data_1YK9 # _entry.id 1YK9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.351 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1YK9 pdb_00001yk9 10.2210/pdb1yk9/pdb RCSB RCSB031610 ? ? WWPDB D_1000031610 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YK9 _pdbx_database_status.recvd_initial_deposition_date 2005-01-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ketkar, A.D.' 1 'Shenoy, A.R.' 2 'Ramagopal, U.A.' 3 'Visweswariah, S.S.' 4 'Suguna, K.' 5 'TB Structural Genomics Consortium (TBSGC)' 6 # _citation.id primary _citation.title ;A Structural Basis for the Role of Nucleotide Specifying Residues in Regulating the Oligomerization of the Rv1625c Adenylyl Cyclase from M.tuberculosis ; _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 356 _citation.page_first 904 _citation.page_last 916 _citation.year 2006 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16403515 _citation.pdbx_database_id_DOI 10.1016/j.jmb.2005.12.017 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ketkar, A.D.' 1 ? primary 'Shenoy, A.R.' 2 ? primary 'Ramagopal, U.A.' 3 ? primary 'Visweswariah, S.S.' 4 ? primary 'Suguna, K.' 5 ? # _cell.entry_id 1YK9 _cell.length_a 71.020 _cell.length_b 71.020 _cell.length_c 43.739 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 1YK9 _symmetry.space_group_name_H-M 'P 41' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Adenylate cyclase' 22372.295 1 4.6.1.1 'K296E, F363R, D365C' 'Rv1625c catalytic domain' ? 2 water nat water 18.015 71 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'ATP pyrophosphate-lyase, Adenylyl cyclase' # _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 ;RNIIADKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIEVSGDSYMVVSGVPRPRPDHTQAL ADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFRYCVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDD FVLRERGHINVKGKGVMRTWYLIGRKVAADPGEVRGAEPRTAGV ; _entity_poly.pdbx_seq_one_letter_code_can ;RNIIADKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIEVSGDSYMVVSGVPRPRPDHTQAL ADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFRYCVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDD FVLRERGHINVKGKGVMRTWYLIGRKVAADPGEVRGAEPRTAGV ; _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 ARG n 1 2 ASN n 1 3 ILE n 1 4 ILE n 1 5 ALA n 1 6 ASP n 1 7 LYS n 1 8 TYR n 1 9 ASP n 1 10 GLU n 1 11 ALA n 1 12 SER n 1 13 VAL n 1 14 LEU n 1 15 PHE n 1 16 ALA n 1 17 ASP n 1 18 ILE n 1 19 VAL n 1 20 GLY n 1 21 PHE n 1 22 THR n 1 23 GLU n 1 24 ARG n 1 25 ALA n 1 26 SER n 1 27 SER n 1 28 THR n 1 29 ALA n 1 30 PRO n 1 31 ALA n 1 32 ASP n 1 33 LEU n 1 34 VAL n 1 35 ARG n 1 36 PHE n 1 37 LEU n 1 38 ASP n 1 39 ARG n 1 40 LEU n 1 41 TYR n 1 42 SER n 1 43 ALA n 1 44 PHE n 1 45 ASP n 1 46 GLU n 1 47 LEU n 1 48 VAL n 1 49 ASP n 1 50 GLN n 1 51 HIS n 1 52 GLY n 1 53 LEU n 1 54 GLU n 1 55 LYS n 1 56 ILE n 1 57 GLU n 1 58 VAL n 1 59 SER n 1 60 GLY n 1 61 ASP n 1 62 SER n 1 63 TYR n 1 64 MET n 1 65 VAL n 1 66 VAL n 1 67 SER n 1 68 GLY n 1 69 VAL n 1 70 PRO n 1 71 ARG n 1 72 PRO n 1 73 ARG n 1 74 PRO n 1 75 ASP n 1 76 HIS n 1 77 THR n 1 78 GLN n 1 79 ALA n 1 80 LEU n 1 81 ALA n 1 82 ASP n 1 83 PHE n 1 84 ALA n 1 85 LEU n 1 86 ASP n 1 87 MET n 1 88 THR n 1 89 ASN n 1 90 VAL n 1 91 ALA n 1 92 ALA n 1 93 GLN n 1 94 LEU n 1 95 LYS n 1 96 ASP n 1 97 PRO n 1 98 ARG n 1 99 GLY n 1 100 ASN n 1 101 PRO n 1 102 VAL n 1 103 PRO n 1 104 LEU n 1 105 ARG n 1 106 VAL n 1 107 GLY n 1 108 LEU n 1 109 ALA n 1 110 THR n 1 111 GLY n 1 112 PRO n 1 113 VAL n 1 114 VAL n 1 115 ALA n 1 116 GLY n 1 117 VAL n 1 118 VAL n 1 119 GLY n 1 120 SER n 1 121 ARG n 1 122 ARG n 1 123 PHE n 1 124 ARG n 1 125 TYR n 1 126 CYS n 1 127 VAL n 1 128 TRP n 1 129 GLY n 1 130 ASP n 1 131 ALA n 1 132 VAL n 1 133 ASN n 1 134 VAL n 1 135 ALA n 1 136 SER n 1 137 ARG n 1 138 MET n 1 139 GLU n 1 140 SER n 1 141 THR n 1 142 ASP n 1 143 SER n 1 144 VAL n 1 145 GLY n 1 146 GLN n 1 147 ILE n 1 148 GLN n 1 149 VAL n 1 150 PRO n 1 151 ASP n 1 152 GLU n 1 153 VAL n 1 154 TYR n 1 155 GLU n 1 156 ARG n 1 157 LEU n 1 158 LYS n 1 159 ASP n 1 160 ASP n 1 161 PHE n 1 162 VAL n 1 163 LEU n 1 164 ARG n 1 165 GLU n 1 166 ARG n 1 167 GLY n 1 168 HIS n 1 169 ILE n 1 170 ASN n 1 171 VAL n 1 172 LYS n 1 173 GLY n 1 174 LYS n 1 175 GLY n 1 176 VAL n 1 177 MET n 1 178 ARG n 1 179 THR n 1 180 TRP n 1 181 TYR n 1 182 LEU n 1 183 ILE n 1 184 GLY n 1 185 ARG n 1 186 LYS n 1 187 VAL n 1 188 ALA n 1 189 ALA n 1 190 ASP n 1 191 PRO n 1 192 GLY n 1 193 GLU n 1 194 VAL n 1 195 ARG n 1 196 GLY n 1 197 ALA n 1 198 GLU n 1 199 PRO n 1 200 ARG n 1 201 THR n 1 202 ALA n 1 203 GLY n 1 204 VAL 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 Mycobacterium _entity_src_gen.pdbx_gene_src_gene Rv1625c _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Mycobacterium tuberculosis' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1773 _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 BL21' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 511693 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species 'Escherichia coli' _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain BL21 _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 pRSET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code CYA1_MYCTU _struct_ref.pdbx_db_accession O30820 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;RNIIADKYDEASVLFADIVGFTERASSTAPADLVRFLDRLYSAFDELVDQHGLEKIKVSGDSYMVVSGVPRPRPDHTQAL ADFALDMTNVAAQLKDPRGNPVPLRVGLATGPVVAGVVGSRRFFYDVWGDAVNVASRMESTDSVGQIQVPDEVYERLKDD FVLRERGHINVKGKGVMRTWYLIGRKVAADPGEVRGAEPRTAGV ; _struct_ref.pdbx_align_begin 240 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1YK9 _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 204 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O30820 _struct_ref_seq.db_align_beg 240 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 443 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 240 _struct_ref_seq.pdbx_auth_seq_align_end 443 # 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 1YK9 GLU A 57 ? UNP O30820 LYS 296 'engineered mutation' 296 1 1 1YK9 ARG A 124 ? UNP O30820 PHE 363 'engineered mutation' 363 2 1 1YK9 CYS A 126 ? UNP O30820 ASP 365 'engineered mutation' 365 3 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 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 1YK9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.66 _exptl_crystal.density_percent_sol 53.4 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.pdbx_details 'PEG 8000, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2004-06-01 _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 'sagitally focusing Si(111) crystals' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9793 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X9A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X9A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9793 # _reflns.entry_id 1YK9 _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 19.98 _reflns.d_resolution_high 2.65 _reflns.number_obs 6355 _reflns.number_all 6356 _reflns.percent_possible_obs 99.3 _reflns.pdbx_Rmerge_I_obs 0.109 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 11.8 _reflns.B_iso_Wilson_estimate 9.5 _reflns.pdbx_redundancy 4.0 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.65 _reflns_shell.d_res_low 2.74 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.46 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.8 _reflns_shell.pdbx_redundancy 3.9 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 628 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1YK9 _refine.ls_number_reflns_obs 6079 _refine.ls_number_reflns_all 6345 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF 2007090.86 _refine.pdbx_data_cutoff_low_absF .000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.98 _refine.ls_d_res_high 2.70 _refine.ls_percent_reflns_obs 99.3 _refine.ls_R_factor_obs 0.205 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.205 _refine.ls_R_factor_R_free 0.245 _refine.ls_R_factor_R_free_error .010 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.6 _refine.ls_number_reflns_R_free 582 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 34.5 _refine.aniso_B[1][1] -.30 _refine.aniso_B[2][2] .13 _refine.aniso_B[3][3] .17 _refine.aniso_B[1][2] .00 _refine.aniso_B[1][3] .00 _refine.aniso_B[2][3] .00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 1.16565 _refine.solvent_model_param_bsol 300 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1YK9 _refine_analyze.Luzzati_coordinate_error_obs .23 _refine_analyze.Luzzati_sigma_a_obs .30 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free .35 _refine_analyze.Luzzati_sigma_a_free .41 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1410 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 71 _refine_hist.number_atoms_total 1481 _refine_hist.d_res_high 2.70 _refine_hist.d_res_low 19.98 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d .010 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg .9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 26.4 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.16 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 4.80 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 7.44 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 8.07 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 9.78 2.50 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.70 _refine_ls_shell.d_res_low 2.87 _refine_ls_shell.number_reflns_R_work 912 _refine_ls_shell.R_factor_R_work 0.236 _refine_ls_shell.percent_reflns_obs 100.0 _refine_ls_shell.R_factor_R_free 0.388 _refine_ls_shell.R_factor_R_free_error .039 _refine_ls_shell.percent_reflns_R_free 9.7 _refine_ls_shell.number_reflns_R_free 98 _refine_ls_shell.number_reflns_obs 912 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 WATER_REP.PARAM WATER.TOP 'X-RAY DIFFRACTION' # _struct.entry_id 1YK9 _struct.title 'Crystal structure of a mutant form of the mycobacterial adenylyl cyclase Rv1625c' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YK9 _struct_keywords.pdbx_keywords LYASE _struct_keywords.text 'beta-alpha-beta sandwich, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, LYASE' # 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 ? # _struct_biol.id 1 _struct_biol.details ? _struct_biol.pdbx_parent_biol_id ? # 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 ARG A 35 ? SER A 42 ? ARG A 274 SER A 281 1 ? 8 HELX_P HELX_P2 2 ASP A 45 ? ASP A 49 ? ASP A 284 ASP A 288 5 ? 5 HELX_P HELX_P3 3 ASP A 75 ? ASP A 82 ? ASP A 314 ASP A 321 1 ? 8 HELX_P HELX_P4 4 ASP A 82 ? ALA A 91 ? ASP A 321 ALA A 330 1 ? 10 HELX_P HELX_P5 5 ASP A 130 ? ALA A 135 ? ASP A 369 ALA A 374 1 ? 6 HELX_P HELX_P6 6 SER A 136 ? THR A 141 ? SER A 375 THR A 380 1 ? 6 HELX_P HELX_P7 7 PRO A 150 ? ARG A 156 ? PRO A 389 ARG A 395 1 ? 7 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id ASP _struct_mon_prot_cis.label_seq_id 96 _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 ASP _struct_mon_prot_cis.auth_seq_id 335 _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 97 _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_2 336 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 0.65 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 2 ? C ? 2 ? # 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 ? parallel B 1 2 ? anti-parallel C 1 2 ? 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 GLU A 54 ? LYS A 55 ? GLU A 293 LYS A 294 A 2 TYR A 63 ? VAL A 66 ? TYR A 302 VAL A 305 A 3 ALA A 11 ? ILE A 18 ? ALA A 250 ILE A 257 A 4 LEU A 104 ? GLY A 111 ? LEU A 343 GLY A 350 A 5 ILE A 147 ? GLN A 148 ? ILE A 386 GLN A 387 B 1 VAL A 113 ? ALA A 115 ? VAL A 352 ALA A 354 B 2 VAL A 127 ? GLY A 129 ? VAL A 366 GLY A 368 C 1 PHE A 161 ? GLU A 165 ? PHE A 400 GLU A 404 C 2 TYR A 181 ? LYS A 186 ? TYR A 420 LYS A 425 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N GLU A 54 ? N GLU A 293 O VAL A 66 ? O VAL A 305 A 2 3 O VAL A 65 ? O VAL A 304 N LEU A 14 ? N LEU A 253 A 3 4 N VAL A 13 ? N VAL A 252 O ALA A 109 ? O ALA A 348 A 4 5 N VAL A 106 ? N VAL A 345 O GLN A 148 ? O GLN A 387 B 1 2 N VAL A 114 ? N VAL A 353 O TRP A 128 ? O TRP A 367 C 1 2 N VAL A 162 ? N VAL A 401 O GLY A 184 ? O GLY A 423 # _database_PDB_matrix.entry_id 1YK9 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] .000000 _database_PDB_matrix.origx[1][3] .000000 _database_PDB_matrix.origx[2][1] .000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] .000000 _database_PDB_matrix.origx[3][1] .000000 _database_PDB_matrix.origx[3][2] .000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] .00000 _database_PDB_matrix.origx_vector[2] .00000 _database_PDB_matrix.origx_vector[3] .00000 # _atom_sites.entry_id 1YK9 _atom_sites.fract_transf_matrix[1][1] .014081 _atom_sites.fract_transf_matrix[1][2] .000000 _atom_sites.fract_transf_matrix[1][3] .000000 _atom_sites.fract_transf_matrix[2][1] .000000 _atom_sites.fract_transf_matrix[2][2] .014081 _atom_sites.fract_transf_matrix[2][3] .000000 _atom_sites.fract_transf_matrix[3][1] .000000 _atom_sites.fract_transf_matrix[3][2] .000000 _atom_sites.fract_transf_matrix[3][3] .022863 _atom_sites.fract_transf_vector[1] .00000 _atom_sites.fract_transf_vector[2] .00000 _atom_sites.fract_transf_vector[3] .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 ARG 1 240 ? ? ? A . n A 1 2 ASN 2 241 ? ? ? A . n A 1 3 ILE 3 242 ? ? ? A . n A 1 4 ILE 4 243 ? ? ? A . n A 1 5 ALA 5 244 ? ? ? A . n A 1 6 ASP 6 245 245 ASP ASP A . n A 1 7 LYS 7 246 246 LYS LYS A . n A 1 8 TYR 8 247 247 TYR TYR A . n A 1 9 ASP 9 248 248 ASP ASP A . n A 1 10 GLU 10 249 249 GLU GLU A . n A 1 11 ALA 11 250 250 ALA ALA A . n A 1 12 SER 12 251 251 SER SER A . n A 1 13 VAL 13 252 252 VAL VAL A . n A 1 14 LEU 14 253 253 LEU LEU A . n A 1 15 PHE 15 254 254 PHE PHE A . n A 1 16 ALA 16 255 255 ALA ALA A . n A 1 17 ASP 17 256 256 ASP ASP A . n A 1 18 ILE 18 257 257 ILE ILE A . n A 1 19 VAL 19 258 258 VAL VAL A . n A 1 20 GLY 20 259 259 GLY GLY A . n A 1 21 PHE 21 260 260 PHE PHE A . n A 1 22 THR 22 261 261 THR THR A . n A 1 23 GLU 23 262 262 GLU GLU A . n A 1 24 ARG 24 263 263 ARG ARG A . n A 1 25 ALA 25 264 264 ALA ALA A . n A 1 26 SER 26 265 265 SER SER A . n A 1 27 SER 27 266 266 SER SER A . n A 1 28 THR 28 267 267 THR THR A . n A 1 29 ALA 29 268 268 ALA ALA A . n A 1 30 PRO 30 269 269 PRO PRO A . n A 1 31 ALA 31 270 270 ALA ALA A . n A 1 32 ASP 32 271 271 ASP ASP A . n A 1 33 LEU 33 272 272 LEU LEU A . n A 1 34 VAL 34 273 273 VAL VAL A . n A 1 35 ARG 35 274 274 ARG ARG A . n A 1 36 PHE 36 275 275 PHE PHE A . n A 1 37 LEU 37 276 276 LEU LEU A . n A 1 38 ASP 38 277 277 ASP ASP A . n A 1 39 ARG 39 278 278 ARG ARG A . n A 1 40 LEU 40 279 279 LEU LEU A . n A 1 41 TYR 41 280 280 TYR TYR A . n A 1 42 SER 42 281 281 SER SER A . n A 1 43 ALA 43 282 282 ALA ALA A . n A 1 44 PHE 44 283 283 PHE PHE A . n A 1 45 ASP 45 284 284 ASP ASP A . n A 1 46 GLU 46 285 285 GLU GLU A . n A 1 47 LEU 47 286 286 LEU LEU A . n A 1 48 VAL 48 287 287 VAL VAL A . n A 1 49 ASP 49 288 288 ASP ASP A . n A 1 50 GLN 50 289 289 GLN GLN A . n A 1 51 HIS 51 290 290 HIS HIS A . n A 1 52 GLY 52 291 291 GLY GLY A . n A 1 53 LEU 53 292 292 LEU LEU A . n A 1 54 GLU 54 293 293 GLU GLU A . n A 1 55 LYS 55 294 294 LYS LYS A . n A 1 56 ILE 56 295 295 ILE ILE A . n A 1 57 GLU 57 296 296 GLU GLU A . n A 1 58 VAL 58 297 297 VAL VAL A . n A 1 59 SER 59 298 298 SER SER A . n A 1 60 GLY 60 299 299 GLY GLY A . n A 1 61 ASP 61 300 300 ASP ASP A . n A 1 62 SER 62 301 301 SER SER A . n A 1 63 TYR 63 302 302 TYR TYR A . n A 1 64 MET 64 303 303 MET MET A . n A 1 65 VAL 65 304 304 VAL VAL A . n A 1 66 VAL 66 305 305 VAL VAL A . n A 1 67 SER 67 306 306 SER SER A . n A 1 68 GLY 68 307 307 GLY GLY A . n A 1 69 VAL 69 308 308 VAL VAL A . n A 1 70 PRO 70 309 309 PRO PRO A . n A 1 71 ARG 71 310 310 ARG ALA A . n A 1 72 PRO 72 311 311 PRO PRO A . n A 1 73 ARG 73 312 312 ARG ARG A . n A 1 74 PRO 74 313 313 PRO PRO A . n A 1 75 ASP 75 314 314 ASP ASP A . n A 1 76 HIS 76 315 315 HIS HIS A . n A 1 77 THR 77 316 316 THR THR A . n A 1 78 GLN 78 317 317 GLN GLN A . n A 1 79 ALA 79 318 318 ALA ALA A . n A 1 80 LEU 80 319 319 LEU LEU A . n A 1 81 ALA 81 320 320 ALA ALA A . n A 1 82 ASP 82 321 321 ASP ASP A . n A 1 83 PHE 83 322 322 PHE PHE A . n A 1 84 ALA 84 323 323 ALA ALA A . n A 1 85 LEU 85 324 324 LEU LEU A . n A 1 86 ASP 86 325 325 ASP ASP A . n A 1 87 MET 87 326 326 MET MET A . n A 1 88 THR 88 327 327 THR THR A . n A 1 89 ASN 89 328 328 ASN ASN A . n A 1 90 VAL 90 329 329 VAL VAL A . n A 1 91 ALA 91 330 330 ALA ALA A . n A 1 92 ALA 92 331 331 ALA ALA A . n A 1 93 GLN 93 332 332 GLN GLN A . n A 1 94 LEU 94 333 333 LEU LEU A . n A 1 95 LYS 95 334 334 LYS LYS A . n A 1 96 ASP 96 335 335 ASP ASP A . n A 1 97 PRO 97 336 336 PRO PRO A . n A 1 98 ARG 98 337 337 ARG ARG A . n A 1 99 GLY 99 338 338 GLY GLY A . n A 1 100 ASN 100 339 339 ASN ASN A . n A 1 101 PRO 101 340 340 PRO PRO A . n A 1 102 VAL 102 341 341 VAL VAL A . n A 1 103 PRO 103 342 342 PRO PRO A . n A 1 104 LEU 104 343 343 LEU LEU A . n A 1 105 ARG 105 344 344 ARG ARG A . n A 1 106 VAL 106 345 345 VAL VAL A . n A 1 107 GLY 107 346 346 GLY GLY A . n A 1 108 LEU 108 347 347 LEU LEU A . n A 1 109 ALA 109 348 348 ALA ALA A . n A 1 110 THR 110 349 349 THR THR A . n A 1 111 GLY 111 350 350 GLY GLY A . n A 1 112 PRO 112 351 351 PRO PRO A . n A 1 113 VAL 113 352 352 VAL VAL A . n A 1 114 VAL 114 353 353 VAL VAL A . n A 1 115 ALA 115 354 354 ALA ALA A . n A 1 116 GLY 116 355 355 GLY GLY A . n A 1 117 VAL 117 356 356 VAL VAL A . n A 1 118 VAL 118 357 357 VAL VAL A . n A 1 119 GLY 119 358 358 GLY GLY A . n A 1 120 SER 120 359 359 SER SER A . n A 1 121 ARG 121 360 360 ARG ARG A . n A 1 122 ARG 122 361 361 ARG ALA A . n A 1 123 PHE 123 362 362 PHE PHE A . n A 1 124 ARG 124 363 363 ARG ARG A . n A 1 125 TYR 125 364 364 TYR TYR A . n A 1 126 CYS 126 365 365 CYS CYS A . n A 1 127 VAL 127 366 366 VAL VAL A . n A 1 128 TRP 128 367 367 TRP TRP A . n A 1 129 GLY 129 368 368 GLY GLY A . n A 1 130 ASP 130 369 369 ASP ASP A . n A 1 131 ALA 131 370 370 ALA ALA A . n A 1 132 VAL 132 371 371 VAL VAL A . n A 1 133 ASN 133 372 372 ASN ASN A . n A 1 134 VAL 134 373 373 VAL VAL A . n A 1 135 ALA 135 374 374 ALA ALA A . n A 1 136 SER 136 375 375 SER SER A . n A 1 137 ARG 137 376 376 ARG ARG A . n A 1 138 MET 138 377 377 MET MET A . n A 1 139 GLU 139 378 378 GLU GLU A . n A 1 140 SER 140 379 379 SER SER A . n A 1 141 THR 141 380 380 THR THR A . n A 1 142 ASP 142 381 381 ASP ASP A . n A 1 143 SER 143 382 382 SER SER A . n A 1 144 VAL 144 383 383 VAL VAL A . n A 1 145 GLY 145 384 384 GLY GLY A . n A 1 146 GLN 146 385 385 GLN GLN A . n A 1 147 ILE 147 386 386 ILE ILE A . n A 1 148 GLN 148 387 387 GLN GLN A . n A 1 149 VAL 149 388 388 VAL VAL A . n A 1 150 PRO 150 389 389 PRO PRO A . n A 1 151 ASP 151 390 390 ASP ASP A . n A 1 152 GLU 152 391 391 GLU GLU A . n A 1 153 VAL 153 392 392 VAL VAL A . n A 1 154 TYR 154 393 393 TYR TYR A . n A 1 155 GLU 155 394 394 GLU GLU A . n A 1 156 ARG 156 395 395 ARG ARG A . n A 1 157 LEU 157 396 396 LEU LEU A . n A 1 158 LYS 158 397 397 LYS LYS A . n A 1 159 ASP 159 398 398 ASP ASP A . n A 1 160 ASP 160 399 399 ASP ASP A . n A 1 161 PHE 161 400 400 PHE PHE A . n A 1 162 VAL 162 401 401 VAL VAL A . n A 1 163 LEU 163 402 402 LEU LEU A . n A 1 164 ARG 164 403 403 ARG ARG A . n A 1 165 GLU 165 404 404 GLU GLU A . n A 1 166 ARG 166 405 405 ARG ARG A . n A 1 167 GLY 167 406 406 GLY GLY A . n A 1 168 HIS 168 407 407 HIS HIS A . n A 1 169 ILE 169 408 408 ILE ILE A . n A 1 170 ASN 170 409 409 ASN ASN A . n A 1 171 VAL 171 410 410 VAL VAL A . n A 1 172 LYS 172 411 411 LYS LYS A . n A 1 173 GLY 173 412 412 GLY GLY A . n A 1 174 LYS 174 413 413 LYS LYS A . n A 1 175 GLY 175 414 414 GLY GLY A . n A 1 176 VAL 176 415 415 VAL VAL A . n A 1 177 MET 177 416 416 MET MET A . n A 1 178 ARG 178 417 417 ARG ARG A . n A 1 179 THR 179 418 418 THR THR A . n A 1 180 TRP 180 419 419 TRP TRP A . n A 1 181 TYR 181 420 420 TYR TYR A . n A 1 182 LEU 182 421 421 LEU LEU A . n A 1 183 ILE 183 422 422 ILE ILE A . n A 1 184 GLY 184 423 423 GLY GLY A . n A 1 185 ARG 185 424 424 ARG ALA A . n A 1 186 LYS 186 425 425 LYS LYS A . n A 1 187 VAL 187 426 426 VAL VAL A . n A 1 188 ALA 188 427 427 ALA ALA A . n A 1 189 ALA 189 428 428 ALA ALA A . n A 1 190 ASP 190 429 ? ? ? A . n A 1 191 PRO 191 430 ? ? ? A . n A 1 192 GLY 192 431 ? ? ? A . n A 1 193 GLU 193 432 ? ? ? A . n A 1 194 VAL 194 433 ? ? ? A . n A 1 195 ARG 195 434 ? ? ? A . n A 1 196 GLY 196 435 ? ? ? A . n A 1 197 ALA 197 436 ? ? ? A . n A 1 198 GLU 198 437 ? ? ? A . n A 1 199 PRO 199 438 ? ? ? A . n A 1 200 ARG 200 439 ? ? ? A . n A 1 201 THR 201 440 ? ? ? A . n A 1 202 ALA 202 441 ? ? ? A . n A 1 203 GLY 203 442 ? ? ? A . n A 1 204 VAL 204 443 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'TB Structural Genomics Consortium' _pdbx_SG_project.initial_of_center TBSGC # 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 HOH 1 1 1 HOH HOH A . B 2 HOH 2 2 2 HOH HOH A . B 2 HOH 3 3 3 HOH HOH A . B 2 HOH 4 4 4 HOH HOH A . B 2 HOH 5 5 5 HOH HOH A . B 2 HOH 6 6 6 HOH HOH A . B 2 HOH 7 7 7 HOH HOH A . B 2 HOH 8 8 8 HOH HOH A . B 2 HOH 9 9 9 HOH HOH A . B 2 HOH 10 10 10 HOH HOH A . B 2 HOH 11 11 11 HOH HOH A . B 2 HOH 12 12 12 HOH HOH A . B 2 HOH 13 13 13 HOH HOH A . B 2 HOH 14 14 14 HOH HOH A . B 2 HOH 15 15 15 HOH HOH A . B 2 HOH 16 16 16 HOH HOH A . B 2 HOH 17 17 17 HOH HOH A . B 2 HOH 18 18 18 HOH HOH A . B 2 HOH 19 19 19 HOH HOH A . B 2 HOH 20 20 20 HOH HOH A . B 2 HOH 21 21 21 HOH HOH A . B 2 HOH 22 22 22 HOH HOH A . B 2 HOH 23 23 23 HOH HOH A . B 2 HOH 24 24 24 HOH HOH A . B 2 HOH 25 25 25 HOH HOH A . B 2 HOH 26 26 26 HOH HOH A . B 2 HOH 27 27 27 HOH HOH A . B 2 HOH 28 28 28 HOH HOH A . B 2 HOH 29 29 29 HOH HOH A . B 2 HOH 30 30 30 HOH HOH A . B 2 HOH 31 31 31 HOH HOH A . B 2 HOH 32 32 32 HOH HOH A . B 2 HOH 33 33 33 HOH HOH A . B 2 HOH 34 34 34 HOH HOH A . B 2 HOH 35 35 35 HOH HOH A . B 2 HOH 36 36 36 HOH HOH A . B 2 HOH 37 37 37 HOH HOH A . B 2 HOH 38 38 38 HOH HOH A . B 2 HOH 39 39 39 HOH HOH A . B 2 HOH 40 40 40 HOH HOH A . B 2 HOH 41 41 41 HOH HOH A . B 2 HOH 42 42 42 HOH HOH A . B 2 HOH 43 43 43 HOH HOH A . B 2 HOH 44 44 44 HOH HOH A . B 2 HOH 45 45 45 HOH HOH A . B 2 HOH 46 46 46 HOH HOH A . B 2 HOH 47 47 47 HOH HOH A . B 2 HOH 48 48 48 HOH HOH A . B 2 HOH 49 49 49 HOH HOH A . B 2 HOH 50 50 50 HOH HOH A . B 2 HOH 51 51 51 HOH HOH A . B 2 HOH 52 52 52 HOH HOH A . B 2 HOH 53 53 53 HOH HOH A . B 2 HOH 54 54 54 HOH HOH A . B 2 HOH 55 55 55 HOH HOH A . B 2 HOH 56 56 56 HOH HOH A . B 2 HOH 57 57 57 HOH HOH A . B 2 HOH 58 58 58 HOH HOH A . B 2 HOH 59 59 59 HOH HOH A . B 2 HOH 60 60 60 HOH HOH A . B 2 HOH 61 61 61 HOH HOH A . B 2 HOH 62 62 62 HOH HOH A . B 2 HOH 63 63 63 HOH HOH A . B 2 HOH 64 64 64 HOH HOH A . B 2 HOH 65 65 65 HOH HOH A . B 2 HOH 66 66 66 HOH HOH A . B 2 HOH 67 67 67 HOH HOH A . B 2 HOH 68 68 68 HOH HOH A . B 2 HOH 69 69 69 HOH HOH A . B 2 HOH 70 70 70 HOH HOH A . B 2 HOH 71 71 71 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 # _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 2006-01-24 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2021-11-10 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 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 4 'Structure model' database_2 2 4 'Structure model' struct_ref_seq_dif # 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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_ref_seq_dif.details' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 PHASER phasing . ? 4 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 CD _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 LYS _pdbx_validate_rmsd_angle.auth_seq_id_1 411 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CE _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 LYS _pdbx_validate_rmsd_angle.auth_seq_id_2 411 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 NZ _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 LYS _pdbx_validate_rmsd_angle.auth_seq_id_3 411 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 127.94 _pdbx_validate_rmsd_angle.angle_target_value 111.70 _pdbx_validate_rmsd_angle.angle_deviation 16.24 _pdbx_validate_rmsd_angle.angle_standard_deviation 2.30 _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 TYR A 247 ? ? -110.78 -73.36 2 1 ASP A 248 ? ? 30.42 -123.88 3 1 PHE A 260 ? ? -110.09 79.92 4 1 GLU A 262 ? ? -152.59 -20.43 5 1 ARG A 263 ? ? -62.37 -81.94 6 1 ALA A 264 ? ? -149.89 13.57 7 1 THR A 267 ? ? 81.34 107.96 8 1 ASP A 271 ? ? 71.46 -56.53 9 1 VAL A 273 ? ? 32.60 37.04 10 1 ARG A 274 ? ? -141.23 -29.89 11 1 ASP A 288 ? ? -56.98 91.52 12 1 GLN A 289 ? ? -154.56 -48.43 13 1 HIS A 290 ? ? -143.25 -159.97 14 1 ILE A 295 ? ? -112.71 -88.09 15 1 VAL A 297 ? ? -163.36 113.46 16 1 ASP A 314 ? ? -91.49 53.11 17 1 ALA A 331 ? ? -143.33 -23.06 18 1 LYS A 334 ? ? -132.56 -40.96 19 1 ARG A 337 ? ? 56.59 106.50 20 1 PRO A 342 ? ? -93.75 38.28 21 1 VAL A 356 ? ? 46.67 90.23 22 1 SER A 359 ? ? 48.28 -171.64 23 1 ARG A 360 ? ? 63.28 -39.05 24 1 CYS A 365 ? ? 56.32 -177.80 25 1 THR A 380 ? ? -107.38 76.87 26 1 VAL A 383 ? ? 23.18 -74.27 27 1 ARG A 405 ? ? -107.65 -71.03 28 1 ILE A 408 ? ? -127.00 -135.65 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ARG 310 ? CG ? A ARG 71 CG 2 1 Y 1 A ARG 310 ? CD ? A ARG 71 CD 3 1 Y 1 A ARG 310 ? NE ? A ARG 71 NE 4 1 Y 1 A ARG 310 ? CZ ? A ARG 71 CZ 5 1 Y 1 A ARG 310 ? NH1 ? A ARG 71 NH1 6 1 Y 1 A ARG 310 ? NH2 ? A ARG 71 NH2 7 1 Y 1 A ARG 361 ? CG ? A ARG 122 CG 8 1 Y 1 A ARG 361 ? CD ? A ARG 122 CD 9 1 Y 1 A ARG 361 ? NE ? A ARG 122 NE 10 1 Y 1 A ARG 361 ? CZ ? A ARG 122 CZ 11 1 Y 1 A ARG 361 ? NH1 ? A ARG 122 NH1 12 1 Y 1 A ARG 361 ? NH2 ? A ARG 122 NH2 13 1 Y 1 A ARG 424 ? CG ? A ARG 185 CG 14 1 Y 1 A ARG 424 ? CD ? A ARG 185 CD 15 1 Y 1 A ARG 424 ? NE ? A ARG 185 NE 16 1 Y 1 A ARG 424 ? CZ ? A ARG 185 CZ 17 1 Y 1 A ARG 424 ? NH1 ? A ARG 185 NH1 18 1 Y 1 A ARG 424 ? NH2 ? A ARG 185 NH2 # 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 ARG 240 ? A ARG 1 2 1 Y 1 A ASN 241 ? A ASN 2 3 1 Y 1 A ILE 242 ? A ILE 3 4 1 Y 1 A ILE 243 ? A ILE 4 5 1 Y 1 A ALA 244 ? A ALA 5 6 1 Y 1 A ASP 429 ? A ASP 190 7 1 Y 1 A PRO 430 ? A PRO 191 8 1 Y 1 A GLY 431 ? A GLY 192 9 1 Y 1 A GLU 432 ? A GLU 193 10 1 Y 1 A VAL 433 ? A VAL 194 11 1 Y 1 A ARG 434 ? A ARG 195 12 1 Y 1 A GLY 435 ? A GLY 196 13 1 Y 1 A ALA 436 ? A ALA 197 14 1 Y 1 A GLU 437 ? A GLU 198 15 1 Y 1 A PRO 438 ? A PRO 199 16 1 Y 1 A ARG 439 ? A ARG 200 17 1 Y 1 A THR 440 ? A THR 201 18 1 Y 1 A ALA 441 ? A ALA 202 19 1 Y 1 A GLY 442 ? A GLY 203 20 1 Y 1 A VAL 443 ? A VAL 204 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #