data_3QKG # _entry.id 3QKG # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3QKG RCSB RCSB063757 WWPDB D_1000063757 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3QKG _pdbx_database_status.recvd_initial_deposition_date 2011-02-01 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Meining, W.' 1 'Skerra, A.' 2 # _citation.id primary _citation.title 'The crystal structure of human alpha(1)-microglobulin reveals a potential haem-binding site.' _citation.journal_abbrev Biochem.J. _citation.journal_volume 445 _citation.page_first 175 _citation.page_last 182 _citation.year 2012 _citation.journal_id_ASTM BIJOAK _citation.country UK _citation.journal_id_ISSN 0264-6021 _citation.journal_id_CSD 0043 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22512701 _citation.pdbx_database_id_DOI 10.1042/BJ20120448 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Meining, W.' 1 primary 'Skerra, A.' 2 # _cell.entry_id 3QKG _cell.length_a 66.721 _cell.length_b 66.721 _cell.length_c 80.255 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? _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.entry_id 3QKG _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _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 man 'Protein AMBP' 21956.834 1 ? C34S lipocalin ? 2 non-polymer syn 'NICKEL (II) ION' 58.693 1 ? ? ? ? 3 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 4 water nat water 18.015 47 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;Alpha-1-microglobulin, Protein HC, Alpha-1 microglycoprotein, Complex-forming glycoprotein heterogeneous in charge, Inter-alpha-trypsin inhibitor light chain, ITI-LC, Bikunin, EDC1, HI-30, Uronic-acid-rich protein, Trypstatin ; # _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 ;GPVPTPPDNIQVQENFNISRIYGKWYNLAIGSTSPWLKKIMDRMTVSTLVLGEGATEAEISMTSTRWRKGVCEETSGAYE KTDTDGKFLYHKSKWNITMESYVVHTNYDEYAIFLTKKFSRHHGPTITAKLYGRAPQLRETLLQDFRVVAQGVGIPEDSI FTMADRGECVPGEQEPEPILIPRSAWSHPQFEK ; _entity_poly.pdbx_seq_one_letter_code_can ;GPVPTPPDNIQVQENFNISRIYGKWYNLAIGSTSPWLKKIMDRMTVSTLVLGEGATEAEISMTSTRWRKGVCEETSGAYE KTDTDGKFLYHKSKWNITMESYVVHTNYDEYAIFLTKKFSRHHGPTITAKLYGRAPQLRETLLQDFRVVAQGVGIPEDSI FTMADRGECVPGEQEPEPILIPRSAWSHPQFEK ; _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 GLY n 1 2 PRO n 1 3 VAL n 1 4 PRO n 1 5 THR n 1 6 PRO n 1 7 PRO n 1 8 ASP n 1 9 ASN n 1 10 ILE n 1 11 GLN n 1 12 VAL n 1 13 GLN n 1 14 GLU n 1 15 ASN n 1 16 PHE n 1 17 ASN n 1 18 ILE n 1 19 SER n 1 20 ARG n 1 21 ILE n 1 22 TYR n 1 23 GLY n 1 24 LYS n 1 25 TRP n 1 26 TYR n 1 27 ASN n 1 28 LEU n 1 29 ALA n 1 30 ILE n 1 31 GLY n 1 32 SER n 1 33 THR n 1 34 SER n 1 35 PRO n 1 36 TRP n 1 37 LEU n 1 38 LYS n 1 39 LYS n 1 40 ILE n 1 41 MET n 1 42 ASP n 1 43 ARG n 1 44 MET n 1 45 THR n 1 46 VAL n 1 47 SER n 1 48 THR n 1 49 LEU n 1 50 VAL n 1 51 LEU n 1 52 GLY n 1 53 GLU n 1 54 GLY n 1 55 ALA n 1 56 THR n 1 57 GLU n 1 58 ALA n 1 59 GLU n 1 60 ILE n 1 61 SER n 1 62 MET n 1 63 THR n 1 64 SER n 1 65 THR n 1 66 ARG n 1 67 TRP n 1 68 ARG n 1 69 LYS n 1 70 GLY n 1 71 VAL n 1 72 CYS n 1 73 GLU n 1 74 GLU n 1 75 THR n 1 76 SER n 1 77 GLY n 1 78 ALA n 1 79 TYR n 1 80 GLU n 1 81 LYS n 1 82 THR n 1 83 ASP n 1 84 THR n 1 85 ASP n 1 86 GLY n 1 87 LYS n 1 88 PHE n 1 89 LEU n 1 90 TYR n 1 91 HIS n 1 92 LYS n 1 93 SER n 1 94 LYS n 1 95 TRP n 1 96 ASN n 1 97 ILE n 1 98 THR n 1 99 MET n 1 100 GLU n 1 101 SER n 1 102 TYR n 1 103 VAL n 1 104 VAL n 1 105 HIS n 1 106 THR n 1 107 ASN n 1 108 TYR n 1 109 ASP n 1 110 GLU n 1 111 TYR n 1 112 ALA n 1 113 ILE n 1 114 PHE n 1 115 LEU n 1 116 THR n 1 117 LYS n 1 118 LYS n 1 119 PHE n 1 120 SER n 1 121 ARG n 1 122 HIS n 1 123 HIS n 1 124 GLY n 1 125 PRO n 1 126 THR n 1 127 ILE n 1 128 THR n 1 129 ALA n 1 130 LYS n 1 131 LEU n 1 132 TYR n 1 133 GLY n 1 134 ARG n 1 135 ALA n 1 136 PRO n 1 137 GLN n 1 138 LEU n 1 139 ARG n 1 140 GLU n 1 141 THR n 1 142 LEU n 1 143 LEU n 1 144 GLN n 1 145 ASP n 1 146 PHE n 1 147 ARG n 1 148 VAL n 1 149 VAL n 1 150 ALA n 1 151 GLN n 1 152 GLY n 1 153 VAL n 1 154 GLY n 1 155 ILE n 1 156 PRO n 1 157 GLU n 1 158 ASP n 1 159 SER n 1 160 ILE n 1 161 PHE n 1 162 THR n 1 163 MET n 1 164 ALA n 1 165 ASP n 1 166 ARG n 1 167 GLY n 1 168 GLU n 1 169 CYS n 1 170 VAL n 1 171 PRO n 1 172 GLY n 1 173 GLU n 1 174 GLN n 1 175 GLU n 1 176 PRO n 1 177 GLU n 1 178 PRO n 1 179 ILE n 1 180 LEU n 1 181 ILE n 1 182 PRO n 1 183 ARG n 1 184 SER n 1 185 ALA n 1 186 TRP n 1 187 SER n 1 188 HIS n 1 189 PRO n 1 190 GLN n 1 191 PHE n 1 192 GLU n 1 193 LYS 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 human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'AMBP, HCP, ITIL' _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 83333 _entity_src_gen.host_org_genus ? _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 K-12 _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 Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pa1m2 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code AMBP_HUMAN _struct_ref.pdbx_db_accession P02760 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;GPVPTPPDNIQVQENFNISRIYGKWYNLAIGSTCPWLKKIMDRMTVSTLVLGEGATEAEISMTSTRWRKGVCEETSGAYE KTDTDGKFLYHKSKWNITMESYVVHTNYDEYAIFLTKKFSRHHGPTITAKLYGRAPQLRETLLQDFRVVAQGVGIPEDSI FTMADRGECVPGEQEPEPILIPR ; _struct_ref.pdbx_align_begin 20 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3QKG _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 183 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P02760 _struct_ref_seq.db_align_beg 20 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 202 _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 183 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3QKG SER A 34 ? UNP P02760 CYS 53 'ENGINEERED MUTATION' 34 1 1 3QKG SER A 184 ? UNP P02760 ? ? 'EXPRESSION TAG' 184 2 1 3QKG ALA A 185 ? UNP P02760 ? ? 'EXPRESSION TAG' 185 3 1 3QKG TRP A 186 ? UNP P02760 ? ? 'EXPRESSION TAG' 186 4 1 3QKG SER A 187 ? UNP P02760 ? ? 'EXPRESSION TAG' 187 5 1 3QKG HIS A 188 ? UNP P02760 ? ? 'EXPRESSION TAG' 188 6 1 3QKG PRO A 189 ? UNP P02760 ? ? 'EXPRESSION TAG' 189 7 1 3QKG GLN A 190 ? UNP P02760 ? ? 'EXPRESSION TAG' 190 8 1 3QKG PHE A 191 ? UNP P02760 ? ? 'EXPRESSION TAG' 191 9 1 3QKG GLU A 192 ? UNP P02760 ? ? 'EXPRESSION TAG' 192 10 1 3QKG LYS A 193 ? UNP P02760 ? ? 'EXPRESSION TAG' 193 11 # 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 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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 NI non-polymer . 'NICKEL (II) ION' ? 'Ni 2' 58.693 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 3QKG _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.32 _exptl_crystal.density_percent_sol 47.06 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '100 mM Tris-HCl, 1.1 M sodium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K' # _diffrn.id 1 _diffrn.ambient_temp 105 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2011-04-29 _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 'Si-111 crystal' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9184 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'BESSY BEAMLINE 14.1' _diffrn_source.pdbx_synchrotron_site BESSY _diffrn_source.pdbx_synchrotron_beamline 14.1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9184 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 3QKG _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 2.5 _reflns.d_resolution_low 46.89 _reflns.d_resolution_high 2.17 _reflns.number_obs 10877 _reflns.number_all ? _reflns.percent_possible_obs 96.5 _reflns.pdbx_Rmerge_I_obs 0.073 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 10.4 _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_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.17 _reflns_shell.d_res_low 2.29 _reflns_shell.percent_possible_all 80.0 _reflns_shell.Rmerge_I_obs 1.38 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 7.3 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3QKG _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 9044 _refine.ls_number_reflns_all 8341 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 46.89 _refine.ls_d_res_high 2.30 _refine.ls_percent_reflns_obs 99.33 _refine.ls_R_factor_obs 0.21478 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21260 _refine.ls_R_factor_R_free 0.25952 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 452 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.955 _refine.correlation_coeff_Fo_to_Fc_free 0.940 _refine.B_iso_mean 71.936 _refine.aniso_B[1][1] -2.35 _refine.aniso_B[2][2] -2.35 _refine.aniso_B[3][3] 3.52 _refine.aniso_B[1][2] -1.17 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _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' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _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 0.309 _refine.pdbx_overall_ESU_R_Free 0.237 _refine.overall_SU_ML 0.224 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 19.515 _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 1317 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 7 _refine_hist.number_atoms_solvent 47 _refine_hist.number_atoms_total 1371 _refine_hist.d_res_high 2.30 _refine_hist.d_res_low 46.89 # 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 0.017 0.022 ? 1353 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.703 1.941 ? 1829 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 7.447 5.000 ? 163 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 36.585 23.548 ? 62 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 20.913 15.000 ? 237 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 24.331 15.000 ? 9 'X-RAY DIFFRACTION' ? r_chiral_restr 0.114 0.200 ? 199 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.021 ? 1011 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? '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 0.896 1.500 ? 812 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.674 2.000 ? 1316 'X-RAY DIFFRACTION' ? r_scbond_it 2.708 3.000 ? 541 'X-RAY DIFFRACTION' ? r_scangle_it 4.428 4.500 ? 513 '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 2.30 _refine_ls_shell.d_res_low 2.36 _refine_ls_shell.number_reflns_R_work 655 _refine_ls_shell.R_factor_R_work 0.340 _refine_ls_shell.percent_reflns_obs 98.85 _refine_ls_shell.R_factor_R_free 0.485 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 31 _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 3QKG _struct.title 'Crystal structure of alpha-1-microglobulin at 2.3 A resolution' _struct.pdbx_descriptor 'Protein AMBP' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3QKG _struct_keywords.pdbx_keywords 'IMMUNE SYSTEM' _struct_keywords.text 'Beta barrel, binding protein, Bound chromophore, Human plasma, Immune system' # 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 3 ? D N N 4 ? # _struct_biol.id 1 _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 ASN A 17 ? TYR A 22 ? ASN A 17 TYR A 22 5 ? 6 HELX_P HELX_P2 2 SER A 34 ? MET A 41 ? SER A 34 MET A 41 1 ? 8 HELX_P HELX_P3 3 ARG A 139 ? VAL A 153 ? ARG A 139 VAL A 153 1 ? 15 # _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 disulf1 disulf ? ? A CYS 72 SG ? ? ? 1_555 A CYS 169 SG ? ? A CYS 72 A CYS 169 1_555 ? ? ? ? ? ? ? 2.045 ? metalc1 metalc ? ? B NI . NI ? ? ? 1_555 D HOH . O ? ? A NI 194 A HOH 199 1_555 ? ? ? ? ? ? ? 1.729 ? metalc2 metalc ? ? A HIS 122 NE2 ? ? ? 1_555 B NI . NI ? ? A HIS 122 A NI 194 1_555 ? ? ? ? ? ? ? 1.936 ? metalc3 metalc ? ? B NI . NI ? ? ? 1_555 D HOH . O ? ? A NI 194 A HOH 196 1_555 ? ? ? ? ? ? ? 2.237 ? metalc4 metalc ? ? B NI . NI ? ? ? 1_555 D HOH . O ? ? A NI 194 A HOH 198 1_555 ? ? ? ? ? ? ? 2.249 ? metalc5 metalc ? ? B NI . NI ? ? ? 1_555 D HOH . O ? ? A NI 194 A HOH 197 1_555 ? ? ? ? ? ? ? 2.255 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? metalc ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 10 _struct_sheet.details ? # 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 A 4 5 ? anti-parallel A 5 6 ? anti-parallel A 6 7 ? anti-parallel A 7 8 ? anti-parallel A 8 9 ? anti-parallel A 9 10 ? 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 ILE A 160 ? THR A 162 ? ILE A 160 THR A 162 A 2 GLY A 23 ? SER A 32 ? GLY A 23 SER A 32 A 3 THR A 126 ? GLY A 133 ? THR A 126 GLY A 133 A 4 TYR A 111 ? LYS A 118 ? TYR A 111 LYS A 118 A 5 ILE A 97 ? THR A 106 ? ILE A 97 THR A 106 A 6 LYS A 87 ? LYS A 92 ? LYS A 87 LYS A 92 A 7 CYS A 72 ? LYS A 81 ? CYS A 72 LYS A 81 A 8 GLU A 59 ? TRP A 67 ? GLU A 59 TRP A 67 A 9 SER A 47 ? GLU A 53 ? SER A 47 GLU A 53 A 10 GLY A 23 ? SER A 32 ? GLY A 23 SER A 32 # 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 O PHE A 161 ? O PHE A 161 N ILE A 30 ? N ILE A 30 A 2 3 N TYR A 26 ? N TYR A 26 O GLY A 133 ? O GLY A 133 A 3 4 O THR A 128 ? O THR A 128 N THR A 116 ? N THR A 116 A 4 5 O LYS A 117 ? O LYS A 117 N GLU A 100 ? N GLU A 100 A 5 6 O ILE A 97 ? O ILE A 97 N LYS A 92 ? N LYS A 92 A 6 7 O LEU A 89 ? O LEU A 89 N GLU A 80 ? N GLU A 80 A 7 8 O THR A 75 ? O THR A 75 N SER A 64 ? N SER A 64 A 8 9 O THR A 63 ? O THR A 63 N VAL A 50 ? N VAL A 50 A 9 10 O SER A 47 ? O SER A 47 N ASN A 27 ? N ASN A 27 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE NI A 194' AC2 Software ? ? ? ? 8 'BINDING SITE FOR RESIDUE GOL A 195' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 HIS A 122 ? HIS A 122 . ? 1_555 ? 2 AC1 6 HIS A 123 ? HIS A 123 . ? 5_555 ? 3 AC1 6 HOH D . ? HOH A 196 . ? 1_555 ? 4 AC1 6 HOH D . ? HOH A 197 . ? 1_555 ? 5 AC1 6 HOH D . ? HOH A 198 . ? 1_555 ? 6 AC1 6 HOH D . ? HOH A 199 . ? 1_555 ? 7 AC2 8 TRP A 67 ? TRP A 67 . ? 1_555 ? 8 AC2 8 GLY A 70 ? GLY A 70 . ? 6_555 ? 9 AC2 8 GLY A 70 ? GLY A 70 . ? 1_555 ? 10 AC2 8 CYS A 72 ? CYS A 72 . ? 1_555 ? 11 AC2 8 VAL A 170 ? VAL A 170 . ? 1_555 ? 12 AC2 8 PRO A 171 ? PRO A 171 . ? 1_555 ? 13 AC2 8 HOH D . ? HOH A 220 . ? 6_555 ? 14 AC2 8 HOH D . ? HOH A 220 . ? 1_555 ? # _database_PDB_matrix.entry_id 3QKG _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 3QKG _atom_sites.fract_transf_matrix[1][1] 0.014988 _atom_sites.fract_transf_matrix[1][2] 0.008653 _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] 0.017306 _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] 0.012460 _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 NI 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 GLY 1 1 ? ? ? A . n A 1 2 PRO 2 2 ? ? ? A . n A 1 3 VAL 3 3 ? ? ? A . n A 1 4 PRO 4 4 ? ? ? A . n A 1 5 THR 5 5 ? ? ? A . n A 1 6 PRO 6 6 ? ? ? A . n A 1 7 PRO 7 7 ? ? ? A . n A 1 8 ASP 8 8 8 ASP ASP A . n A 1 9 ASN 9 9 9 ASN ASN A . n A 1 10 ILE 10 10 10 ILE ILE A . n A 1 11 GLN 11 11 11 GLN GLN A . n A 1 12 VAL 12 12 12 VAL VAL A . n A 1 13 GLN 13 13 13 GLN GLN A . n A 1 14 GLU 14 14 14 GLU GLU A . n A 1 15 ASN 15 15 15 ASN ASN A . n A 1 16 PHE 16 16 16 PHE PHE A . n A 1 17 ASN 17 17 17 ASN ASN A . n A 1 18 ILE 18 18 18 ILE ILE A . n A 1 19 SER 19 19 19 SER SER A . n A 1 20 ARG 20 20 20 ARG ARG A . n A 1 21 ILE 21 21 21 ILE ILE A . n A 1 22 TYR 22 22 22 TYR TYR A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 LYS 24 24 24 LYS LYS A . n A 1 25 TRP 25 25 25 TRP TRP A . n A 1 26 TYR 26 26 26 TYR TYR A . n A 1 27 ASN 27 27 27 ASN ASN A . n A 1 28 LEU 28 28 28 LEU LEU A . n A 1 29 ALA 29 29 29 ALA ALA A . n A 1 30 ILE 30 30 30 ILE ILE A . n A 1 31 GLY 31 31 31 GLY GLY A . n A 1 32 SER 32 32 32 SER SER A . n A 1 33 THR 33 33 33 THR THR A . n A 1 34 SER 34 34 34 SER SER A . n A 1 35 PRO 35 35 35 PRO PRO A . n A 1 36 TRP 36 36 36 TRP TRP A . n A 1 37 LEU 37 37 37 LEU LEU A . n A 1 38 LYS 38 38 38 LYS LYS A . n A 1 39 LYS 39 39 39 LYS LYS A . n A 1 40 ILE 40 40 40 ILE ILE A . n A 1 41 MET 41 41 41 MET MET A . n A 1 42 ASP 42 42 42 ASP ASP A . n A 1 43 ARG 43 43 43 ARG ARG A . n A 1 44 MET 44 44 44 MET MET A . n A 1 45 THR 45 45 45 THR THR A . n A 1 46 VAL 46 46 46 VAL VAL A . n A 1 47 SER 47 47 47 SER SER A . n A 1 48 THR 48 48 48 THR THR A . n A 1 49 LEU 49 49 49 LEU LEU A . n A 1 50 VAL 50 50 50 VAL VAL A . n A 1 51 LEU 51 51 51 LEU LEU A . n A 1 52 GLY 52 52 52 GLY GLY A . n A 1 53 GLU 53 53 53 GLU GLU A . n A 1 54 GLY 54 54 54 GLY GLY A . n A 1 55 ALA 55 55 55 ALA ALA A . n A 1 56 THR 56 56 56 THR THR A . n A 1 57 GLU 57 57 57 GLU GLU A . n A 1 58 ALA 58 58 58 ALA ALA A . n A 1 59 GLU 59 59 59 GLU GLU A . n A 1 60 ILE 60 60 60 ILE ILE A . n A 1 61 SER 61 61 61 SER SER A . n A 1 62 MET 62 62 62 MET MET A . n A 1 63 THR 63 63 63 THR THR A . n A 1 64 SER 64 64 64 SER SER A . n A 1 65 THR 65 65 65 THR THR A . n A 1 66 ARG 66 66 66 ARG ARG A . n A 1 67 TRP 67 67 67 TRP TRP A . n A 1 68 ARG 68 68 68 ARG ARG A . n A 1 69 LYS 69 69 69 LYS LYS A . n A 1 70 GLY 70 70 70 GLY GLY A . n A 1 71 VAL 71 71 71 VAL VAL A . n A 1 72 CYS 72 72 72 CYS CYS A . n A 1 73 GLU 73 73 73 GLU GLU A . n A 1 74 GLU 74 74 74 GLU GLU A . n A 1 75 THR 75 75 75 THR THR A . n A 1 76 SER 76 76 76 SER SER A . n A 1 77 GLY 77 77 77 GLY GLY A . n A 1 78 ALA 78 78 78 ALA ALA A . n A 1 79 TYR 79 79 79 TYR TYR A . n A 1 80 GLU 80 80 80 GLU GLU A . n A 1 81 LYS 81 81 81 LYS LYS A . n A 1 82 THR 82 82 82 THR THR A . n A 1 83 ASP 83 83 83 ASP ASP A . n A 1 84 THR 84 84 84 THR THR A . n A 1 85 ASP 85 85 85 ASP ASP A . n A 1 86 GLY 86 86 86 GLY GLY A . n A 1 87 LYS 87 87 87 LYS LYS A . n A 1 88 PHE 88 88 88 PHE PHE A . n A 1 89 LEU 89 89 89 LEU LEU A . n A 1 90 TYR 90 90 90 TYR TYR A . n A 1 91 HIS 91 91 91 HIS HIS A . n A 1 92 LYS 92 92 92 LYS LYS A . n A 1 93 SER 93 93 93 SER SER A . n A 1 94 LYS 94 94 94 LYS LYS A . n A 1 95 TRP 95 95 95 TRP TRP A . n A 1 96 ASN 96 96 96 ASN ASN A . n A 1 97 ILE 97 97 97 ILE ILE A . n A 1 98 THR 98 98 98 THR THR A . n A 1 99 MET 99 99 99 MET MET A . n A 1 100 GLU 100 100 100 GLU GLU A . n A 1 101 SER 101 101 101 SER SER A . n A 1 102 TYR 102 102 102 TYR TYR A . n A 1 103 VAL 103 103 103 VAL VAL A . n A 1 104 VAL 104 104 104 VAL VAL A . n A 1 105 HIS 105 105 105 HIS HIS A . n A 1 106 THR 106 106 106 THR THR A . n A 1 107 ASN 107 107 107 ASN ASN A . n A 1 108 TYR 108 108 108 TYR TYR A . n A 1 109 ASP 109 109 109 ASP ASP A . n A 1 110 GLU 110 110 110 GLU GLU A . n A 1 111 TYR 111 111 111 TYR TYR A . n A 1 112 ALA 112 112 112 ALA ALA A . n A 1 113 ILE 113 113 113 ILE ILE A . n A 1 114 PHE 114 114 114 PHE PHE A . n A 1 115 LEU 115 115 115 LEU LEU A . n A 1 116 THR 116 116 116 THR THR A . n A 1 117 LYS 117 117 117 LYS LYS A . n A 1 118 LYS 118 118 118 LYS LYS A . n A 1 119 PHE 119 119 119 PHE PHE A . n A 1 120 SER 120 120 120 SER SER A . n A 1 121 ARG 121 121 121 ARG ARG A . n A 1 122 HIS 122 122 122 HIS HIS A . n A 1 123 HIS 123 123 123 HIS HIS A . n A 1 124 GLY 124 124 124 GLY GLY A . n A 1 125 PRO 125 125 125 PRO PRO A . n A 1 126 THR 126 126 126 THR THR A . n A 1 127 ILE 127 127 127 ILE ILE A . n A 1 128 THR 128 128 128 THR THR A . n A 1 129 ALA 129 129 129 ALA ALA A . n A 1 130 LYS 130 130 130 LYS LYS A . n A 1 131 LEU 131 131 131 LEU LEU A . n A 1 132 TYR 132 132 132 TYR TYR A . n A 1 133 GLY 133 133 133 GLY GLY A . n A 1 134 ARG 134 134 134 ARG ARG A . n A 1 135 ALA 135 135 135 ALA ALA A . n A 1 136 PRO 136 136 136 PRO PRO A . n A 1 137 GLN 137 137 137 GLN GLN A . n A 1 138 LEU 138 138 138 LEU LEU A . n A 1 139 ARG 139 139 139 ARG ARG A . n A 1 140 GLU 140 140 140 GLU GLU A . n A 1 141 THR 141 141 141 THR THR A . n A 1 142 LEU 142 142 142 LEU LEU A . n A 1 143 LEU 143 143 143 LEU LEU A . n A 1 144 GLN 144 144 144 GLN GLN A . n A 1 145 ASP 145 145 145 ASP ASP A . n A 1 146 PHE 146 146 146 PHE PHE A . n A 1 147 ARG 147 147 147 ARG ARG A . n A 1 148 VAL 148 148 148 VAL VAL A . n A 1 149 VAL 149 149 149 VAL VAL A . n A 1 150 ALA 150 150 150 ALA ALA A . n A 1 151 GLN 151 151 151 GLN GLN A . n A 1 152 GLY 152 152 152 GLY GLY A . n A 1 153 VAL 153 153 153 VAL VAL A . n A 1 154 GLY 154 154 154 GLY GLY A . n A 1 155 ILE 155 155 155 ILE ILE A . n A 1 156 PRO 156 156 156 PRO PRO A . n A 1 157 GLU 157 157 157 GLU GLU A . n A 1 158 ASP 158 158 158 ASP ASP A . n A 1 159 SER 159 159 159 SER SER A . n A 1 160 ILE 160 160 160 ILE ILE A . n A 1 161 PHE 161 161 161 PHE PHE A . n A 1 162 THR 162 162 162 THR THR A . n A 1 163 MET 163 163 163 MET MET A . n A 1 164 ALA 164 164 164 ALA ALA A . n A 1 165 ASP 165 165 165 ASP ASP A . n A 1 166 ARG 166 166 166 ARG ARG A . n A 1 167 GLY 167 167 167 GLY GLY A . n A 1 168 GLU 168 168 168 GLU GLU A . n A 1 169 CYS 169 169 169 CYS CYS A . n A 1 170 VAL 170 170 170 VAL VAL A . n A 1 171 PRO 171 171 171 PRO PRO A . n A 1 172 GLY 172 172 ? ? ? A . n A 1 173 GLU 173 173 ? ? ? A . n A 1 174 GLN 174 174 ? ? ? A . n A 1 175 GLU 175 175 ? ? ? A . n A 1 176 PRO 176 176 ? ? ? A . n A 1 177 GLU 177 177 ? ? ? A . n A 1 178 PRO 178 178 ? ? ? A . n A 1 179 ILE 179 179 ? ? ? A . n A 1 180 LEU 180 180 ? ? ? A . n A 1 181 ILE 181 181 ? ? ? A . n A 1 182 PRO 182 182 ? ? ? A . n A 1 183 ARG 183 183 ? ? ? A . n A 1 184 SER 184 184 ? ? ? A . n A 1 185 ALA 185 185 ? ? ? A . n A 1 186 TRP 186 186 ? ? ? A . n A 1 187 SER 187 187 ? ? ? A . n A 1 188 HIS 188 188 ? ? ? A . n A 1 189 PRO 189 189 ? ? ? A . n A 1 190 GLN 190 190 ? ? ? A . n A 1 191 PHE 191 191 ? ? ? A . n A 1 192 GLU 192 192 ? ? ? A . n A 1 193 LYS 193 193 ? ? ? 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 NI 1 194 1 NI NI A . C 3 GOL 1 195 1 GOL GOL A . D 4 HOH 1 196 1 HOH HOH A . D 4 HOH 2 197 2 HOH HOH A . D 4 HOH 3 198 3 HOH HOH A . D 4 HOH 4 199 4 HOH HOH A . D 4 HOH 5 200 5 HOH HOH A . D 4 HOH 6 201 6 HOH HOH A . D 4 HOH 7 202 7 HOH HOH A . D 4 HOH 8 203 8 HOH HOH A . D 4 HOH 9 204 9 HOH HOH A . D 4 HOH 10 205 10 HOH HOH A . D 4 HOH 11 206 11 HOH HOH A . D 4 HOH 12 207 12 HOH HOH A . D 4 HOH 13 208 13 HOH HOH A . D 4 HOH 14 209 14 HOH HOH A . D 4 HOH 15 210 15 HOH HOH A . D 4 HOH 16 211 16 HOH HOH A . D 4 HOH 17 212 17 HOH HOH A . D 4 HOH 18 213 18 HOH HOH A . D 4 HOH 19 214 19 HOH HOH A . D 4 HOH 20 215 20 HOH HOH A . D 4 HOH 21 216 21 HOH HOH A . D 4 HOH 22 217 22 HOH HOH A . D 4 HOH 23 218 23 HOH HOH A . D 4 HOH 24 219 24 HOH HOH A . D 4 HOH 25 220 25 HOH HOH A . D 4 HOH 26 221 26 HOH HOH A . D 4 HOH 27 222 27 HOH HOH A . D 4 HOH 28 223 28 HOH HOH A . D 4 HOH 29 224 29 HOH HOH A . D 4 HOH 30 225 30 HOH HOH A . D 4 HOH 31 226 31 HOH HOH A . D 4 HOH 32 227 32 HOH HOH A . D 4 HOH 33 228 33 HOH HOH A . D 4 HOH 34 229 34 HOH HOH A . D 4 HOH 35 230 35 HOH HOH A . D 4 HOH 36 231 36 HOH HOH A . D 4 HOH 37 232 37 HOH HOH A . D 4 HOH 38 233 38 HOH HOH A . D 4 HOH 39 234 39 HOH HOH A . D 4 HOH 40 235 40 HOH HOH A . D 4 HOH 41 236 41 HOH HOH A . D 4 HOH 42 237 42 HOH HOH A . D 4 HOH 43 238 43 HOH HOH A . D 4 HOH 44 239 44 HOH HOH A . D 4 HOH 45 240 45 HOH HOH A . D 4 HOH 46 241 46 HOH HOH A . D 4 HOH 47 242 47 HOH HOH A . # _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 # _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_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? D HOH . ? A HOH 199 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 NE2 ? A HIS 122 ? A HIS 122 ? 1_555 92.8 ? 2 O ? D HOH . ? A HOH 199 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 O ? D HOH . ? A HOH 196 ? 1_555 178.5 ? 3 NE2 ? A HIS 122 ? A HIS 122 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 O ? D HOH . ? A HOH 196 ? 1_555 87.6 ? 4 O ? D HOH . ? A HOH 199 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 O ? D HOH . ? A HOH 198 ? 1_555 124.1 ? 5 NE2 ? A HIS 122 ? A HIS 122 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 O ? D HOH . ? A HOH 198 ? 1_555 95.2 ? 6 O ? D HOH . ? A HOH 196 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 O ? D HOH . ? A HOH 198 ? 1_555 57.3 ? 7 O ? D HOH . ? A HOH 199 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 O ? D HOH . ? A HOH 197 ? 1_555 107.6 ? 8 NE2 ? A HIS 122 ? A HIS 122 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 O ? D HOH . ? A HOH 197 ? 1_555 159.1 ? 9 O ? D HOH . ? A HOH 196 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 O ? D HOH . ? A HOH 197 ? 1_555 72.2 ? 10 O ? D HOH . ? A HOH 198 ? 1_555 NI ? B NI . ? A NI 194 ? 1_555 O ? D HOH . ? A HOH 197 ? 1_555 69.6 ? # 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 2012-02-08 2 'Structure model' 1 1 2012-06-20 3 'Structure model' 1 2 2013-06-19 4 'Structure model' 1 3 2017-11-08 # _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 ? # 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' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 4 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined -18.1030 16.9850 -1.2880 0.5226 0.3116 0.0604 -0.0737 -0.0008 0.0341 6.7347 6.0569 6.7829 2.4013 -0.7132 1.1743 -0.4377 0.2940 -0.2103 0.1032 0.2054 -0.0532 0.2347 0.3580 0.2323 'X-RAY DIFFRACTION' 2 ? refined -15.8210 12.5320 12.0420 1.6242 0.9307 0.4704 -0.0650 -0.0420 0.0222 1.3449 4.0462 5.0214 2.5567 6.5378 -6.0837 -0.0763 -0.5462 -0.3688 1.3359 -0.0883 -0.1471 0.0993 0.3715 0.1646 'X-RAY DIFFRACTION' 3 ? refined -22.4660 15.2970 4.0240 0.5163 0.4512 0.0725 -0.0848 -0.0110 0.0079 2.3128 6.0564 2.1614 2.9719 -1.1821 -0.8751 0.0077 -0.1102 0.0179 0.3647 0.0516 -0.0337 -0.0595 0.1959 -0.0593 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _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 'X-RAY DIFFRACTION' 1 1 A 8 ? ? A 34 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 35 ? ? A 79 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 80 ? ? A 171 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 MrBUMP phasing . ? 2 REFMAC refinement 5.5.0109 ? 3 XDS 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 OE2 A GLU 110 ? ? NH1 A ARG 139 ? ? 1.97 2 1 N A SER 159 ? ? O A HOH 241 ? ? 2.01 3 1 O A PRO 156 ? ? O A ASP 158 ? ? 2.12 4 1 O A HOH 196 ? ? O A HOH 198 ? ? 2.15 # 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 ARG A 43 ? ? -53.40 2.28 2 1 LYS A 69 ? ? 54.72 -124.92 3 1 THR A 82 ? ? -123.61 -164.16 4 1 ASN A 96 ? ? 72.19 33.08 5 1 TYR A 108 ? ? 73.00 -45.60 6 1 GLU A 110 ? ? -137.87 -48.24 7 1 LEU A 138 ? ? -74.19 -97.52 8 1 ARG A 139 ? ? 110.67 100.83 9 1 ASP A 158 ? ? -58.64 174.40 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 1 ? A GLY 1 2 1 Y 1 A PRO 2 ? A PRO 2 3 1 Y 1 A VAL 3 ? A VAL 3 4 1 Y 1 A PRO 4 ? A PRO 4 5 1 Y 1 A THR 5 ? A THR 5 6 1 Y 1 A PRO 6 ? A PRO 6 7 1 Y 1 A PRO 7 ? A PRO 7 8 1 Y 1 A GLY 172 ? A GLY 172 9 1 Y 1 A GLU 173 ? A GLU 173 10 1 Y 1 A GLN 174 ? A GLN 174 11 1 Y 1 A GLU 175 ? A GLU 175 12 1 Y 1 A PRO 176 ? A PRO 176 13 1 Y 1 A GLU 177 ? A GLU 177 14 1 Y 1 A PRO 178 ? A PRO 178 15 1 Y 1 A ILE 179 ? A ILE 179 16 1 Y 1 A LEU 180 ? A LEU 180 17 1 Y 1 A ILE 181 ? A ILE 181 18 1 Y 1 A PRO 182 ? A PRO 182 19 1 Y 1 A ARG 183 ? A ARG 183 20 1 Y 1 A SER 184 ? A SER 184 21 1 Y 1 A ALA 185 ? A ALA 185 22 1 Y 1 A TRP 186 ? A TRP 186 23 1 Y 1 A SER 187 ? A SER 187 24 1 Y 1 A HIS 188 ? A HIS 188 25 1 Y 1 A PRO 189 ? A PRO 189 26 1 Y 1 A GLN 190 ? A GLN 190 27 1 Y 1 A PHE 191 ? A PHE 191 28 1 Y 1 A GLU 192 ? A GLU 192 29 1 Y 1 A LYS 193 ? A LYS 193 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'NICKEL (II) ION' NI 3 GLYCEROL GOL 4 water HOH #