data_7C4U # _entry.id 7C4U # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.339 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 7C4U WWPDB D_1300017030 EMDB EMD-30288 # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'MicroED structure of orthorhombic Vancomycin at 1.2 A resolution' _pdbx_database_related.db_id EMD-30288 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7C4U _pdbx_database_status.recvd_initial_deposition_date 2020-05-18 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Fan, Q.' 1 0000-0001-9133-8039 'Zhou, H.' 2 0000-0002-6267-1585 'Li, X.' 3 0000-0002-8451-9947 'Wang, J.' 4 0000-0002-1704-9922 # _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 GE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_id_ASTM ACIEAY _citation.journal_id_CSD 0179 _citation.journal_id_ISSN 1521-3773 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 59 _citation.language ? _citation.page_first 15141 _citation.page_last 15146 _citation.title 'Precise Control Over Kinetics of Molecular Assembly: Production of Particles with Tunable Sizes and Crystalline Forms.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/anie.202003922 _citation.pdbx_database_id_PubMed 32432368 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Fan, Q.' 1 ? primary 'Li, L.' 2 ? primary 'Xue, H.' 3 ? primary 'Zhou, H.' 4 ? primary 'Zhao, L.' 5 ? primary 'Liu, J.' 6 ? primary 'Mao, J.' 7 ? primary 'Wu, S.' 8 ? primary 'Zhang, S.' 9 ? primary 'Wu, C.' 10 ? primary 'Li, X.' 11 ? primary 'Zhou, X.' 12 ? primary 'Wang, J.' 13 ? # _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 7C4U _cell.details ? _cell.formula_units_Z ? _cell.length_a 20.060 _cell.length_a_esd ? _cell.length_b 33.020 _cell.length_b_esd ? _cell.length_c 41.720 _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 7C4U _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' _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 nat Vancomycin 1149.977 2 ? ? ? ? 2 branched man 'vancosamine-(1-2)-beta-D-glucopyranose' 323.340 2 ? ? ? ? 3 non-polymer man 'CHLORIDE ION' 35.453 1 ? ? ? ? 4 water nat water 18.015 50 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(MLU)(OMZ)N(GHP)(GHP)(OMY)(3FG)' _entity_poly.pdbx_seq_one_letter_code_can XXNGGYX _entity_poly.pdbx_strand_id A,B _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 MLU n 1 2 OMZ n 1 3 ASN n 1 4 GHP n 1 5 GHP n 1 6 OMY n 1 7 3FG 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 1 _entity_src_nat.pdbx_end_seq_num 7 _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Amycolatopsis orientalis' _entity_src_nat.pdbx_ncbi_taxonomy_id 31958 _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 PDB _struct_ref.db_code 7C4U _struct_ref.pdbx_db_accession 7C4U _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 7C4U A 1 ? 7 ? 7C4U 1 ? 7 ? 1 7 2 1 7C4U B 1 ? 7 ? 7C4U 1 ? 7 ? 1 7 # 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 3FG 'L-peptide linking' . '(2S)-amino(3,5-dihydroxyphenyl)ethanoic acid' ? 'C8 H9 N O4' 183.161 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 BGC 'D-saccharide, beta linking' . beta-D-glucopyranose 'beta-D-glucose; D-glucose; glucose' 'C6 H12 O6' 180.156 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 GHP 'D-peptide linking' . '(2R)-amino(4-hydroxyphenyl)ethanoic acid' ? 'C8 H9 N O3' 167.162 HOH non-polymer . WATER ? 'H2 O' 18.015 MLU 'D-peptide linking' . N-methyl-D-leucine ? 'C7 H15 N O2' 145.199 OMY 'L-peptide linking' n '(betaR)-3-chloro-beta-hydroxy-L-tyrosine' ? 'C9 H10 Cl N O4' 231.633 OMZ 'D-peptide linking' . '(betaR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE' ? 'C9 H10 Cl N O4' 231.633 RER 'L-saccharide, alpha linking' . vancosamine '(1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose' 'C7 H15 N O3' 161.199 # _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 7C4U _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON CRYSTALLOGRAPHY' _exptl.method_details ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.preparation ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 _diffrn.pdbx_serial_crystal_experiment ? # _diffrn_detector.details ? _diffrn_detector.detector ? _diffrn_detector.diffrn_id 1 _diffrn_detector.type ? _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-06-01 _diffrn_detector.pdbx_frequency ? # _reflns_shell.d_res_high 1.20 _reflns_shell.d_res_low 1.30 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.70 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all 1907 _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 75.6 _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 0.740 _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 7.45 _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 1 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_CC_half 0.781 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? # _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 32.720 _refine.B_iso_mean 11.4269 _refine.B_iso_min 4.420 _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 7C4U _refine.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _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 1.2000 _refine.ls_d_res_low 7.5710 _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 6839 _refine.ls_number_reflns_R_free 342 _refine.ls_number_reflns_R_work 6497 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 75.1500 _refine.ls_percent_reflns_R_free 5.0000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2027 _refine.ls_R_factor_R_free 0.2159 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2020 _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.pdbx_R_complete ? _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 1.350 _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 THROUGHOUT _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details 'Random selection' _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 24.0000 _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 0.1100 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _refine_hist.cycle_id final _refine_hist.details ? _refine_hist.d_res_high 1.20 _refine_hist.d_res_low 7.57 _refine_hist.number_atoms_solvent 50 _refine_hist.number_atoms_total 253 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total 14 _refine_hist.pdbx_B_iso_mean_ligand 10.18 _refine_hist.pdbx_B_iso_mean_solvent 18.86 _refine_hist.pdbx_number_atoms_protein ? _refine_hist.pdbx_number_atoms_nucleic_acid ? _refine_hist.pdbx_number_atoms_ligand 43 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # 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_R_complete _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 'ELECTRON CRYSTALLOGRAPHY' 1.2 1.5097 . . 168 3202 76.0000 5 . . 0.2740 0.0000 0.2408 . . . . . . . . . . . 'ELECTRON CRYSTALLOGRAPHY' 1.5097 7.5709 . . 174 3295 75.0000 5 . . 0.1998 0.0000 0.1905 . . . . . . . . . . . # _struct.entry_id 7C4U _struct.title 'MicroED structure of orthorhombic Vancomycin at 1.2 A resolution' _struct.pdbx_descriptor Vancomycin _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7C4U _struct_keywords.text 'MicroED, Vancomycin, superbacteria, Antibiotic' _struct_keywords.pdbx_keywords ANTIBIOTIC # 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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 4 ? G N N 4 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A MLU 1 C ? ? ? 1_555 A OMZ 2 N ? ? A MLU 1 A OMZ 2 1_555 ? ? ? ? ? ? ? 1.319 ? ? covale2 covale both ? A OMZ 2 C ? ? ? 1_555 A ASN 3 N ? ? A OMZ 2 A ASN 3 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale3 covale none ? A OMZ 2 OH ? ? ? 1_555 A GHP 4 C5 ? ? A OMZ 2 A GHP 4 1_555 ? ? ? ? ? ? ? 1.374 ? ? covale4 covale both ? A ASN 3 C ? ? ? 1_555 A GHP 4 N ? ? A ASN 3 A GHP 4 1_555 ? ? ? ? ? ? ? 1.320 ? ? covale5 covale both ? A GHP 4 C ? ? ? 1_555 A GHP 5 N ? ? A GHP 4 A GHP 5 1_555 ? ? ? ? ? ? ? 1.314 ? ? covale6 covale none ? A GHP 4 C3 ? ? ? 1_555 A OMY 6 OCZ ? ? A GHP 4 A OMY 6 1_555 ? ? ? ? ? ? ? 1.372 ? ? covale7 covale one ? A GHP 4 O4 ? ? ? 1_555 C BGC . C1 ? ? A GHP 4 C BGC 1 1_555 ? ? ? ? ? ? ? 1.371 sing ? covale8 covale both ? A GHP 5 C ? ? ? 1_555 A OMY 6 N ? ? A GHP 5 A OMY 6 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale9 covale none ? A GHP 5 C3 ? ? ? 1_555 A 3FG 7 CG1 ? ? A GHP 5 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.487 ? ? covale10 covale both ? A OMY 6 C ? ? ? 1_555 A 3FG 7 N ? ? A OMY 6 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.318 ? ? covale11 covale both ? B MLU 1 C ? ? ? 1_555 B OMZ 2 N ? ? B MLU 1 B OMZ 2 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale12 covale both ? B OMZ 2 C ? ? ? 1_555 B ASN 3 N ? ? B OMZ 2 B ASN 3 1_555 ? ? ? ? ? ? ? 1.311 ? ? covale13 covale none ? B OMZ 2 OH ? ? ? 1_555 B GHP 4 C5 ? ? B OMZ 2 B GHP 4 1_555 ? ? ? ? ? ? ? 1.369 ? ? covale14 covale both ? B ASN 3 C ? ? ? 1_555 B GHP 4 N ? ? B ASN 3 B GHP 4 1_555 ? ? ? ? ? ? ? 1.314 ? ? covale15 covale both ? B GHP 4 C ? ? ? 1_555 B GHP 5 N ? ? B GHP 4 B GHP 5 1_555 ? ? ? ? ? ? ? 1.309 ? ? covale16 covale none ? B GHP 4 C3 ? ? ? 1_555 B OMY 6 OCZ ? ? B GHP 4 B OMY 6 1_555 ? ? ? ? ? ? ? 1.374 ? ? covale17 covale one ? B GHP 4 O4 ? ? ? 1_555 D BGC . C1 ? ? B GHP 4 D BGC 1 1_555 ? ? ? ? ? ? ? 1.376 sing ? covale18 covale both ? B GHP 5 C ? ? ? 1_555 B OMY 6 N ? ? B GHP 5 B OMY 6 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale19 covale none ? B GHP 5 C3 ? ? ? 1_555 B 3FG 7 CG1 ? ? B GHP 5 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.490 ? ? covale20 covale both ? B OMY 6 C ? ? ? 1_555 B 3FG 7 N ? ? B OMY 6 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.311 ? ? covale21 covale both ? C BGC . O2 ? ? ? 1_555 C RER . C1 ? ? C BGC 1 C RER 2 1_555 ? ? ? ? ? ? ? 1.374 ? ? covale22 covale both ? D BGC . O2 ? ? ? 1_555 D RER . C1 ? ? D BGC 1 D RER 2 1_555 ? ? ? ? ? ? ? 1.373 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GHP 5 A . ? GHP 5 A OMY 6 A ? OMY 6 A 1 4.80 2 GHP 5 B . ? GHP 5 B OMY 6 B ? OMY 6 B 1 -5.84 # _atom_sites.entry_id 7C4U _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.049850 _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] 0.030285 _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] 0.023969 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C CL N O # 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 MLU 1 1 1 MLU MLU A . n A 1 2 OMZ 2 2 2 OMZ OMZ A . n A 1 3 ASN 3 3 3 ASN ASN A . n A 1 4 GHP 4 4 4 GHP GHP A . n A 1 5 GHP 5 5 5 GHP GHP A . n A 1 6 OMY 6 6 6 OMY OMY A . n A 1 7 3FG 7 7 7 3FG 3FG A . n B 1 1 MLU 1 1 1 MLU MLU B . n B 1 2 OMZ 2 2 2 OMZ OMZ B . n B 1 3 ASN 3 3 3 ASN ASN B . n B 1 4 GHP 4 4 4 GHP GHP B . n B 1 5 GHP 5 5 5 GHP GHP B . n B 1 6 OMY 6 6 6 OMY OMY B . n B 1 7 3FG 7 7 7 3FG 3FG B . 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 E 3 CL 1 101 1 CL CL A . F 4 HOH 1 201 49 HOH HOH A . F 4 HOH 2 202 21 HOH HOH A . F 4 HOH 3 203 1 HOH HOH A . F 4 HOH 4 204 11 HOH HOH A . F 4 HOH 5 205 5 HOH HOH A . F 4 HOH 6 206 34 HOH HOH A . F 4 HOH 7 207 47 HOH HOH A . F 4 HOH 8 208 8 HOH HOH A . F 4 HOH 9 209 29 HOH HOH A . F 4 HOH 10 210 22 HOH HOH A . F 4 HOH 11 211 26 HOH HOH A . F 4 HOH 12 212 32 HOH HOH A . F 4 HOH 13 213 48 HOH HOH A . F 4 HOH 14 214 35 HOH HOH A . F 4 HOH 15 215 12 HOH HOH A . F 4 HOH 16 216 37 HOH HOH A . F 4 HOH 17 217 25 HOH HOH A . F 4 HOH 18 218 45 HOH HOH A . G 4 HOH 1 201 10 HOH HOH B . G 4 HOH 2 202 15 HOH HOH B . G 4 HOH 3 203 24 HOH HOH B . G 4 HOH 4 204 20 HOH HOH B . G 4 HOH 5 205 28 HOH HOH B . G 4 HOH 6 206 23 HOH HOH B . G 4 HOH 7 207 17 HOH HOH B . G 4 HOH 8 208 40 HOH HOH B . G 4 HOH 9 209 3 HOH HOH B . G 4 HOH 10 210 14 HOH HOH B . G 4 HOH 11 211 2 HOH HOH B . G 4 HOH 12 212 46 HOH HOH B . G 4 HOH 13 213 30 HOH HOH B . G 4 HOH 14 214 43 HOH HOH B . G 4 HOH 15 215 19 HOH HOH B . G 4 HOH 16 216 27 HOH HOH B . G 4 HOH 17 217 33 HOH HOH B . G 4 HOH 18 218 39 HOH HOH B . G 4 HOH 19 219 7 HOH HOH B . G 4 HOH 20 220 44 HOH HOH B . G 4 HOH 21 221 38 HOH HOH B . G 4 HOH 22 222 42 HOH HOH B . G 4 HOH 23 223 41 HOH HOH B . G 4 HOH 24 224 50 HOH HOH B . G 4 HOH 25 225 36 HOH HOH B . G 4 HOH 26 226 6 HOH HOH B . G 4 HOH 27 227 4 HOH HOH B . G 4 HOH 28 228 13 HOH HOH B . G 4 HOH 29 229 9 HOH HOH B . G 4 HOH 30 230 16 HOH HOH B . G 4 HOH 31 231 18 HOH HOH B . G 4 HOH 32 232 31 HOH HOH B . # _pdbx_molecule_features.prd_id PRD_000204 _pdbx_molecule_features.name VANCOMYCIN _pdbx_molecule_features.type Glycopeptide _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000204 A 1 PRD_000204 C 2 PRD_000204 B 2 PRD_000204 D # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA monomeric 1 2 author_and_software_defined_assembly PISA monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C,E,F 2 1 B,D,G # 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)' 300 ? 1 MORE -7 ? 1 'SSA (A^2)' 1400 ? 2 'ABSA (A^2)' 200 ? 2 MORE 2 ? 2 'SSA (A^2)' 1410 ? # _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 2020-08-12 2 'Structure model' 1 1 2020-08-19 3 'Structure model' 1 2 2020-08-26 4 'Structure model' 1 3 2021-03-17 # _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_details.details ? # 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' 'Data collection' 2 3 'Structure model' 'Data collection' 3 4 'Structure model' 'Database references' # 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 2 'Structure model' pdbx_entity_branch_descriptor 2 2 'Structure model' pdbx_entity_branch_link 3 3 'Structure model' pdbx_entity_branch_descriptor 4 4 'Structure model' citation 5 4 'Structure model' citation_author # 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_volume' 2 4 'Structure model' '_citation.page_first' 3 4 'Structure model' '_citation.page_last' 4 4 'Structure model' '_citation_author.identifier_ORCID' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.15_3459 1 ? 'data extraction' ? ? PDB deposit@deposit.rcsb.org 'Apr. 1, 2019' ? ? ? C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ ? PDB_EXTRACT ? ? package 3.25 2 # _pdbx_entry_details.entry_id 7C4U _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ;VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE AND VANCOSAMINE. HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOUGHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y # _em_3d_fitting.entry_id 7C4U _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol 'RIGID BODY FIT' _em_3d_fitting.ref_space RECIPROCAL _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.id 1 _em_3d_fitting_list.details ? _em_3d_fitting_list.pdb_chain_id A _em_3d_fitting_list.pdb_chain_residue_range 1-7 _em_3d_fitting_list.pdb_entry_id 1FVM # _em_3d_reconstruction.entry_id 7C4U _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles ? _em_3d_reconstruction.resolution 1.2 _em_3d_reconstruction.resolution_method 'DIFFRACTION PATTERN/LAYERLINES' _em_3d_reconstruction.symmetry_type '3D CRYSTAL' _em_3d_reconstruction.method CRYSTALLOGRAPHY _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 7.0 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name Vancomycin _em_entity_assembly.source NATURAL _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 7C4U _em_imaging.accelerating_voltage 200 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter 100 _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen NITROGEN _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TECNAI F20' _em_imaging.mode DIFFRACTION _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_max ? _em_imaging.nominal_defocus_min ? _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model 'GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER' _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 200 _em_sample_support.grid_type Homemade _em_sample_support.method ? _em_sample_support.film_material ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature 298 _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity 50 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.entry_id 7C4U _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7C4U _em_experiment.id 1 _em_experiment.aggregation_state '3D ARRAY' _em_experiment.reconstruction_method CRYSTALLOGRAPHY _em_experiment.entity_assembly_id 1 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 CZ _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 OMZ _pdbx_validate_close_contact.auth_seq_id_1 2 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 C5 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 GHP _pdbx_validate_close_contact.auth_seq_id_2 4 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.13 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ASN _pdbx_validate_torsion.auth_asym_id B _pdbx_validate_torsion.auth_seq_id 3 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi 177.98 _pdbx_validate_torsion.psi -144.77 # _em_3d_crystal_entity.id 1 _em_3d_crystal_entity.image_processing_id 1 _em_3d_crystal_entity.angle_alpha 90.00 _em_3d_crystal_entity.angle_beta 90.00 _em_3d_crystal_entity.angle_gamma 90.00 _em_3d_crystal_entity.length_a 20.06 _em_3d_crystal_entity.length_b 33.02 _em_3d_crystal_entity.length_c 41.72 _em_3d_crystal_entity.space_group_name 'P 2 21 21' _em_3d_crystal_entity.space_group_num 18 # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type NONE _em_ctf_correction.details ? # _em_diffraction.id 1 _em_diffraction.camera_length 730 _em_diffraction.imaging_id 1 _em_diffraction.tilt_angle_list ? # _em_diffraction_shell.id 1 _em_diffraction_shell.em_diffraction_stats_id 1 _em_diffraction_shell.fourier_space_coverage 75.6 _em_diffraction_shell.high_resolution 1.20 _em_diffraction_shell.low_resolution 1.30 _em_diffraction_shell.multiplicity 7.45 _em_diffraction_shell.num_structure_factors 1907 _em_diffraction_shell.phase_residual 1 # _em_diffraction_stats.id 1 _em_diffraction_stats.details ? _em_diffraction_stats.image_processing_id 1 _em_diffraction_stats.fourier_space_coverage 74.7 _em_diffraction_stats.high_resolution 1.2 _em_diffraction_stats.num_intensities_measured 64605 _em_diffraction_stats.num_structure_factors 6840 _em_diffraction_stats.overall_phase_error 0 _em_diffraction_stats.overall_phase_residual 1 _em_diffraction_stats.phase_error_rejection_criteria 60 _em_diffraction_stats.r_merge 0.185 _em_diffraction_stats.r_sym 0.185 # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.units ? _em_entity_assembly_molwt.value ? # _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 31958 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Amycolatopsis orientalis' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 0.0286 _em_image_recording.average_exposure_time 5.72 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN ULTRASCAN 4000 (4k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'IMAGE ACQUISITION' ? ? ? ? ? 1 2 MASKING ? ? ? ? ? ? 3 'CTF CORRECTION' ? ? ? 1 ? ? 4 'LAYERLINE INDEXING' ? ? ? ? ? ? 5 'DIFFRACTION INDEXING' ? ? ? ? ? ? 6 'MODEL FITTING' ? 'CCP4 package' ? ? 1 ? 7 OTHER ? ? ? ? ? ? 8 'MOLECULAR REPLACEMENT' ? ? ? 1 ? ? 9 'LATTICE DISTORTION CORRECTION' ? ? ? 1 ? ? 10 'SYMMETRY DETERMINATION' ? ? ? 1 ? ? 11 'CRYSTALLOGRAPHY MERGING' ? ? ? 1 ? ? 12 RECONSTRUCTION ? ? ? 1 ? ? 13 'MODEL REFINEMENT' ? PHENIX ? ? 1 ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Science Foundation (NSF, China)' China 51925307 1 'National Science Foundation (NSF, China)' China 21733010 2 # 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 C 2 BGC 1 C BGC 1 A BGC 8 n C 2 RER 2 C RER 2 A RER 9 n D 2 BGC 1 D BGC 1 B BGC 8 n D 2 RER 2 D RER 2 B RER 9 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier BGC 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpb BGC 'COMMON NAME' GMML 1.0 b-D-glucopyranose BGC 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-Glcp BGC 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Glc # _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 'WURCS=2.0/2,2,1/[a2122h-1b_1-5][ad621m-1a_1-5_3*C_3*N]/1-2/a2-b1' WURCS PDB2Glycan 1.1.0 2 2 '[][D-1-deoxy-Glcp]{[(2+1)][a-L-2-deoxy-Fucp3N]{}}' 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 RER _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.details ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 2 BGC 1 n 2 RER 2 n # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 3FG ? ? 3FG ? ? 'SUBJECT OF INVESTIGATION' ? 2 BGC ? ? BGC ? ? 'SUBJECT OF INVESTIGATION' ? 3 CL ? ? CL ? ? 'SUBJECT OF INVESTIGATION' ? 4 GHP ? ? GHP ? ? 'SUBJECT OF INVESTIGATION' ? 5 MLU ? ? MLU ? ? 'SUBJECT OF INVESTIGATION' ? 6 OMY ? ? OMY ? ? 'SUBJECT OF INVESTIGATION' ? 7 OMZ ? ? OMZ ? ? 'SUBJECT OF INVESTIGATION' ? 8 RER ? ? RER ? ? 'SUBJECT OF INVESTIGATION' ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'CHLORIDE ION' CL 4 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #