72 72 72 ILE ILE A . n A 1 73 MET 73 73 73 MET MET A . n A 1 74 GLY 74 74 74 GLY GLY A . n A 1 75 TYR 75 75 75 TYR TYR A . n A 1 76 LEU 76 76 76 LEU LEU A . n A 1 77 VAL 77 77 77 VAL VAL A . n A 1 78 ASN 78 78 78 ASN ASN A . n A 1 79 SER 79 79 79 SER SER A . n A 1 80 THR 80 80 80 THR THR A . n A 1 81 SER 81 81 81 SER SER A . n A 1 82 TYR 82 82 82 TYR TYR A . n A 1 83 PHE 83 83 83 PHE PHE A . n A 1 84 PHE 84 84 84 PHE PHE A . n A 1 85 ASN 85 85 85 ASN ASN A . n A 1 86 GLU 86 86 86 GLU GLU A . n A 1 87 SER 87 87 87 SER SER A . n A 1 88 ASP 88 88 88 ASP ASP A . n A 1 89 ALA 89 89 89 ALA ALA A . n A 1 90 LYS 90 90 90 LYS LYS A . n A 1 91 LEU 91 91 91 LEU LEU A . n A 1 92 ALA 92 92 92 ALA ALA A . n A 1 93 SER 93 93 93 SER SER A . n A 1 94 GLN 94 94 94 GLN GLN A . n A 1 95 TYR 95 95 95 TYR TYR A . n A 1 96 VAL 96 96 96 VAL VAL A . n A 1 97 PHE 97 97 97 PHE PHE A . n A 1 98 LYS 98 98 98 LYS LYS A . n A 1 99 GLY 99 99 99 GLY GLY A . n A 1 100 SER 100 100 100 SER SER A . n A 1 101 THR 101 101 101 THR THR A . n A 1 102 ILE 102 102 102 ILE ILE A . n A 1 103 VAL 103 103 103 VAL VAL A . n A 1 104 THR 104 104 104 THR THR A . n A 1 105 LEU 105 105 105 LEU LEU A . n A 1 106 PRO 106 106 106 PRO PRO A . n A 1 107 TYR 107 107 107 TYR TYR A . n A 1 108 SER 108 108 108 SER SER A . n A 1 109 GLY 109 109 109 GLY GLY A . n A 1 110 ASN 110 110 110 ASN ASN A . n A 1 111 TYR 111 111 111 TYR TYR A . n A 1 112 GLU 112 112 112 GLU GLU A . n A 1 113 ARG 113 113 113 ARG ARG A . n A 1 114 LEU 114 114 114 LEU LEU A . n A 1 115 GLN 115 115 115 GLN GLN A . n A 1 116 ASN 116 116 116 ASN ASN A . n A 1 117 ALA 117 117 117 ALA ALA A . n A 1 118 ALA 118 118 118 ALA ALA A . n A 1 119 GLY 119 119 119 GLY GLY A . n A 1 120 LYS 120 120 120 LYS LYS A . n A 1 121 VAL 121 121 121 VAL VAL A . n A 1 122 ARG 122 122 122 ARG ARG A . n A 1 123 GLU 123 123 123 GLU GLU A . n A 1 124 LYS 124 124 124 LYS LYS A . n A 1 125 ILE 125 125 125 ILE ILE A . n A 1 126 PRO 126 126 126 PRO PRO A . n A 1 127 LEU 127 127 127 LEU LEU A . n A 1 128 GLY 128 128 128 GLY GLY A . n A 1 129 PHE 129 129 129 PHE PHE A . n A 1 130 ARG 130 130 130 ARG ARG A . n A 1 131 ALA 131 131 131 ALA ALA A . n A 1 132 PHE 132 132 132 PHE PHE A . n A 1 133 ASP 133 133 133 ASP ASP A . n A 1 134 SER 134 134 134 SER SER A . n A 1 135 ALA 135 135 135 ALA ALA A . n A 1 136 ILE 136 136 136 ILE ILE A . n A 1 137 THR 137 137 137 THR THR A . n A 1 138 SER 138 138 138 SER SER A . n A 1 139 LEU 139 139 139 LEU LEU A . n A 1 140 PHE 140 140 140 PHE PHE A . n A 1 141 HIS 141 141 141 HIS HIS A . n A 1 142 TYR 142 142 142 TYR TYR A . n A 1 143 ASP 143 143 143 ASP ASP A . n A 1 144 SER 144 144 144 SER SER A . n A 1 145 THR 145 145 145 THR THR A . n A 1 146 ALA 146 146 146 ALA ALA A . n A 1 147 ALA 147 147 147 ALA ALA A . n A 1 148 ALA 148 148 148 ALA ALA A . n A 1 149 GLY 149 149 149 GLY GLY A . n A 1 150 ALA 150 150 150 ALA ALA A . n A 1 151 PHE 151 151 151 PHE PHE A . n A 1 152 LEU 152 152 152 LEU LEU A . n A 1 153 VAL 153 153 153 VAL VAL A . n A 1 154 ILE 154 154 154 ILE ILE A . n A 1 155 ILE 155 155 155 ILE ILE A . n A 1 156 GLN 156 156 156 GLN GLN A . n A 1 157 THR 157 157 157 THR THR A . n A 1 158 THR 158 158 158 THR THR A . n A 1 159 ALA 159 159 159 ALA ALA A . n A 1 160 GLU 160 160 160 GLU GLU A . n A 1 161 ALA 161 161 161 ALA ALA A . n A 1 162 SER 162 162 162 SER SER A . n A 1 163 ARG 163 163 163 ARG ARG A . n A 1 164 PHE 164 164 164 PHE PHE A . n A 1 165 LYS 165 165 165 LYS LYS A . n A 1 166 TYR 166 166 166 TYR TYR A . n A 1 167 ILE 167 167 167 ILE ILE A . n A 1 168 GLU 168 168 168 GLU GLU A . n A 1 169 GLY 169 169 169 GLY GLY A . n A 1 170 GLN 170 170 170 GLN GLN A . n A 1 171 ILE 171 171 171 ILE ILE A . n A 1 172 ILE 172 172 172 ILE ILE A . n A 1 173 LYS 173 173 173 LYS LYS A . n A 1 174 ARG 174 174 174 ARG ARG A . n A 1 175 ILE 175 175 175 ILE ILE A . n A 1 176 PRO 176 176 176 PRO PRO A . n A 1 177 LYS 177 177 177 LYS LYS A . n A 1 178 ASN 178 178 178 ASN ASN A . n A 1 179 GLU 179 179 179 GLU GLU A . n A 1 180 VAL 180 180 180 VAL VAL A . n A 1 181 PRO 181 181 181 PRO PRO A . n A 1 182 SER 182 182 182 SER SER A . n A 1 183 PRO 183 183 183 PRO PRO A . n A 1 184 ALA 184 184 184 ALA ALA A . n A 1 185 ALA 185 185 185 ALA ALA A . n A 1 186 LEU 186 186 186 LEU LEU A . n A 1 187 SER 187 187 187 SER SER A . n A 1 188 LEU 188 188 188 LEU LEU A . n A 1 189 GLU 189 189 189 GLU GLU A . n A 1 190 ASN 190 190 190 ASN ASN A . n A 1 191 GLU 191 191 191 GLU GLU A . n A 1 192 TRP 192 192 192 TRP TRP A . n A 1 193 SER 193 193 193 SER SER A . n A 1 194 ALA 194 194 194 ALA ALA A . n A 1 195 LEU 195 195 195 LEU LEU A . n A 1 196 SER 196 196 196 SER SER A . n A 1 197 LYS 197 197 197 LYS LYS A . n A 1 198 GLN 198 198 198 GLN GLN A . n A 1 199 ILE 199 199 199 ILE ILE A . n A 1 200 GLN 200 200 200 GLN GLN A . n A 1 201 LEU 201 201 201 LEU LEU A . n A 1 202 ALA 202 202 202 ALA ALA A . n A 1 203 GLN 203 203 203 GLN GLN A . n A 1 204 THR 204 204 204 THR THR A . n A 1 205 ASN 205 205 205 ASN ASN A . n A 1 206 ASN 206 206 206 ASN ASN A . n A 1 207 GLY 207 207 207 GLY GLY A . n A 1 208 ALA 208 208 208 ALA ALA A . n A 1 209 PHE 209 209 209 PHE PHE A . n A 1 210 ARG 210 210 210 ARG ARG A . n A 1 211 THR 211 211 211 THR THR A . n A 1 212 PRO 212 212 212 PRO PRO A . n A 1 213 VAL 213 213 213 VAL VAL A . n A 1 214 VAL 214 214 214 VAL VAL A . n A 1 215 ILE 215 215 215 ILE ILE A . n A 1 216 ILE 216 216 216 ILE ILE A . n A 1 217 ASP 217 217 217 ASP ASP A . n A 1 218 ASN 218 218 218 ASN ASN A . n A 1 219 LYS 219 219 219 LYS LYS A . n A 1 220 GLY 220 220 220 GLY GLY A . n A 1 221 GLN 221 221 221 GLN GLN A . n A 1 222 ARG 222 222 222 ARG ARG A . n A 1 223 VAL 223 223 223 VAL VAL A . n A 1 224 GLU 224 224 224 GLU GLU A . n A 1 225 ILE 225 225 225 ILE ILE A . n A 1 226 LYS 226 226 226 LYS LYS A . n A 1 227 ASP 227 227 227 ASP ASP A . n A 1 228 VAL 228 228 228 VAL VAL A . n A 1 229 ASN 229 229 229 ASN ASN A . n A 1 230 SER 230 230 230 SER SER A . n A 1 231 LYS 231 231 231 LYS LYS A . n A 1 232 VAL 232 232 232 VAL VAL A . n A 1 233 VAL 233 233 233 VAL VAL A . n A 1 234 THR 234 234 234 THR THR A . n A 1 235 ASN 235 235 235 ASN ASN A . n A 1 236 ASN 236 236 236 ASN ASN A . n A 1 237 ILE 237 237 237 ILE ILE A . n A 1 238 LYS 238 238 238 LYS LYS A . n A 1 239 LEU 239 239 239 LEU LEU A . n A 1 240 LEU 240 240 240 LEU LEU A . n A 1 241 LEU 241 241 241 LEU LEU A . n A 1 242 ASN 242 242 242 ASN ASN A . n A 1 243 LYS 243 243 243 LYS LYS A . n A 1 244 GLN 244 244 244 GLN GLN A . n A 1 245 ASN 245 245 245 ASN ASN A . n A 1 246 ILE 246 246 246 ILE ILE A . n A 1 247 ALA 247 247 247 ALA ALA A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NAG 1 248 248 NAG NAG A . C 2 NAG 1 249 249 NAG NAG A . D 2 NAG 1 250 250 NAG NAG A . E 3 HOH 1 251 1 HOH HOH A . E 3 HOH 2 252 2 HOH HOH A . E 3 HOH 3 253 3 HOH HOH A . E 3 HOH 4 254 4 HOH HOH A . E 3 HOH 5 255 5 HOH HOH A . E 3 HOH 6 256 6 HOH HOH A . E 3 HOH 7 257 7 HOH HOH A . E 3 HOH 8 258 8 HOH HOH A . E 3 HOH 9 259 9 HOH HOH A . E 3 HOH 10 260 10 HOH HOH A . E 3 HOH 11 261 11 HOH HOH A . E 3 HOH 12 262 12 HOH HOH A . E 3 HOH 13 263 13 HOH HOH A . E 3 HOH 14 264 14 HOH HOH A . E 3 HOH 15 265 15 HOH HOH A . E 3 HOH 16 266 16 HOH HOH A . E 3 HOH 17 267 17 HOH HOH A . E 3 HOH 18 268 18 HOH HOH A . E 3 HOH 19 269 19 HOH HOH A . E 3 HOH 20 270 20 HOH HOH A . E 3 HOH 21 271 21 HOH HOH A . E 3 HOH 22 272 22 HOH HOH A . E 3 HOH 23 273 23 HOH HOH A . E 3 HOH 24 274 24 HOH HOH A . E 3 HOH 25 275 25 HOH HOH A . E 3 HOH 26 276 26 HOH HOH A . E 3 HOH 27 277 27 HOH HOH A . E 3 HOH 28 278 28 HOH HOH A . E 3 HOH 29 279 29 HOH HOH A . E 3 HOH 30 280 30 HOH HOH A . E 3 HOH 31 281 31 HOH HOH A . E 3 HOH 32 282 32 HOH HOH A . E 3 HOH 33 283 33 HOH HOH A . E 3 HOH 34 284 34 HOH HOH A . E 3 HOH 35 285 35 HOH HOH A . E 3 HOH 36 286 36 HOH HOH A . E 3 HOH 37 287 37 HOH HOH A . E 3 HOH 38 288 38 HOH HOH A . E 3 HOH 39 289 39 HOH HOH A . E 3 HOH 40 290 40 HOH HOH A . E 3 HOH 41 291 41 HOH HOH A . E 3 HOH 42 292 42 HOH HOH A . E 3 HOH 43 293 43 HOH HOH A . E 3 HOH 44 294 44 HOH HOH A . E 3 HOH 45 295 45 HOH HOH A . E 3 HOH 46 296 46 HOH HOH A . E 3 HOH 47 297 47 HOH HOH A . E 3 HOH 48 298 48 HOH HOH A . E 3 HOH 49 299 49 HOH HOH A . E 3 HOH 50 300 50 HOH HOH A . E 3 HOH 51 301 51 HOH HOH A . E 3 HOH 52 302 52 HOH HOH A . E 3 HOH 53 303 53 HOH HOH A . E 3 HOH 54 304 54 HOH HOH A . E 3 HOH 55 305 55 HOH HOH A . E 3 HOH 56 306 56 HOH HOH A . E 3 HOH 57 307 57 HOH HOH A . E 3 HOH 58 308 58 HOH HOH A . E 3 HOH 59 309 59 HOH HOH A . E 3 HOH 60 310 60 HOH HOH A . E 3 HOH 61 311 61 HOH HOH A . E 3 HOH 62 312 62 HOH HOH A . E 3 HOH 63 313 63 HOH HOH A . E 3 HOH 64 314 64 HOH HOH A . E 3 HOH 65 315 65 HOH HOH A . E 3 HOH 66 316 66 HOH HOH A . E 3 HOH 67 317 67 HOH HOH A . E 3 HOH 68 318 68 HOH HOH A . E 3 HOH 69 319 69 HOH HOH A . E 3 HOH 70 320 70 HOH HOH A . E 3 HOH 71 321 71 HOH HOH A . E 3 HOH 72 322 72 HOH HOH A . E 3 HOH 73 323 73 HOH HOH A . E 3 HOH 74 324 74 HOH HOH A . E 3 HOH 75 325 75 HOH HOH A . E 3 HOH 76 326 76 HOH HOH A . E 3 HOH 77 327 77 HOH HOH A . E 3 HOH 78 328 78 HOH HOH A . E 3 HOH 79 329 79 HOH HOH A . E 3 HOH 80 330 80 HOH HOH A . E 3 HOH 81 331 81 HOH HOH A . E 3 HOH 82 332 82 HOH HOH A . E 3 HOH 83 333 83 HOH HOH A . E 3 HOH 84 334 84 HOH HOH A . E 3 HOH 85 335 85 HOH HOH A . E 3 HOH 86 336 86 HOH HOH A . E 3 HOH 87 337 87 HOH HOH A . E 3 HOH 88 338 88 HOH HOH A . E 3 HOH 89 339 89 HOH HOH A . E 3 HOH 90 340 90 HOH HOH A . E 3 HOH 91 341 91 HOH HOH A . E 3 HOH 92 342 92 HOH HOH A . E 3 HOH 93 343 93 HOH HOH A . E 3 HOH 94 344 94 HOH HOH A . E 3 HOH 95 345 95 HOH HOH A . E 3 HOH 96 346 96 HOH HOH A . E 3 HOH 97 347 97 HOH HOH A . E 3 HOH 98 348 98 HOH HOH A . E 3 HOH 99 349 99 HOH HOH A . E 3 HOH 100 350 100 HOH HOH A . E 3 HOH 101 351 101 HOH HOH A . E 3 HOH 102 352 102 HOH HOH A . E 3 HOH 103 353 103 HOH HOH A . E 3 HOH 104 354 104 HOH HOH A . E 3 HOH 105 355 105 HOH HOH A . E 3 HOH 106 356 106 HOH HOH A . E 3 HOH 107 357 107 HOH HOH A . E 3 HOH 108 358 108 HOH HOH A . E 3 HOH 109 359 109 HOH HOH A . E 3 HOH 110 360 110 HOH HOH A . E 3 HOH 111 361 111 HOH HOH A . E 3 HOH 112 362 112 HOH HOH A . E 3 HOH 113 363 113 HOH HOH A . E 3 HOH 114 364 114 HOH HOH A . E 3 HOH 115 365 115 HOH HOH A . E 3 HOH 116 366 116 HOH HOH A . E 3 HOH 117 367 117 HOH HOH A . E 3 HOH 118 368 118 HOH HOH A . E 3 HOH 119 369 119 HOH HOH A . E 3 HOH 120 370 120 HOH HOH A . E 3 HOH 121 371 121 HOH HOH A . E 3 HOH 122 372 122 HOH HOH A . E 3 HOH 123 373 123 HOH HOH A . E 3 HOH 124 374 124 HOH HOH A . E 3 HOH 125 375 125 HOH HOH A . E 3 HOH 126 376 126 HOH HOH A . E 3 HOH 127 377 127 HOH HOH A . E 3 HOH 128 378 128 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A ASN 2 A ASN 2 ? ASN 'GLYCOSYLATION SITE' 2 A ASN 78 A ASN 78 ? ASN 'GLYCOSYLATION SITE' 3 A ASN 85 A ASN 85 ? ASN 'GLYCOSYLATION SITE' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _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_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 350 ? E HOH . 2 1 A HOH 351 ? E HOH . # 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 2003-08-05 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 4 'Structure model' repository Remediation 'Carbohydrate remediation' ? # 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' 'Non-polymer description' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Structure summary' # 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' chem_comp 2 4 'Structure model' entity 3 4 'Structure model' pdbx_chem_comp_identifier 4 4 'Structure model' pdbx_entity_nonpoly 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_ref_seq_dif 7 4 'Structure model' struct_site 8 4 'Structure model' struct_site_gen # 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 4 'Structure model' '_chem_comp.name' 2 4 'Structure model' '_chem_comp.type' 3 4 'Structure model' '_entity.pdbx_description' 4 4 'Structure model' '_pdbx_entity_nonpoly.name' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 4 'Structure model' '_struct_conn.pdbx_role' 7 4 'Structure model' '_struct_ref_seq_dif.details' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CNS phasing . ? 4 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A ILE 246 ? ? 1_555 O A ILE 246 ? ? 2_557 2.05 2 1 CB A ALA 247 ? ? 1_555 CB A ALA 247 ? ? 2_557 2.14 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASN A 78 ? ? 52.95 -119.63 2 1 THR A 158 ? ? -113.58 -71.21 3 1 ASN A 236 ? ? -161.46 -71.82 4 1 ILE A 246 ? ? -106.34 -87.20 # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 3 water HOH #