data_1SK3 # _entry.id 1SK3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1SK3 RCSB RCSB021779 WWPDB D_1000021779 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1OHT _pdbx_database_related.details 'Peptidoglycan Recognition Protein-Lb' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1SK3 _pdbx_database_status.recvd_initial_deposition_date 2004-03-04 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Guan, R.' 1 'Malchiodi, E.L.' 2 'Qian, W.' 3 'Schuck, P.' 4 'Mariuzza, R.A.' 5 # _citation.id primary _citation.title 'Crystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ialpha' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 279 _citation.page_first 31873 _citation.page_last 31882 _citation.year 2004 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15140887 _citation.pdbx_database_id_DOI 10.1074/jbc.M404920200 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Guan, R.' 1 primary 'Malchiodi, E.L.' 2 primary 'Qian, W.' 3 primary 'Schuck, P.' 4 primary 'Mariuzza, R.A.' 5 # _cell.entry_id 1SK3 _cell.length_a 102.632 _cell.length_b 102.632 _cell.length_c 41.496 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SK3 _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 'Peptidoglycan recognition protein I-alpha' 18271.795 1 ? ? ? ? 2 non-polymer syn 'NICKEL (II) ION' 58.693 2 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 4 water nat water 18.015 11 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Peptidoglycan recognition protein intermediate alpha, PGRP-I-alpha, PGLYRPIalpha' # _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 ;VCPNIIKRSAWEARETHCPKMNLPAKYVIIIHTAGTSCTVSTDCQTVVRNIQSFHMDTRNFCDIGYHFLVGQDGGVYEGV GWHIQGSHTYGFNDIALGIAFIGYFVEKPPNAAALEAAQDLIQCAVVEGYLTPNYLLMGHSDVVNILSPGQALYNIISTW PHFKH ; _entity_poly.pdbx_seq_one_letter_code_can ;VCPNIIKRSAWEARETHCPKMNLPAKYVIIIHTAGTSCTVSTDCQTVVRNIQSFHMDTRNFCDIGYHFLVGQDGGVYEGV GWHIQGSHTYGFNDIALGIAFIGYFVEKPPNAAALEAAQDLIQCAVVEGYLTPNYLLMGHSDVVNILSPGQALYNIISTW PHFKH ; _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 VAL n 1 2 CYS n 1 3 PRO n 1 4 ASN n 1 5 ILE n 1 6 ILE n 1 7 LYS n 1 8 ARG n 1 9 SER n 1 10 ALA n 1 11 TRP n 1 12 GLU n 1 13 ALA n 1 14 ARG n 1 15 GLU n 1 16 THR n 1 17 HIS n 1 18 CYS n 1 19 PRO n 1 20 LYS n 1 21 MET n 1 22 ASN n 1 23 LEU n 1 24 PRO n 1 25 ALA n 1 26 LYS n 1 27 TYR n 1 28 VAL n 1 29 ILE n 1 30 ILE n 1 31 ILE n 1 32 HIS n 1 33 THR n 1 34 ALA n 1 35 GLY n 1 36 THR n 1 37 SER n 1 38 CYS n 1 39 THR n 1 40 VAL n 1 41 SER n 1 42 THR n 1 43 ASP n 1 44 CYS n 1 45 GLN n 1 46 THR n 1 47 VAL n 1 48 VAL n 1 49 ARG n 1 50 ASN n 1 51 ILE n 1 52 GLN n 1 53 SER n 1 54 PHE n 1 55 HIS n 1 56 MET n 1 57 ASP n 1 58 THR n 1 59 ARG n 1 60 ASN n 1 61 PHE n 1 62 CYS n 1 63 ASP n 1 64 ILE n 1 65 GLY n 1 66 TYR n 1 67 HIS n 1 68 PHE n 1 69 LEU n 1 70 VAL n 1 71 GLY n 1 72 GLN n 1 73 ASP n 1 74 GLY n 1 75 GLY n 1 76 VAL n 1 77 TYR n 1 78 GLU n 1 79 GLY n 1 80 VAL n 1 81 GLY n 1 82 TRP n 1 83 HIS n 1 84 ILE n 1 85 GLN n 1 86 GLY n 1 87 SER n 1 88 HIS n 1 89 THR n 1 90 TYR n 1 91 GLY n 1 92 PHE n 1 93 ASN n 1 94 ASP n 1 95 ILE n 1 96 ALA n 1 97 LEU n 1 98 GLY n 1 99 ILE n 1 100 ALA n 1 101 PHE n 1 102 ILE n 1 103 GLY n 1 104 TYR n 1 105 PHE n 1 106 VAL n 1 107 GLU n 1 108 LYS n 1 109 PRO n 1 110 PRO n 1 111 ASN n 1 112 ALA n 1 113 ALA n 1 114 ALA n 1 115 LEU n 1 116 GLU n 1 117 ALA n 1 118 ALA n 1 119 GLN n 1 120 ASP n 1 121 LEU n 1 122 ILE n 1 123 GLN n 1 124 CYS n 1 125 ALA n 1 126 VAL n 1 127 VAL n 1 128 GLU n 1 129 GLY n 1 130 TYR n 1 131 LEU n 1 132 THR n 1 133 PRO n 1 134 ASN n 1 135 TYR n 1 136 LEU n 1 137 LEU n 1 138 MET n 1 139 GLY n 1 140 HIS n 1 141 SER n 1 142 ASP n 1 143 VAL n 1 144 VAL n 1 145 ASN n 1 146 ILE n 1 147 LEU n 1 148 SER n 1 149 PRO n 1 150 GLY n 1 151 GLN n 1 152 ALA n 1 153 LEU n 1 154 TYR n 1 155 ASN n 1 156 ILE n 1 157 ILE n 1 158 SER n 1 159 THR n 1 160 TRP n 1 161 PRO n 1 162 HIS n 1 163 PHE n 1 164 LYS n 1 165 HIS 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 Homo _entity_src_gen.pdbx_gene_src_gene PGRPIA _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 'Escherichia coli' _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21 DE3' _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 pt7-7 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PGRP3_HUMAN _struct_ref.pdbx_db_accession Q96LB9 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;VCPNIIKRSAWEARETHCPKMNLPAKYVIIIHTAGTSCTVSTDCQTVVRNIQSFHMDTRNFCDIGYHFLVGQDGGVYEGV GWHIQGSHTYGFNDIALGIAFIGYFVEKPPNAAALEAAQDLIQCAVVEGYLTPNYLLMGHSDVVNILSPGQALYNIISTW PHFKH ; _struct_ref.pdbx_align_begin 177 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1SK3 _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 165 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q96LB9 _struct_ref_seq.db_align_beg 177 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 341 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 177 _struct_ref_seq.pdbx_auth_seq_align_end 341 # 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 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 1SK3 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 64.36 _exptl_crystal.description ? _exptl_crystal.density_Matthews 3.45 _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _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 8.5 _exptl_crystal_grow.pdbx_details 'PEG-MME 2000, nickleous sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2003-11-09 _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 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X25' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X25 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 1SK3 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 30 _reflns.d_resolution_high 2.8 _reflns.number_obs 6416 _reflns.number_all 6416 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs 0.131 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 58.9 _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_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.80 _reflns_shell.d_res_low 2.90 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.505 _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 627 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1SK3 _refine.ls_number_reflns_obs 6405 _refine.ls_number_reflns_all 6405 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 1047715.81 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.63 _refine.ls_d_res_high 2.80 _refine.ls_percent_reflns_obs 100.0 _refine.ls_R_factor_obs 0.219 _refine.ls_R_factor_all 0.219 _refine.ls_R_factor_R_work 0.219 _refine.ls_R_factor_R_free 0.253 _refine.ls_R_factor_R_free_error 0.014 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.4 _refine.ls_number_reflns_R_free 346 _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 33.6 _refine.aniso_B[1][1] 2.35 _refine.aniso_B[2][2] 2.35 _refine.aniso_B[3][3] -4.70 _refine.aniso_B[1][2] 7.23 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.360846 _refine.solvent_model_param_bsol 34.5311 _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 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _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.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1SK3 _refine_analyze.Luzzati_coordinate_error_obs 0.35 _refine_analyze.Luzzati_sigma_a_obs 0.52 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.45 _refine_analyze.Luzzati_sigma_a_free 0.59 _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 1286 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 7 _refine_hist.number_atoms_solvent 11 _refine_hist.number_atoms_total 1304 _refine_hist.d_res_high 2.80 _refine_hist.d_res_low 29.63 # 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 1.5 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 24.0 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.95 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.80 _refine_ls_shell.d_res_low 2.98 _refine_ls_shell.number_reflns_R_work 1042 _refine_ls_shell.R_factor_R_work 0.329 _refine_ls_shell.percent_reflns_obs 99.9 _refine_ls_shell.R_factor_R_free ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free ? _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 ? 'X-RAY DIFFRACTION' 3 ION.PARAM ? 'X-RAY DIFFRACTION' # _struct.entry_id 1SK3 _struct.title 'Crystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ialpha' _struct.pdbx_descriptor 'Peptidoglycan recognition protein I-alpha' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1SK3 _struct_keywords.pdbx_keywords 'IMMUNE SYSTEM' _struct_keywords.text 'alpha/beta mix, 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 2 ? D N N 3 ? E N N 4 ? # _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 VAL A 40 ? THR A 58 ? VAL A 216 THR A 234 1 ? 19 HELX_P HELX_P2 2 ASN A 111 ? GLU A 128 ? ASN A 287 GLU A 304 1 ? 18 HELX_P HELX_P3 3 SER A 141 ? VAL A 143 ? SER A 317 VAL A 319 5 ? 3 HELX_P HELX_P4 4 GLY A 150 ? SER A 158 ? GLY A 326 SER A 334 1 ? 9 # _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 2 SG ? ? ? 1_555 A CYS 124 SG ? ? A CYS 178 A CYS 300 1_555 ? ? ? ? ? ? ? 2.042 ? disulf2 disulf ? ? A CYS 18 SG ? ? ? 1_555 A CYS 62 SG ? ? A CYS 194 A CYS 238 1_555 ? ? ? ? ? ? ? 2.041 ? disulf3 disulf ? ? A CYS 38 SG ? ? ? 1_555 A CYS 44 SG ? ? A CYS 214 A CYS 220 1_555 ? ? ? ? ? ? ? 2.043 ? metalc1 metalc ? ? B NI . NI ? ? ? 1_555 A VAL 1 O ? ? A NI 21 A VAL 177 1_555 ? ? ? ? ? ? ? 2.090 ? metalc2 metalc ? ? B NI . NI ? ? ? 1_555 A ASP 120 OD2 ? ? A NI 21 A ASP 296 1_555 ? ? ? ? ? ? ? 2.127 ? metalc3 metalc ? ? B NI . NI ? ? ? 1_555 E HOH . O ? ? A NI 21 A HOH 1 1_555 ? ? ? ? ? ? ? 2.452 ? metalc4 metalc ? ? B NI . NI ? ? ? 1_555 A VAL 1 N ? ? A NI 21 A VAL 177 1_555 ? ? ? ? ? ? ? 2.575 ? metalc5 metalc ? ? B NI . NI ? ? ? 1_555 A HIS 162 NE2 ? ? A NI 21 A HIS 338 6_764 ? ? ? ? ? ? ? 2.141 ? metalc6 metalc ? ? C NI . NI ? ? ? 1_555 A HIS 165 NE2 ? ? A NI 22 A HIS 341 6_764 ? ? ? ? ? ? ? 2.239 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? metalc ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id SER _struct_mon_prot_cis.label_seq_id 148 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id SER _struct_mon_prot_cis.auth_seq_id 324 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 149 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 325 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 0.42 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _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 ? parallel A 3 4 ? parallel A 4 5 ? 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 76 ? GLU A 78 ? VAL A 252 GLU A 254 A 2 PHE A 68 ? VAL A 70 ? PHE A 244 VAL A 246 A 3 ALA A 96 ? PHE A 101 ? ALA A 272 PHE A 277 A 4 ALA A 25 ? HIS A 32 ? ALA A 201 HIS A 208 A 5 LEU A 131 ? GLY A 139 ? LEU A 307 GLY A 315 # 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 TYR A 77 ? O TYR A 253 N LEU A 69 ? N LEU A 245 A 2 3 N PHE A 68 ? N PHE A 244 O ALA A 100 ? O ALA A 276 A 3 4 O ILE A 99 ? O ILE A 275 N ILE A 29 ? N ILE A 205 A 4 5 N ALA A 25 ? N ALA A 201 O THR A 132 ? O THR A 308 # 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 ? ? ? ? 4 'BINDING SITE FOR RESIDUE NI A 21' AC2 Software ? ? ? ? 2 'BINDING SITE FOR RESIDUE NI A 22' AC3 Software ? ? ? ? 2 'BINDING SITE FOR RESIDUE SO4 A 342' # 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 4 HOH E . ? HOH A 1 . ? 1_555 ? 2 AC1 4 VAL A 1 ? VAL A 177 . ? 1_555 ? 3 AC1 4 ASP A 120 ? ASP A 296 . ? 1_555 ? 4 AC1 4 HIS A 162 ? HIS A 338 . ? 6_764 ? 5 AC2 2 GLU A 116 ? GLU A 292 . ? 1_555 ? 6 AC2 2 HIS A 165 ? HIS A 341 . ? 6_764 ? 7 AC3 2 HIS A 17 ? HIS A 193 . ? 1_555 ? 8 AC3 2 ARG A 59 ? ARG A 235 . ? 3_665 ? # _database_PDB_matrix.entry_id 1SK3 _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 1SK3 _atom_sites.fract_transf_matrix[1][1] 0.009744 _atom_sites.fract_transf_matrix[1][2] 0.005625 _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] 0.011251 _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] 0.024099 _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 VAL 1 177 177 VAL VAL A . n A 1 2 CYS 2 178 178 CYS CYS A . n A 1 3 PRO 3 179 179 PRO PRO A . n A 1 4 ASN 4 180 180 ASN ASN A . n A 1 5 ILE 5 181 181 ILE ILE A . n A 1 6 ILE 6 182 182 ILE ILE A . n A 1 7 LYS 7 183 183 LYS LYS A . n A 1 8 ARG 8 184 184 ARG ARG A . n A 1 9 SER 9 185 185 SER SER A . n A 1 10 ALA 10 186 186 ALA ALA A . n A 1 11 TRP 11 187 187 TRP TRP A . n A 1 12 GLU 12 188 188 GLU GLU A . n A 1 13 ALA 13 189 189 ALA ALA A . n A 1 14 ARG 14 190 190 ARG ARG A . n A 1 15 GLU 15 191 191 GLU GLU A . n A 1 16 THR 16 192 192 THR THR A . n A 1 17 HIS 17 193 193 HIS HIS A . n A 1 18 CYS 18 194 194 CYS CYS A . n A 1 19 PRO 19 195 195 PRO PRO A . n A 1 20 LYS 20 196 196 LYS LYS A . n A 1 21 MET 21 197 197 MET MET A . n A 1 22 ASN 22 198 198 ASN ASN A . n A 1 23 LEU 23 199 199 LEU LEU A . n A 1 24 PRO 24 200 200 PRO PRO A . n A 1 25 ALA 25 201 201 ALA ALA A . n A 1 26 LYS 26 202 202 LYS LYS A . n A 1 27 TYR 27 203 203 TYR TYR A . n A 1 28 VAL 28 204 204 VAL VAL A . n A 1 29 ILE 29 205 205 ILE ILE A . n A 1 30 ILE 30 206 206 ILE ILE A . n A 1 31 ILE 31 207 207 ILE ILE A . n A 1 32 HIS 32 208 208 HIS HIS A . n A 1 33 THR 33 209 209 THR THR A . n A 1 34 ALA 34 210 210 ALA ALA A . n A 1 35 GLY 35 211 211 GLY GLY A . n A 1 36 THR 36 212 212 THR THR A . n A 1 37 SER 37 213 213 SER SER A . n A 1 38 CYS 38 214 214 CYS CYS A . n A 1 39 THR 39 215 215 THR THR A . n A 1 40 VAL 40 216 216 VAL VAL A . n A 1 41 SER 41 217 217 SER SER A . n A 1 42 THR 42 218 218 THR THR A . n A 1 43 ASP 43 219 219 ASP ASP A . n A 1 44 CYS 44 220 220 CYS CYS A . n A 1 45 GLN 45 221 221 GLN GLN A . n A 1 46 THR 46 222 222 THR THR A . n A 1 47 VAL 47 223 223 VAL VAL A . n A 1 48 VAL 48 224 224 VAL VAL A . n A 1 49 ARG 49 225 225 ARG ARG A . n A 1 50 ASN 50 226 226 ASN ASN A . n A 1 51 ILE 51 227 227 ILE ILE A . n A 1 52 GLN 52 228 228 GLN GLN A . n A 1 53 SER 53 229 229 SER SER A . n A 1 54 PHE 54 230 230 PHE PHE A . n A 1 55 HIS 55 231 231 HIS HIS A . n A 1 56 MET 56 232 232 MET MET A . n A 1 57 ASP 57 233 233 ASP ASP A . n A 1 58 THR 58 234 234 THR THR A . n A 1 59 ARG 59 235 235 ARG ARG A . n A 1 60 ASN 60 236 236 ASN ASN A . n A 1 61 PHE 61 237 237 PHE PHE A . n A 1 62 CYS 62 238 238 CYS CYS A . n A 1 63 ASP 63 239 239 ASP ASP A . n A 1 64 ILE 64 240 240 ILE ILE A . n A 1 65 GLY 65 241 241 GLY GLY A . n A 1 66 TYR 66 242 242 TYR TYR A . n A 1 67 HIS 67 243 243 HIS HIS A . n A 1 68 PHE 68 244 244 PHE PHE A . n A 1 69 LEU 69 245 245 LEU LEU A . n A 1 70 VAL 70 246 246 VAL VAL A . n A 1 71 GLY 71 247 247 GLY GLY A . n A 1 72 GLN 72 248 248 GLN GLN A . n A 1 73 ASP 73 249 249 ASP ASP A . n A 1 74 GLY 74 250 250 GLY GLY A . n A 1 75 GLY 75 251 251 GLY GLY A . n A 1 76 VAL 76 252 252 VAL VAL A . n A 1 77 TYR 77 253 253 TYR TYR A . n A 1 78 GLU 78 254 254 GLU GLU A . n A 1 79 GLY 79 255 255 GLY GLY A . n A 1 80 VAL 80 256 256 VAL VAL A . n A 1 81 GLY 81 257 257 GLY GLY A . n A 1 82 TRP 82 258 258 TRP TRP A . n A 1 83 HIS 83 259 259 HIS HIS A . n A 1 84 ILE 84 260 260 ILE ILE A . n A 1 85 GLN 85 261 261 GLN GLN A . n A 1 86 GLY 86 262 262 GLY GLY A . n A 1 87 SER 87 263 263 SER SER A . n A 1 88 HIS 88 264 264 HIS HIS A . n A 1 89 THR 89 265 265 THR THR A . n A 1 90 TYR 90 266 266 TYR TYR A . n A 1 91 GLY 91 267 267 GLY GLY A . n A 1 92 PHE 92 268 268 PHE PHE A . n A 1 93 ASN 93 269 269 ASN ASN A . n A 1 94 ASP 94 270 270 ASP ASP A . n A 1 95 ILE 95 271 271 ILE ILE A . n A 1 96 ALA 96 272 272 ALA ALA A . n A 1 97 LEU 97 273 273 LEU LEU A . n A 1 98 GLY 98 274 274 GLY GLY A . n A 1 99 ILE 99 275 275 ILE ILE A . n A 1 100 ALA 100 276 276 ALA ALA A . n A 1 101 PHE 101 277 277 PHE PHE A . n A 1 102 ILE 102 278 278 ILE ILE A . n A 1 103 GLY 103 279 279 GLY GLY A . n A 1 104 TYR 104 280 280 TYR TYR A . n A 1 105 PHE 105 281 281 PHE PHE A . n A 1 106 VAL 106 282 282 VAL VAL A . n A 1 107 GLU 107 283 283 GLU GLU A . n A 1 108 LYS 108 284 284 LYS LYS A . n A 1 109 PRO 109 285 285 PRO PRO A . n A 1 110 PRO 110 286 286 PRO PRO A . n A 1 111 ASN 111 287 287 ASN ASN A . n A 1 112 ALA 112 288 288 ALA ALA A . n A 1 113 ALA 113 289 289 ALA ALA A . n A 1 114 ALA 114 290 290 ALA ALA A . n A 1 115 LEU 115 291 291 LEU LEU A . n A 1 116 GLU 116 292 292 GLU GLU A . n A 1 117 ALA 117 293 293 ALA ALA A . n A 1 118 ALA 118 294 294 ALA ALA A . n A 1 119 GLN 119 295 295 GLN GLN A . n A 1 120 ASP 120 296 296 ASP ASP A . n A 1 121 LEU 121 297 297 LEU LEU A . n A 1 122 ILE 122 298 298 ILE ILE A . n A 1 123 GLN 123 299 299 GLN GLN A . n A 1 124 CYS 124 300 300 CYS CYS A . n A 1 125 ALA 125 301 301 ALA ALA A . n A 1 126 VAL 126 302 302 VAL VAL A . n A 1 127 VAL 127 303 303 VAL VAL A . n A 1 128 GLU 128 304 304 GLU GLU A . n A 1 129 GLY 129 305 305 GLY GLY A . n A 1 130 TYR 130 306 306 TYR TYR A . n A 1 131 LEU 131 307 307 LEU LEU A . n A 1 132 THR 132 308 308 THR THR A . n A 1 133 PRO 133 309 309 PRO PRO A . n A 1 134 ASN 134 310 310 ASN ASN A . n A 1 135 TYR 135 311 311 TYR TYR A . n A 1 136 LEU 136 312 312 LEU LEU A . n A 1 137 LEU 137 313 313 LEU LEU A . n A 1 138 MET 138 314 314 MET MET A . n A 1 139 GLY 139 315 315 GLY GLY A . n A 1 140 HIS 140 316 316 HIS HIS A . n A 1 141 SER 141 317 317 SER SER A . n A 1 142 ASP 142 318 318 ASP ASP A . n A 1 143 VAL 143 319 319 VAL VAL A . n A 1 144 VAL 144 320 320 VAL VAL A . n A 1 145 ASN 145 321 321 ASN ASN A . n A 1 146 ILE 146 322 322 ILE ILE A . n A 1 147 LEU 147 323 323 LEU LEU A . n A 1 148 SER 148 324 324 SER SER A . n A 1 149 PRO 149 325 325 PRO PRO A . n A 1 150 GLY 150 326 326 GLY GLY A . n A 1 151 GLN 151 327 327 GLN GLN A . n A 1 152 ALA 152 328 328 ALA ALA A . n A 1 153 LEU 153 329 329 LEU LEU A . n A 1 154 TYR 154 330 330 TYR TYR A . n A 1 155 ASN 155 331 331 ASN ASN A . n A 1 156 ILE 156 332 332 ILE ILE A . n A 1 157 ILE 157 333 333 ILE ILE A . n A 1 158 SER 158 334 334 SER SER A . n A 1 159 THR 159 335 335 THR THR A . n A 1 160 TRP 160 336 336 TRP TRP A . n A 1 161 PRO 161 337 337 PRO PRO A . n A 1 162 HIS 162 338 338 HIS HIS A . n A 1 163 PHE 163 339 339 PHE PHE A . n A 1 164 LYS 164 340 340 LYS LYS A . n A 1 165 HIS 165 341 341 HIS HIS 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 21 1 NI NI2 A . C 2 NI 1 22 2 NI NI2 A . D 3 SO4 1 342 276 SO4 SO4 A . E 4 HOH 1 1 1 HOH HOH A . E 4 HOH 2 2 2 HOH HOH A . E 4 HOH 3 3 3 HOH HOH A . E 4 HOH 4 4 4 HOH HOH A . E 4 HOH 5 5 5 HOH HOH A . E 4 HOH 6 6 6 HOH HOH A . E 4 HOH 7 7 7 HOH HOH A . E 4 HOH 8 8 8 HOH HOH A . E 4 HOH 9 9 9 HOH HOH A . E 4 HOH 10 10 10 HOH HOH A . E 4 HOH 11 11 11 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,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_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 ? A VAL 1 ? A VAL 177 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 OD2 ? A ASP 120 ? A ASP 296 ? 1_555 110.7 ? 2 O ? A VAL 1 ? A VAL 177 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 O ? E HOH . ? A HOH 1 ? 1_555 74.5 ? 3 OD2 ? A ASP 120 ? A ASP 296 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 O ? E HOH . ? A HOH 1 ? 1_555 85.1 ? 4 O ? A VAL 1 ? A VAL 177 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 N ? A VAL 1 ? A VAL 177 ? 1_555 71.8 ? 5 OD2 ? A ASP 120 ? A ASP 296 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 N ? A VAL 1 ? A VAL 177 ? 1_555 176.4 ? 6 O ? E HOH . ? A HOH 1 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 N ? A VAL 1 ? A VAL 177 ? 1_555 93.2 ? 7 O ? A VAL 1 ? A VAL 177 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 NE2 ? A HIS 162 ? A HIS 338 ? 6_764 139.3 ? 8 OD2 ? A ASP 120 ? A ASP 296 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 NE2 ? A HIS 162 ? A HIS 338 ? 6_764 94.0 ? 9 O ? E HOH . ? A HOH 1 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 NE2 ? A HIS 162 ? A HIS 338 ? 6_764 76.0 ? 10 N ? A VAL 1 ? A VAL 177 ? 1_555 NI ? B NI . ? A NI 21 ? 1_555 NE2 ? A HIS 162 ? A HIS 338 ? 6_764 82.5 ? # 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 2004-07-13 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 HKL-2000 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 AMoRE phasing . ? 4 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 ND2 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 ASN _pdbx_validate_symm_contact.auth_seq_id_1 180 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 ND2 _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 ASN _pdbx_validate_symm_contact.auth_seq_id_2 180 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 6_765 _pdbx_validate_symm_contact.dist 2.01 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 C _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 LEU _pdbx_validate_rmsd_angle.auth_seq_id_1 199 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 N _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 PRO _pdbx_validate_rmsd_angle.auth_seq_id_2 200 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 CA _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 PRO _pdbx_validate_rmsd_angle.auth_seq_id_3 200 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 110.18 _pdbx_validate_rmsd_angle.angle_target_value 119.30 _pdbx_validate_rmsd_angle.angle_deviation -9.12 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.50 _pdbx_validate_rmsd_angle.linker_flag Y # 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 PRO A 179 ? ? -64.23 -178.06 2 1 ILE A 181 ? ? 31.86 93.88 3 1 GLU A 188 ? ? 68.19 60.03 4 1 ALA A 210 ? ? 63.93 -5.47 5 1 ASN A 236 ? ? 70.46 37.61 6 1 ASP A 239 ? ? -162.23 -162.59 7 1 GLN A 248 ? ? -69.21 5.08 8 1 HIS A 259 ? ? -69.48 1.97 9 1 SER A 324 ? ? -170.33 143.85 10 1 HIS A 338 ? ? 58.34 10.19 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'NICKEL (II) ION' NI 3 'SULFATE ION' SO4 4 water HOH #