data_4CSB # _entry.id 4CSB # _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 4CSB PDBE EBI-59876 WWPDB D_1290059876 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4CSB _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2014-03-06 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Whittingham, J.L.' 1 'Blagova, E.V.' 2 'Finn, C.E.' 3 'Luo, H.' 4 'Miranda-CasoLuengo, R.' 5 'Turkenburg, J.P.' 6 'Leech, A.P.' 7 'Walton, P.H.' 8 'Meijers, W.G.' 9 'Wilkinson, A.J.' 10 # _citation.id primary _citation.title 'Structure of the Virulence-Associated Protein Vapd from the Intracellular Pathogen Rhodococcus Equi.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 70 _citation.page_first 2139 _citation.page_last ? _citation.year 2014 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25084333 _citation.pdbx_database_id_DOI 10.1107/S1399004714012632 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Whittingham, J.L.' 1 ? primary 'Blagova, E.V.' 2 ? primary 'Finn, C.E.' 3 ? primary 'Luo, H.' 4 ? primary 'Miranda-Casoluengo, R.' 5 ? primary 'Turkenburg, J.P.' 6 ? primary 'Leech, A.P.' 7 ? primary 'Walton, P.H.' 8 ? primary 'Murzin, A.G.' 9 ? primary 'Meijer, W.G.' 10 ? primary 'Wilkinson, A.J.' 11 ? # _cell.entry_id 4CSB _cell.length_a 142.844 _cell.length_b 142.844 _cell.length_c 142.844 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CSB _symmetry.space_group_name_H-M 'F 4 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 209 # 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 'VIRULENCE ASSOCIATED PROTEIN VAPD' 13481.826 1 ? ? ? ? 2 non-polymer man 'octyl beta-D-glucopyranoside' 292.369 3 ? ? ? ? 3 water nat water 18.015 64 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'VIRULENCE-ASSOCIATED PROTEIN D' # _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 ;MAIPEDKEYDVSGRVVSALVYQYFIVTVDDAEDKKGKTFQGDAGGVTIPGVDFFWGTLHTPDLEKLYSDTVSFQYNAAAT FLNINFFDSKGERLGYVLAGAAGTVSGIGGGTGGWELEHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;MAIPEDKEYDVSGRVVSALVYQYFIVTVDDAEDKKGKTFQGDAGGVTIPGVDFFWGTLHTPDLEKLYSDTVSFQYNAAAT FLNINFFDSKGERLGYVLAGAAGTVSGIGGGTGGWELEHHHHHH ; _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 MET n 1 2 ALA n 1 3 ILE n 1 4 PRO n 1 5 GLU n 1 6 ASP n 1 7 LYS n 1 8 GLU n 1 9 TYR n 1 10 ASP n 1 11 VAL n 1 12 SER n 1 13 GLY n 1 14 ARG n 1 15 VAL n 1 16 VAL n 1 17 SER n 1 18 ALA n 1 19 LEU n 1 20 VAL n 1 21 TYR n 1 22 GLN n 1 23 TYR n 1 24 PHE n 1 25 ILE n 1 26 VAL n 1 27 THR n 1 28 VAL n 1 29 ASP n 1 30 ASP n 1 31 ALA n 1 32 GLU n 1 33 ASP n 1 34 LYS n 1 35 LYS n 1 36 GLY n 1 37 LYS n 1 38 THR n 1 39 PHE n 1 40 GLN n 1 41 GLY n 1 42 ASP n 1 43 ALA n 1 44 GLY n 1 45 GLY n 1 46 VAL n 1 47 THR n 1 48 ILE n 1 49 PRO n 1 50 GLY n 1 51 VAL n 1 52 ASP n 1 53 PHE n 1 54 PHE n 1 55 TRP n 1 56 GLY n 1 57 THR n 1 58 LEU n 1 59 HIS n 1 60 THR n 1 61 PRO n 1 62 ASP n 1 63 LEU n 1 64 GLU n 1 65 LYS n 1 66 LEU n 1 67 TYR n 1 68 SER n 1 69 ASP n 1 70 THR n 1 71 VAL n 1 72 SER n 1 73 PHE n 1 74 GLN n 1 75 TYR n 1 76 ASN n 1 77 ALA n 1 78 ALA n 1 79 ALA n 1 80 THR n 1 81 PHE n 1 82 LEU n 1 83 ASN n 1 84 ILE n 1 85 ASN n 1 86 PHE n 1 87 PHE n 1 88 ASP n 1 89 SER n 1 90 LYS n 1 91 GLY n 1 92 GLU n 1 93 ARG n 1 94 LEU n 1 95 GLY n 1 96 TYR n 1 97 VAL n 1 98 LEU n 1 99 ALA n 1 100 GLY n 1 101 ALA n 1 102 ALA n 1 103 GLY n 1 104 THR n 1 105 VAL n 1 106 SER n 1 107 GLY n 1 108 ILE n 1 109 GLY n 1 110 GLY n 1 111 GLY n 1 112 THR n 1 113 GLY n 1 114 GLY n 1 115 TRP n 1 116 GLU n 1 117 LEU n 1 118 GLU n 1 119 HIS n 1 120 HIS n 1 121 HIS n 1 122 HIS n 1 123 HIS n 1 124 HIS 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 ? _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 103S _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 'RHODOCOCCUS EQUI' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 685727 _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 PET22B _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code B4F3C5_RHOE1 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession B4F3C5 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4CSB _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 116 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession B4F3C5 _struct_ref_seq.db_align_beg 50 _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 20 _struct_ref_seq.pdbx_auth_seq_align_end 134 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4CSB MET A 1 ? UNP B4F3C5 ? ? 'expression tag' 19 1 1 4CSB LEU A 117 ? UNP B4F3C5 ? ? 'expression tag' 135 2 1 4CSB GLU A 118 ? UNP B4F3C5 ? ? 'expression tag' 136 3 1 4CSB HIS A 119 ? UNP B4F3C5 ? ? 'expression tag' 137 4 1 4CSB HIS A 120 ? UNP B4F3C5 ? ? 'expression tag' 138 5 1 4CSB HIS A 121 ? UNP B4F3C5 ? ? 'expression tag' 139 6 1 4CSB HIS A 122 ? UNP B4F3C5 ? ? 'expression tag' 140 7 1 4CSB HIS A 123 ? UNP B4F3C5 ? ? 'expression tag' 141 8 1 4CSB HIS A 124 ? UNP B4F3C5 ? ? 'expression tag' 142 9 # 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 BOG D-saccharide n 'octyl beta-D-glucopyranoside' ? 'C14 H28 O6' 292.369 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 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 4CSB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.2 _exptl_crystal.density_percent_sol 43 _exptl_crystal.description NONE _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;PROTEIN:20 MG ML-1 VAPD-CORE IN 20 MM HEPES PH 7.5, 500 MM NACL RESERVOIR: 2.2M AMMONIUM SULPHATE, 0.2M SODIUM THIOCYANATE, 0.1% WV-1 BETA-D-OCTYL GLUCOSIDE ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2013-03-17 _diffrn_detector.details MIRRORS # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I02' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I02 _diffrn_source.pdbx_wavelength 0.9795 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4CSB _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 82.50 _reflns.d_resolution_high 1.90 _reflns.number_obs 10376 _reflns.number_all ? _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs 0.09 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 21.00 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.9 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.90 _reflns_shell.d_res_low 1.94 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.83 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.70 _reflns_shell.pdbx_redundancy 12.0 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4CSB _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 9823 _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 82.47 _refine.ls_d_res_high 1.90 _refine.ls_percent_reflns_obs 99.54 _refine.ls_R_factor_obs 0.16077 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.15923 _refine.ls_R_factor_R_free 0.19078 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 497 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.966 _refine.correlation_coeff_Fo_to_Fc_free 0.960 _refine.B_iso_mean 28.742 _refine.aniso_B[1][1] 0.00 _refine.aniso_B[2][2] 0.00 _refine.aniso_B[3][3] 0.00 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 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 ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROTEIN STRUCTURE IS VAPD-CORE IN WHICH THE DISORDERED N-TERMINUS (RESIDUE 1-19) IS ABSENT FROM THE PROTEIN CONSTRUCT. ; _refine.pdbx_starting_model NONE _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 0.122 _refine.pdbx_overall_ESU_R_Free 0.115 _refine.overall_SU_ML 0.079 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 2.731 _refine.overall_SU_R_Cruickshank_DPI ? _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 857 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 60 _refine_hist.number_atoms_solvent 64 _refine_hist.number_atoms_total 981 _refine_hist.d_res_high 1.90 _refine_hist.d_res_low 82.47 # 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 r_bond_refined_d 0.020 0.020 ? 903 'X-RAY DIFFRACTION' ? r_bond_other_d 0.005 0.020 ? 811 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.141 1.989 ? 1220 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.711 3.000 ? 1872 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.326 5.000 ? 111 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 33.302 24.865 ? 37 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 15.025 15.000 ? 113 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 8.236 15.000 ? 1 'X-RAY DIFFRACTION' ? r_chiral_restr 0.224 0.200 ? 137 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 1005 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 206 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 2.968 2.645 ? 449 'X-RAY DIFFRACTION' ? r_mcbond_other 2.881 2.640 ? 448 'X-RAY DIFFRACTION' ? r_mcangle_it 4.283 3.931 ? 559 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 4.231 3.220 ? 454 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? '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 1.900 _refine_ls_shell.d_res_low 1.949 _refine_ls_shell.number_reflns_R_work 708 _refine_ls_shell.R_factor_R_work 0.192 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.221 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 37 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 4CSB _struct.title 'Structure of the Virulence-Associated Protein VapD from the intracellular pathogen Rhodococcus equi.' _struct.pdbx_descriptor 'VIRULENCE ASSOCIATED PROTEIN VAPD' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4CSB _struct_keywords.pdbx_keywords 'UNKNOWN FUNCTION' _struct_keywords.text 'UNKNOWN-FUNCTION, BACTERIAL PATHOGEN, VIRULENCE PROTEIN, BETA BARREL, UNKNOWN FUNCTION' # 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 2 ? E N N 3 ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id ASP _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 62 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id THR _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 70 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ASP _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 80 _struct_conf.end_auth_comp_id THR _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 88 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 9 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_sheet.id AA _struct_sheet.type ? _struct_sheet.number_strands 9 _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 AA 1 2 ? anti-parallel AA 2 3 ? anti-parallel AA 3 4 ? anti-parallel AA 4 5 ? anti-parallel AA 5 6 ? anti-parallel AA 6 7 ? anti-parallel AA 7 8 ? anti-parallel AA 8 9 ? 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 AA 1 LYS A 7 ? SER A 17 ? LYS A 25 SER A 35 AA 2 GLY A 50 ? THR A 60 ? GLY A 68 THR A 78 AA 3 ARG A 93 ? ALA A 101 ? ARG A 111 ALA A 119 AA 4 PHE A 81 ? PHE A 87 ? PHE A 99 PHE A 105 AA 5 SER A 72 ? ALA A 78 ? SER A 90 ALA A 96 AA 6 GLY A 107 ? GLU A 116 ? GLY A 125 GLU A 134 AA 7 THR A 38 ? THR A 47 ? THR A 56 THR A 65 AA 8 TYR A 21 ? ASP A 30 ? TYR A 39 ASP A 48 AA 9 LYS A 7 ? SER A 17 ? LYS A 25 SER A 35 # 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 AA 1 2 N SER A 17 ? N SER A 35 O GLY A 50 ? O GLY A 68 AA 2 3 N HIS A 59 ? N HIS A 77 O TYR A 96 ? O TYR A 114 AA 3 4 N ALA A 99 ? N ALA A 117 O LEU A 82 ? O LEU A 100 AA 4 5 N PHE A 87 ? N PHE A 105 O SER A 72 ? O SER A 90 AA 5 6 N ALA A 77 ? N ALA A 95 O GLY A 107 ? O GLY A 125 AA 6 7 N GLU A 116 ? N GLU A 134 O THR A 38 ? O THR A 56 AA 7 8 N ALA A 43 ? N ALA A 61 O GLN A 22 ? O GLN A 40 AA 8 9 N ASP A 29 ? N ASP A 47 O ASP A 10 ? O ASP A 28 # _database_PDB_matrix.entry_id 4CSB _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 4CSB _atom_sites.fract_transf_matrix[1][1] 0.007001 _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] 0.007001 _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] 0.007001 _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 # 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 MET 1 19 ? ? ? A . n A 1 2 ALA 2 20 ? ? ? A . n A 1 3 ILE 3 21 ? ? ? A . n A 1 4 PRO 4 22 22 PRO PRO A . n A 1 5 GLU 5 23 23 GLU GLU A . n A 1 6 ASP 6 24 24 ASP ASP A . n A 1 7 LYS 7 25 25 LYS LYS A . n A 1 8 GLU 8 26 26 GLU GLU A . n A 1 9 TYR 9 27 27 TYR TYR A . n A 1 10 ASP 10 28 28 ASP ASP A . n A 1 11 VAL 11 29 29 VAL VAL A . n A 1 12 SER 12 30 30 SER SER A . n A 1 13 GLY 13 31 31 GLY GLY A . n A 1 14 ARG 14 32 32 ARG ARG A . n A 1 15 VAL 15 33 33 VAL VAL A . n A 1 16 VAL 16 34 34 VAL VAL A . n A 1 17 SER 17 35 35 SER SER A . n A 1 18 ALA 18 36 36 ALA ALA A . n A 1 19 LEU 19 37 37 LEU LEU A . n A 1 20 VAL 20 38 38 VAL VAL A . n A 1 21 TYR 21 39 39 TYR TYR A . n A 1 22 GLN 22 40 40 GLN GLN A . n A 1 23 TYR 23 41 41 TYR TYR A . n A 1 24 PHE 24 42 42 PHE PHE A . n A 1 25 ILE 25 43 43 ILE ILE A . n A 1 26 VAL 26 44 44 VAL VAL A . n A 1 27 THR 27 45 45 THR THR A . n A 1 28 VAL 28 46 46 VAL VAL A . n A 1 29 ASP 29 47 47 ASP ASP A . n A 1 30 ASP 30 48 48 ASP ASP A . n A 1 31 ALA 31 49 49 ALA ALA A . n A 1 32 GLU 32 50 50 GLU GLU A . n A 1 33 ASP 33 51 51 ASP ASP A . n A 1 34 LYS 34 52 52 LYS LYS A . n A 1 35 LYS 35 53 53 LYS LYS A . n A 1 36 GLY 36 54 54 GLY GLY A . n A 1 37 LYS 37 55 55 LYS LYS A . n A 1 38 THR 38 56 56 THR THR A . n A 1 39 PHE 39 57 57 PHE PHE A . n A 1 40 GLN 40 58 58 GLN GLN A . n A 1 41 GLY 41 59 59 GLY GLY A . n A 1 42 ASP 42 60 60 ASP ASP A . n A 1 43 ALA 43 61 61 ALA ALA A . n A 1 44 GLY 44 62 62 GLY GLY A . n A 1 45 GLY 45 63 63 GLY GLY A . n A 1 46 VAL 46 64 64 VAL VAL A . n A 1 47 THR 47 65 65 THR THR A . n A 1 48 ILE 48 66 66 ILE ILE A . n A 1 49 PRO 49 67 67 PRO PRO A . n A 1 50 GLY 50 68 68 GLY GLY A . n A 1 51 VAL 51 69 69 VAL VAL A . n A 1 52 ASP 52 70 70 ASP ASP A . n A 1 53 PHE 53 71 71 PHE PHE A . n A 1 54 PHE 54 72 72 PHE PHE A . n A 1 55 TRP 55 73 73 TRP TRP A . n A 1 56 GLY 56 74 74 GLY GLY A . n A 1 57 THR 57 75 75 THR THR A . n A 1 58 LEU 58 76 76 LEU LEU A . n A 1 59 HIS 59 77 77 HIS HIS A . n A 1 60 THR 60 78 78 THR THR A . n A 1 61 PRO 61 79 79 PRO PRO A . n A 1 62 ASP 62 80 80 ASP ASP A . n A 1 63 LEU 63 81 81 LEU LEU A . n A 1 64 GLU 64 82 82 GLU GLU A . n A 1 65 LYS 65 83 83 LYS LYS A . n A 1 66 LEU 66 84 84 LEU LEU A . n A 1 67 TYR 67 85 85 TYR TYR A . n A 1 68 SER 68 86 86 SER SER A . n A 1 69 ASP 69 87 87 ASP ASP A . n A 1 70 THR 70 88 88 THR THR A . n A 1 71 VAL 71 89 89 VAL VAL A . n A 1 72 SER 72 90 90 SER SER A . n A 1 73 PHE 73 91 91 PHE PHE A . n A 1 74 GLN 74 92 92 GLN GLN A . n A 1 75 TYR 75 93 93 TYR TYR A . n A 1 76 ASN 76 94 94 ASN ASN A . n A 1 77 ALA 77 95 95 ALA ALA A . n A 1 78 ALA 78 96 96 ALA ALA A . n A 1 79 ALA 79 97 97 ALA ALA A . n A 1 80 THR 80 98 98 THR THR A . n A 1 81 PHE 81 99 99 PHE PHE A . n A 1 82 LEU 82 100 100 LEU LEU A . n A 1 83 ASN 83 101 101 ASN ASN A . n A 1 84 ILE 84 102 102 ILE ILE A . n A 1 85 ASN 85 103 103 ASN ASN A . n A 1 86 PHE 86 104 104 PHE PHE A . n A 1 87 PHE 87 105 105 PHE PHE A . n A 1 88 ASP 88 106 106 ASP ASP A . n A 1 89 SER 89 107 107 SER SER A . n A 1 90 LYS 90 108 108 LYS LYS A . n A 1 91 GLY 91 109 109 GLY GLY A . n A 1 92 GLU 92 110 110 GLU GLU A . n A 1 93 ARG 93 111 111 ARG ARG A . n A 1 94 LEU 94 112 112 LEU LEU A . n A 1 95 GLY 95 113 113 GLY GLY A . n A 1 96 TYR 96 114 114 TYR TYR A . n A 1 97 VAL 97 115 115 VAL VAL A . n A 1 98 LEU 98 116 116 LEU LEU A . n A 1 99 ALA 99 117 117 ALA ALA A . n A 1 100 GLY 100 118 118 GLY GLY A . n A 1 101 ALA 101 119 119 ALA ALA A . n A 1 102 ALA 102 120 120 ALA ALA A . n A 1 103 GLY 103 121 121 GLY GLY A . n A 1 104 THR 104 122 122 THR THR A . n A 1 105 VAL 105 123 123 VAL VAL A . n A 1 106 SER 106 124 124 SER SER A . n A 1 107 GLY 107 125 125 GLY GLY A . n A 1 108 ILE 108 126 126 ILE ILE A . n A 1 109 GLY 109 127 127 GLY GLY A . n A 1 110 GLY 110 128 128 GLY GLY A . n A 1 111 GLY 111 129 129 GLY GLY A . n A 1 112 THR 112 130 130 THR THR A . n A 1 113 GLY 113 131 131 GLY GLY A . n A 1 114 GLY 114 132 132 GLY GLY A . n A 1 115 TRP 115 133 133 TRP TRP A . n A 1 116 GLU 116 134 134 GLU GLU A . n A 1 117 LEU 117 135 ? ? ? A . n A 1 118 GLU 118 136 ? ? ? A . n A 1 119 HIS 119 137 ? ? ? A . n A 1 120 HIS 120 138 ? ? ? A . n A 1 121 HIS 121 139 ? ? ? A . n A 1 122 HIS 122 140 ? ? ? A . n A 1 123 HIS 123 141 ? ? ? A . n A 1 124 HIS 124 142 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 BOG 1 1135 1135 BOG BOG A . C 2 BOG 1 1136 1136 BOG BOG A . D 2 BOG 1 1137 1137 BOG BOG A . E 3 HOH 1 2001 2001 HOH HOH A . E 3 HOH 2 2002 2002 HOH HOH A . E 3 HOH 3 2003 2003 HOH HOH A . E 3 HOH 4 2004 2004 HOH HOH A . E 3 HOH 5 2005 2005 HOH HOH A . E 3 HOH 6 2006 2006 HOH HOH A . E 3 HOH 7 2007 2007 HOH HOH A . E 3 HOH 8 2008 2008 HOH HOH A . E 3 HOH 9 2009 2009 HOH HOH A . E 3 HOH 10 2010 2010 HOH HOH A . E 3 HOH 11 2011 2011 HOH HOH A . E 3 HOH 12 2012 2012 HOH HOH A . E 3 HOH 13 2013 2013 HOH HOH A . E 3 HOH 14 2014 2014 HOH HOH A . E 3 HOH 15 2015 2015 HOH HOH A . E 3 HOH 16 2016 2016 HOH HOH A . E 3 HOH 17 2017 2017 HOH HOH A . E 3 HOH 18 2018 2018 HOH HOH A . E 3 HOH 19 2019 2019 HOH HOH A . E 3 HOH 20 2020 2020 HOH HOH A . E 3 HOH 21 2021 2021 HOH HOH A . E 3 HOH 22 2022 2022 HOH HOH A . E 3 HOH 23 2023 2023 HOH HOH A . E 3 HOH 24 2024 2024 HOH HOH A . E 3 HOH 25 2025 2025 HOH HOH A . E 3 HOH 26 2026 2026 HOH HOH A . E 3 HOH 27 2027 2027 HOH HOH A . E 3 HOH 28 2028 2028 HOH HOH A . E 3 HOH 29 2029 2029 HOH HOH A . E 3 HOH 30 2030 2030 HOH HOH A . E 3 HOH 31 2031 2031 HOH HOH A . E 3 HOH 32 2032 2032 HOH HOH A . E 3 HOH 33 2033 2033 HOH HOH A . E 3 HOH 34 2034 2034 HOH HOH A . E 3 HOH 35 2035 2035 HOH HOH A . E 3 HOH 36 2036 2036 HOH HOH A . E 3 HOH 37 2037 2037 HOH HOH A . E 3 HOH 38 2038 2038 HOH HOH A . E 3 HOH 39 2039 2039 HOH HOH A . E 3 HOH 40 2040 2040 HOH HOH A . E 3 HOH 41 2041 2041 HOH HOH A . E 3 HOH 42 2042 2042 HOH HOH A . E 3 HOH 43 2043 2043 HOH HOH A . E 3 HOH 44 2044 2044 HOH HOH A . E 3 HOH 45 2045 2045 HOH HOH A . E 3 HOH 46 2046 2046 HOH HOH A . E 3 HOH 47 2047 2047 HOH HOH A . E 3 HOH 48 2048 2048 HOH HOH A . E 3 HOH 49 2049 2049 HOH HOH A . E 3 HOH 50 2050 2050 HOH HOH A . E 3 HOH 51 2051 2051 HOH HOH A . E 3 HOH 52 2052 2052 HOH HOH A . E 3 HOH 53 2053 2053 HOH HOH A . E 3 HOH 54 2054 2054 HOH HOH A . E 3 HOH 55 2055 2055 HOH HOH A . E 3 HOH 56 2056 2056 HOH HOH A . E 3 HOH 57 2057 2057 HOH HOH A . E 3 HOH 58 2058 2058 HOH HOH A . E 3 HOH 59 2059 2059 HOH HOH A . E 3 HOH 60 2060 2060 HOH HOH A . E 3 HOH 61 2061 2061 HOH HOH A . E 3 HOH 62 2062 2062 HOH HOH A . E 3 HOH 63 2063 2063 HOH HOH A . E 3 HOH 64 2064 2064 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 2017 ? E HOH . 2 1 A HOH 2026 ? E HOH . 3 1 A HOH 2036 ? E HOH . 4 1 A HOH 2061 ? E HOH . 5 1 A HOH 2064 ? E HOH . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2014-04-16 2 'Structure model' 1 1 2014-08-06 3 'Structure model' 1 2 2014-08-13 4 'Structure model' 1 3 2014-08-20 5 'Structure model' 1 4 2017-09-06 6 'Structure model' 1 5 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 6 '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 2 'Structure model' 'Structure summary' 3 3 'Structure model' 'Database references' 4 4 'Structure model' 'Database references' 5 5 'Structure model' Advisory 6 5 'Structure model' 'Data collection' 7 6 'Structure model' 'Data collection' 8 6 'Structure model' 'Derived calculations' 9 6 'Structure model' Other 10 6 '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 5 'Structure model' diffrn_detector 2 5 'Structure model' pdbx_unobs_or_zero_occ_atoms 3 6 'Structure model' chem_comp 4 6 'Structure model' entity 5 6 'Structure model' pdbx_chem_comp_identifier 6 6 'Structure model' pdbx_database_status 7 6 'Structure model' pdbx_entity_nonpoly 8 6 'Structure model' struct_site 9 6 '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 5 'Structure model' '_diffrn_detector.type' 2 6 'Structure model' '_chem_comp.mon_nstd_flag' 3 6 'Structure model' '_chem_comp.name' 4 6 'Structure model' '_chem_comp.type' 5 6 'Structure model' '_entity.pdbx_description' 6 6 'Structure model' '_pdbx_database_status.status_code_sf' 7 6 'Structure model' '_pdbx_entity_nonpoly.name' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language REFMAC refinement 5.8.0033 ? 1 ? ? ? ? MOSFLM 'data reduction' . ? 2 ? ? ? ? SCALA 'data scaling' . ? 3 ? ? ? ? SHELX phasing . ? 4 ? ? ? ? # _pdbx_database_remark.id 700 _pdbx_database_remark.text ; SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. ; # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 2001 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 2058 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.13 # 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 LEU A 37 ? ? 73.96 -62.93 2 1 GLU A 50 ? ? 58.25 -128.11 3 1 ASP A 80 ? ? -160.21 97.69 4 1 THR A 98 ? ? 81.70 -3.82 # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 2023 ? 7.43 . 2 1 O ? A HOH 2026 ? 5.94 . 3 1 O ? A HOH 2061 ? . 6.47 4 1 O ? A HOH 2063 ? 6.78 . 5 1 O ? A HOH 2064 ? 5.82 . # 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 MET 19 ? A MET 1 2 1 Y 1 A ALA 20 ? A ALA 2 3 1 Y 1 A ILE 21 ? A ILE 3 4 1 Y 1 A LEU 135 ? A LEU 117 5 1 Y 1 A GLU 136 ? A GLU 118 6 1 Y 1 A HIS 137 ? A HIS 119 7 1 Y 1 A HIS 138 ? A HIS 120 8 1 Y 1 A HIS 139 ? A HIS 121 9 1 Y 1 A HIS 140 ? A HIS 122 10 1 Y 1 A HIS 141 ? A HIS 123 11 1 Y 1 A HIS 142 ? A HIS 124 # _pdbx_chem_comp_identifier.comp_id BOG _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1.0 _pdbx_chem_comp_identifier.identifier b-octylglucoside # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'octyl beta-D-glucopyranoside' BOG 3 water HOH #