data_4NYR # _entry.id 4NYR # _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 4NYR RCSB RCSB083824 WWPDB D_1000083824 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4NYQ . unspecified PDB 4NYS . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4NYR _pdbx_database_status.recvd_initial_deposition_date 2013-12-11 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Coussens, N.P.' 1 'Gallat, F.-X.' 2 'Ramaswamy, S.' 3 'Yagi, K.' 4 'Tobe, S.S.' 5 'Stay, B.' 6 'Chavas, L.M.G.' 7 # _citation.id primary _citation.title ;Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata. ; _citation.journal_abbrev Iucrj _citation.journal_volume 3 _citation.page_first 282 _citation.page_last 293 _citation.year 2016 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 2052-2525 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 27437115 _citation.pdbx_database_id_DOI 10.1107/S2052252516008903 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Banerjee, S.' 1 ? primary 'Coussens, N.P.' 2 ? primary 'Gallat, F.X.' 3 ? primary 'Sathyanarayanan, N.' 4 ? primary 'Srikanth, J.' 5 ? primary 'Yagi, K.J.' 6 ? primary 'Gray, J.S.' 7 ? primary 'Tobe, S.S.' 8 ? primary 'Stay, B.' 9 ? primary 'Chavas, L.M.' 10 ? primary 'Ramaswamy, S.' 11 ? # _cell.entry_id 4NYR _cell.length_a 32.280 _cell.length_b 33.220 _cell.length_c 40.180 _cell.angle_alpha 99.50 _cell.angle_beta 100.28 _cell.angle_gamma 104.11 _cell.Z_PDB 1 _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 4NYR _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _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 nat 'Milk protein' 18749.201 1 ? ? ? ? 2 branched man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose' 424.401 2 ? ? ? ? 3 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 1 ? ? ? ? 4 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 5 water nat water 18.015 88 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name Lili-Mip # _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 ;IAAILVANAKEPCPPENLQLTPRALVGKWYLRTTSPDIFKQVSNITEFYSAHGNDYYGTVTDYSPEYGLEAHRVNLTVSG RTLKFYMNDTHEYDSKYEILAVDKDYFIFYGHPPAAPSGLALIHYRQSCPKEDVIKRVKKALKNVCLDYKYFGNDTSVPC HYVE ; _entity_poly.pdbx_seq_one_letter_code_can ;IAAILVANAKEPCPPENLQLTPRALVGKWYLRTTSPDIFKQVSNITEFYSAHGNDYYGTVTDYSPEYGLEAHRVNLTVSG RTLKFYMNDTHEYDSKYEILAVDKDYFIFYGHPPAAPSGLALIHYRQSCPKEDVIKRVKKALKNVCLDYKYFGNDTSVPC HYVE ; _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 ILE n 1 2 ALA n 1 3 ALA n 1 4 ILE n 1 5 LEU n 1 6 VAL n 1 7 ALA n 1 8 ASN n 1 9 ALA n 1 10 LYS n 1 11 GLU n 1 12 PRO n 1 13 CYS n 1 14 PRO n 1 15 PRO n 1 16 GLU n 1 17 ASN n 1 18 LEU n 1 19 GLN n 1 20 LEU n 1 21 THR n 1 22 PRO n 1 23 ARG n 1 24 ALA n 1 25 LEU n 1 26 VAL n 1 27 GLY n 1 28 LYS n 1 29 TRP n 1 30 TYR n 1 31 LEU n 1 32 ARG n 1 33 THR n 1 34 THR n 1 35 SER n 1 36 PRO n 1 37 ASP n 1 38 ILE n 1 39 PHE n 1 40 LYS n 1 41 GLN n 1 42 VAL n 1 43 SER n 1 44 ASN n 1 45 ILE n 1 46 THR n 1 47 GLU n 1 48 PHE n 1 49 TYR n 1 50 SER n 1 51 ALA n 1 52 HIS n 1 53 GLY n 1 54 ASN n 1 55 ASP n 1 56 TYR n 1 57 TYR n 1 58 GLY n 1 59 THR n 1 60 VAL n 1 61 THR n 1 62 ASP n 1 63 TYR n 1 64 SER n 1 65 PRO n 1 66 GLU n 1 67 TYR n 1 68 GLY n 1 69 LEU n 1 70 GLU n 1 71 ALA n 1 72 HIS n 1 73 ARG n 1 74 VAL n 1 75 ASN n 1 76 LEU n 1 77 THR n 1 78 VAL n 1 79 SER n 1 80 GLY n 1 81 ARG n 1 82 THR n 1 83 LEU n 1 84 LYS n 1 85 PHE n 1 86 TYR n 1 87 MET n 1 88 ASN n 1 89 ASP n 1 90 THR n 1 91 HIS n 1 92 GLU n 1 93 TYR n 1 94 ASP n 1 95 SER n 1 96 LYS n 1 97 TYR n 1 98 GLU n 1 99 ILE n 1 100 LEU n 1 101 ALA n 1 102 VAL n 1 103 ASP n 1 104 LYS n 1 105 ASP n 1 106 TYR n 1 107 PHE n 1 108 ILE n 1 109 PHE n 1 110 TYR n 1 111 GLY n 1 112 HIS n 1 113 PRO n 1 114 PRO n 1 115 ALA n 1 116 ALA n 1 117 PRO n 1 118 SER n 1 119 GLY n 1 120 LEU n 1 121 ALA n 1 122 LEU n 1 123 ILE n 1 124 HIS n 1 125 TYR n 1 126 ARG n 1 127 GLN n 1 128 SER n 1 129 CYS n 1 130 PRO n 1 131 LYS n 1 132 GLU n 1 133 ASP n 1 134 VAL n 1 135 ILE n 1 136 LYS n 1 137 ARG n 1 138 VAL n 1 139 LYS n 1 140 LYS n 1 141 ALA n 1 142 LEU n 1 143 LYS n 1 144 ASN n 1 145 VAL n 1 146 CYS n 1 147 LEU n 1 148 ASP n 1 149 TYR n 1 150 LYS n 1 151 TYR n 1 152 PHE n 1 153 GLY n 1 154 ASN n 1 155 ASP n 1 156 THR n 1 157 SER n 1 158 VAL n 1 159 PRO n 1 160 CYS n 1 161 HIS n 1 162 TYR n 1 163 VAL n 1 164 GLU n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num ? _entity_src_nat.pdbx_end_seq_num ? _entity_src_nat.common_name 'Pacific beetle cockroach' _entity_src_nat.pdbx_organism_scientific 'Diploptera punctata' _entity_src_nat.pdbx_ncbi_taxonomy_id 6984 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q6SVB6_DIPPU _struct_ref.pdbx_db_accession Q6SVB6 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;IAAILVANAKEPCPPENLQLTPRALVGKWYLRTTSPDIFKQVSNITEFYSAHGNDYYGTVTDYSPEYGLEAHRVNLTVSG RTLKFYMNDTHEYDSKYEILAVDKDYFIFYGHPPAAPSGLALIHYRQSCPKEDVIKRVKKALKNVCLDYKYFGNDTSVPC HYVE ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4NYR _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 164 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q6SVB6 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 164 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg -8 _struct_ref_seq.pdbx_auth_seq_align_end 155 # 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ? 'C8 H15 N O6' 221.208 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 4NYR _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.14 _exptl_crystal.density_percent_sol 42.52 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'In-vivo crystallization' _exptl_crystal_grow.temp 300 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details 'Spontaneous crystallization inside the midguts of a living viviparous cockroach, pH 6.0, In-vivo crystallization, temperature 300K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 70 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 2M-F' _diffrn_detector.pdbx_collection_date 2013-05-13 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 2.7 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-1A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-1A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 2.7 # _reflns.entry_id 4NYR _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.49 _reflns.number_obs 5421 _reflns.number_all 5421 _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 38.07 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 20 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.49 _reflns_shell.d_res_low 2.56 _reflns_shell.percent_possible_all 96.7 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 22.43 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 820 _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_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4NYR _refine.ls_number_reflns_obs 4876 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 38.58 _refine.ls_d_res_high 2.49 _refine.ls_percent_reflns_obs 99.83 _refine.ls_R_factor_obs 0.16159 _refine.ls_R_factor_all 0.16159 _refine.ls_R_factor_R_work 0.15368 _refine.ls_R_factor_R_free 0.23262 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.1 _refine.ls_number_reflns_R_free 546 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.952 _refine.correlation_coeff_Fo_to_Fc_free 0.886 _refine.B_iso_mean 17.473 _refine.aniso_B[1][1] -0.25 _refine.aniso_B[2][2] -0.22 _refine.aniso_B[3][3] 0.29 _refine.aniso_B[1][2] 0.17 _refine.aniso_B[1][3] -0.05 _refine.aniso_B[2][3] 0.38 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 0.323 _refine.overall_SU_ML 0.204 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 9.127 _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1248 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 76 _refine_hist.number_atoms_solvent 88 _refine_hist.number_atoms_total 1412 _refine_hist.d_res_high 2.49 _refine_hist.d_res_low 38.58 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.013 0.019 ? 1369 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.906 2.021 ? 1867 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 7.515 5.000 ? 152 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 36.737 23.548 ? 62 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 18.433 15.000 ? 205 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 21.681 15.000 ? 6 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.122 0.200 ? 206 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.008 0.021 ? 1042 ? 'X-RAY DIFFRACTION' r_mcbond_it 1.181 1.532 ? 611 ? 'X-RAY DIFFRACTION' r_mcangle_it 2.031 2.290 ? 762 ? 'X-RAY DIFFRACTION' r_scbond_it 1.836 1.842 ? 758 ? 'X-RAY DIFFRACTION' r_long_range_B_refined 5.678 13.791 ? 2089 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.491 _refine_ls_shell.d_res_low 2.556 _refine_ls_shell.number_reflns_R_work 357 _refine_ls_shell.R_factor_R_work 0.184 _refine_ls_shell.percent_reflns_obs 97.79 _refine_ls_shell.R_factor_R_free 0.345 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 41 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 793 _refine_ls_shell.redundancy_reflns_obs ? # _struct.entry_id 4NYR _struct.title ;In-vivo crystallisation (midguts of a viviparous cockroach) and structure at 2.5 A resolution of a glycosylated, lipid-binding, lipocalin-like protein ; _struct.pdbx_descriptor 'Milk protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4NYR _struct_keywords.pdbx_keywords 'LIPID BINDING PROTEIN' _struct_keywords.text 'In-vivo crystallization, cockroach, SAD phasing, lipocalin, Lipocalin fold, Fatty acid binding protein, LIPID 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 2 ? D N N 3 ? E N N 4 ? F N N 5 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 LYS A 131 ? ASN A 144 ? LYS A 122 ASN A 135 1 ? 14 HELX_P HELX_P2 2 ASP A 148 ? PHE A 152 ? ASP A 139 PHE A 143 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 13 SG ? ? ? 1_555 A CYS 146 SG ? ? A CYS 4 A CYS 137 1_555 ? ? ? ? ? ? ? 2.064 ? ? disulf2 disulf ? ? A CYS 129 SG ? ? ? 1_555 A CYS 160 SG ? ? A CYS 120 A CYS 151 1_555 ? ? ? ? ? ? ? 2.038 ? ? covale1 covale one ? A ASN 44 ND2 ? ? ? 1_555 B NAG . C1 ? ? A ASN 35 B NAG 1 1_555 ? ? ? ? ? ? ? 1.441 ? N-Glycosylation covale2 covale one ? A ASN 88 ND2 ? ? ? 1_555 C NAG . C1 ? ? A ASN 79 C NAG 1 1_555 ? ? ? ? ? ? ? 1.462 ? N-Glycosylation covale3 covale one ? A ASN 154 ND2 ? ? ? 1_555 D NAG . C1 ? ? A ASN 145 A NAG 205 1_555 ? ? ? ? ? ? ? 1.439 ? N-Glycosylation covale4 covale both ? B NAG . O4 ? ? ? 1_555 B NAG . C1 ? ? B NAG 1 B NAG 2 1_555 ? ? ? ? ? ? ? 1.417 ? ? covale5 covale both ? C NAG . O4 ? ? ? 1_555 C NAG . C1 ? ? C NAG 1 C NAG 2 1_555 ? ? ? ? ? ? ? 1.439 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id SER _struct_mon_prot_cis.label_seq_id 35 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id SER _struct_mon_prot_cis.auth_seq_id 26 _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 36 _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 27 _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 -1.26 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 10 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel A 6 7 ? anti-parallel A 7 8 ? anti-parallel A 8 9 ? anti-parallel A 9 10 ? 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 GLY A 153 ? ASN A 154 ? GLY A 144 ASN A 145 A 2 GLY A 27 ? SER A 35 ? GLY A 18 SER A 26 A 3 LEU A 120 ? TYR A 125 ? LEU A 111 TYR A 116 A 4 TYR A 106 ? GLY A 111 ? TYR A 97 GLY A 102 A 5 SER A 95 ? VAL A 102 ? SER A 86 VAL A 93 A 6 THR A 82 ? MET A 87 ? THR A 73 MET A 78 A 7 GLY A 68 ? SER A 79 ? GLY A 59 SER A 70 A 8 ASP A 55 ? SER A 64 ? ASP A 46 SER A 55 A 9 SER A 43 ? HIS A 52 ? SER A 34 HIS A 43 A 10 GLY A 27 ? SER A 35 ? GLY A 18 SER A 26 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O GLY A 153 ? O GLY A 144 N THR A 34 ? N THR A 25 A 2 3 N THR A 33 ? N THR A 24 O ILE A 123 ? O ILE A 114 A 3 4 O HIS A 124 ? O HIS A 115 N PHE A 107 ? N PHE A 98 A 4 5 O ILE A 108 ? O ILE A 99 N LEU A 100 ? N LEU A 91 A 5 6 O SER A 95 ? O SER A 86 N PHE A 85 ? N PHE A 76 A 6 7 O THR A 82 ? O THR A 73 N SER A 79 ? N SER A 70 A 7 8 O LEU A 76 ? O LEU A 67 N TYR A 56 ? N TYR A 47 A 8 9 O TYR A 57 ? O TYR A 48 N SER A 50 ? N SER A 41 A 9 10 O GLU A 47 ? O GLU A 38 N TRP A 29 ? N TRP A 20 # _database_PDB_matrix.entry_id 4NYR _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 4NYR _atom_sites.fract_transf_matrix[1][1] 0.030979 _atom_sites.fract_transf_matrix[1][2] 0.007786 _atom_sites.fract_transf_matrix[1][3] 0.007503 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.031039 _atom_sites.fract_transf_matrix[2][3] 0.006949 _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] 0.025920 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # 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 ILE 1 -8 ? ? ? A . n A 1 2 ALA 2 -7 ? ? ? A . n A 1 3 ALA 3 -6 ? ? ? A . n A 1 4 ILE 4 -5 ? ? ? A . n A 1 5 LEU 5 -4 ? ? ? A . n A 1 6 VAL 6 -3 ? ? ? A . n A 1 7 ALA 7 -2 ? ? ? A . n A 1 8 ASN 8 -1 ? ? ? A . n A 1 9 ALA 9 0 ? ? ? A . n A 1 10 LYS 10 1 1 LYS LYS A . n A 1 11 GLU 11 2 2 GLU GLU A . n A 1 12 PRO 12 3 3 PRO PRO A . n A 1 13 CYS 13 4 4 CYS CYS A . n A 1 14 PRO 14 5 5 PRO PRO A . n A 1 15 PRO 15 6 6 PRO PRO A . n A 1 16 GLU 16 7 7 GLU GLU A . n A 1 17 ASN 17 8 8 ASN ASN A . n A 1 18 LEU 18 9 9 LEU LEU A . n A 1 19 GLN 19 10 10 GLN GLN A . n A 1 20 LEU 20 11 11 LEU LEU A . n A 1 21 THR 21 12 12 THR THR A . n A 1 22 PRO 22 13 13 PRO PRO A . n A 1 23 ARG 23 14 14 ARG ARG A . n A 1 24 ALA 24 15 15 ALA ALA A . n A 1 25 LEU 25 16 16 LEU LEU A . n A 1 26 VAL 26 17 17 VAL VAL A . n A 1 27 GLY 27 18 18 GLY GLY A . n A 1 28 LYS 28 19 19 LYS LYS A . n A 1 29 TRP 29 20 20 TRP TRP A . n A 1 30 TYR 30 21 21 TYR TYR A . n A 1 31 LEU 31 22 22 LEU LEU A . n A 1 32 ARG 32 23 23 ARG ARG A . n A 1 33 THR 33 24 24 THR THR A . n A 1 34 THR 34 25 25 THR THR A . n A 1 35 SER 35 26 26 SER SER A . n A 1 36 PRO 36 27 27 PRO PRO A . n A 1 37 ASP 37 28 28 ASP ASP A . n A 1 38 ILE 38 29 29 ILE ILE A . n A 1 39 PHE 39 30 30 PHE PHE A . n A 1 40 LYS 40 31 31 LYS LYS A . n A 1 41 GLN 41 32 32 GLN GLN A . n A 1 42 VAL 42 33 33 VAL VAL A . n A 1 43 SER 43 34 34 SER SER A . n A 1 44 ASN 44 35 35 ASN ASN A . n A 1 45 ILE 45 36 36 ILE ILE A . n A 1 46 THR 46 37 37 THR THR A . n A 1 47 GLU 47 38 38 GLU GLU A . n A 1 48 PHE 48 39 39 PHE PHE A . n A 1 49 TYR 49 40 40 TYR TYR A . n A 1 50 SER 50 41 41 SER SER A . n A 1 51 ALA 51 42 42 ALA ALA A . n A 1 52 HIS 52 43 43 HIS HIS A . n A 1 53 GLY 53 44 44 GLY GLY A . n A 1 54 ASN 54 45 45 ASN ASN A . n A 1 55 ASP 55 46 46 ASP ASP A . n A 1 56 TYR 56 47 47 TYR TYR A . n A 1 57 TYR 57 48 48 TYR TYR A . n A 1 58 GLY 58 49 49 GLY GLY A . n A 1 59 THR 59 50 50 THR THR A . n A 1 60 VAL 60 51 51 VAL VAL A . n A 1 61 THR 61 52 52 THR THR A . n A 1 62 ASP 62 53 53 ASP ASP A . n A 1 63 TYR 63 54 54 TYR TYR A . n A 1 64 SER 64 55 55 SER SER A . n A 1 65 PRO 65 56 56 PRO PRO A . n A 1 66 GLU 66 57 57 GLU GLU A . n A 1 67 TYR 67 58 58 TYR TYR A . n A 1 68 GLY 68 59 59 GLY GLY A . n A 1 69 LEU 69 60 60 LEU LEU A . n A 1 70 GLU 70 61 61 GLU GLU A . n A 1 71 ALA 71 62 62 ALA ALA A . n A 1 72 HIS 72 63 63 HIS HIS A . n A 1 73 ARG 73 64 64 ARG ARG A . n A 1 74 VAL 74 65 65 VAL VAL A . n A 1 75 ASN 75 66 66 ASN ASN A . n A 1 76 LEU 76 67 67 LEU LEU A . n A 1 77 THR 77 68 68 THR THR A . n A 1 78 VAL 78 69 69 VAL VAL A . n A 1 79 SER 79 70 70 SER SER A . n A 1 80 GLY 80 71 71 GLY GLY A . n A 1 81 ARG 81 72 72 ARG ARG A . n A 1 82 THR 82 73 73 THR THR A . n A 1 83 LEU 83 74 74 LEU LEU A . n A 1 84 LYS 84 75 75 LYS LYS A . n A 1 85 PHE 85 76 76 PHE PHE A . n A 1 86 TYR 86 77 77 TYR TYR A . n A 1 87 MET 87 78 78 MET MET A . n A 1 88 ASN 88 79 79 ASN ASN A . n A 1 89 ASP 89 80 80 ASP ASP A . n A 1 90 THR 90 81 81 THR THR A . n A 1 91 HIS 91 82 82 HIS HIS A . n A 1 92 GLU 92 83 83 GLU GLU A . n A 1 93 TYR 93 84 84 TYR TYR A . n A 1 94 ASP 94 85 85 ASP ASP A . n A 1 95 SER 95 86 86 SER SER A . n A 1 96 LYS 96 87 87 LYS LYS A . n A 1 97 TYR 97 88 88 TYR TYR A . n A 1 98 GLU 98 89 89 GLU GLU A . n A 1 99 ILE 99 90 90 ILE ILE A . n A 1 100 LEU 100 91 91 LEU LEU A . n A 1 101 ALA 101 92 92 ALA ALA A . n A 1 102 VAL 102 93 93 VAL VAL A . n A 1 103 ASP 103 94 94 ASP ASP A . n A 1 104 LYS 104 95 95 LYS LYS A . n A 1 105 ASP 105 96 96 ASP ASP A . n A 1 106 TYR 106 97 97 TYR TYR A . n A 1 107 PHE 107 98 98 PHE PHE A . n A 1 108 ILE 108 99 99 ILE ILE A . n A 1 109 PHE 109 100 100 PHE PHE A . n A 1 110 TYR 110 101 101 TYR TYR A . n A 1 111 GLY 111 102 102 GLY GLY A . n A 1 112 HIS 112 103 103 HIS HIS A . n A 1 113 PRO 113 104 104 PRO PRO A . n A 1 114 PRO 114 105 105 PRO PRO A . n A 1 115 ALA 115 106 106 ALA ALA A . n A 1 116 ALA 116 107 107 ALA ALA A . n A 1 117 PRO 117 108 108 PRO PRO A . n A 1 118 SER 118 109 109 SER SER A . n A 1 119 GLY 119 110 110 GLY GLY A . n A 1 120 LEU 120 111 111 LEU LEU A . n A 1 121 ALA 121 112 112 ALA ALA A . n A 1 122 LEU 122 113 113 LEU LEU A . n A 1 123 ILE 123 114 114 ILE ILE A . n A 1 124 HIS 124 115 115 HIS HIS A . n A 1 125 TYR 125 116 116 TYR TYR A . n A 1 126 ARG 126 117 117 ARG ARG A . n A 1 127 GLN 127 118 118 GLN GLN A . n A 1 128 SER 128 119 119 SER SER A . n A 1 129 CYS 129 120 120 CYS CYS A . n A 1 130 PRO 130 121 121 PRO PRO A . n A 1 131 LYS 131 122 122 LYS LYS A . n A 1 132 GLU 132 123 123 GLU GLU A . n A 1 133 ASP 133 124 124 ASP ASP A . n A 1 134 VAL 134 125 125 VAL VAL A . n A 1 135 ILE 135 126 126 ILE ILE A . n A 1 136 LYS 136 127 127 LYS LYS A . n A 1 137 ARG 137 128 128 ARG ARG A . n A 1 138 VAL 138 129 129 VAL VAL A . n A 1 139 LYS 139 130 130 LYS LYS A . n A 1 140 LYS 140 131 131 LYS LYS A . n A 1 141 ALA 141 132 132 ALA ALA A . n A 1 142 LEU 142 133 133 LEU LEU A . n A 1 143 LYS 143 134 134 LYS LYS A . n A 1 144 ASN 144 135 135 ASN ASN A . n A 1 145 VAL 145 136 136 VAL VAL A . n A 1 146 CYS 146 137 137 CYS CYS A . n A 1 147 LEU 147 138 138 LEU LEU A . n A 1 148 ASP 148 139 139 ASP ASP A . n A 1 149 TYR 149 140 140 TYR TYR A . n A 1 150 LYS 150 141 141 LYS LYS A . n A 1 151 TYR 151 142 142 TYR TYR A . n A 1 152 PHE 152 143 143 PHE PHE A . n A 1 153 GLY 153 144 144 GLY GLY A . n A 1 154 ASN 154 145 145 ASN ASN A . n A 1 155 ASP 155 146 146 ASP ASP A . n A 1 156 THR 156 147 147 THR THR A . n A 1 157 SER 157 148 148 SER SER A . n A 1 158 VAL 158 149 149 VAL VAL A . n A 1 159 PRO 159 150 150 PRO PRO A . n A 1 160 CYS 160 151 151 CYS CYS A . n A 1 161 HIS 161 152 152 HIS HIS A . n A 1 162 TYR 162 153 153 TYR TYR A . n A 1 163 VAL 163 154 ? ? ? A . n A 1 164 GLU 164 155 ? ? ? 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 D 3 NAG 1 205 159 NAG NAG A . E 4 GOL 1 206 1 GOL GOL A . F 5 HOH 1 301 1 HOH HOH A . F 5 HOH 2 302 2 HOH HOH A . F 5 HOH 3 303 3 HOH HOH A . F 5 HOH 4 304 4 HOH HOH A . F 5 HOH 5 305 5 HOH HOH A . F 5 HOH 6 306 6 HOH HOH A . F 5 HOH 7 307 7 HOH HOH A . F 5 HOH 8 308 8 HOH HOH A . F 5 HOH 9 309 9 HOH HOH A . F 5 HOH 10 310 10 HOH HOH A . F 5 HOH 11 311 11 HOH HOH A . F 5 HOH 12 312 12 HOH HOH A . F 5 HOH 13 313 13 HOH HOH A . F 5 HOH 14 314 14 HOH HOH A . F 5 HOH 15 315 15 HOH HOH A . F 5 HOH 16 316 16 HOH HOH A . F 5 HOH 17 317 17 HOH HOH A . F 5 HOH 18 318 18 HOH HOH A . F 5 HOH 19 319 19 HOH HOH A . F 5 HOH 20 320 20 HOH HOH A . F 5 HOH 21 321 21 HOH HOH A . F 5 HOH 22 322 22 HOH HOH A . F 5 HOH 23 323 23 HOH HOH A . F 5 HOH 24 324 24 HOH HOH A . F 5 HOH 25 325 25 HOH HOH A . F 5 HOH 26 326 26 HOH HOH A . F 5 HOH 27 327 27 HOH HOH A . F 5 HOH 28 328 28 HOH HOH A . F 5 HOH 29 329 29 HOH HOH A . F 5 HOH 30 330 30 HOH HOH A . F 5 HOH 31 331 31 HOH HOH A . F 5 HOH 32 332 32 HOH HOH A . F 5 HOH 33 333 33 HOH HOH A . F 5 HOH 34 334 34 HOH HOH A . F 5 HOH 35 335 35 HOH HOH A . F 5 HOH 36 336 36 HOH HOH A . F 5 HOH 37 337 37 HOH HOH A . F 5 HOH 38 338 38 HOH HOH A . F 5 HOH 39 339 39 HOH HOH A . F 5 HOH 40 340 40 HOH HOH A . F 5 HOH 41 341 41 HOH HOH A . F 5 HOH 42 342 42 HOH HOH A . F 5 HOH 43 343 43 HOH HOH A . F 5 HOH 44 344 44 HOH HOH A . F 5 HOH 45 345 45 HOH HOH A . F 5 HOH 46 346 46 HOH HOH A . F 5 HOH 47 347 47 HOH HOH A . F 5 HOH 48 348 48 HOH HOH A . F 5 HOH 49 349 49 HOH HOH A . F 5 HOH 50 350 50 HOH HOH A . F 5 HOH 51 351 51 HOH HOH A . F 5 HOH 52 352 53 HOH HOH A . F 5 HOH 53 353 54 HOH HOH A . F 5 HOH 54 354 55 HOH HOH A . F 5 HOH 55 355 56 HOH HOH A . F 5 HOH 56 356 57 HOH HOH A . F 5 HOH 57 357 58 HOH HOH A . F 5 HOH 58 358 59 HOH HOH A . F 5 HOH 59 359 60 HOH HOH A . F 5 HOH 60 360 61 HOH HOH A . F 5 HOH 61 361 62 HOH HOH A . F 5 HOH 62 362 63 HOH HOH A . F 5 HOH 63 363 64 HOH HOH A . F 5 HOH 64 364 65 HOH HOH A . F 5 HOH 65 365 66 HOH HOH A . F 5 HOH 66 366 67 HOH HOH A . F 5 HOH 67 367 68 HOH HOH A . F 5 HOH 68 368 69 HOH HOH A . F 5 HOH 69 369 70 HOH HOH A . F 5 HOH 70 370 71 HOH HOH A . F 5 HOH 71 371 72 HOH HOH A . F 5 HOH 72 372 73 HOH HOH A . F 5 HOH 73 373 74 HOH HOH A . F 5 HOH 74 374 75 HOH HOH A . F 5 HOH 75 375 76 HOH HOH A . F 5 HOH 76 376 77 HOH HOH A . F 5 HOH 77 377 78 HOH HOH A . F 5 HOH 78 378 79 HOH HOH A . F 5 HOH 79 379 81 HOH HOH A . F 5 HOH 80 380 83 HOH HOH A . F 5 HOH 81 381 85 HOH HOH A . F 5 HOH 82 382 87 HOH HOH A . F 5 HOH 83 383 88 HOH HOH A . F 5 HOH 84 384 89 HOH HOH A . F 5 HOH 85 385 90 HOH HOH A . F 5 HOH 86 386 91 HOH HOH A . F 5 HOH 87 387 92 HOH HOH A . F 5 HOH 88 388 93 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A ASN 154 A ASN 145 ? ASN 'GLYCOSYLATION SITE' 2 A ASN 44 A ASN 35 ? ASN 'GLYCOSYLATION SITE' 3 A ASN 88 A ASN 79 ? ASN 'GLYCOSYLATION SITE' # _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,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2014-01-01 2 'Structure model' 1 1 2016-07-20 3 'Structure model' 1 2 2017-11-22 4 'Structure model' 1 3 2020-01-01 5 'Structure model' 2 0 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' 'Database references' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 5 'Structure model' 'Atomic model' 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' software 2 4 'Structure model' citation 3 4 'Structure model' citation_author 4 4 'Structure model' struct_conn 5 5 'Structure model' atom_site 6 5 'Structure model' chem_comp 7 5 'Structure model' entity 8 5 'Structure model' pdbx_branch_scheme 9 5 'Structure model' pdbx_chem_comp_identifier 10 5 'Structure model' pdbx_entity_branch 11 5 'Structure model' pdbx_entity_branch_descriptor 12 5 'Structure model' pdbx_entity_branch_link 13 5 'Structure model' pdbx_entity_branch_list 14 5 'Structure model' pdbx_entity_nonpoly 15 5 'Structure model' pdbx_nonpoly_scheme 16 5 'Structure model' pdbx_struct_assembly_gen 17 5 'Structure model' struct_asym 18 5 'Structure model' struct_conn 19 5 'Structure model' struct_site 20 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 4 'Structure model' '_citation.journal_abbrev' 2 4 'Structure model' '_citation.pdbx_database_id_PubMed' 3 4 'Structure model' '_citation.title' 4 4 'Structure model' '_citation_author.name' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 5 'Structure model' '_atom_site.auth_asym_id' 7 5 'Structure model' '_atom_site.auth_seq_id' 8 5 'Structure model' '_atom_site.label_asym_id' 9 5 'Structure model' '_atom_site.label_entity_id' 10 5 'Structure model' '_chem_comp.name' 11 5 'Structure model' '_chem_comp.type' 12 5 'Structure model' '_pdbx_entity_nonpoly.entity_id' 13 5 'Structure model' '_pdbx_entity_nonpoly.name' 14 5 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 15 5 'Structure model' '_struct_conn.pdbx_dist_value' 16 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 17 5 'Structure model' '_struct_conn.pdbx_role' 18 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 19 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 26 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 27 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SOLVE phasing . ? 1 REFMAC refinement 5.7.0032 ? 2 XDS 'data reduction' . ? 3 XSCALE 'data scaling' . ? 4 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 CB _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 PHE _pdbx_validate_rmsd_angle.auth_seq_id_1 100 _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 PHE _pdbx_validate_rmsd_angle.auth_seq_id_2 100 _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 PHE _pdbx_validate_rmsd_angle.auth_seq_id_3 100 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 92.95 _pdbx_validate_rmsd_angle.angle_target_value 110.40 _pdbx_validate_rmsd_angle.angle_deviation -17.45 _pdbx_validate_rmsd_angle.angle_standard_deviation 2.00 _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 ALA A 92 ? ? -174.13 139.29 2 1 ALA A 107 ? ? -154.40 71.54 # 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 ILE -8 ? A ILE 1 2 1 Y 1 A ALA -7 ? A ALA 2 3 1 Y 1 A ALA -6 ? A ALA 3 4 1 Y 1 A ILE -5 ? A ILE 4 5 1 Y 1 A LEU -4 ? A LEU 5 6 1 Y 1 A VAL -3 ? A VAL 6 7 1 Y 1 A ALA -2 ? A ALA 7 8 1 Y 1 A ASN -1 ? A ASN 8 9 1 Y 1 A ALA 0 ? A ALA 9 10 1 Y 1 A VAL 154 ? A VAL 163 11 1 Y 1 A GLU 155 ? A GLU 164 # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero B 2 NAG 1 B NAG 1 A NAG 154 n B 2 NAG 2 B NAG 2 A NAG 155 n C 2 NAG 1 C NAG 1 A NAG 157 n C 2 NAG 2 C NAG 2 A NAG 158 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 2 DGlcpNAcb1-4DGlcpNAcb1- 'Glycam Condensed Sequence' GMML 1.0 2 2 'WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1' WURCS PDB2Glycan 1.1.0 3 2 '[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}' LINUCS PDB-CARE ? # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.details ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 2 NAG 1 n 2 NAG 2 n # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 4 GLYCEROL GOL 5 water HOH #