data_5DZO # _entry.id 5DZO # _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 5DZO WWPDB D_1000214080 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5DZO _pdbx_database_status.recvd_initial_deposition_date 2015-09-25 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Yuan, S.' 1 'Rao, Z.' 2 'Wang, X.' 3 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country CN _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Protein Cell' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1674-8018 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 6 _citation.language ? _citation.page_first 814 _citation.page_last 824 _citation.title 'TIM-1 acts a dual-attachment receptor for Ebolavirus by interacting directly with viral GP and the PS on the viral envelope.' _citation.year 2015 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1007/s13238-015-0220-y _citation.pdbx_database_id_PubMed 26487564 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Yuan, S.' 1 primary 'Cao, L.' 2 primary 'Ling, H.' 3 primary 'Dang, M.' 4 primary 'Sun, Y.' 5 primary 'Zhang, X.' 6 primary 'Chen, Y.' 7 primary 'Zhang, L.' 8 primary 'Su, D.' 9 primary 'Wang, X.' 10 primary 'Rao, Z.' 11 # _cell.entry_id 5DZO _cell.length_a 50.739 _cell.length_b 50.739 _cell.length_c 84.162 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DZO _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # 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 'Hepatitis A virus cellular receptor 1' 11846.519 1 ? ? 'UNP RESIDUES 22-127' ? 2 non-polymer syn 'NITRATE ION' 62.005 2 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 4 water nat water 18.015 156 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;HAVcr-1,Kidney injury molecule 1,KIM-1,T-cell immunoglobulin and mucin domain-containing protein 1,TIMD-1,T-cell immunoglobulin mucin receptor 1,TIM-1,T-cell membrane protein 1 ; # _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 ;MVKVGGEAGPSVTLPCHYSGAVTSMCWNRGSCSLFTCQNGIVWTNGTHVTYRKDTRYKLLGDLSRRDVSLTIENTAVSDS GVYCCRVEHRGWFNDMKITVSLEIVPP ; _entity_poly.pdbx_seq_one_letter_code_can ;MVKVGGEAGPSVTLPCHYSGAVTSMCWNRGSCSLFTCQNGIVWTNGTHVTYRKDTRYKLLGDLSRRDVSLTIENTAVSDS GVYCCRVEHRGWFNDMKITVSLEIVPP ; _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 MET n 1 2 VAL n 1 3 LYS n 1 4 VAL n 1 5 GLY n 1 6 GLY n 1 7 GLU n 1 8 ALA n 1 9 GLY n 1 10 PRO n 1 11 SER n 1 12 VAL n 1 13 THR n 1 14 LEU n 1 15 PRO n 1 16 CYS n 1 17 HIS n 1 18 TYR n 1 19 SER n 1 20 GLY n 1 21 ALA n 1 22 VAL n 1 23 THR n 1 24 SER n 1 25 MET n 1 26 CYS n 1 27 TRP n 1 28 ASN n 1 29 ARG n 1 30 GLY n 1 31 SER n 1 32 CYS n 1 33 SER n 1 34 LEU n 1 35 PHE n 1 36 THR n 1 37 CYS n 1 38 GLN n 1 39 ASN n 1 40 GLY n 1 41 ILE n 1 42 VAL n 1 43 TRP n 1 44 THR n 1 45 ASN n 1 46 GLY n 1 47 THR n 1 48 HIS n 1 49 VAL n 1 50 THR n 1 51 TYR n 1 52 ARG n 1 53 LYS n 1 54 ASP n 1 55 THR n 1 56 ARG n 1 57 TYR n 1 58 LYS n 1 59 LEU n 1 60 LEU n 1 61 GLY n 1 62 ASP n 1 63 LEU n 1 64 SER n 1 65 ARG n 1 66 ARG n 1 67 ASP n 1 68 VAL n 1 69 SER n 1 70 LEU n 1 71 THR n 1 72 ILE n 1 73 GLU n 1 74 ASN n 1 75 THR n 1 76 ALA n 1 77 VAL n 1 78 SER n 1 79 ASP n 1 80 SER n 1 81 GLY n 1 82 VAL n 1 83 TYR n 1 84 CYS n 1 85 CYS n 1 86 ARG n 1 87 VAL n 1 88 GLU n 1 89 HIS n 1 90 ARG n 1 91 GLY n 1 92 TRP n 1 93 PHE n 1 94 ASN n 1 95 ASP n 1 96 MET n 1 97 LYS n 1 98 ILE n 1 99 THR n 1 100 VAL n 1 101 SER n 1 102 LEU n 1 103 GLU n 1 104 ILE n 1 105 VAL n 1 106 PRO n 1 107 PRO 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 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 107 _entity_src_gen.gene_src_common_name Human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'HAVCR1, KIM1, TIM1, TIMD1' _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 562 _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 ? _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 HAVR1_HUMAN _struct_ref.pdbx_db_accession Q96D42 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;VKVGGEAGPSVTLPCHYSGAVTSMCWNRGSCSLFTCQNGIVWTNGTHVTYRKDTRYKLLGDLSRRDVSLTIENTAVSDSG VYCCRVEHRGWFNDMKITVSLEIVPP ; _struct_ref.pdbx_align_begin 22 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5DZO _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 107 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q96D42 _struct_ref_seq.db_align_beg 22 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 127 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 5 _struct_ref_seq.pdbx_auth_seq_align_end 110 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 5DZO _struct_ref_seq_dif.mon_id MET _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _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 Q96D42 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'initiating methionine' _struct_ref_seq_dif.pdbx_auth_seq_num 4 _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 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 NO3 non-polymer . 'NITRATE ION' ? 'N O3 -1' 62.005 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.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5DZO _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.30 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 46.53 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 289 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '1.5 M sodium nitrate, 0.1 M sodium acetate trihydrate, pH 4.6' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-10-08 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _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.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'SSRF BEAMLINE BL17U' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.0 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL17U _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5DZO _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.300 _reflns.d_resolution_low 50.000 _reflns.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.number_all ? _reflns.number_obs 27042 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 97.400 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 12.100 _reflns.pdbx_Rmerge_I_obs 0.069 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 34.178 _reflns.pdbx_netI_over_sigmaI 10.400 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.017 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 328083 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 1.300 1.350 ? ? ? ? ? 2196 ? 81.800 ? ? ? ? 0.173 ? ? ? ? ? ? ? ? 8.500 ? 0.889 ? ? ? ? 0 1 1 ? ? 1.350 1.400 ? ? ? ? ? 2613 ? 95.900 ? ? ? ? 0.151 ? ? ? ? ? ? ? ? 11.000 ? 0.878 ? ? ? ? 0 2 1 ? ? 1.400 1.460 ? ? ? ? ? 2689 ? 99.200 ? ? ? ? 0.131 ? ? ? ? ? ? ? ? 13.000 ? 1.039 ? ? ? ? 0 3 1 ? ? 1.460 1.540 ? ? ? ? ? 2713 ? 99.200 ? ? ? ? 0.111 ? ? ? ? ? ? ? ? 12.600 ? 1.076 ? ? ? ? 0 4 1 ? ? 1.540 1.640 ? ? ? ? ? 2730 ? 99.200 ? ? ? ? 0.096 ? ? ? ? ? ? ? ? 12.600 ? 0.921 ? ? ? ? 0 5 1 ? ? 1.640 1.760 ? ? ? ? ? 2720 ? 99.400 ? ? ? ? 0.084 ? ? ? ? ? ? ? ? 13.000 ? 1.048 ? ? ? ? 0 6 1 ? ? 1.760 1.940 ? ? ? ? ? 2757 ? 99.600 ? ? ? ? 0.073 ? ? ? ? ? ? ? ? 12.300 ? 1.069 ? ? ? ? 0 7 1 ? ? 1.940 2.220 ? ? ? ? ? 2795 ? 99.900 ? ? ? ? 0.064 ? ? ? ? ? ? ? ? 12.900 ? 1.082 ? ? ? ? 0 8 1 ? ? 2.220 2.800 ? ? ? ? ? 2823 ? 99.900 ? ? ? ? 0.057 ? ? ? ? ? ? ? ? 12.600 ? 1.017 ? ? ? ? 0 9 1 ? ? 2.800 50.000 ? ? ? ? ? 3006 ? 99.500 ? ? ? ? 0.068 ? ? ? ? ? ? ? ? 12.000 ? 1.061 ? ? ? ? 0 10 1 ? ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5DZO _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 26993 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.40 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 33.004 _refine.ls_d_res_high 1.301 _refine.ls_percent_reflns_obs 97.50 _refine.ls_R_factor_obs 0.1574 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1565 _refine.ls_R_factor_R_free 0.1761 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.75 _refine.ls_number_reflns_R_free 1282 _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 ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.07 _refine.pdbx_overall_phase_error 15.77 _refine.overall_SU_B ? _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 825 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 9 _refine_hist.number_atoms_solvent 156 _refine_hist.number_atoms_total 990 _refine_hist.d_res_high 1.301 _refine_hist.d_res_low 33.004 # 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 f_bond_d 0.013 ? ? 859 'X-RAY DIFFRACTION' ? f_angle_d 1.411 ? ? 1164 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 12.359 ? ? 306 'X-RAY DIFFRACTION' ? f_chiral_restr 0.068 ? ? 131 'X-RAY DIFFRACTION' ? f_plane_restr 0.008 ? ? 149 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _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_all _refine_ls_shell.R_factor_all 'X-RAY DIFFRACTION' . 1.3011 1.3532 2350 0.1500 83.00 0.1686 . . 113 . . 'X-RAY DIFFRACTION' . 1.3532 1.4148 2802 0.1519 97.00 0.1774 . . 131 . . 'X-RAY DIFFRACTION' . 1.4148 1.4894 2851 0.1511 99.00 0.1798 . . 156 . . 'X-RAY DIFFRACTION' . 1.4894 1.5827 2892 0.1425 99.00 0.1642 . . 128 . . 'X-RAY DIFFRACTION' . 1.5827 1.7049 2860 0.1484 99.00 0.1478 . . 158 . . 'X-RAY DIFFRACTION' . 1.7049 1.8765 2881 0.1549 100.00 0.1758 . . 161 . . 'X-RAY DIFFRACTION' . 1.8765 2.1480 2961 0.1551 100.00 0.1737 . . 121 . . 'X-RAY DIFFRACTION' . 2.1480 2.7060 2961 0.1662 100.00 0.1877 . . 171 . . 'X-RAY DIFFRACTION' . 2.7060 33.0147 3153 0.1583 100.00 0.1784 . . 143 . . # _struct.entry_id 5DZO _struct.title 'Crystal structure of human T-cell immunoglobulin and mucin domain protein 1' _struct.pdbx_descriptor 'Hepatitis A virus cellular receptor 1' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5DZO _struct_keywords.text 'receptor, Ig V domain, IMMUNE SYSTEM' _struct_keywords.pdbx_keywords '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 ? # 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 AA1 ASP A 62 ? ARG A 66 ? ASP A 65 ARG A 69 5 ? 5 HELX_P HELX_P2 AA2 ALA A 76 ? SER A 80 ? ALA A 79 SER A 83 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 disulf1 disulf ? ? A CYS 16 SG ? ? ? 1_555 A CYS 85 SG ? ? A CYS 19 A CYS 88 1_555 ? ? ? ? ? ? ? 2.016 ? disulf2 disulf ? ? A CYS 26 SG ? ? ? 1_555 A CYS 37 SG ? ? A CYS 29 A CYS 40 1_555 ? ? ? ? ? ? ? 2.035 ? disulf3 disulf ? ? A CYS 32 SG ? ? ? 1_555 A CYS 84 SG ? ? A CYS 35 A CYS 87 1_555 ? ? ? ? ? ? ? 2.037 ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 6 ? AA2 ? 3 ? # 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 AA1 1 2 ? parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel AA1 4 5 ? anti-parallel AA1 5 6 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? 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 AA1 1 VAL A 2 ? GLU A 7 ? VAL A 5 GLU A 10 AA1 2 MET A 96 ? VAL A 105 ? MET A 99 VAL A 108 AA1 3 GLY A 81 ? VAL A 87 ? GLY A 84 VAL A 90 AA1 4 MET A 25 ? ARG A 29 ? MET A 28 ARG A 32 AA1 5 GLY A 40 ? THR A 44 ? GLY A 43 THR A 47 AA1 6 VAL A 49 ? ARG A 52 ? VAL A 52 ARG A 55 AA2 1 VAL A 12 ? LEU A 14 ? VAL A 15 LEU A 17 AA2 2 LEU A 70 ? ILE A 72 ? LEU A 73 ILE A 75 AA2 3 TYR A 57 ? LYS A 58 ? TYR A 60 LYS A 61 # 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 AA1 1 2 N VAL A 2 ? N VAL A 5 O SER A 101 ? O SER A 104 AA1 2 3 O VAL A 100 ? O VAL A 103 N TYR A 83 ? N TYR A 86 AA1 3 4 O ARG A 86 ? O ARG A 89 N CYS A 26 ? N CYS A 29 AA1 4 5 N TRP A 27 ? N TRP A 30 O ILE A 41 ? O ILE A 44 AA1 5 6 N TRP A 43 ? N TRP A 46 O THR A 50 ? O THR A 53 AA2 1 2 N LEU A 14 ? N LEU A 17 O LEU A 70 ? O LEU A 73 AA2 2 3 O THR A 71 ? O THR A 74 N LYS A 58 ? N LYS A 61 # 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 A NO3 201 ? 9 'binding site for residue NO3 A 201' AC2 Software A NO3 202 ? 7 'binding site for residue NO3 A 202' AC3 Software A NA 203 ? 2 'binding site for residue NA A 203' # 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 9 ASN A 28 ? ASN A 31 . ? 1_555 ? 2 AC1 9 SER A 31 ? SER A 34 . ? 1_555 ? 3 AC1 9 CYS A 32 ? CYS A 35 . ? 1_555 ? 4 AC1 9 SER A 33 ? SER A 36 . ? 1_555 ? 5 AC1 9 PHE A 35 ? PHE A 38 . ? 1_555 ? 6 AC1 9 CYS A 37 ? CYS A 40 . ? 1_555 ? 7 AC1 9 CYS A 84 ? CYS A 87 . ? 1_555 ? 8 AC1 9 ARG A 86 ? ARG A 89 . ? 1_555 ? 9 AC1 9 HOH E . ? HOH A 360 . ? 1_555 ? 10 AC2 7 VAL A 82 ? VAL A 85 . ? 6_545 ? 11 AC2 7 GLY A 91 ? GLY A 94 . ? 1_555 ? 12 AC2 7 TRP A 92 ? TRP A 95 . ? 1_555 ? 13 AC2 7 TRP A 92 ? TRP A 95 . ? 7_645 ? 14 AC2 7 PHE A 93 ? PHE A 96 . ? 1_555 ? 15 AC2 7 ASN A 94 ? ASN A 97 . ? 1_555 ? 16 AC2 7 HOH E . ? HOH A 311 . ? 1_555 ? 17 AC3 2 SER A 19 ? SER A 22 . ? 1_555 ? 18 AC3 2 HIS A 89 ? HIS A 92 . ? 1_555 ? # _atom_sites.entry_id 5DZO _atom_sites.fract_transf_matrix[1][1] 0.019709 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.019709 _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] 0.011882 _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 NA 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 MET 1 4 4 MET MET A . n A 1 2 VAL 2 5 5 VAL VAL A . n A 1 3 LYS 3 6 6 LYS LYS A . n A 1 4 VAL 4 7 7 VAL VAL A . n A 1 5 GLY 5 8 8 GLY GLY A . n A 1 6 GLY 6 9 9 GLY GLY A . n A 1 7 GLU 7 10 10 GLU GLU A . n A 1 8 ALA 8 11 11 ALA ALA A . n A 1 9 GLY 9 12 12 GLY GLY A . n A 1 10 PRO 10 13 13 PRO PRO A . n A 1 11 SER 11 14 14 SER SER A . n A 1 12 VAL 12 15 15 VAL VAL A . n A 1 13 THR 13 16 16 THR THR A . n A 1 14 LEU 14 17 17 LEU LEU A . n A 1 15 PRO 15 18 18 PRO PRO A . n A 1 16 CYS 16 19 19 CYS CYS A . n A 1 17 HIS 17 20 20 HIS HIS A . n A 1 18 TYR 18 21 21 TYR TYR A . n A 1 19 SER 19 22 22 SER SER A . n A 1 20 GLY 20 23 23 GLY GLY A . n A 1 21 ALA 21 24 24 ALA ALA A . n A 1 22 VAL 22 25 25 VAL VAL A . n A 1 23 THR 23 26 26 THR THR A . n A 1 24 SER 24 27 27 SER SER A . n A 1 25 MET 25 28 28 MET MET A . n A 1 26 CYS 26 29 29 CYS CYS A . n A 1 27 TRP 27 30 30 TRP TRP A . n A 1 28 ASN 28 31 31 ASN ASN A . n A 1 29 ARG 29 32 32 ARG ARG A . n A 1 30 GLY 30 33 33 GLY GLY A . n A 1 31 SER 31 34 34 SER SER A . n A 1 32 CYS 32 35 35 CYS CYS A . n A 1 33 SER 33 36 36 SER SER A . n A 1 34 LEU 34 37 37 LEU LEU A . n A 1 35 PHE 35 38 38 PHE PHE A . n A 1 36 THR 36 39 39 THR THR A . n A 1 37 CYS 37 40 40 CYS CYS A . n A 1 38 GLN 38 41 41 GLN GLN A . n A 1 39 ASN 39 42 42 ASN ASN A . n A 1 40 GLY 40 43 43 GLY GLY A . n A 1 41 ILE 41 44 44 ILE ILE A . n A 1 42 VAL 42 45 45 VAL VAL A . n A 1 43 TRP 43 46 46 TRP TRP A . n A 1 44 THR 44 47 47 THR THR A . n A 1 45 ASN 45 48 48 ASN ASN A . n A 1 46 GLY 46 49 49 GLY GLY A . n A 1 47 THR 47 50 50 THR THR A . n A 1 48 HIS 48 51 51 HIS HIS A . n A 1 49 VAL 49 52 52 VAL VAL A . n A 1 50 THR 50 53 53 THR THR A . n A 1 51 TYR 51 54 54 TYR TYR A . n A 1 52 ARG 52 55 55 ARG ARG A . n A 1 53 LYS 53 56 56 LYS LYS A . n A 1 54 ASP 54 57 57 ASP ASP A . n A 1 55 THR 55 58 58 THR THR A . n A 1 56 ARG 56 59 59 ARG ARG A . n A 1 57 TYR 57 60 60 TYR TYR A . n A 1 58 LYS 58 61 61 LYS LYS A . n A 1 59 LEU 59 62 62 LEU LEU A . n A 1 60 LEU 60 63 63 LEU LEU A . n A 1 61 GLY 61 64 64 GLY GLY A . n A 1 62 ASP 62 65 65 ASP ASP A . n A 1 63 LEU 63 66 66 LEU LEU A . n A 1 64 SER 64 67 67 SER SER A . n A 1 65 ARG 65 68 68 ARG ARG A . n A 1 66 ARG 66 69 69 ARG ARG A . n A 1 67 ASP 67 70 70 ASP ASP A . n A 1 68 VAL 68 71 71 VAL VAL A . n A 1 69 SER 69 72 72 SER SER A . n A 1 70 LEU 70 73 73 LEU LEU A . n A 1 71 THR 71 74 74 THR THR A . n A 1 72 ILE 72 75 75 ILE ILE A . n A 1 73 GLU 73 76 76 GLU GLU A . n A 1 74 ASN 74 77 77 ASN ASN A . n A 1 75 THR 75 78 78 THR THR A . n A 1 76 ALA 76 79 79 ALA ALA A . n A 1 77 VAL 77 80 80 VAL VAL A . n A 1 78 SER 78 81 81 SER SER A . n A 1 79 ASP 79 82 82 ASP ASP A . n A 1 80 SER 80 83 83 SER SER A . n A 1 81 GLY 81 84 84 GLY GLY A . n A 1 82 VAL 82 85 85 VAL VAL A . n A 1 83 TYR 83 86 86 TYR TYR A . n A 1 84 CYS 84 87 87 CYS CYS A . n A 1 85 CYS 85 88 88 CYS CYS A . n A 1 86 ARG 86 89 89 ARG ARG A . n A 1 87 VAL 87 90 90 VAL VAL A . n A 1 88 GLU 88 91 91 GLU GLU A . n A 1 89 HIS 89 92 92 HIS HIS A . n A 1 90 ARG 90 93 93 ARG ARG A . n A 1 91 GLY 91 94 94 GLY GLY A . n A 1 92 TRP 92 95 95 TRP TRP A . n A 1 93 PHE 93 96 96 PHE PHE A . n A 1 94 ASN 94 97 97 ASN ASN A . n A 1 95 ASP 95 98 98 ASP ASP A . n A 1 96 MET 96 99 99 MET MET A . n A 1 97 LYS 97 100 100 LYS LYS A . n A 1 98 ILE 98 101 101 ILE ILE A . n A 1 99 THR 99 102 102 THR THR A . n A 1 100 VAL 100 103 103 VAL VAL A . n A 1 101 SER 101 104 104 SER SER A . n A 1 102 LEU 102 105 105 LEU LEU A . n A 1 103 GLU 103 106 106 GLU GLU A . n A 1 104 ILE 104 107 107 ILE ILE A . n A 1 105 VAL 105 108 108 VAL VAL A . n A 1 106 PRO 106 109 109 PRO PRO A . n A 1 107 PRO 107 110 110 PRO PRO 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 NO3 1 201 1 NO3 NO3 A . C 2 NO3 1 202 2 NO3 NO3 A . D 3 NA 1 203 1 NA NA A . E 4 HOH 1 301 65 HOH HOH A . E 4 HOH 2 302 134 HOH HOH A . E 4 HOH 3 303 113 HOH HOH A . E 4 HOH 4 304 132 HOH HOH A . E 4 HOH 5 305 37 HOH HOH A . E 4 HOH 6 306 75 HOH HOH A . E 4 HOH 7 307 60 HOH HOH A . E 4 HOH 8 308 73 HOH HOH A . E 4 HOH 9 309 127 HOH HOH A . E 4 HOH 10 310 77 HOH HOH A . E 4 HOH 11 311 89 HOH HOH A . E 4 HOH 12 312 138 HOH HOH A . E 4 HOH 13 313 2 HOH HOH A . E 4 HOH 14 314 98 HOH HOH A . E 4 HOH 15 315 154 HOH HOH A . E 4 HOH 16 316 117 HOH HOH A . E 4 HOH 17 317 12 HOH HOH A . E 4 HOH 18 318 59 HOH HOH A . E 4 HOH 19 319 8 HOH HOH A . E 4 HOH 20 320 42 HOH HOH A . E 4 HOH 21 321 18 HOH HOH A . E 4 HOH 22 322 46 HOH HOH A . E 4 HOH 23 323 11 HOH HOH A . E 4 HOH 24 324 39 HOH HOH A . E 4 HOH 25 325 36 HOH HOH A . E 4 HOH 26 326 33 HOH HOH A . E 4 HOH 27 327 6 HOH HOH A . E 4 HOH 28 328 31 HOH HOH A . E 4 HOH 29 329 61 HOH HOH A . E 4 HOH 30 330 145 HOH HOH A . E 4 HOH 31 331 62 HOH HOH A . E 4 HOH 32 332 3 HOH HOH A . E 4 HOH 33 333 5 HOH HOH A . E 4 HOH 34 334 94 HOH HOH A . E 4 HOH 35 335 19 HOH HOH A . E 4 HOH 36 336 85 HOH HOH A . E 4 HOH 37 337 108 HOH HOH A . E 4 HOH 38 338 29 HOH HOH A . E 4 HOH 39 339 43 HOH HOH A . E 4 HOH 40 340 101 HOH HOH A . E 4 HOH 41 341 44 HOH HOH A . E 4 HOH 42 342 107 HOH HOH A . E 4 HOH 43 343 38 HOH HOH A . E 4 HOH 44 344 120 HOH HOH A . E 4 HOH 45 345 121 HOH HOH A . E 4 HOH 46 346 16 HOH HOH A . E 4 HOH 47 347 118 HOH HOH A . E 4 HOH 48 348 69 HOH HOH A . E 4 HOH 49 349 104 HOH HOH A . E 4 HOH 50 350 140 HOH HOH A . E 4 HOH 51 351 30 HOH HOH A . E 4 HOH 52 352 9 HOH HOH A . E 4 HOH 53 353 21 HOH HOH A . E 4 HOH 54 354 34 HOH HOH A . E 4 HOH 55 355 144 HOH HOH A . E 4 HOH 56 356 15 HOH HOH A . E 4 HOH 57 357 130 HOH HOH A . E 4 HOH 58 358 97 HOH HOH A . E 4 HOH 59 359 14 HOH HOH A . E 4 HOH 60 360 17 HOH HOH A . E 4 HOH 61 361 40 HOH HOH A . E 4 HOH 62 362 119 HOH HOH A . E 4 HOH 63 363 66 HOH HOH A . E 4 HOH 64 364 48 HOH HOH A . E 4 HOH 65 365 22 HOH HOH A . E 4 HOH 66 366 7 HOH HOH A . E 4 HOH 67 367 1 HOH HOH A . E 4 HOH 68 368 80 HOH HOH A . E 4 HOH 69 369 54 HOH HOH A . E 4 HOH 70 370 112 HOH HOH A . E 4 HOH 71 371 88 HOH HOH A . E 4 HOH 72 372 53 HOH HOH A . E 4 HOH 73 373 57 HOH HOH A . E 4 HOH 74 374 102 HOH HOH A . E 4 HOH 75 375 56 HOH HOH A . E 4 HOH 76 376 105 HOH HOH A . E 4 HOH 77 377 4 HOH HOH A . E 4 HOH 78 378 86 HOH HOH A . E 4 HOH 79 379 78 HOH HOH A . E 4 HOH 80 380 55 HOH HOH A . E 4 HOH 81 381 20 HOH HOH A . E 4 HOH 82 382 136 HOH HOH A . E 4 HOH 83 383 83 HOH HOH A . E 4 HOH 84 384 45 HOH HOH A . E 4 HOH 85 385 23 HOH HOH A . E 4 HOH 86 386 93 HOH HOH A . E 4 HOH 87 387 74 HOH HOH A . E 4 HOH 88 388 67 HOH HOH A . E 4 HOH 89 389 24 HOH HOH A . E 4 HOH 90 390 99 HOH HOH A . E 4 HOH 91 391 139 HOH HOH A . E 4 HOH 92 392 41 HOH HOH A . E 4 HOH 93 393 32 HOH HOH A . E 4 HOH 94 394 72 HOH HOH A . E 4 HOH 95 395 52 HOH HOH A . E 4 HOH 96 396 27 HOH HOH A . E 4 HOH 97 397 28 HOH HOH A . E 4 HOH 98 398 10 HOH HOH A . E 4 HOH 99 399 133 HOH HOH A . E 4 HOH 100 400 50 HOH HOH A . E 4 HOH 101 401 148 HOH HOH A . E 4 HOH 102 402 76 HOH HOH A . E 4 HOH 103 403 35 HOH HOH A . E 4 HOH 104 404 70 HOH HOH A . E 4 HOH 105 405 64 HOH HOH A . E 4 HOH 106 406 49 HOH HOH A . E 4 HOH 107 407 114 HOH HOH A . E 4 HOH 108 408 58 HOH HOH A . E 4 HOH 109 409 25 HOH HOH A . E 4 HOH 110 410 71 HOH HOH A . E 4 HOH 111 411 51 HOH HOH A . E 4 HOH 112 412 91 HOH HOH A . E 4 HOH 113 413 123 HOH HOH A . E 4 HOH 114 414 13 HOH HOH A . E 4 HOH 115 415 125 HOH HOH A . E 4 HOH 116 416 68 HOH HOH A . E 4 HOH 117 417 106 HOH HOH A . E 4 HOH 118 418 150 HOH HOH A . E 4 HOH 119 419 143 HOH HOH A . E 4 HOH 120 420 137 HOH HOH A . E 4 HOH 121 421 124 HOH HOH A . E 4 HOH 122 422 109 HOH HOH A . E 4 HOH 123 423 111 HOH HOH A . E 4 HOH 124 424 81 HOH HOH A . E 4 HOH 125 425 126 HOH HOH A . E 4 HOH 126 426 47 HOH HOH A . E 4 HOH 127 427 147 HOH HOH A . E 4 HOH 128 428 151 HOH HOH A . E 4 HOH 129 429 149 HOH HOH A . E 4 HOH 130 430 100 HOH HOH A . E 4 HOH 131 431 152 HOH HOH A . E 4 HOH 132 432 79 HOH HOH A . E 4 HOH 133 433 116 HOH HOH A . E 4 HOH 134 434 146 HOH HOH A . E 4 HOH 135 435 26 HOH HOH A . E 4 HOH 136 436 84 HOH HOH A . E 4 HOH 137 437 122 HOH HOH A . E 4 HOH 138 438 95 HOH HOH A . E 4 HOH 139 439 141 HOH HOH A . E 4 HOH 140 440 82 HOH HOH A . E 4 HOH 141 441 90 HOH HOH A . E 4 HOH 142 442 63 HOH HOH A . E 4 HOH 143 443 135 HOH HOH A . E 4 HOH 144 444 87 HOH HOH A . E 4 HOH 145 445 153 HOH HOH A . E 4 HOH 146 446 92 HOH HOH A . E 4 HOH 147 447 142 HOH HOH A . E 4 HOH 148 448 115 HOH HOH A . E 4 HOH 149 449 131 HOH HOH A . E 4 HOH 150 450 129 HOH HOH A . E 4 HOH 151 451 110 HOH HOH A . E 4 HOH 152 452 96 HOH HOH A . E 4 HOH 153 453 103 HOH HOH A . E 4 HOH 154 454 155 HOH HOH A . E 4 HOH 155 455 128 HOH HOH A . E 4 HOH 156 456 156 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_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 2015-11-25 2 'Structure model' 1 1 2016-02-10 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # 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 18.0879 0.4697 10.9214 0.0957 0.0881 0.0996 -0.0107 -0.0027 -0.0083 0.8591 0.7730 1.8203 -0.0778 -0.5151 -0.2455 0.0366 -0.0498 0.0090 0.0255 -0.0012 -0.0235 -0.0779 0.0480 -0.0354 'X-RAY DIFFRACTION' 2 ? refined 21.0495 -11.7093 3.7992 0.1637 0.0928 0.1207 0.0144 0.0054 -0.0042 3.2987 0.8319 0.1627 -1.4673 -0.2709 -0.0388 -0.0184 0.0382 -0.2413 -0.0712 -0.0451 0.1232 0.2773 0.0576 -0.0107 'X-RAY DIFFRACTION' 3 ? refined 18.5827 -1.5061 -0.0393 0.1271 0.0943 0.0750 -0.0037 0.0135 -0.0063 2.0673 1.9982 0.6115 0.9603 -0.5211 -0.8141 -0.1033 0.1183 0.0171 -0.2732 0.0365 -0.0297 0.2415 0.0355 0.0020 'X-RAY DIFFRACTION' 4 ? refined 20.0825 5.1207 -2.6500 0.1524 0.1090 0.1683 -0.0082 0.0064 0.0335 1.7302 1.0017 4.8903 -0.5439 1.7140 0.7202 -0.1928 0.4660 0.3274 0.0133 0.0049 0.0575 -0.5479 0.1499 0.1686 'X-RAY DIFFRACTION' 5 ? refined 12.3662 4.6681 3.5189 0.1062 0.0739 0.0912 0.0255 0.0055 0.0058 7.1130 2.2924 2.8779 2.7044 1.9093 0.5244 -0.0291 -0.0293 0.2496 -0.0323 -0.0227 0.1039 -0.2115 -0.1051 0.0033 'X-RAY DIFFRACTION' 6 ? refined 24.7432 8.6230 9.1006 0.1531 0.0924 0.1208 -0.0298 -0.0012 -0.0042 6.7501 8.8848 4.1205 3.7394 -2.7520 1.0520 0.1530 -0.1268 0.1962 -0.0034 0.0133 -0.4202 -0.5369 0.3095 -0.0100 'X-RAY DIFFRACTION' 7 ? refined 11.3477 -2.0530 8.8835 0.0817 0.0853 0.0602 -0.0096 -0.0019 -0.0056 4.2912 0.8814 1.3032 0.1104 -0.6189 -0.2827 0.0101 -0.0197 0.0288 -0.0135 0.0207 0.0683 -0.0038 -0.1425 -0.0208 'X-RAY DIFFRACTION' 8 ? refined 33.7270 -7.0856 3.7242 0.1256 0.1728 0.1530 0.0165 -0.0144 -0.0034 3.4603 1.1570 4.5568 -1.9910 -0.2280 0.3591 -0.0254 0.0482 0.4838 0.0120 0.1237 -0.4965 0.1796 0.2718 -0.1077 'X-RAY DIFFRACTION' 9 ? refined 12.4783 -4.6729 14.7132 0.1106 0.1098 0.0852 -0.0000 0.0013 0.0014 2.0075 1.5652 3.2599 0.1831 -2.5365 -0.3362 -0.0197 -0.2220 -0.1927 0.0597 0.0299 0.1288 0.0846 -0.0314 -0.0767 # 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 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 4 through 32 ) ; 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 33 through 42 ) ; 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 43 through 47 ) ; 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 48 through 55 ) ; 'X-RAY DIFFRACTION' 5 5 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 56 through 65 ) ; 'X-RAY DIFFRACTION' 6 6 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 66 through 72 ) ; 'X-RAY DIFFRACTION' 7 7 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 73 through 90 ) ; 'X-RAY DIFFRACTION' 8 8 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 91 through 98 ) ; 'X-RAY DIFFRACTION' 9 9 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 99 through 110 ) ; # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.9_1692 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.15 3 # 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 OD1 A ASN 97 ? ? O A HOH 301 ? ? 1.82 2 1 O A HOH 433 ? ? O A HOH 452 ? ? 2.03 3 1 O A HOH 304 ? ? O A HOH 381 ? ? 2.04 4 1 NZ A LYS 56 ? ? O A HOH 302 ? ? 2.18 # 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 CD A GLU 10 ? ? 1_555 OE2 A GLU 10 ? ? 8_555 0.38 2 1 OE2 A GLU 10 ? ? 1_555 OE2 A GLU 10 ? ? 8_555 0.87 3 1 OE1 A GLU 10 ? ? 1_555 OE2 A GLU 10 ? ? 8_555 1.40 4 1 CD A GLU 10 ? ? 1_555 CD A GLU 10 ? ? 8_555 1.59 5 1 CG A GLU 10 ? ? 1_555 OE2 A GLU 10 ? ? 8_555 1.80 6 1 O A HOH 315 ? ? 1_555 O A HOH 399 ? ? 8_555 1.87 7 1 O A HOH 415 ? ? 1_555 O A HOH 440 ? ? 6_455 1.88 8 1 O A HOH 395 ? ? 1_555 O A HOH 429 ? ? 4_555 1.96 # 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 CYS A 40 ? ? 25.45 74.90 2 1 ASN A 42 ? ? -118.62 54.84 # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 456 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.49 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # _pdbx_audit_support.funding_organization 'Ministry of Science and Technology 973 Project' _pdbx_audit_support.country China _pdbx_audit_support.grant_number 2014CB542800 _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'NITRATE ION' NO3 3 'SODIUM ION' NA 4 water HOH #