data_3NV2 # _entry.id 3NV2 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3NV2 RCSB RCSB060314 WWPDB D_1000060314 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3NV1 'The same protein without ligand' unspecified PDB 3NV3 'The same protein with biantennary oligosaccharide' unspecified PDB 3NV4 'The same protein with Sialyllactose' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3NV2 _pdbx_database_status.recvd_initial_deposition_date 2010-07-07 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Yoshida, H.' 1 'Kamitori, S.' 2 # _citation.id primary _citation.title 'X-ray structures of human galectin-9 C-terminal domain in complexes with a biantennary oligosaccharide and sialyllactose' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 285 _citation.page_first 36969 _citation.page_last 36976 _citation.year 2010 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20861009 _citation.pdbx_database_id_DOI 10.1074/jbc.M110.163402 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Yoshida, H.' 1 primary 'Teraoka, M.' 2 primary 'Nishi, N.' 3 primary 'Nakakita, S.' 4 primary 'Nakamura, T.' 5 primary 'Hirashima, M.' 6 primary 'Kamitori, S.' 7 # _cell.entry_id 3NV2 _cell.length_a 70.805 _cell.length_b 70.805 _cell.length_c 50.209 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3NV2 _symmetry.space_group_name_H-M 'P 63' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _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 9 short isoform variant' 15729.982 1 ? ? 'C-terminal carbohydrate recognition domain, residues 186-323' ? 2 non-polymer syn 'NICKEL (II) ION' 58.693 1 ? ? ? ? 3 non-polymer man BETA-D-GALACTOSE 180.156 1 ? ? ? ? 4 non-polymer man '2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE' 221.208 1 ? ? ? ? 5 water nat water 18.015 140 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name Galectin-9 # _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 ;YPHPAYPMPFITTILGGLYPSKSILLSGTVLPSAQRFHINLCSGNHIAFHLNPRFDENAVVRNTQIDNSWGSEERSLPRK MPFVRGQSFSVWILCEAHCLKVAVDGQHLFEYYHRLRNLPTINRLEVGGDIQLTHVQT ; _entity_poly.pdbx_seq_one_letter_code_can ;YPHPAYPMPFITTILGGLYPSKSILLSGTVLPSAQRFHINLCSGNHIAFHLNPRFDENAVVRNTQIDNSWGSEERSLPRK MPFVRGQSFSVWILCEAHCLKVAVDGQHLFEYYHRLRNLPTINRLEVGGDIQLTHVQT ; _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 PRO n 1 3 HIS n 1 4 PRO n 1 5 ALA n 1 6 TYR n 1 7 PRO n 1 8 MET n 1 9 PRO n 1 10 PHE n 1 11 ILE n 1 12 THR n 1 13 THR n 1 14 ILE n 1 15 LEU n 1 16 GLY n 1 17 GLY n 1 18 LEU n 1 19 TYR n 1 20 PRO n 1 21 SER n 1 22 LYS n 1 23 SER n 1 24 ILE n 1 25 LEU n 1 26 LEU n 1 27 SER n 1 28 GLY n 1 29 THR n 1 30 VAL n 1 31 LEU n 1 32 PRO n 1 33 SER n 1 34 ALA n 1 35 GLN n 1 36 ARG n 1 37 PHE n 1 38 HIS n 1 39 ILE n 1 40 ASN n 1 41 LEU n 1 42 CYS n 1 43 SER n 1 44 GLY n 1 45 ASN n 1 46 HIS n 1 47 ILE n 1 48 ALA n 1 49 PHE n 1 50 HIS n 1 51 LEU n 1 52 ASN n 1 53 PRO n 1 54 ARG n 1 55 PHE n 1 56 ASP n 1 57 GLU n 1 58 ASN n 1 59 ALA n 1 60 VAL n 1 61 VAL n 1 62 ARG n 1 63 ASN n 1 64 THR n 1 65 GLN n 1 66 ILE n 1 67 ASP n 1 68 ASN n 1 69 SER n 1 70 TRP n 1 71 GLY n 1 72 SER n 1 73 GLU n 1 74 GLU n 1 75 ARG n 1 76 SER n 1 77 LEU n 1 78 PRO n 1 79 ARG n 1 80 LYS n 1 81 MET n 1 82 PRO n 1 83 PHE n 1 84 VAL n 1 85 ARG n 1 86 GLY n 1 87 GLN n 1 88 SER n 1 89 PHE n 1 90 SER n 1 91 VAL n 1 92 TRP n 1 93 ILE n 1 94 LEU n 1 95 CYS n 1 96 GLU n 1 97 ALA n 1 98 HIS n 1 99 CYS n 1 100 LEU n 1 101 LYS n 1 102 VAL n 1 103 ALA n 1 104 VAL n 1 105 ASP n 1 106 GLY n 1 107 GLN n 1 108 HIS n 1 109 LEU n 1 110 PHE n 1 111 GLU n 1 112 TYR n 1 113 TYR n 1 114 HIS n 1 115 ARG n 1 116 LEU n 1 117 ARG n 1 118 ASN n 1 119 LEU n 1 120 PRO n 1 121 THR n 1 122 ILE n 1 123 ASN n 1 124 ARG n 1 125 LEU n 1 126 GLU n 1 127 VAL n 1 128 GLY n 1 129 GLY n 1 130 ASP n 1 131 ILE n 1 132 GLN n 1 133 LEU n 1 134 THR n 1 135 HIS n 1 136 VAL n 1 137 GLN n 1 138 THR n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type PLASMID _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pGEX-4T-2 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q53FQ0_HUMAN _struct_ref.pdbx_db_accession Q53FQ0 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;YPHPAYPMPFITTILGGLYPSKSILLSGTVLPSAQRFHINLCSGNHIAFHLNPRFDENAVVRNTQIDNSWGSEERSLPRK MPFVRGQSFSVWILCEAHCLKVAVDGQHLFEYYHRLRNLPTINRLEVGGDIQLTHVQT ; _struct_ref.pdbx_align_begin 186 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3NV2 _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 138 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q53FQ0 _struct_ref_seq.db_align_beg 186 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 323 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 186 _struct_ref_seq.pdbx_auth_seq_align_end 323 # 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 GAL D-saccharide . BETA-D-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 NDG D-saccharide . '2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE' ? 'C8 H15 N O6' 221.208 NI non-polymer . 'NICKEL (II) ION' ? 'Ni 2' 58.693 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3NV2 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.31 _exptl_crystal.density_percent_sol 46.75 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.pdbx_details '20% PEG MME 2000, 0.1M Tris pH 8.5, 0.01M nickel chloride hexahydrate, VAPOR DIFFUSION, HANGING 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 'ADSC QUANTUM 210r' _diffrn_detector.pdbx_collection_date 2009-11-28 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _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 'PHOTON FACTORY BEAMLINE AR-NW12A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline AR-NW12A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 3NV2 _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.34 _reflns.number_obs 6135 _reflns.number_all ? _reflns.pdbx_number_measured_all 68565 _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs 0.075 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 8.7 _reflns.B_iso_Wilson_estimate 24.1 _reflns.pdbx_redundancy 11.2 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.34 _reflns_shell.d_res_low 2.38 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.385 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 7.4 _reflns_shell.pdbx_redundancy 11.2 _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_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3NV2 _refine.ls_number_reflns_obs 5989 _refine.ls_number_reflns_all 5989 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 40669.38 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 38.85 _refine.ls_d_res_high 2.34 _refine.ls_percent_reflns_obs 97.5 _refine.ls_R_factor_obs 0.179 _refine.ls_R_factor_all 0.185 _refine.ls_R_factor_R_work 0.179 _refine.ls_R_factor_R_free 0.231 _refine.ls_R_factor_R_free_error 0.009 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 11.0 _refine.ls_number_reflns_R_free 659 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 1.56 _refine.aniso_B[2][2] 1.56 _refine.aniso_B[3][3] -3.12 _refine.aniso_B[1][2] 2.79 _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 0.364624 _refine.solvent_model_param_bsol 60.142 _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 'PDB entry 3KOE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_ESU_R ? _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 3NV2 _refine_analyze.Luzzati_coordinate_error_obs 0.21 _refine_analyze.Luzzati_sigma_a_obs 0.12 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.30 _refine_analyze.Luzzati_sigma_a_free 0.25 _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 1090 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 27 _refine_hist.number_atoms_solvent 140 _refine_hist.number_atoms_total 1257 _refine_hist.d_res_high 2.34 _refine_hist.d_res_low 38.85 # 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 0.005 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.5 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 27.2 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.76 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.34 _refine_ls_shell.d_res_low 2.49 _refine_ls_shell.number_reflns_R_work 829 _refine_ls_shell.R_factor_R_work 0.171 _refine_ls_shell.percent_reflns_obs 92.8 _refine_ls_shell.R_factor_R_free 0.256 _refine_ls_shell.R_factor_R_free_error 0.025 _refine_ls_shell.percent_reflns_R_free 11.5 _refine_ls_shell.number_reflns_R_free 108 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 829 _refine_ls_shell.redundancy_reflns_obs ? # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 protein_rep.param protein.top 'X-RAY DIFFRACTION' 2 carbohydrate.param carbohydrate.top 'X-RAY DIFFRACTION' 3 ion.param ion.top 'X-RAY DIFFRACTION' 4 water_rep.param water.top # _struct.entry_id 3NV2 _struct.title 'Crystal structure of human galectin-9 C-terminal CRD in complex with N-acetyllactosamine' _struct.pdbx_descriptor 'Galectin 9 short isoform variant' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3NV2 _struct_keywords.pdbx_keywords 'SUGAR BINDING PROTEIN' _struct_keywords.text 'Sugar binding, 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 ? D N N 4 ? E N N 5 ? # _struct_biol.id 1 _struct_biol.details 'AUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.' # _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 ASN _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 118 _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 122 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ASN _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 303 _struct_conf.end_auth_comp_id ILE _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 307 _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 covale1 covale ? ? C GAL . C1 ? ? ? 1_555 D NDG . O4 ? ? A GAL 501 A NDG 502 1_555 ? ? ? ? ? ? ? 1.388 ? metalc1 metalc ? ? B NI . NI ? ? ? 1_555 E HOH . O ? ? A NI 401 A HOH 16 1_555 ? ? ? ? ? ? ? 2.183 ? metalc2 metalc ? ? A HIS 135 NE2 ? ? ? 1_555 B NI . NI ? ? A HIS 320 A NI 401 1_555 ? ? ? ? ? ? ? 2.246 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id MET _struct_mon_prot_cis.label_seq_id 8 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id MET _struct_mon_prot_cis.auth_seq_id 193 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 9 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 194 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 0.08 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 5 ? # 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 # 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 PHE A 10 ? THR A 13 ? PHE A 195 THR A 198 A 2 ARG A 124 ? GLY A 129 ? ARG A 309 GLY A 314 A 3 PHE A 37 ? SER A 43 ? PHE A 222 SER A 228 A 4 HIS A 46 ? ARG A 54 ? HIS A 231 ARG A 239 A 5 ALA A 59 ? ILE A 66 ? ALA A 244 ILE A 251 A 6 SER A 69 ? TRP A 70 ? SER A 254 TRP A 255 B 1 GLN A 107 ? TYR A 113 ? GLN A 292 TYR A 298 B 2 CYS A 99 ? VAL A 104 ? CYS A 284 VAL A 289 B 3 SER A 88 ? CYS A 95 ? SER A 273 CYS A 280 B 4 SER A 23 ? VAL A 30 ? SER A 208 VAL A 215 B 5 ILE A 131 ? GLN A 137 ? ILE A 316 GLN A 322 # 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 THR A 12 ? N THR A 197 O LEU A 125 ? O LEU A 310 A 2 3 O ARG A 124 ? O ARG A 309 N CYS A 42 ? N CYS A 227 A 3 4 N SER A 43 ? N SER A 228 O HIS A 46 ? O HIS A 231 A 4 5 N ARG A 54 ? N ARG A 239 O ALA A 59 ? O ALA A 244 A 5 6 N ILE A 66 ? N ILE A 251 O SER A 69 ? O SER A 254 B 1 2 O LEU A 109 ? O LEU A 294 N VAL A 102 ? N VAL A 287 B 2 3 O LYS A 101 ? O LYS A 286 N LEU A 94 ? N LEU A 279 B 3 4 O VAL A 91 ? O VAL A 276 N LEU A 26 ? N LEU A 211 B 4 5 N THR A 29 ? N THR A 214 O GLN A 132 ? O GLN A 317 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE NI A 401' AC2 Software ? ? ? ? 9 'BINDING SITE FOR RESIDUE GAL A 501' AC3 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE NDG A 502' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 HOH E . ? HOH A 16 . ? 3_565 ? 2 AC1 6 HOH E . ? HOH A 16 . ? 2_665 ? 3 AC1 6 HOH E . ? HOH A 16 . ? 1_555 ? 4 AC1 6 HIS A 135 ? HIS A 320 . ? 1_555 ? 5 AC1 6 HIS A 135 ? HIS A 320 . ? 2_665 ? 6 AC1 6 HIS A 135 ? HIS A 320 . ? 3_565 ? 7 AC2 9 HOH E . ? HOH A 1 . ? 1_555 ? 8 AC2 9 HOH E . ? HOH A 3 . ? 1_555 ? 9 AC2 9 HIS A 50 ? HIS A 235 . ? 1_555 ? 10 AC2 9 ASN A 52 ? ASN A 237 . ? 1_555 ? 11 AC2 9 ARG A 54 ? ARG A 239 . ? 1_555 ? 12 AC2 9 ASN A 63 ? ASN A 248 . ? 1_555 ? 13 AC2 9 TRP A 70 ? TRP A 255 . ? 1_555 ? 14 AC2 9 GLU A 73 ? GLU A 258 . ? 1_555 ? 15 AC2 9 NDG D . ? NDG A 502 . ? 1_555 ? 16 AC3 5 HOH E . ? HOH A 8 . ? 1_555 ? 17 AC3 5 ARG A 54 ? ARG A 239 . ? 1_555 ? 18 AC3 5 GLU A 73 ? GLU A 258 . ? 1_555 ? 19 AC3 5 ARG A 75 ? ARG A 260 . ? 1_555 ? 20 AC3 5 GAL C . ? GAL A 501 . ? 1_555 ? # _database_PDB_matrix.entry_id 3NV2 _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 3NV2 _atom_sites.fract_transf_matrix[1][1] 0.014123 _atom_sites.fract_transf_matrix[1][2] 0.008154 _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] 0.016308 _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] 0.019917 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N NI O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 TYR 1 186 ? ? ? A . n A 1 2 PRO 2 187 ? ? ? A . n A 1 3 HIS 3 188 188 HIS HIS A . n A 1 4 PRO 4 189 189 PRO PRO A . n A 1 5 ALA 5 190 190 ALA ALA A . n A 1 6 TYR 6 191 191 TYR TYR A . n A 1 7 PRO 7 192 192 PRO PRO A . n A 1 8 MET 8 193 193 MET MET A . n A 1 9 PRO 9 194 194 PRO PRO A . n A 1 10 PHE 10 195 195 PHE PHE A . n A 1 11 ILE 11 196 196 ILE ILE A . n A 1 12 THR 12 197 197 THR THR A . n A 1 13 THR 13 198 198 THR THR A . n A 1 14 ILE 14 199 199 ILE ILE A . n A 1 15 LEU 15 200 200 LEU LEU A . n A 1 16 GLY 16 201 201 GLY GLY A . n A 1 17 GLY 17 202 202 GLY GLY A . n A 1 18 LEU 18 203 203 LEU LEU A . n A 1 19 TYR 19 204 204 TYR TYR A . n A 1 20 PRO 20 205 205 PRO PRO A . n A 1 21 SER 21 206 206 SER SER A . n A 1 22 LYS 22 207 207 LYS LYS A . n A 1 23 SER 23 208 208 SER SER A . n A 1 24 ILE 24 209 209 ILE ILE A . n A 1 25 LEU 25 210 210 LEU LEU A . n A 1 26 LEU 26 211 211 LEU LEU A . n A 1 27 SER 27 212 212 SER SER A . n A 1 28 GLY 28 213 213 GLY GLY A . n A 1 29 THR 29 214 214 THR THR A . n A 1 30 VAL 30 215 215 VAL VAL A . n A 1 31 LEU 31 216 216 LEU LEU A . n A 1 32 PRO 32 217 217 PRO PRO A . n A 1 33 SER 33 218 218 SER SER A . n A 1 34 ALA 34 219 219 ALA ALA A . n A 1 35 GLN 35 220 220 GLN GLN A . n A 1 36 ARG 36 221 221 ARG ARG A . n A 1 37 PHE 37 222 222 PHE PHE A . n A 1 38 HIS 38 223 223 HIS HIS A . n A 1 39 ILE 39 224 224 ILE ILE A . n A 1 40 ASN 40 225 225 ASN ASN A . n A 1 41 LEU 41 226 226 LEU LEU A . n A 1 42 CYS 42 227 227 CYS CYS A . n A 1 43 SER 43 228 228 SER SER A . n A 1 44 GLY 44 229 229 GLY GLY A . n A 1 45 ASN 45 230 230 ASN ASN A . n A 1 46 HIS 46 231 231 HIS HIS A . n A 1 47 ILE 47 232 232 ILE ILE A . n A 1 48 ALA 48 233 233 ALA ALA A . n A 1 49 PHE 49 234 234 PHE PHE A . n A 1 50 HIS 50 235 235 HIS HIS A . n A 1 51 LEU 51 236 236 LEU LEU A . n A 1 52 ASN 52 237 237 ASN ASN A . n A 1 53 PRO 53 238 238 PRO PRO A . n A 1 54 ARG 54 239 239 ARG ARG A . n A 1 55 PHE 55 240 240 PHE PHE A . n A 1 56 ASP 56 241 241 ASP ASP A . n A 1 57 GLU 57 242 242 GLU GLU A . n A 1 58 ASN 58 243 243 ASN ASN A . n A 1 59 ALA 59 244 244 ALA ALA A . n A 1 60 VAL 60 245 245 VAL VAL A . n A 1 61 VAL 61 246 246 VAL VAL A . n A 1 62 ARG 62 247 247 ARG ARG A . n A 1 63 ASN 63 248 248 ASN ASN A . n A 1 64 THR 64 249 249 THR THR A . n A 1 65 GLN 65 250 250 GLN GLN A . n A 1 66 ILE 66 251 251 ILE ILE A . n A 1 67 ASP 67 252 252 ASP ASP A . n A 1 68 ASN 68 253 253 ASN ASN A . n A 1 69 SER 69 254 254 SER SER A . n A 1 70 TRP 70 255 255 TRP TRP A . n A 1 71 GLY 71 256 256 GLY GLY A . n A 1 72 SER 72 257 257 SER SER A . n A 1 73 GLU 73 258 258 GLU GLU A . n A 1 74 GLU 74 259 259 GLU GLU A . n A 1 75 ARG 75 260 260 ARG ARG A . n A 1 76 SER 76 261 261 SER SER A . n A 1 77 LEU 77 262 262 LEU LEU A . n A 1 78 PRO 78 263 263 PRO PRO A . n A 1 79 ARG 79 264 264 ARG ARG A . n A 1 80 LYS 80 265 265 LYS LYS A . n A 1 81 MET 81 266 266 MET MET A . n A 1 82 PRO 82 267 267 PRO PRO A . n A 1 83 PHE 83 268 268 PHE PHE A . n A 1 84 VAL 84 269 269 VAL VAL A . n A 1 85 ARG 85 270 270 ARG ARG A . n A 1 86 GLY 86 271 271 GLY GLY A . n A 1 87 GLN 87 272 272 GLN GLN A . n A 1 88 SER 88 273 273 SER SER A . n A 1 89 PHE 89 274 274 PHE PHE A . n A 1 90 SER 90 275 275 SER SER A . n A 1 91 VAL 91 276 276 VAL VAL A . n A 1 92 TRP 92 277 277 TRP TRP A . n A 1 93 ILE 93 278 278 ILE ILE A . n A 1 94 LEU 94 279 279 LEU LEU A . n A 1 95 CYS 95 280 280 CYS CYS A . n A 1 96 GLU 96 281 281 GLU GLU A . n A 1 97 ALA 97 282 282 ALA ALA A . n A 1 98 HIS 98 283 283 HIS HIS A . n A 1 99 CYS 99 284 284 CYS CYS A . n A 1 100 LEU 100 285 285 LEU LEU A . n A 1 101 LYS 101 286 286 LYS LYS A . n A 1 102 VAL 102 287 287 VAL VAL A . n A 1 103 ALA 103 288 288 ALA ALA A . n A 1 104 VAL 104 289 289 VAL VAL A . n A 1 105 ASP 105 290 290 ASP ASP A . n A 1 106 GLY 106 291 291 GLY GLY A . n A 1 107 GLN 107 292 292 GLN GLN A . n A 1 108 HIS 108 293 293 HIS HIS A . n A 1 109 LEU 109 294 294 LEU LEU A . n A 1 110 PHE 110 295 295 PHE PHE A . n A 1 111 GLU 111 296 296 GLU GLU A . n A 1 112 TYR 112 297 297 TYR TYR A . n A 1 113 TYR 113 298 298 TYR TYR A . n A 1 114 HIS 114 299 299 HIS HIS A . n A 1 115 ARG 115 300 300 ARG ARG A . n A 1 116 LEU 116 301 301 LEU LEU A . n A 1 117 ARG 117 302 302 ARG ARG A . n A 1 118 ASN 118 303 303 ASN ASN A . n A 1 119 LEU 119 304 304 LEU LEU A . n A 1 120 PRO 120 305 305 PRO PRO A . n A 1 121 THR 121 306 306 THR THR A . n A 1 122 ILE 122 307 307 ILE ILE A . n A 1 123 ASN 123 308 308 ASN ASN A . n A 1 124 ARG 124 309 309 ARG ARG A . n A 1 125 LEU 125 310 310 LEU LEU A . n A 1 126 GLU 126 311 311 GLU GLU A . n A 1 127 VAL 127 312 312 VAL VAL A . n A 1 128 GLY 128 313 313 GLY GLY A . n A 1 129 GLY 129 314 314 GLY GLY A . n A 1 130 ASP 130 315 315 ASP ASP A . n A 1 131 ILE 131 316 316 ILE ILE A . n A 1 132 GLN 132 317 317 GLN GLN A . n A 1 133 LEU 133 318 318 LEU LEU A . n A 1 134 THR 134 319 319 THR THR A . n A 1 135 HIS 135 320 320 HIS HIS A . n A 1 136 VAL 136 321 321 VAL VAL A . n A 1 137 GLN 137 322 322 GLN GLN A . n A 1 138 THR 138 323 323 THR THR A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2780 ? 1 MORE -22 ? 1 'SSA (A^2)' 17740 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5000000000 -0.8660254038 0.0000000000 35.4025000000 0.8660254038 -0.5000000000 0.0000000000 61.3189287150 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5000000000 0.8660254038 0.0000000000 -35.4025000000 -0.8660254038 -0.5000000000 0.0000000000 61.3189287150 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id NI _pdbx_struct_special_symmetry.auth_seq_id 401 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id NI _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id O _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id E _pdbx_struct_conn_angle.ptnr1_label_comp_id HOH _pdbx_struct_conn_angle.ptnr1_label_seq_id . _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id HOH _pdbx_struct_conn_angle.ptnr1_auth_seq_id 16 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id NI _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id B _pdbx_struct_conn_angle.ptnr2_label_comp_id NI _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id NI _pdbx_struct_conn_angle.ptnr2_auth_seq_id 401 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id NE2 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id A _pdbx_struct_conn_angle.ptnr3_label_comp_id HIS _pdbx_struct_conn_angle.ptnr3_label_seq_id 135 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id A _pdbx_struct_conn_angle.ptnr3_auth_comp_id HIS _pdbx_struct_conn_angle.ptnr3_auth_seq_id 320 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 99.4 _pdbx_struct_conn_angle.value_esd ? # 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 2010-09-22 2 'Structure model' 1 1 2011-07-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 MOLREP phasing . ? 2 CNS refinement 1.1 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_entry_details.entry_id 3NV2 _pdbx_entry_details.nonpolymer_details 'THE LIGANDS GAL AND NDG FORM N-ACETYLLACTOSAMINE.' _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? # 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 O A ASN 243 ? ? 1_555 O A HOH 67 ? ? 6_654 2.07 2 1 O A HOH 16 ? ? 1_555 O A HOH 16 ? ? 3_565 2.17 # 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 SER A 206 ? ? 86.32 -6.05 2 1 ASP A 252 ? ? 65.09 -122.27 # 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 TYR 186 ? A TYR 1 2 1 Y 1 A PRO 187 ? A PRO 2 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'NICKEL (II) ION' NI 3 BETA-D-GALACTOSE GAL 4 '2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE' NDG 5 water HOH # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NI 1 401 401 NI NI2 A . C 3 GAL 1 501 501 GAL GAL A . D 4 NDG 2 502 502 NDG NAG A . E 5 HOH 1 1 1 HOH HOH A . E 5 HOH 2 2 2 HOH HOH A . E 5 HOH 3 3 3 HOH HOH A . E 5 HOH 4 4 4 HOH HOH A . E 5 HOH 5 5 5 HOH HOH A . E 5 HOH 6 6 6 HOH HOH A . E 5 HOH 7 7 7 HOH HOH A . E 5 HOH 8 8 8 HOH HOH A . E 5 HOH 9 9 9 HOH HOH A . E 5 HOH 10 10 10 HOH HOH A . E 5 HOH 11 11 11 HOH HOH A . E 5 HOH 12 12 12 HOH HOH A . E 5 HOH 13 13 13 HOH HOH A . E 5 HOH 14 14 14 HOH HOH A . E 5 HOH 15 15 15 HOH HOH A . E 5 HOH 16 16 16 HOH HOH A . E 5 HOH 17 17 17 HOH HOH A . E 5 HOH 18 18 18 HOH HOH A . E 5 HOH 19 19 19 HOH HOH A . E 5 HOH 20 20 20 HOH HOH A . E 5 HOH 21 21 21 HOH HOH A . E 5 HOH 22 22 22 HOH HOH A . E 5 HOH 23 23 23 HOH HOH A . E 5 HOH 24 24 24 HOH HOH A . E 5 HOH 25 25 25 HOH HOH A . E 5 HOH 26 26 26 HOH HOH A . E 5 HOH 27 27 27 HOH HOH A . E 5 HOH 28 28 28 HOH HOH A . E 5 HOH 29 29 29 HOH HOH A . E 5 HOH 30 30 30 HOH HOH A . E 5 HOH 31 31 31 HOH HOH A . E 5 HOH 32 32 32 HOH HOH A . E 5 HOH 33 33 33 HOH HOH A . E 5 HOH 34 34 34 HOH HOH A . E 5 HOH 35 35 35 HOH HOH A . E 5 HOH 36 36 36 HOH HOH A . E 5 HOH 37 37 37 HOH HOH A . E 5 HOH 38 38 38 HOH HOH A . E 5 HOH 39 39 39 HOH HOH A . E 5 HOH 40 40 40 HOH HOH A . E 5 HOH 41 41 41 HOH HOH A . E 5 HOH 42 42 42 HOH HOH A . E 5 HOH 43 43 43 HOH HOH A . E 5 HOH 44 44 44 HOH HOH A . E 5 HOH 45 45 45 HOH HOH A . E 5 HOH 46 46 46 HOH HOH A . E 5 HOH 47 47 47 HOH HOH A . E 5 HOH 48 48 48 HOH HOH A . E 5 HOH 49 49 49 HOH HOH A . E 5 HOH 50 50 50 HOH HOH A . E 5 HOH 51 51 51 HOH HOH A . E 5 HOH 52 52 52 HOH HOH A . E 5 HOH 53 53 53 HOH HOH A . E 5 HOH 54 54 54 HOH HOH A . E 5 HOH 55 55 55 HOH HOH A . E 5 HOH 56 56 56 HOH HOH A . E 5 HOH 57 57 57 HOH HOH A . E 5 HOH 58 58 58 HOH HOH A . E 5 HOH 59 59 59 HOH HOH A . E 5 HOH 60 60 60 HOH HOH A . E 5 HOH 61 61 61 HOH HOH A . E 5 HOH 62 62 62 HOH HOH A . E 5 HOH 63 63 63 HOH HOH A . E 5 HOH 64 64 64 HOH HOH A . E 5 HOH 65 65 65 HOH HOH A . E 5 HOH 66 66 66 HOH HOH A . E 5 HOH 67 67 67 HOH HOH A . E 5 HOH 68 68 68 HOH HOH A . E 5 HOH 69 69 69 HOH HOH A . E 5 HOH 70 70 70 HOH HOH A . E 5 HOH 71 71 71 HOH HOH A . E 5 HOH 72 72 72 HOH HOH A . E 5 HOH 73 73 73 HOH HOH A . E 5 HOH 74 74 74 HOH HOH A . E 5 HOH 75 75 75 HOH HOH A . E 5 HOH 76 76 76 HOH HOH A . E 5 HOH 77 77 77 HOH HOH A . E 5 HOH 78 78 78 HOH HOH A . E 5 HOH 79 79 79 HOH HOH A . E 5 HOH 80 80 80 HOH HOH A . E 5 HOH 81 81 81 HOH HOH A . E 5 HOH 82 82 82 HOH HOH A . E 5 HOH 83 83 83 HOH HOH A . E 5 HOH 84 84 84 HOH HOH A . E 5 HOH 85 85 85 HOH HOH A . E 5 HOH 86 86 86 HOH HOH A . E 5 HOH 87 87 87 HOH HOH A . E 5 HOH 88 88 88 HOH HOH A . E 5 HOH 89 89 89 HOH HOH A . E 5 HOH 90 90 90 HOH HOH A . E 5 HOH 91 91 91 HOH HOH A . E 5 HOH 92 92 92 HOH HOH A . E 5 HOH 93 93 93 HOH HOH A . E 5 HOH 94 94 94 HOH HOH A . E 5 HOH 95 95 95 HOH HOH A . E 5 HOH 96 96 96 HOH HOH A . E 5 HOH 97 97 97 HOH HOH A . E 5 HOH 98 98 98 HOH HOH A . E 5 HOH 99 99 99 HOH HOH A . E 5 HOH 100 100 100 HOH HOH A . E 5 HOH 101 101 101 HOH HOH A . E 5 HOH 102 102 102 HOH HOH A . E 5 HOH 103 103 103 HOH HOH A . E 5 HOH 104 104 104 HOH HOH A . E 5 HOH 105 105 105 HOH HOH A . E 5 HOH 106 106 106 HOH HOH A . E 5 HOH 107 107 107 HOH HOH A . E 5 HOH 108 108 108 HOH HOH A . E 5 HOH 109 109 109 HOH HOH A . E 5 HOH 110 110 110 HOH HOH A . E 5 HOH 111 111 111 HOH HOH A . E 5 HOH 112 112 112 HOH HOH A . E 5 HOH 113 113 113 HOH HOH A . E 5 HOH 114 114 114 HOH HOH A . E 5 HOH 115 115 115 HOH HOH A . E 5 HOH 116 116 116 HOH HOH A . E 5 HOH 117 117 117 HOH HOH A . E 5 HOH 118 118 118 HOH HOH A . E 5 HOH 119 119 119 HOH HOH A . E 5 HOH 120 120 120 HOH HOH A . E 5 HOH 121 121 121 HOH HOH A . E 5 HOH 122 122 122 HOH HOH A . E 5 HOH 123 123 123 HOH HOH A . E 5 HOH 124 124 124 HOH HOH A . E 5 HOH 125 125 125 HOH HOH A . E 5 HOH 126 126 126 HOH HOH A . E 5 HOH 127 127 127 HOH HOH A . E 5 HOH 128 128 128 HOH HOH A . E 5 HOH 129 129 129 HOH HOH A . E 5 HOH 130 130 130 HOH HOH A . E 5 HOH 131 131 131 HOH HOH A . E 5 HOH 132 132 132 HOH HOH A . E 5 HOH 133 133 133 HOH HOH A . E 5 HOH 134 134 134 HOH HOH A . E 5 HOH 135 135 135 HOH HOH A . E 5 HOH 136 136 136 HOH HOH A . E 5 HOH 137 137 137 HOH HOH A . E 5 HOH 138 138 138 HOH HOH A . E 5 HOH 139 139 139 HOH HOH A . E 5 HOH 140 140 140 HOH HOH A . #