data_2YXS # _entry.id 2YXS # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.332 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2YXS RCSB RCSB027268 WWPDB D_1000027268 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2YV8 'The same protein without ligand' unspecified TargetDB hso002002300.2 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2YXS _pdbx_database_status.recvd_initial_deposition_date 2007-04-27 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kishishita, S.' 1 ? 'Nishino, A.' 2 ? 'Murayama, K.' 3 ? 'Terada, T.' 4 ? 'Shirouzu, M.' 5 ? 'Yokoyama, S.' 6 ? 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 7 ? # _citation.id primary _citation.title 'Crystal Structure of N-terminal domain of human galectin-8 with D-lactose' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kishishita, S.' 1 ? primary 'Nishino, A.' 2 ? primary 'Murayama, K.' 3 ? primary 'Terada, T.' 4 ? primary 'Shirouzu, M.' 5 ? primary 'Yokoyama, S.' 6 ? # _cell.entry_id 2YXS _cell.length_a 45.913 _cell.length_b 50.551 _cell.length_c 69.336 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 2YXS _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 'Galectin-8 variant' 18102.559 1 ? ? 'N-terminal domain' ? 2 branched man 'beta-D-galactopyranose-(1-4)-beta-D-glucopyranose' 342.297 1 ? ? ? ? 3 water nat water 18.015 152 ? ? ? ? # _entity_name_com.entity_id 2 _entity_name_com.name beta-lactose # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;GSSGSSGMMLSLNNLQNIIYNPVIPYVGTIPDQLDPGTLIVICGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRA GCIVCNTLINEKWGREEITYDTPFKREKSFEIVI(MSE)VLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSI GFSGPSSG ; _entity_poly.pdbx_seq_one_letter_code_can ;GSSGSSGMMLSLNNLQNIIYNPVIPYVGTIPDQLDPGTLIVICGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRA GCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSG PSSG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier hso002002300.2 # 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 SER n 1 3 SER n 1 4 GLY n 1 5 SER n 1 6 SER n 1 7 GLY n 1 8 MET n 1 9 MET n 1 10 LEU n 1 11 SER n 1 12 LEU n 1 13 ASN n 1 14 ASN n 1 15 LEU n 1 16 GLN n 1 17 ASN n 1 18 ILE n 1 19 ILE n 1 20 TYR n 1 21 ASN n 1 22 PRO n 1 23 VAL n 1 24 ILE n 1 25 PRO n 1 26 TYR n 1 27 VAL n 1 28 GLY n 1 29 THR n 1 30 ILE n 1 31 PRO n 1 32 ASP n 1 33 GLN n 1 34 LEU n 1 35 ASP n 1 36 PRO n 1 37 GLY n 1 38 THR n 1 39 LEU n 1 40 ILE n 1 41 VAL n 1 42 ILE n 1 43 CYS n 1 44 GLY n 1 45 HIS n 1 46 VAL n 1 47 PRO n 1 48 SER n 1 49 ASP n 1 50 ALA n 1 51 ASP n 1 52 ARG n 1 53 PHE n 1 54 GLN n 1 55 VAL n 1 56 ASP n 1 57 LEU n 1 58 GLN n 1 59 ASN n 1 60 GLY n 1 61 SER n 1 62 SER n 1 63 VAL n 1 64 LYS n 1 65 PRO n 1 66 ARG n 1 67 ALA n 1 68 ASP n 1 69 VAL n 1 70 ALA n 1 71 PHE n 1 72 HIS n 1 73 PHE n 1 74 ASN n 1 75 PRO n 1 76 ARG n 1 77 PHE n 1 78 LYS n 1 79 ARG n 1 80 ALA n 1 81 GLY n 1 82 CYS n 1 83 ILE n 1 84 VAL n 1 85 CYS n 1 86 ASN n 1 87 THR n 1 88 LEU n 1 89 ILE n 1 90 ASN n 1 91 GLU n 1 92 LYS n 1 93 TRP n 1 94 GLY n 1 95 ARG n 1 96 GLU n 1 97 GLU n 1 98 ILE n 1 99 THR n 1 100 TYR n 1 101 ASP n 1 102 THR n 1 103 PRO n 1 104 PHE n 1 105 LYS n 1 106 ARG n 1 107 GLU n 1 108 LYS n 1 109 SER n 1 110 PHE n 1 111 GLU n 1 112 ILE n 1 113 VAL n 1 114 ILE n 1 115 MSE n 1 116 VAL n 1 117 LEU n 1 118 LYS n 1 119 ASP n 1 120 LYS n 1 121 PHE n 1 122 GLN n 1 123 VAL n 1 124 ALA n 1 125 VAL n 1 126 ASN n 1 127 GLY n 1 128 LYS n 1 129 HIS n 1 130 THR n 1 131 LEU n 1 132 LEU n 1 133 TYR n 1 134 GLY n 1 135 HIS n 1 136 ARG n 1 137 ILE n 1 138 GLY n 1 139 PRO n 1 140 GLU n 1 141 LYS n 1 142 ILE n 1 143 ASP n 1 144 THR n 1 145 LEU n 1 146 GLY n 1 147 ILE n 1 148 TYR n 1 149 GLY n 1 150 LYS n 1 151 VAL n 1 152 ASN n 1 153 ILE n 1 154 HIS n 1 155 SER n 1 156 ILE n 1 157 GLY n 1 158 PHE n 1 159 SER n 1 160 GLY n 1 161 PRO n 1 162 SER n 1 163 SER n 1 164 GLY 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 ? _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 'Cell-free protein synthesis' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ? _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 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 PK050620-06 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q59E97_HUMAN _struct_ref.pdbx_db_accession Q59E97 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MMLSLNNLQNIIYNPVIPYVGTIPDQLDPGTLIVICGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRAGCIVCNT LINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGF ; _struct_ref.pdbx_align_begin 22 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2YXS _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 8 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 158 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q59E97 _struct_ref_seq.db_align_beg 22 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 172 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 8 _struct_ref_seq.pdbx_auth_seq_align_end 158 # 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 2YXS GLY A 1 ? UNP Q59E97 ? ? 'expression tag' 1 1 1 2YXS SER A 2 ? UNP Q59E97 ? ? 'expression tag' 2 2 1 2YXS SER A 3 ? UNP Q59E97 ? ? 'expression tag' 3 3 1 2YXS GLY A 4 ? UNP Q59E97 ? ? 'expression tag' 4 4 1 2YXS SER A 5 ? UNP Q59E97 ? ? 'expression tag' 5 5 1 2YXS SER A 6 ? UNP Q59E97 ? ? 'expression tag' 6 6 1 2YXS GLY A 7 ? UNP Q59E97 ? ? 'expression tag' 7 7 1 2YXS SER A 159 ? UNP Q59E97 ? ? 'expression tag' 159 8 1 2YXS GLY A 160 ? UNP Q59E97 ? ? 'expression tag' 160 9 1 2YXS PRO A 161 ? UNP Q59E97 ? ? 'expression tag' 161 10 1 2YXS SER A 162 ? UNP Q59E97 ? ? 'expression tag' 162 11 1 2YXS SER A 163 ? UNP Q59E97 ? ? 'expression tag' 163 12 1 2YXS GLY A 164 ? UNP Q59E97 ? ? 'expression tag' 164 13 # 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 BGC 'D-saccharide, beta linking' . beta-D-glucopyranose 'beta-D-glucose; D-glucose; glucose' 'C6 H12 O6' 180.156 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GAL 'D-saccharide, beta linking' . beta-D-galactopyranose 'beta-D-galactose; D-galactose; galactose' 'C6 H12 O6' 180.156 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 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 2YXS _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.22 _exptl_crystal.density_percent_sol 44.62 _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 5.5 _exptl_crystal_grow.pdbx_details '0.1M bis-tris, 25% PEG3350, 1mM lactose, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _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 'RIGAKU JUPITER 210' _diffrn_detector.pdbx_collection_date 2006-09-22 _diffrn_detector.details mirrors # _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 'SPRING-8 BEAMLINE BL26B2' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL26B2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 2YXS _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.13 _reflns.number_obs 9421 _reflns.number_all ? _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.074 _reflns.pdbx_netI_over_sigmaI 32.8 _reflns.B_iso_Wilson_estimate 5.5 _reflns.pdbx_redundancy 6.56 _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.13 _reflns_shell.d_res_low 2.21 _reflns_shell.percent_possible_all 99.2 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.13 _reflns_shell.meanI_over_sigI_obs 12.6 _reflns_shell.pdbx_redundancy ? _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 ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 2YXS _refine.ls_number_reflns_obs 9191 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 100747.62 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 33.99 _refine.ls_d_res_high 2.13 _refine.ls_percent_reflns_obs 97.3 _refine.ls_R_factor_obs 0.19 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.19 _refine.ls_R_factor_R_free 0.234 _refine.ls_R_factor_R_free_error 0.011 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.4 _refine.ls_number_reflns_R_free 494 _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 15.6 _refine.aniso_B[1][1] 3.56 _refine.aniso_B[2][2] -0.78 _refine.aniso_B[3][3] -2.78 _refine.aniso_B[1][2] 0.00 _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 0.321209 _refine.solvent_model_param_bsol 25.4063 _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 2YV8 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 2YXS _refine_analyze.Luzzati_coordinate_error_obs 0.21 _refine_analyze.Luzzati_sigma_a_obs 0.07 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.26 _refine_analyze.Luzzati_sigma_a_free 0.12 _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 1180 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 23 _refine_hist.number_atoms_solvent 152 _refine_hist.number_atoms_total 1355 _refine_hist.d_res_high 2.13 _refine_hist.d_res_low 33.99 # 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 0.006 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.3 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 26.2 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.74 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.27 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 1.85 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 2.03 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 2.74 2.50 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.13 _refine_ls_shell.d_res_low 2.26 _refine_ls_shell.number_reflns_R_work 1364 _refine_ls_shell.R_factor_R_work 0.177 _refine_ls_shell.percent_reflns_obs 92.7 _refine_ls_shell.R_factor_R_free 0.213 _refine_ls_shell.R_factor_R_free_error 0.027 _refine_ls_shell.percent_reflns_R_free 4.4 _refine_ls_shell.number_reflns_R_free 63 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 protein_rep.param protein.top 'X-RAY DIFFRACTION' 2 water_rep.param water.top 'X-RAY DIFFRACTION' 3 lat_xplor_param lat_xplor_top 'X-RAY DIFFRACTION' # _struct.entry_id 2YXS _struct.title 'Crystal Structure of N-terminal domain of human galectin-8 with D-lactose' _struct.pdbx_descriptor 'Galectin-8 variant' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2YXS _struct_keywords.pdbx_keywords 'SUGAR BINDING PROTEIN' _struct_keywords.text ;suger-binding, lactose, galectin, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SUGAR BINDING PROTEIN ; # 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 ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id GLY _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 138 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ILE _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 142 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id GLY _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 138 _struct_conf.end_auth_comp_id ILE _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 142 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A ILE 114 C ? ? ? 1_555 A MSE 115 N ? ? A ILE 114 A MSE 115 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale2 covale both ? A MSE 115 C ? ? ? 1_555 A VAL 116 N ? ? A MSE 115 A VAL 116 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale3 covale both ? B BGC . O4 ? ? ? 1_555 B GAL . C1 ? ? B BGC 1 B GAL 2 1_555 ? ? ? ? ? ? ? 1.444 sing ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 ILE 24 A . ? ILE 24 A PRO 25 A ? PRO 25 A 1 0.33 2 LYS 64 A . ? LYS 64 A PRO 65 A ? PRO 65 A 1 -0.19 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 6 ? C ? 6 ? # 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 B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel B 5 6 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel C 3 4 ? anti-parallel C 4 5 ? anti-parallel C 5 6 ? 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 GLN A 16 ? TYR A 20 ? GLN A 16 TYR A 20 A 2 ASN A 152 ? SER A 159 ? ASN A 152 SER A 159 A 3 THR A 38 ? HIS A 45 ? THR A 38 HIS A 45 A 4 SER A 109 ? VAL A 116 ? SER A 109 VAL A 116 A 5 LYS A 120 ? VAL A 125 ? LYS A 120 VAL A 125 A 6 LYS A 128 ? GLY A 134 ? LYS A 128 GLY A 134 B 1 TYR A 26 ? THR A 29 ? TYR A 26 THR A 29 B 2 THR A 144 ? GLY A 149 ? THR A 144 GLY A 149 B 3 PHE A 53 ? ASN A 59 ? PHE A 53 ASN A 59 B 4 ASP A 68 ? ARG A 76 ? ASP A 68 ARG A 76 B 5 CYS A 82 ? ILE A 89 ? CYS A 82 ILE A 89 B 6 LYS A 92 ? TRP A 93 ? LYS A 92 TRP A 93 C 1 TYR A 26 ? THR A 29 ? TYR A 26 THR A 29 C 2 THR A 144 ? GLY A 149 ? THR A 144 GLY A 149 C 3 PHE A 53 ? ASN A 59 ? PHE A 53 ASN A 59 C 4 ASP A 68 ? ARG A 76 ? ASP A 68 ARG A 76 C 5 CYS A 82 ? ILE A 89 ? CYS A 82 ILE A 89 C 6 GLU A 97 ? THR A 99 ? GLU A 97 THR A 99 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N ILE A 19 ? N ILE A 19 O ILE A 156 ? O ILE A 156 A 2 3 O SER A 159 ? O SER A 159 N LEU A 39 ? N LEU A 39 A 3 4 N ILE A 42 ? N ILE A 42 O ILE A 112 ? O ILE A 112 A 4 5 N MSE A 115 ? N MSE A 115 O GLN A 122 ? O GLN A 122 A 5 6 N VAL A 123 ? N VAL A 123 O THR A 130 ? O THR A 130 B 1 2 N GLY A 28 ? N GLY A 28 O LEU A 145 ? O LEU A 145 B 2 3 O GLY A 146 ? O GLY A 146 N ASP A 56 ? N ASP A 56 B 3 4 N VAL A 55 ? N VAL A 55 O PHE A 73 ? O PHE A 73 B 4 5 N ARG A 76 ? N ARG A 76 O CYS A 82 ? O CYS A 82 B 5 6 N ILE A 89 ? N ILE A 89 O LYS A 92 ? O LYS A 92 C 1 2 N GLY A 28 ? N GLY A 28 O LEU A 145 ? O LEU A 145 C 2 3 O GLY A 146 ? O GLY A 146 N ASP A 56 ? N ASP A 56 C 3 4 N VAL A 55 ? N VAL A 55 O PHE A 73 ? O PHE A 73 C 4 5 N ARG A 76 ? N ARG A 76 O CYS A 82 ? O CYS A 82 C 5 6 N CYS A 85 ? N CYS A 85 O GLU A 97 ? O GLU A 97 # _database_PDB_matrix.entry_id 2YXS _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 2YXS _atom_sites.fract_transf_matrix[1][1] 0.021780 _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] 0.019782 _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] 0.014423 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S SE # 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 SER 2 2 ? ? ? A . n A 1 3 SER 3 3 ? ? ? A . n A 1 4 GLY 4 4 ? ? ? A . n A 1 5 SER 5 5 ? ? ? A . n A 1 6 SER 6 6 ? ? ? A . n A 1 7 GLY 7 7 ? ? ? A . n A 1 8 MET 8 8 ? ? ? A . n A 1 9 MET 9 9 ? ? ? A . n A 1 10 LEU 10 10 ? ? ? A . n A 1 11 SER 11 11 ? ? ? A . n A 1 12 LEU 12 12 ? ? ? A . n A 1 13 ASN 13 13 ? ? ? A . n A 1 14 ASN 14 14 ? ? ? A . n A 1 15 LEU 15 15 15 LEU LEU A . n A 1 16 GLN 16 16 16 GLN GLN 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 ILE 19 19 19 ILE ILE A . n A 1 20 TYR 20 20 20 TYR TYR A . n A 1 21 ASN 21 21 21 ASN ASN A . n A 1 22 PRO 22 22 22 PRO PRO A . n A 1 23 VAL 23 23 23 VAL VAL A . n A 1 24 ILE 24 24 24 ILE ILE A . n A 1 25 PRO 25 25 25 PRO PRO A . n A 1 26 TYR 26 26 26 TYR TYR A . n A 1 27 VAL 27 27 27 VAL VAL A . n A 1 28 GLY 28 28 28 GLY GLY A . n A 1 29 THR 29 29 29 THR THR A . n A 1 30 ILE 30 30 30 ILE ILE A . n A 1 31 PRO 31 31 31 PRO PRO A . n A 1 32 ASP 32 32 32 ASP ASP A . n A 1 33 GLN 33 33 33 GLN GLN A . n A 1 34 LEU 34 34 34 LEU LEU A . n A 1 35 ASP 35 35 35 ASP ASP A . n A 1 36 PRO 36 36 36 PRO PRO A . n A 1 37 GLY 37 37 37 GLY GLY A . n A 1 38 THR 38 38 38 THR THR A . n A 1 39 LEU 39 39 39 LEU LEU A . n A 1 40 ILE 40 40 40 ILE ILE A . n A 1 41 VAL 41 41 41 VAL VAL A . n A 1 42 ILE 42 42 42 ILE ILE A . n A 1 43 CYS 43 43 43 CYS CYS A . n A 1 44 GLY 44 44 44 GLY GLY A . n A 1 45 HIS 45 45 45 HIS HIS A . n A 1 46 VAL 46 46 46 VAL VAL A . n A 1 47 PRO 47 47 47 PRO PRO A . n A 1 48 SER 48 48 48 SER SER A . n A 1 49 ASP 49 49 49 ASP ASP A . n A 1 50 ALA 50 50 50 ALA ALA A . n A 1 51 ASP 51 51 51 ASP ASP A . n A 1 52 ARG 52 52 52 ARG ARG A . n A 1 53 PHE 53 53 53 PHE PHE A . n A 1 54 GLN 54 54 54 GLN GLN A . n A 1 55 VAL 55 55 55 VAL VAL A . n A 1 56 ASP 56 56 56 ASP ASP A . n A 1 57 LEU 57 57 57 LEU LEU A . n A 1 58 GLN 58 58 58 GLN GLN A . n A 1 59 ASN 59 59 59 ASN ASN A . n A 1 60 GLY 60 60 60 GLY GLY A . n A 1 61 SER 61 61 61 SER SER A . n A 1 62 SER 62 62 62 SER SER A . n A 1 63 VAL 63 63 63 VAL VAL A . n A 1 64 LYS 64 64 64 LYS LYS A . n A 1 65 PRO 65 65 65 PRO PRO A . n A 1 66 ARG 66 66 66 ARG ARG A . n A 1 67 ALA 67 67 67 ALA ALA A . n A 1 68 ASP 68 68 68 ASP ASP A . n A 1 69 VAL 69 69 69 VAL VAL A . n A 1 70 ALA 70 70 70 ALA ALA A . n A 1 71 PHE 71 71 71 PHE PHE A . n A 1 72 HIS 72 72 72 HIS HIS A . n A 1 73 PHE 73 73 73 PHE PHE A . n A 1 74 ASN 74 74 74 ASN ASN A . n A 1 75 PRO 75 75 75 PRO PRO A . n A 1 76 ARG 76 76 76 ARG ARG A . n A 1 77 PHE 77 77 77 PHE PHE A . n A 1 78 LYS 78 78 78 LYS LYS A . n A 1 79 ARG 79 79 79 ARG ARG A . n A 1 80 ALA 80 80 80 ALA ALA A . n A 1 81 GLY 81 81 81 GLY GLY A . n A 1 82 CYS 82 82 82 CYS CYS A . n A 1 83 ILE 83 83 83 ILE ILE A . n A 1 84 VAL 84 84 84 VAL VAL A . n A 1 85 CYS 85 85 85 CYS CYS A . n A 1 86 ASN 86 86 86 ASN ASN A . n A 1 87 THR 87 87 87 THR THR A . n A 1 88 LEU 88 88 88 LEU LEU A . n A 1 89 ILE 89 89 89 ILE ILE A . n A 1 90 ASN 90 90 90 ASN ASN A . n A 1 91 GLU 91 91 91 GLU GLU A . n A 1 92 LYS 92 92 92 LYS LYS A . n A 1 93 TRP 93 93 93 TRP TRP A . n A 1 94 GLY 94 94 94 GLY GLY A . n A 1 95 ARG 95 95 95 ARG ARG A . n A 1 96 GLU 96 96 96 GLU GLU A . n A 1 97 GLU 97 97 97 GLU GLU A . n A 1 98 ILE 98 98 98 ILE ILE A . n A 1 99 THR 99 99 99 THR THR A . n A 1 100 TYR 100 100 100 TYR TYR A . n A 1 101 ASP 101 101 101 ASP ASP A . n A 1 102 THR 102 102 102 THR THR A . n A 1 103 PRO 103 103 103 PRO PRO A . n A 1 104 PHE 104 104 104 PHE PHE A . n A 1 105 LYS 105 105 105 LYS LYS A . n A 1 106 ARG 106 106 106 ARG ARG A . n A 1 107 GLU 107 107 107 GLU GLU A . n A 1 108 LYS 108 108 108 LYS LYS A . n A 1 109 SER 109 109 109 SER SER A . n A 1 110 PHE 110 110 110 PHE PHE A . n A 1 111 GLU 111 111 111 GLU GLU A . n A 1 112 ILE 112 112 112 ILE ILE A . n A 1 113 VAL 113 113 113 VAL VAL A . n A 1 114 ILE 114 114 114 ILE ILE A . n A 1 115 MSE 115 115 115 MSE MSE A . n A 1 116 VAL 116 116 116 VAL VAL A . n A 1 117 LEU 117 117 117 LEU LEU A . n A 1 118 LYS 118 118 118 LYS LYS A . n A 1 119 ASP 119 119 119 ASP ASP A . n A 1 120 LYS 120 120 120 LYS LYS A . n A 1 121 PHE 121 121 121 PHE PHE A . n A 1 122 GLN 122 122 122 GLN GLN A . n A 1 123 VAL 123 123 123 VAL VAL A . n A 1 124 ALA 124 124 124 ALA ALA A . n A 1 125 VAL 125 125 125 VAL VAL A . n A 1 126 ASN 126 126 126 ASN ASN A . n A 1 127 GLY 127 127 127 GLY GLY A . n A 1 128 LYS 128 128 128 LYS LYS A . n A 1 129 HIS 129 129 129 HIS HIS A . n A 1 130 THR 130 130 130 THR THR A . n A 1 131 LEU 131 131 131 LEU LEU A . n A 1 132 LEU 132 132 132 LEU LEU A . n A 1 133 TYR 133 133 133 TYR TYR A . n A 1 134 GLY 134 134 134 GLY GLY A . n A 1 135 HIS 135 135 135 HIS HIS A . n A 1 136 ARG 136 136 136 ARG ARG A . n A 1 137 ILE 137 137 137 ILE ILE A . n A 1 138 GLY 138 138 138 GLY GLY A . n A 1 139 PRO 139 139 139 PRO PRO A . n A 1 140 GLU 140 140 140 GLU GLU A . n A 1 141 LYS 141 141 141 LYS LYS A . n A 1 142 ILE 142 142 142 ILE ILE A . n A 1 143 ASP 143 143 143 ASP ASP A . n A 1 144 THR 144 144 144 THR THR A . n A 1 145 LEU 145 145 145 LEU LEU A . n A 1 146 GLY 146 146 146 GLY GLY A . n A 1 147 ILE 147 147 147 ILE ILE A . n A 1 148 TYR 148 148 148 TYR TYR A . n A 1 149 GLY 149 149 149 GLY GLY A . n A 1 150 LYS 150 150 150 LYS LYS A . n A 1 151 VAL 151 151 151 VAL VAL A . n A 1 152 ASN 152 152 152 ASN ASN A . n A 1 153 ILE 153 153 153 ILE ILE A . n A 1 154 HIS 154 154 154 HIS HIS A . n A 1 155 SER 155 155 155 SER SER A . n A 1 156 ILE 156 156 156 ILE ILE A . n A 1 157 GLY 157 157 157 GLY GLY A . n A 1 158 PHE 158 158 158 PHE PHE A . n A 1 159 SER 159 159 159 SER SER A . n A 1 160 GLY 160 160 160 GLY GLY A . n A 1 161 PRO 161 161 161 PRO PRO A . n A 1 162 SER 162 162 162 SER SER A . n A 1 163 SER 163 163 163 SER SER A . n A 1 164 GLY 164 164 164 GLY GLY A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'NPPSFA, National Project on Protein Structural and Functional Analyses' _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # 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 C 3 HOH 1 402 1 HOH TIP A . C 3 HOH 2 403 2 HOH TIP A . C 3 HOH 3 404 3 HOH TIP A . C 3 HOH 4 405 4 HOH TIP A . C 3 HOH 5 406 5 HOH TIP A . C 3 HOH 6 407 6 HOH TIP A . C 3 HOH 7 408 7 HOH TIP A . C 3 HOH 8 409 8 HOH TIP A . C 3 HOH 9 410 10 HOH TIP A . C 3 HOH 10 411 11 HOH TIP A . C 3 HOH 11 412 12 HOH TIP A . C 3 HOH 12 413 13 HOH TIP A . C 3 HOH 13 414 14 HOH TIP A . C 3 HOH 14 415 15 HOH TIP A . C 3 HOH 15 416 16 HOH TIP A . C 3 HOH 16 417 17 HOH TIP A . C 3 HOH 17 418 18 HOH TIP A . C 3 HOH 18 419 19 HOH TIP A . C 3 HOH 19 420 20 HOH TIP A . C 3 HOH 20 421 21 HOH TIP A . C 3 HOH 21 422 22 HOH TIP A . C 3 HOH 22 423 23 HOH TIP A . C 3 HOH 23 424 24 HOH TIP A . C 3 HOH 24 425 25 HOH TIP A . C 3 HOH 25 426 26 HOH TIP A . C 3 HOH 26 427 27 HOH TIP A . C 3 HOH 27 428 28 HOH TIP A . C 3 HOH 28 429 29 HOH TIP A . C 3 HOH 29 430 30 HOH TIP A . C 3 HOH 30 431 31 HOH TIP A . C 3 HOH 31 432 32 HOH TIP A . C 3 HOH 32 433 33 HOH TIP A . C 3 HOH 33 434 34 HOH TIP A . C 3 HOH 34 435 35 HOH TIP A . C 3 HOH 35 436 36 HOH TIP A . C 3 HOH 36 437 37 HOH TIP A . C 3 HOH 37 438 38 HOH TIP A . C 3 HOH 38 439 39 HOH TIP A . C 3 HOH 39 440 40 HOH TIP A . C 3 HOH 40 441 41 HOH TIP A . C 3 HOH 41 442 42 HOH TIP A . C 3 HOH 42 443 43 HOH TIP A . C 3 HOH 43 444 44 HOH TIP A . C 3 HOH 44 445 45 HOH TIP A . C 3 HOH 45 446 46 HOH TIP A . C 3 HOH 46 447 47 HOH TIP A . C 3 HOH 47 448 48 HOH TIP A . C 3 HOH 48 449 49 HOH TIP A . C 3 HOH 49 450 50 HOH TIP A . C 3 HOH 50 451 51 HOH TIP A . C 3 HOH 51 452 52 HOH TIP A . C 3 HOH 52 453 53 HOH TIP A . C 3 HOH 53 454 54 HOH TIP A . C 3 HOH 54 455 55 HOH TIP A . C 3 HOH 55 456 56 HOH TIP A . C 3 HOH 56 457 57 HOH TIP A . C 3 HOH 57 458 58 HOH TIP A . C 3 HOH 58 459 59 HOH TIP A . C 3 HOH 59 460 60 HOH TIP A . C 3 HOH 60 461 61 HOH TIP A . C 3 HOH 61 462 62 HOH TIP A . C 3 HOH 62 463 63 HOH TIP A . C 3 HOH 63 464 64 HOH TIP A . C 3 HOH 64 465 65 HOH TIP A . C 3 HOH 65 466 66 HOH TIP A . C 3 HOH 66 467 67 HOH TIP A . C 3 HOH 67 468 68 HOH TIP A . C 3 HOH 68 469 69 HOH TIP A . C 3 HOH 69 470 70 HOH TIP A . C 3 HOH 70 471 71 HOH TIP A . C 3 HOH 71 472 72 HOH TIP A . C 3 HOH 72 473 73 HOH TIP A . C 3 HOH 73 474 74 HOH TIP A . C 3 HOH 74 475 75 HOH TIP A . C 3 HOH 75 476 77 HOH TIP A . C 3 HOH 76 477 78 HOH TIP A . C 3 HOH 77 478 79 HOH TIP A . C 3 HOH 78 479 80 HOH TIP A . C 3 HOH 79 480 81 HOH TIP A . C 3 HOH 80 481 82 HOH TIP A . C 3 HOH 81 482 83 HOH TIP A . C 3 HOH 82 483 84 HOH TIP A . C 3 HOH 83 484 85 HOH TIP A . C 3 HOH 84 485 86 HOH TIP A . C 3 HOH 85 486 87 HOH TIP A . C 3 HOH 86 487 88 HOH TIP A . C 3 HOH 87 488 89 HOH TIP A . C 3 HOH 88 489 90 HOH TIP A . C 3 HOH 89 490 92 HOH TIP A . C 3 HOH 90 491 93 HOH TIP A . C 3 HOH 91 492 94 HOH TIP A . C 3 HOH 92 493 95 HOH TIP A . C 3 HOH 93 494 96 HOH TIP A . C 3 HOH 94 495 97 HOH TIP A . C 3 HOH 95 496 98 HOH TIP A . C 3 HOH 96 497 99 HOH TIP A . C 3 HOH 97 498 100 HOH TIP A . C 3 HOH 98 499 101 HOH TIP A . C 3 HOH 99 500 102 HOH TIP A . C 3 HOH 100 501 103 HOH TIP A . C 3 HOH 101 502 104 HOH TIP A . C 3 HOH 102 503 105 HOH TIP A . C 3 HOH 103 504 106 HOH TIP A . C 3 HOH 104 505 107 HOH TIP A . C 3 HOH 105 506 108 HOH TIP A . C 3 HOH 106 507 109 HOH TIP A . C 3 HOH 107 508 110 HOH TIP A . C 3 HOH 108 509 111 HOH TIP A . C 3 HOH 109 510 112 HOH TIP A . C 3 HOH 110 511 113 HOH TIP A . C 3 HOH 111 512 114 HOH TIP A . C 3 HOH 112 513 115 HOH TIP A . C 3 HOH 113 514 116 HOH TIP A . C 3 HOH 114 515 117 HOH TIP A . C 3 HOH 115 516 118 HOH TIP A . C 3 HOH 116 517 119 HOH TIP A . C 3 HOH 117 518 120 HOH TIP A . C 3 HOH 118 519 121 HOH TIP A . C 3 HOH 119 520 122 HOH TIP A . C 3 HOH 120 521 123 HOH TIP A . C 3 HOH 121 522 124 HOH TIP A . C 3 HOH 122 523 125 HOH TIP A . C 3 HOH 123 524 126 HOH TIP A . C 3 HOH 124 525 127 HOH TIP A . C 3 HOH 125 526 128 HOH TIP A . C 3 HOH 126 527 129 HOH TIP A . C 3 HOH 127 528 130 HOH TIP A . C 3 HOH 128 529 131 HOH TIP A . C 3 HOH 129 530 132 HOH TIP A . C 3 HOH 130 531 133 HOH TIP A . C 3 HOH 131 532 134 HOH TIP A . C 3 HOH 132 533 135 HOH TIP A . C 3 HOH 133 534 136 HOH TIP A . C 3 HOH 134 535 137 HOH TIP A . C 3 HOH 135 536 138 HOH TIP A . C 3 HOH 136 537 139 HOH TIP A . C 3 HOH 137 538 140 HOH TIP A . C 3 HOH 138 539 141 HOH TIP A . C 3 HOH 139 540 142 HOH TIP A . C 3 HOH 140 541 143 HOH TIP A . C 3 HOH 141 542 144 HOH TIP A . C 3 HOH 142 543 145 HOH TIP A . C 3 HOH 143 544 146 HOH TIP A . C 3 HOH 144 545 147 HOH TIP A . C 3 HOH 145 546 148 HOH TIP A . C 3 HOH 146 547 149 HOH TIP A . C 3 HOH 147 548 150 HOH TIP A . C 3 HOH 148 549 151 HOH TIP A . C 3 HOH 149 550 152 HOH TIP A . C 3 HOH 150 551 153 HOH TIP A . C 3 HOH 151 552 154 HOH TIP A . C 3 HOH 152 553 155 HOH TIP A . # _pdbx_molecule_features.prd_id PRD_900004 _pdbx_molecule_features.name beta-lactose _pdbx_molecule_features.type Oligosaccharide _pdbx_molecule_features.class Nutrient _pdbx_molecule_features.details oligosaccharide # _pdbx_molecule.instance_id 1 _pdbx_molecule.prd_id PRD_900004 _pdbx_molecule.asym_id B # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id MSE _pdbx_struct_mod_residue.label_seq_id 115 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id MSE _pdbx_struct_mod_residue.auth_seq_id 115 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id MET _pdbx_struct_mod_residue.details SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 # _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 2008-05-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 2 0 2020-07-29 4 'Structure model' 2 1 2020-09-09 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 3 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Non-polymer description' 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Atomic model' 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' 6 3 'Structure model' 'Derived calculations' 7 3 'Structure model' 'Non-polymer description' 8 3 'Structure model' 'Structure summary' 9 4 'Structure model' 'Database references' 10 4 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' atom_site 2 3 'Structure model' chem_comp 3 3 'Structure model' entity 4 3 'Structure model' entity_name_com 5 3 'Structure model' pdbx_branch_scheme 6 3 'Structure model' pdbx_chem_comp_identifier 7 3 'Structure model' pdbx_entity_branch 8 3 'Structure model' pdbx_entity_branch_descriptor 9 3 'Structure model' pdbx_entity_branch_link 10 3 'Structure model' pdbx_entity_branch_list 11 3 'Structure model' pdbx_entity_nonpoly 12 3 'Structure model' pdbx_molecule_features 13 3 'Structure model' pdbx_nonpoly_scheme 14 3 'Structure model' struct_conn 15 3 'Structure model' struct_ref_seq_dif 16 3 'Structure model' struct_site 17 3 'Structure model' struct_site_gen 18 4 'Structure model' chem_comp 19 4 'Structure model' citation 20 4 'Structure model' struct # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_atom_site.B_iso_or_equiv' 2 3 'Structure model' '_atom_site.Cartn_x' 3 3 'Structure model' '_atom_site.Cartn_y' 4 3 'Structure model' '_atom_site.Cartn_z' 5 3 'Structure model' '_atom_site.auth_asym_id' 6 3 'Structure model' '_atom_site.auth_atom_id' 7 3 'Structure model' '_atom_site.auth_comp_id' 8 3 'Structure model' '_atom_site.auth_seq_id' 9 3 'Structure model' '_atom_site.label_atom_id' 10 3 'Structure model' '_atom_site.label_comp_id' 11 3 'Structure model' '_chem_comp.formula' 12 3 'Structure model' '_chem_comp.formula_weight' 13 3 'Structure model' '_chem_comp.id' 14 3 'Structure model' '_chem_comp.mon_nstd_flag' 15 3 'Structure model' '_chem_comp.name' 16 3 'Structure model' '_chem_comp.type' 17 3 'Structure model' '_entity.formula_weight' 18 3 'Structure model' '_entity.pdbx_description' 19 3 'Structure model' '_entity.type' 20 3 'Structure model' '_struct_ref_seq_dif.details' 21 4 'Structure model' '_chem_comp.pdbx_synonyms' 22 4 'Structure model' '_citation.title' 23 4 'Structure model' '_struct.title' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 HKL-2000 'data reduction' . ? 2 HKL-2000 'data scaling' . ? 3 MOLREP phasing . ? 4 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASN A 21 ? ? 36.87 57.79 2 1 ARG A 79 ? ? 64.59 -135.08 3 1 ASP A 101 ? ? -100.17 78.73 # 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 SER 2 ? A SER 2 3 1 Y 1 A SER 3 ? A SER 3 4 1 Y 1 A GLY 4 ? A GLY 4 5 1 Y 1 A SER 5 ? A SER 5 6 1 Y 1 A SER 6 ? A SER 6 7 1 Y 1 A GLY 7 ? A GLY 7 8 1 Y 1 A MET 8 ? A MET 8 9 1 Y 1 A MET 9 ? A MET 9 10 1 Y 1 A LEU 10 ? A LEU 10 11 1 Y 1 A SER 11 ? A SER 11 12 1 Y 1 A LEU 12 ? A LEU 12 13 1 Y 1 A ASN 13 ? A ASN 13 14 1 Y 1 A ASN 14 ? A ASN 14 # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero B 2 BGC 1 B BGC 1 A LAT 401 n B 2 GAL 2 B GAL 2 A LAT 401 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier BGC 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpb BGC 'COMMON NAME' GMML 1.0 b-D-glucopyranose BGC 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-Glcp BGC 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Glc GAL 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGalpb GAL 'COMMON NAME' GMML 1.0 b-D-galactopyranose GAL 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-Galp GAL 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Gal # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 2 DGalpb1-4DGlcpb1-ROH 'Glycam Condensed Sequence' GMML 1.0 2 2 'WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1' WURCS PDB2Glycan 1.1.0 3 2 '[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}' LINUCS PDB-CARE ? # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.comp_id_1 GAL _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.details ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 2 BGC 1 n 2 GAL 2 n # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #