data_4XQM # _entry.id 4XQM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4XQM WWPDB D_1000206128 # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB 'uncomplexed NMR structure' 2LVX unspecified PDB . 2N1H unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 4XQM _pdbx_database_status.recvd_initial_deposition_date 2015-01-19 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Olson, L.J.' 1 'Dahms, N.M.' 2 'Kim, J.-J.P.' 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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Biochemistry _citation.journal_id_ASTM BICHAW _citation.journal_id_CSD 0033 _citation.journal_id_ISSN 0006-2960 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 54 _citation.language ? _citation.page_first 4097 _citation.page_last 4111 _citation.title 'Crystal Structure and Functional Analyses of the Lectin Domain of Glucosidase II: Insights into Oligomannose Recognition.' _citation.year 2015 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.biochem.5b00256 _citation.pdbx_database_id_PubMed 26062005 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Olson, L.J.' 1 ? primary 'Orsi, R.' 2 ? primary 'Peterson, F.C.' 3 ? primary 'Parodi, A.J.' 4 ? primary 'Kim, J.J.' 5 ? primary ;D'Alessio, C. ; 6 ? primary 'Dahms, N.M.' 7 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 4XQM _cell.details ? _cell.formula_units_Z ? _cell.length_a 57.571 _cell.length_a_esd ? _cell.length_b 57.571 _cell.length_b_esd ? _cell.length_c 58.321 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XQM _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' _symmetry.pdbx_full_space_group_name_H-M ? # 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 'Glucosidase 2 subunit beta' 10543.977 1 3.2.1.84 ? 'MRH domain (UNP residues 380-473)' ? 2 non-polymer man alpha-D-mannopyranose 180.156 1 ? ? ? ? 3 water nat water 18.015 142 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Alpha-glucosidase 2 subunit beta' # _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 ;YRAIKGMETKREIGGYTYKVVFYENVFQDSILLGNFASQEGNVLKYENGQSCWNGPHRSAIVTVECGVENEIVSVLEAQK CEYLIKMKSPAACS ; _entity_poly.pdbx_seq_one_letter_code_can ;YRAIKGMETKREIGGYTYKVVFYENVFQDSILLGNFASQEGNVLKYENGQSCWNGPHRSAIVTVECGVENEIVSVLEAQK CEYLIKMKSPAACS ; _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 TYR n 1 2 ARG n 1 3 ALA n 1 4 ILE n 1 5 LYS n 1 6 GLY n 1 7 MET n 1 8 GLU n 1 9 THR n 1 10 LYS n 1 11 ARG n 1 12 GLU n 1 13 ILE n 1 14 GLY n 1 15 GLY n 1 16 TYR n 1 17 THR n 1 18 TYR n 1 19 LYS n 1 20 VAL n 1 21 VAL n 1 22 PHE n 1 23 TYR n 1 24 GLU n 1 25 ASN n 1 26 VAL n 1 27 PHE n 1 28 GLN n 1 29 ASP n 1 30 SER n 1 31 ILE n 1 32 LEU n 1 33 LEU n 1 34 GLY n 1 35 ASN n 1 36 PHE n 1 37 ALA n 1 38 SER n 1 39 GLN n 1 40 GLU n 1 41 GLY n 1 42 ASN n 1 43 VAL n 1 44 LEU n 1 45 LYS n 1 46 TYR n 1 47 GLU n 1 48 ASN n 1 49 GLY n 1 50 GLN n 1 51 SER n 1 52 CYS n 1 53 TRP n 1 54 ASN n 1 55 GLY n 1 56 PRO n 1 57 HIS n 1 58 ARG n 1 59 SER n 1 60 ALA n 1 61 ILE n 1 62 VAL n 1 63 THR n 1 64 VAL n 1 65 GLU n 1 66 CYS n 1 67 GLY n 1 68 VAL n 1 69 GLU n 1 70 ASN n 1 71 GLU n 1 72 ILE n 1 73 VAL n 1 74 SER n 1 75 VAL n 1 76 LEU n 1 77 GLU n 1 78 ALA n 1 79 GLN n 1 80 LYS n 1 81 CYS n 1 82 GLU n 1 83 TYR n 1 84 LEU n 1 85 ILE n 1 86 LYS n 1 87 MET n 1 88 LYS n 1 89 SER n 1 90 PRO n 1 91 ALA n 1 92 ALA n 1 93 CYS n 1 94 SER 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 94 _entity_src_gen.gene_src_common_name 'Fission yeast' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'gtb1, gls2-beta, SPCC825.02' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain '972 / ATCC 24843' _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 'Schizosaccharomyces pombe (strain 972 / ATCC 24843)' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 284812 _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 GLU2B_SCHPO _struct_ref.pdbx_db_accession Q9USH8 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;YRAIKGMETKREIGGYTYKVVFYENVFQDSILLGNFASQEGNVLKYENGQSCWNGPHRSAIVTVECGVENEIVSVLEAQK CEYLIKMKSPAACS ; _struct_ref.pdbx_align_begin 380 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4XQM _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 94 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9USH8 _struct_ref_seq.db_align_beg 380 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 473 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 357 _struct_ref_seq.pdbx_auth_seq_align_end 450 # 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 MAN 'D-saccharide, alpha linking' . alpha-D-mannopyranose ? 'C6 H12 O6' 180.156 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 4XQM _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 2.29 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 46.33 _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 8.25 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 292 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;10mg/ml protein in 20mM Tris pH 7.5, 150mM NaCl, 100mM mannose mixed 1:1 with 100 mM triethanolamine HCl pH 8.25, 200 mM potassium glutamate, 28% PEG 4000 ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 98 _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 'IMAGE PLATE' _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'RIGAKU RAXIS IV++' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2013-07-01 # _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 1.54 _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 'ROTATING ANODE' _diffrn_source.target ? _diffrn_source.type 'RIGAKU MICROMAX-007' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.54 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_synchrotron_site ? # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 4XQM _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.620 _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 12000 _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 99.000 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 12.800 _reflns.pdbx_Rmerge_I_obs 0.064 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 49.610 _reflns.pdbx_netI_over_sigmaI 14.500 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.521 _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 153936 _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 1.620 1.650 ? ? ? ? ? 467 ? 79.600 ? ? ? ? 0.395 ? ? ? ? ? ? ? ? 3.700 ? 1.191 ? ? ? ? 0 1 1 ? ? 1.650 1.680 ? ? ? ? ? 604 ? 99.500 ? ? ? ? 0.416 ? ? ? ? ? ? ? ? 6.100 ? 1.282 ? ? ? ? 0 2 1 ? ? 1.680 1.710 ? ? ? ? ? 595 ? 100.000 ? ? ? ? 0.404 ? ? ? ? ? ? ? ? 9.100 ? 1.296 ? ? ? ? 0 3 1 ? ? 1.710 1.750 ? ? ? ? ? 611 ? 100.000 ? ? ? ? 0.352 ? ? ? ? ? ? ? ? 11.200 ? 1.491 ? ? ? ? 0 4 1 ? ? 1.750 1.780 ? ? ? ? ? 620 ? 100.000 ? ? ? ? 0.317 ? ? ? ? ? ? ? ? 12.600 ? 1.489 ? ? ? ? 0 5 1 ? ? 1.780 1.820 ? ? ? ? ? 584 ? 100.000 ? ? ? ? 0.278 ? ? ? ? ? ? ? ? 13.300 ? 1.393 ? ? ? ? 0 6 1 ? ? 1.820 1.870 ? ? ? ? ? 612 ? 100.000 ? ? ? ? 0.234 ? ? ? ? ? ? ? ? 13.500 ? 1.688 ? ? ? ? 0 7 1 ? ? 1.870 1.920 ? ? ? ? ? 611 ? 100.000 ? ? ? ? 0.195 ? ? ? ? ? ? ? ? 13.800 ? 1.832 ? ? ? ? 0 8 1 ? ? 1.920 1.980 ? ? ? ? ? 584 ? 100.000 ? ? ? ? 0.164 ? ? ? ? ? ? ? ? 13.900 ? 1.653 ? ? ? ? 0 9 1 ? ? 1.980 2.040 ? ? ? ? ? 604 ? 100.000 ? ? ? ? 0.148 ? ? ? ? ? ? ? ? 14.000 ? 1.619 ? ? ? ? 0 10 1 ? ? 2.040 2.110 ? ? ? ? ? 606 ? 100.000 ? ? ? ? 0.119 ? ? ? ? ? ? ? ? 14.000 ? 1.651 ? ? ? ? 0 11 1 ? ? 2.110 2.200 ? ? ? ? ? 613 ? 100.000 ? ? ? ? 0.094 ? ? ? ? ? ? ? ? 14.100 ? 1.584 ? ? ? ? 0 12 1 ? ? 2.200 2.300 ? ? ? ? ? 601 ? 100.000 ? ? ? ? 0.093 ? ? ? ? ? ? ? ? 14.100 ? 1.523 ? ? ? ? 0 13 1 ? ? 2.300 2.420 ? ? ? ? ? 607 ? 100.000 ? ? ? ? 0.080 ? ? ? ? ? ? ? ? 14.300 ? 1.495 ? ? ? ? 0 14 1 ? ? 2.420 2.570 ? ? ? ? ? 609 ? 100.000 ? ? ? ? 0.067 ? ? ? ? ? ? ? ? 14.300 ? 1.428 ? ? ? ? 0 15 1 ? ? 2.570 2.770 ? ? ? ? ? 610 ? 100.000 ? ? ? ? 0.060 ? ? ? ? ? ? ? ? 14.400 ? 1.359 ? ? ? ? 0 16 1 ? ? 2.770 3.050 ? ? ? ? ? 601 ? 100.000 ? ? ? ? 0.051 ? ? ? ? ? ? ? ? 14.500 ? 1.517 ? ? ? ? 0 17 1 ? ? 3.050 3.490 ? ? ? ? ? 612 ? 100.000 ? ? ? ? 0.038 ? ? ? ? ? ? ? ? 14.500 ? 1.478 ? ? ? ? 0 18 1 ? ? 3.490 4.400 ? ? ? ? ? 614 ? 100.000 ? ? ? ? 0.030 ? ? ? ? ? ? ? ? 14.600 ? 1.380 ? ? ? ? 0 19 1 ? ? 4.400 50.000 ? ? ? ? ? 635 ? 99.700 ? ? ? ? 0.030 ? ? ? ? ? ? ? ? 14.300 ? 1.574 ? ? ? ? 0 20 1 ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max 50.480 _refine.B_iso_mean 17.6900 _refine.B_iso_min 9.110 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 4XQM _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.6250 _refine.ls_d_res_low 29.1610 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 23378 _refine.ls_number_reflns_R_free 2354 _refine.ls_number_reflns_R_work 21024 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.0200 _refine.ls_percent_reflns_R_free 10.0700 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1703 _refine.ls_R_factor_R_free 0.1969 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1673 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.360 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 18.8100 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.2000 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set 0.8862 _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.6250 _refine_hist.d_res_low 29.1610 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 142 _refine_hist.number_atoms_total 891 _refine_hist.pdbx_number_residues_total 94 _refine_hist.pdbx_B_iso_mean_ligand 18.56 _refine_hist.pdbx_B_iso_mean_solvent 27.24 _refine_hist.pdbx_number_atoms_protein 737 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.009 ? 764 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.396 ? 1027 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.090 ? 114 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.004 ? 130 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 12.802 ? 288 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 1.6251 1.6582 1178 . 105 1073 85.0000 . . . 0.3661 . 0.3156 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 1.6582 1.6943 1352 . 137 1215 99.0000 . . . 0.2432 . 0.2699 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 1.6943 1.7337 1406 . 150 1256 100.0000 . . . 0.2584 . 0.2132 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 1.7337 1.7770 1369 . 120 1249 100.0000 . . . 0.2011 . 0.1926 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 1.7770 1.8251 1403 . 140 1263 100.0000 . . . 0.2140 . 0.1843 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 1.8251 1.8788 1374 . 140 1234 100.0000 . . . 0.1859 . 0.1759 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 1.8788 1.9394 1414 . 144 1270 100.0000 . . . 0.2222 . 0.1755 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 1.9394 2.0087 1374 . 142 1232 100.0000 . . . 0.1927 . 0.1713 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 2.0087 2.0891 1400 . 142 1258 100.0000 . . . 0.2321 . 0.1840 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 2.0891 2.1841 1381 . 152 1229 100.0000 . . . 0.1951 . 0.1536 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 2.1841 2.2993 1384 . 138 1246 100.0000 . . . 0.2172 . 0.1643 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 2.2993 2.4432 1376 . 135 1241 100.0000 . . . 0.2019 . 0.1659 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 2.4432 2.6318 1426 . 142 1284 100.0000 . . . 0.2318 . 0.1670 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 2.6318 2.8964 1368 . 132 1236 100.0000 . . . 0.2165 . 0.1638 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 2.8964 3.3150 1395 . 142 1253 100.0000 . . . 0.1848 . 0.1628 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 3.3150 4.1746 1399 . 156 1243 100.0000 . . . 0.1705 . 0.1316 . . . . . . 17 . . . 'X-RAY DIFFRACTION' 4.1746 29.1652 1379 . 137 1242 100.0000 . . . 0.1420 . 0.1581 . . . . . . 17 . . . # _struct.entry_id 4XQM _struct.title 'Crystal structure of the MRH domain of Glucosidase II beta bound to mannose' _struct.pdbx_descriptor 'MRH domain of Glucosidase II beta (E.C.3.2.1.84)' _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 4XQM _struct_keywords.text 'hydrolase, sugar binding protein' _struct_keywords.pdbx_keywords HYDROLASE # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id PRO _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 90 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id CYS _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 93 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id PRO _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 446 _struct_conf.end_auth_comp_id CYS _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 449 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 4 # _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 disulf1 disulf ? ? A CYS 52 SG ? ? ? 1_555 A CYS 81 SG ? ? A CYS 408 A CYS 437 1_555 ? ? ? ? ? ? ? 2.045 ? ? disulf2 disulf ? ? A CYS 66 SG ? ? ? 1_555 A CYS 93 SG ? ? A CYS 422 A CYS 449 1_555 ? ? ? ? ? ? ? 2.042 ? ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 8 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel AA1 4 5 ? anti-parallel AA1 5 6 ? anti-parallel AA1 6 7 ? parallel AA1 7 8 ? 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 GLU A 8 ? ILE A 13 ? GLU A 364 ILE A 369 AA1 2 TYR A 16 ? VAL A 21 ? TYR A 372 VAL A 377 AA1 3 ASN A 25 ? GLN A 28 ? ASN A 381 GLN A 384 AA1 4 ILE A 31 ? GLU A 40 ? ILE A 387 GLU A 396 AA1 5 VAL A 43 ? ASN A 48 ? VAL A 399 ASN A 404 AA1 6 SER A 59 ? CYS A 66 ? SER A 415 CYS A 422 AA1 7 GLU A 82 ? SER A 89 ? GLU A 438 SER A 445 AA1 8 GLU A 71 ? GLN A 79 ? GLU A 427 GLN A 435 # 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 ARG A 11 ? N ARG A 367 O TYR A 18 ? O TYR A 374 AA1 2 3 N LYS A 19 ? N LYS A 375 O PHE A 27 ? O PHE A 383 AA1 3 4 N VAL A 26 ? N VAL A 382 O LEU A 33 ? O LEU A 389 AA1 4 5 N ALA A 37 ? N ALA A 393 O LYS A 45 ? O LYS A 401 AA1 5 6 N LEU A 44 ? N LEU A 400 O VAL A 62 ? O VAL A 418 AA1 6 7 N THR A 63 ? N THR A 419 O MET A 87 ? O MET A 443 AA1 7 8 O LEU A 84 ? O LEU A 440 N LEU A 76 ? N LEU A 432 # _atom_sites.entry_id 4XQM _atom_sites.fract_transf_matrix[1][1] 0.017370 _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] 0.017370 _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] 0.017146 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 TYR 1 357 357 TYR TYR A . n A 1 2 ARG 2 358 358 ARG ARG A . n A 1 3 ALA 3 359 359 ALA ALA A . n A 1 4 ILE 4 360 360 ILE ILE A . n A 1 5 LYS 5 361 361 LYS LYS A . n A 1 6 GLY 6 362 362 GLY GLY A . n A 1 7 MET 7 363 363 MET MET A . n A 1 8 GLU 8 364 364 GLU GLU A . n A 1 9 THR 9 365 365 THR THR A . n A 1 10 LYS 10 366 366 LYS LYS A . n A 1 11 ARG 11 367 367 ARG ARG A . n A 1 12 GLU 12 368 368 GLU GLU A . n A 1 13 ILE 13 369 369 ILE ILE A . n A 1 14 GLY 14 370 370 GLY GLY A . n A 1 15 GLY 15 371 371 GLY GLY A . n A 1 16 TYR 16 372 372 TYR TYR A . n A 1 17 THR 17 373 373 THR THR A . n A 1 18 TYR 18 374 374 TYR TYR A . n A 1 19 LYS 19 375 375 LYS LYS A . n A 1 20 VAL 20 376 376 VAL VAL A . n A 1 21 VAL 21 377 377 VAL VAL A . n A 1 22 PHE 22 378 378 PHE PHE A . n A 1 23 TYR 23 379 379 TYR TYR A . n A 1 24 GLU 24 380 380 GLU GLU A . n A 1 25 ASN 25 381 381 ASN ASN A . n A 1 26 VAL 26 382 382 VAL VAL A . n A 1 27 PHE 27 383 383 PHE PHE A . n A 1 28 GLN 28 384 384 GLN GLN A . n A 1 29 ASP 29 385 385 ASP ASP A . n A 1 30 SER 30 386 386 SER SER A . n A 1 31 ILE 31 387 387 ILE ILE A . n A 1 32 LEU 32 388 388 LEU LEU A . n A 1 33 LEU 33 389 389 LEU LEU A . n A 1 34 GLY 34 390 390 GLY GLY A . n A 1 35 ASN 35 391 391 ASN ASN A . n A 1 36 PHE 36 392 392 PHE PHE A . n A 1 37 ALA 37 393 393 ALA ALA A . n A 1 38 SER 38 394 394 SER SER A . n A 1 39 GLN 39 395 395 GLN GLN A . n A 1 40 GLU 40 396 396 GLU GLU A . n A 1 41 GLY 41 397 397 GLY GLY A . n A 1 42 ASN 42 398 398 ASN ASN A . n A 1 43 VAL 43 399 399 VAL VAL A . n A 1 44 LEU 44 400 400 LEU LEU A . n A 1 45 LYS 45 401 401 LYS LYS A . n A 1 46 TYR 46 402 402 TYR TYR A . n A 1 47 GLU 47 403 403 GLU GLU A . n A 1 48 ASN 48 404 404 ASN ASN A . n A 1 49 GLY 49 405 405 GLY GLY A . n A 1 50 GLN 50 406 406 GLN GLN A . n A 1 51 SER 51 407 407 SER SER A . n A 1 52 CYS 52 408 408 CYS CYS A . n A 1 53 TRP 53 409 409 TRP TRP A . n A 1 54 ASN 54 410 410 ASN ASN A . n A 1 55 GLY 55 411 411 GLY GLY A . n A 1 56 PRO 56 412 412 PRO PRO A . n A 1 57 HIS 57 413 413 HIS HIS A . n A 1 58 ARG 58 414 414 ARG ARG A . n A 1 59 SER 59 415 415 SER SER A . n A 1 60 ALA 60 416 416 ALA ALA A . n A 1 61 ILE 61 417 417 ILE ILE A . n A 1 62 VAL 62 418 418 VAL VAL A . n A 1 63 THR 63 419 419 THR THR A . n A 1 64 VAL 64 420 420 VAL VAL A . n A 1 65 GLU 65 421 421 GLU GLU A . n A 1 66 CYS 66 422 422 CYS CYS A . n A 1 67 GLY 67 423 423 GLY GLY A . n A 1 68 VAL 68 424 424 VAL VAL A . n A 1 69 GLU 69 425 425 GLU GLU A . n A 1 70 ASN 70 426 426 ASN ASN A . n A 1 71 GLU 71 427 427 GLU GLU A . n A 1 72 ILE 72 428 428 ILE ILE A . n A 1 73 VAL 73 429 429 VAL VAL A . n A 1 74 SER 74 430 430 SER SER A . n A 1 75 VAL 75 431 431 VAL VAL A . n A 1 76 LEU 76 432 432 LEU LEU A . n A 1 77 GLU 77 433 433 GLU GLU A . n A 1 78 ALA 78 434 434 ALA ALA A . n A 1 79 GLN 79 435 435 GLN GLN A . n A 1 80 LYS 80 436 436 LYS LYS A . n A 1 81 CYS 81 437 437 CYS CYS A . n A 1 82 GLU 82 438 438 GLU GLU A . n A 1 83 TYR 83 439 439 TYR TYR A . n A 1 84 LEU 84 440 440 LEU LEU A . n A 1 85 ILE 85 441 441 ILE ILE A . n A 1 86 LYS 86 442 442 LYS LYS A . n A 1 87 MET 87 443 443 MET MET A . n A 1 88 LYS 88 444 444 LYS LYS A . n A 1 89 SER 89 445 445 SER SER A . n A 1 90 PRO 90 446 446 PRO PRO A . n A 1 91 ALA 91 447 447 ALA ALA A . n A 1 92 ALA 92 448 448 ALA ALA A . n A 1 93 CYS 93 449 449 CYS CYS A . n A 1 94 SER 94 450 450 SER SER 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 MAN 1 501 2 MAN MAN A . C 3 HOH 1 601 8 HOH HOH A . C 3 HOH 2 602 94 HOH HOH A . C 3 HOH 3 603 58 HOH HOH A . C 3 HOH 4 604 134 HOH HOH A . C 3 HOH 5 605 86 HOH HOH A . C 3 HOH 6 606 14 HOH HOH A . C 3 HOH 7 607 42 HOH HOH A . C 3 HOH 8 608 22 HOH HOH A . C 3 HOH 9 609 85 HOH HOH A . C 3 HOH 10 610 4 HOH HOH A . C 3 HOH 11 611 29 HOH HOH A . C 3 HOH 12 612 13 HOH HOH A . C 3 HOH 13 613 9 HOH HOH A . C 3 HOH 14 614 63 HOH HOH A . C 3 HOH 15 615 52 HOH HOH A . C 3 HOH 16 616 10 HOH HOH A . C 3 HOH 17 617 17 HOH HOH A . C 3 HOH 18 618 125 HOH HOH A . C 3 HOH 19 619 54 HOH HOH A . C 3 HOH 20 620 26 HOH HOH A . C 3 HOH 21 621 119 HOH HOH A . C 3 HOH 22 622 47 HOH HOH A . C 3 HOH 23 623 21 HOH HOH A . C 3 HOH 24 624 5 HOH HOH A . C 3 HOH 25 625 84 HOH HOH A . C 3 HOH 26 626 99 HOH HOH A . C 3 HOH 27 627 46 HOH HOH A . C 3 HOH 28 628 93 HOH HOH A . C 3 HOH 29 629 18 HOH HOH A . C 3 HOH 30 630 64 HOH HOH A . C 3 HOH 31 631 112 HOH HOH A . C 3 HOH 32 632 117 HOH HOH A . C 3 HOH 33 633 33 HOH HOH A . C 3 HOH 34 634 40 HOH HOH A . C 3 HOH 35 635 65 HOH HOH A . C 3 HOH 36 636 72 HOH HOH A . C 3 HOH 37 637 81 HOH HOH A . C 3 HOH 38 638 11 HOH HOH A . C 3 HOH 39 639 89 HOH HOH A . C 3 HOH 40 640 101 HOH HOH A . C 3 HOH 41 641 38 HOH HOH A . C 3 HOH 42 642 34 HOH HOH A . C 3 HOH 43 643 106 HOH HOH A . C 3 HOH 44 644 19 HOH HOH A . C 3 HOH 45 645 98 HOH HOH A . C 3 HOH 46 646 12 HOH HOH A . C 3 HOH 47 647 141 HOH HOH A . C 3 HOH 48 648 83 HOH HOH A . C 3 HOH 49 649 82 HOH HOH A . C 3 HOH 50 650 3 HOH HOH A . C 3 HOH 51 651 28 HOH HOH A . C 3 HOH 52 652 50 HOH HOH A . C 3 HOH 53 653 74 HOH HOH A . C 3 HOH 54 654 66 HOH HOH A . C 3 HOH 55 655 57 HOH HOH A . C 3 HOH 56 656 95 HOH HOH A . C 3 HOH 57 657 59 HOH HOH A . C 3 HOH 58 658 113 HOH HOH A . C 3 HOH 59 659 30 HOH HOH A . C 3 HOH 60 660 88 HOH HOH A . C 3 HOH 61 661 80 HOH HOH A . C 3 HOH 62 662 56 HOH HOH A . C 3 HOH 63 663 111 HOH HOH A . C 3 HOH 64 664 97 HOH HOH A . C 3 HOH 65 665 43 HOH HOH A . C 3 HOH 66 666 37 HOH HOH A . C 3 HOH 67 667 110 HOH HOH A . C 3 HOH 68 668 31 HOH HOH A . C 3 HOH 69 669 132 HOH HOH A . C 3 HOH 70 670 107 HOH HOH A . C 3 HOH 71 671 128 HOH HOH A . C 3 HOH 72 672 114 HOH HOH A . C 3 HOH 73 673 100 HOH HOH A . C 3 HOH 74 674 71 HOH HOH A . C 3 HOH 75 675 103 HOH HOH A . C 3 HOH 76 676 20 HOH HOH A . C 3 HOH 77 677 67 HOH HOH A . C 3 HOH 78 678 126 HOH HOH A . C 3 HOH 79 679 70 HOH HOH A . C 3 HOH 80 680 79 HOH HOH A . C 3 HOH 81 681 73 HOH HOH A . C 3 HOH 82 682 51 HOH HOH A . C 3 HOH 83 683 139 HOH HOH A . C 3 HOH 84 684 90 HOH HOH A . C 3 HOH 85 685 129 HOH HOH A . C 3 HOH 86 686 123 HOH HOH A . C 3 HOH 87 687 137 HOH HOH A . C 3 HOH 88 688 140 HOH HOH A . C 3 HOH 89 689 76 HOH HOH A . C 3 HOH 90 690 116 HOH HOH A . C 3 HOH 91 691 138 HOH HOH A . C 3 HOH 92 692 75 HOH HOH A . C 3 HOH 93 693 1 HOH HOH A . C 3 HOH 94 694 2 HOH HOH A . C 3 HOH 95 695 6 HOH HOH A . C 3 HOH 96 696 7 HOH HOH A . C 3 HOH 97 697 15 HOH HOH A . C 3 HOH 98 698 16 HOH HOH A . C 3 HOH 99 699 23 HOH HOH A . C 3 HOH 100 700 24 HOH HOH A . C 3 HOH 101 701 25 HOH HOH A . C 3 HOH 102 702 27 HOH HOH A . C 3 HOH 103 703 32 HOH HOH A . C 3 HOH 104 704 35 HOH HOH A . C 3 HOH 105 705 36 HOH HOH A . C 3 HOH 106 706 39 HOH HOH A . C 3 HOH 107 707 41 HOH HOH A . C 3 HOH 108 708 44 HOH HOH A . C 3 HOH 109 709 45 HOH HOH A . C 3 HOH 110 710 48 HOH HOH A . C 3 HOH 111 711 49 HOH HOH A . C 3 HOH 112 712 53 HOH HOH A . C 3 HOH 113 713 55 HOH HOH A . C 3 HOH 114 714 60 HOH HOH A . C 3 HOH 115 715 61 HOH HOH A . C 3 HOH 116 716 62 HOH HOH A . C 3 HOH 117 717 68 HOH HOH A . C 3 HOH 118 718 69 HOH HOH A . C 3 HOH 119 719 77 HOH HOH A . C 3 HOH 120 720 78 HOH HOH A . C 3 HOH 121 721 87 HOH HOH A . C 3 HOH 122 722 91 HOH HOH A . C 3 HOH 123 723 92 HOH HOH A . C 3 HOH 124 724 96 HOH HOH A . C 3 HOH 125 725 102 HOH HOH A . C 3 HOH 126 726 104 HOH HOH A . C 3 HOH 127 727 105 HOH HOH A . C 3 HOH 128 728 108 HOH HOH A . C 3 HOH 129 729 109 HOH HOH A . C 3 HOH 130 730 115 HOH HOH A . C 3 HOH 131 731 118 HOH HOH A . C 3 HOH 132 732 120 HOH HOH A . C 3 HOH 133 733 121 HOH HOH A . C 3 HOH 134 734 122 HOH HOH A . C 3 HOH 135 735 124 HOH HOH A . C 3 HOH 136 736 127 HOH HOH A . C 3 HOH 137 737 130 HOH HOH A . C 3 HOH 138 738 131 HOH HOH A . C 3 HOH 139 739 133 HOH HOH A . C 3 HOH 140 740 135 HOH HOH A . C 3 HOH 141 741 136 HOH HOH A . C 3 HOH 142 742 142 HOH HOH A . # _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_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 607 ? C HOH . 2 1 A HOH 673 ? C HOH . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2015-07-22 2 'Structure model' 1 1 2015-12-16 3 'Structure model' 1 2 2017-09-27 4 'Structure model' 1 3 2019-12-25 5 'Structure model' 1 4 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 5 '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' Other 2 3 'Structure model' 'Author supporting evidence' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Author supporting evidence' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Derived calculations' 8 5 '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' diffrn_detector 2 3 'Structure model' pdbx_audit_support 3 3 'Structure model' pdbx_struct_oper_list 4 4 'Structure model' pdbx_audit_support 5 5 'Structure model' chem_comp 6 5 'Structure model' entity 7 5 'Structure model' pdbx_chem_comp_identifier 8 5 'Structure model' pdbx_entity_nonpoly 9 5 'Structure model' struct_site 10 5 'Structure model' struct_site_gen # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_diffrn_detector.detector' 2 3 'Structure model' '_pdbx_audit_support.funding_organization' 3 3 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 4 4 'Structure model' '_pdbx_audit_support.funding_organization' 5 5 'Structure model' '_chem_comp.name' 6 5 'Structure model' '_chem_comp.type' 7 5 'Structure model' '_entity.pdbx_description' 8 5 'Structure model' '_pdbx_entity_nonpoly.name' # _phasing.method SAD # 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 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 1 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELX ? ? ? . 2 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(phenix.refine: 1.8.2_1309)' 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.15 4 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 5 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 OE1 A GLU 396 ? ? O A HOH 735 ? ? 2.09 2 1 O A HOH 601 ? ? O A HOH 640 ? ? 2.14 3 1 O A HOH 670 ? ? O A HOH 712 ? ? 2.19 # 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 N A TYR 357 ? ? 1_555 O1 A MAN 501 ? ? 7_545 1.92 2 1 O A HOH 643 ? ? 1_555 O A HOH 643 ? ? 2_655 2.19 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 N _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 TYR _pdbx_validate_rmsd_angle.auth_seq_id_1 357 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CA _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 TYR _pdbx_validate_rmsd_angle.auth_seq_id_2 357 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 C _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 TYR _pdbx_validate_rmsd_angle.auth_seq_id_3 357 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 89.27 _pdbx_validate_rmsd_angle.angle_target_value 111.00 _pdbx_validate_rmsd_angle.angle_deviation -21.73 _pdbx_validate_rmsd_angle.angle_standard_deviation 2.70 _pdbx_validate_rmsd_angle.linker_flag N # 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 GLU A 380 ? ? -125.27 -84.60 2 1 ASP A 385 ? ? 49.50 -126.44 3 1 GLU A 433 ? ? -116.02 71.76 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)' 'United States' DK042667 1 'Mizutani Foundation for Glycoscience' 'United States' 10-0056 2 # 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 MAN 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DManpa MAN 'COMMON NAME' GMML 1.0 a-D-mannopyranose MAN 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-Manp MAN 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Man # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 alpha-D-mannopyranose MAN 3 water HOH #