data_2R8D # _entry.id 2R8D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2R8D RCSB RCSB044552 WWPDB D_1000044552 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type TargetDB APC86234.2 . unspecified PDB 2OAI ;Crystal structure of transporter associated domain CorC_HlyC from a Xylella fastidiosa Temecula1 hemolysin (same protein complexed with Ca++) ; unspecified # _pdbx_database_status.entry_id 2R8D _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-09-10 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cuff, M.E.' 1 'Volkart, L.' 2 'Joachimiak, A.' 3 'Midwest Center for Structural Genomics (MCSG)' 4 # _citation.id primary _citation.title 'The structure of transporter associated domain CorC in complex with Mg++ and Mn++ from Xylella fastidiosa.' _citation.journal_abbrev 'TO BE PUBLISHED' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Cuff, M.E.' 1 primary 'Volkart, L.' 2 primary 'Joachimiak, A.' 3 # _cell.length_a 88.061 _cell.length_b 88.061 _cell.length_c 88.061 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 2R8D _cell.pdbx_unique_axis ? _cell.Z_PDB 24 _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.space_group_name_H-M 'I 2 3' _symmetry.entry_id 2R8D _symmetry.Int_Tables_number 197 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _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 Hemolysin 10754.613 1 ? ? 'CorC_HlyC Domain: Residues 349-439' ? 2 non-polymer syn 'MANGANESE (II) ION' 54.938 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 68 ? ? ? ? # _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 ;SNAENTDEDAL(MSE)VTREDGSFLIDGTLPIEELREVLGAELPDGEENNYHTLAG(MSE)CISYFGRIPHVGEYFDWAG WRIEIVDLDGARID(MLY)LLLQRLN ; _entity_poly.pdbx_seq_one_letter_code_can ;SNAENTDEDALMVTREDGSFLIDGTLPIEELREVLGAELPDGEENNYHTLAGMCISYFGRIPHVGEYFDWAGWRIEIVDL DGARIDKLLLQRLN ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier APC86234.2 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 ASN n 1 3 ALA n 1 4 GLU n 1 5 ASN n 1 6 THR n 1 7 ASP n 1 8 GLU n 1 9 ASP n 1 10 ALA n 1 11 LEU n 1 12 MSE n 1 13 VAL n 1 14 THR n 1 15 ARG n 1 16 GLU n 1 17 ASP n 1 18 GLY n 1 19 SER n 1 20 PHE n 1 21 LEU n 1 22 ILE n 1 23 ASP n 1 24 GLY n 1 25 THR n 1 26 LEU n 1 27 PRO n 1 28 ILE n 1 29 GLU n 1 30 GLU n 1 31 LEU n 1 32 ARG n 1 33 GLU n 1 34 VAL n 1 35 LEU n 1 36 GLY n 1 37 ALA n 1 38 GLU n 1 39 LEU n 1 40 PRO n 1 41 ASP n 1 42 GLY n 1 43 GLU n 1 44 GLU n 1 45 ASN n 1 46 ASN n 1 47 TYR n 1 48 HIS n 1 49 THR n 1 50 LEU n 1 51 ALA n 1 52 GLY n 1 53 MSE n 1 54 CYS n 1 55 ILE n 1 56 SER n 1 57 TYR n 1 58 PHE n 1 59 GLY n 1 60 ARG n 1 61 ILE n 1 62 PRO n 1 63 HIS n 1 64 VAL n 1 65 GLY n 1 66 GLU n 1 67 TYR n 1 68 PHE n 1 69 ASP n 1 70 TRP n 1 71 ALA n 1 72 GLY n 1 73 TRP n 1 74 ARG n 1 75 ILE n 1 76 GLU n 1 77 ILE n 1 78 VAL n 1 79 ASP n 1 80 LEU n 1 81 ASP n 1 82 GLY n 1 83 ALA n 1 84 ARG n 1 85 ILE n 1 86 ASP n 1 87 MLY n 1 88 LEU n 1 89 LEU n 1 90 LEU n 1 91 GLN n 1 92 ARG n 1 93 LEU n 1 94 ASN 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 Xylella _entity_src_gen.pdbx_gene_src_gene tlyC _entity_src_gen.gene_src_species 'Xylella fastidiosa' _entity_src_gen.gene_src_strain Temecula1 _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 'Xylella fastidiosa' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 183190 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc 700964 _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(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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(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 pMCSG7 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q87DZ3_XYLFT _struct_ref.pdbx_db_accession Q87DZ3 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ENTDEDALMVTREDGSFLIDGTLPIEELREVLGAELPDGEENNYHTLAGMCISYFGRIPHVGEYFDWAGWRIEIVDLDGA RIDKLLLQRLN ; _struct_ref.pdbx_align_begin 349 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2R8D _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 94 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q87DZ3 _struct_ref_seq.db_align_beg 349 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 439 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 91 # 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 2R8D SER A 1 ? UNP Q87DZ3 ? ? 'EXPRESSION TAG' -2 1 1 2R8D ASN A 2 ? UNP Q87DZ3 ? ? 'EXPRESSION TAG' -1 2 1 2R8D ALA A 3 ? UNP Q87DZ3 ? ? 'EXPRESSION TAG' 0 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 MLY 'L-peptide linking' n N-DIMETHYL-LYSINE ? 'C8 H18 N2 O2' 174.241 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 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.crystals_number 1 _exptl.entry_id 2R8D _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.65 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 53.51 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details '0.1M Tris-HCl pH 8.5, 0.2M MgCl2, 20% PEG 8000, 5mM MnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2007-02-11 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'SAGITALLY FOCUSED Si(111)' _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97925 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97925 _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID # _reflns.entry_id 2R8D _reflns.d_resolution_high 2.000 _reflns.d_resolution_low 50.000 _reflns.number_obs 7134 _reflns.pdbx_Rmerge_I_obs 0.075 _reflns.pdbx_netI_over_sigmaI 9.900 _reflns.pdbx_chi_squared 1.902 _reflns.pdbx_redundancy 4.700 _reflns.percent_possible_obs 91.200 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3 _reflns.number_all 7134 _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate 36 _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_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.00 _reflns_shell.d_res_low 2.05 _reflns_shell.number_measured_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_unique_obs ? _reflns_shell.Rmerge_I_obs 0.356 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 0.575 _reflns_shell.pdbx_redundancy 1.30 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 151 _reflns_shell.percent_possible_all 30.70 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 2R8D _refine.ls_d_res_high 2.000 _refine.ls_d_res_low 25.400 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 91.210 _refine.ls_number_reflns_obs 7129 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_R_factor_obs 0.173 _refine.ls_R_factor_R_work 0.171 _refine.ls_R_factor_R_free 0.220 _refine.ls_percent_reflns_R_free 4.700 _refine.ls_number_reflns_R_free 337 _refine.B_iso_mean 59.580 _refine.correlation_coeff_Fo_to_Fc 0.968 _refine.correlation_coeff_Fo_to_Fc_free 0.946 _refine.pdbx_overall_ESU_R 0.152 _refine.pdbx_overall_ESU_R_Free 0.150 _refine.overall_SU_ML 0.106 _refine.overall_SU_B 7.054 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 7129 _refine.ls_R_factor_all 0.173 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _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_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _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 636 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 68 _refine_hist.number_atoms_total 706 _refine_hist.d_res_high 2.000 _refine_hist.d_res_low 25.400 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 655 0.013 0.022 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 887 1.309 1.971 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 79 5.875 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 34 42.734 23.529 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 107 14.963 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 6 20.481 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 98 0.094 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 499 0.005 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 309 0.185 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 446 0.310 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 40 0.132 0.200 ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined 1 0.005 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 23 0.205 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 5 0.152 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 404 1.201 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 623 1.423 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 291 2.259 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 263 3.391 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.000 _refine_ls_shell.d_res_low 2.053 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 33.330 _refine_ls_shell.number_reflns_R_work 179 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.267 _refine_ls_shell.R_factor_R_free 0.292 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 9 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 188 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2R8D _struct.title ;The structure of transporter associated domain CorC_HlyC from a Xylella fastidiosa Temecula1 hemolysin in complex with Mg++ and Mn++ ; _struct.pdbx_descriptor Hemolysin _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2R8D _struct_keywords.pdbx_keywords TOXIN _struct_keywords.text ;CorC, hemolysin, structural genomics, pfam03471, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TOXIN ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # _struct_biol.id 1 _struct_biol.details 'Authors state that the biological unit of this polypeptide is unknown, likely dimer.' # 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 PRO A 27 ? GLY A 36 ? PRO A 24 GLY A 33 1 ? 10 HELX_P HELX_P2 2 THR A 49 ? GLY A 59 ? THR A 46 GLY A 56 1 ? 11 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc1 metalc ? ? A ASP 79 OD2 ? ? ? 1_555 B MN . MN ? ? A ASP 76 A MN 92 1_555 ? ? ? ? ? ? ? 2.061 ? metalc2 metalc ? ? A ASP 81 OD2 ? ? ? 1_555 B MN . MN ? ? A ASP 78 A MN 92 1_555 ? ? ? ? ? ? ? 2.178 ? metalc3 metalc ? ? A ASP 86 OD2 ? ? ? 1_555 C MG . MG ? ? A ASP 83 A MG 93 1_555 ? ? ? ? ? ? ? 2.125 ? metalc4 metalc ? ? A ASP 86 OD2 ? ? ? 1_555 B MN . MN ? ? A ASP 83 A MN 92 1_555 ? ? ? ? ? ? ? 2.424 ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 93 A HOH 104 1_555 ? ? ? ? ? ? ? 2.264 ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 93 A HOH 96 1_555 ? ? ? ? ? ? ? 2.180 ? metalc7 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 93 A HOH 133 1_555 ? ? ? ? ? ? ? 1.985 ? covale1 covale ? ? A LEU 11 C ? ? ? 1_555 A MSE 12 N ? ? A LEU 8 A MSE 9 1_555 ? ? ? ? ? ? ? 1.324 ? covale2 covale ? ? A MSE 12 C ? ? ? 1_555 A VAL 13 N ? ? A MSE 9 A VAL 10 1_555 ? ? ? ? ? ? ? 1.329 ? covale3 covale ? ? A GLY 52 C ? ? ? 1_555 A MSE 53 N ? ? A GLY 49 A MSE 50 1_555 ? ? ? ? ? ? ? 1.332 ? covale4 covale ? ? A MSE 53 C ? ? ? 1_555 A CYS 54 N ? ? A MSE 50 A CYS 51 1_555 ? ? ? ? ? ? ? 1.325 ? covale5 covale ? ? A ASP 86 C ? ? ? 1_555 A MLY 87 N ? ? A ASP 83 A MLY 84 1_555 ? ? ? ? ? ? ? 1.332 ? covale6 covale ? ? A MLY 87 C ? ? ? 1_555 A LEU 88 N ? ? A MLY 84 A LEU 85 1_555 ? ? ? ? ? ? ? 1.331 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? covale ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel # 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 MSE A 12 ? THR A 14 ? MSE A 9 THR A 11 A 2 PHE A 20 ? ASP A 23 ? PHE A 17 ASP A 20 A 3 ARG A 84 ? ARG A 92 ? ARG A 81 ARG A 89 A 4 TRP A 73 ? ASP A 81 ? TRP A 70 ASP A 78 A 5 TYR A 67 ? TRP A 70 ? TYR A 64 TRP A 67 # 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 VAL A 13 ? N VAL A 10 O LEU A 21 ? O LEU A 18 A 2 3 N PHE A 20 ? N PHE A 17 O LEU A 90 ? O LEU A 87 A 3 4 O GLN A 91 ? O GLN A 88 N ARG A 74 ? N ARG A 71 A 4 5 O TRP A 73 ? O TRP A 70 N TRP A 70 ? N TRP A 67 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE MN A 92' AC2 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE MG A 93' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 ASP A 79 ? ASP A 76 . ? 4_565 ? 2 AC1 6 ASP A 79 ? ASP A 76 . ? 1_555 ? 3 AC1 6 ASP A 81 ? ASP A 78 . ? 4_565 ? 4 AC1 6 ASP A 81 ? ASP A 78 . ? 1_555 ? 5 AC1 6 ASP A 86 ? ASP A 83 . ? 1_555 ? 6 AC1 6 ASP A 86 ? ASP A 83 . ? 4_565 ? 7 AC2 6 ASP A 79 ? ASP A 76 . ? 4_565 ? 8 AC2 6 ASP A 81 ? ASP A 78 . ? 4_565 ? 9 AC2 6 ASP A 86 ? ASP A 83 . ? 1_555 ? 10 AC2 6 HOH D . ? HOH A 96 . ? 1_555 ? 11 AC2 6 HOH D . ? HOH A 104 . ? 1_555 ? 12 AC2 6 HOH D . ? HOH A 133 . ? 1_555 ? # _atom_sites.entry_id 2R8D _atom_sites.fract_transf_matrix[1][1] 0.011356 _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] 0.011356 _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] 0.011356 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MG MN N O S SE # 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 SER 1 -2 ? ? ? A . n A 1 2 ASN 2 -1 ? ? ? A . n A 1 3 ALA 3 0 ? ? ? A . n A 1 4 GLU 4 1 ? ? ? A . n A 1 5 ASN 5 2 ? ? ? A . n A 1 6 THR 6 3 ? ? ? A . n A 1 7 ASP 7 4 ? ? ? A . n A 1 8 GLU 8 5 ? ? ? A . n A 1 9 ASP 9 6 ? ? ? A . n A 1 10 ALA 10 7 7 ALA ALA A . n A 1 11 LEU 11 8 8 LEU LEU A . n A 1 12 MSE 12 9 9 MSE MSE A . n A 1 13 VAL 13 10 10 VAL VAL A . n A 1 14 THR 14 11 11 THR THR A . n A 1 15 ARG 15 12 12 ARG ARG A . n A 1 16 GLU 16 13 13 GLU GLU A . n A 1 17 ASP 17 14 14 ASP ASP A . n A 1 18 GLY 18 15 15 GLY GLY A . n A 1 19 SER 19 16 16 SER SER A . n A 1 20 PHE 20 17 17 PHE PHE A . n A 1 21 LEU 21 18 18 LEU LEU A . n A 1 22 ILE 22 19 19 ILE ILE A . n A 1 23 ASP 23 20 20 ASP ASP A . n A 1 24 GLY 24 21 21 GLY GLY A . n A 1 25 THR 25 22 22 THR THR A . n A 1 26 LEU 26 23 23 LEU LEU A . n A 1 27 PRO 27 24 24 PRO PRO A . n A 1 28 ILE 28 25 25 ILE ILE A . n A 1 29 GLU 29 26 26 GLU GLU A . n A 1 30 GLU 30 27 27 GLU GLU A . n A 1 31 LEU 31 28 28 LEU LEU A . n A 1 32 ARG 32 29 29 ARG ARG A . n A 1 33 GLU 33 30 30 GLU GLU A . n A 1 34 VAL 34 31 31 VAL VAL A . n A 1 35 LEU 35 32 32 LEU LEU A . n A 1 36 GLY 36 33 33 GLY GLY A . n A 1 37 ALA 37 34 34 ALA ALA A . n A 1 38 GLU 38 35 35 GLU GLU A . n A 1 39 LEU 39 36 ? ? ? A . n A 1 40 PRO 40 37 ? ? ? A . n A 1 41 ASP 41 38 ? ? ? A . n A 1 42 GLY 42 39 ? ? ? A . n A 1 43 GLU 43 40 ? ? ? A . n A 1 44 GLU 44 41 ? ? ? A . n A 1 45 ASN 45 42 42 ASN ASN A . n A 1 46 ASN 46 43 43 ASN ASN A . n A 1 47 TYR 47 44 44 TYR TYR A . n A 1 48 HIS 48 45 45 HIS HIS A . n A 1 49 THR 49 46 46 THR THR A . n A 1 50 LEU 50 47 47 LEU LEU A . n A 1 51 ALA 51 48 48 ALA ALA A . n A 1 52 GLY 52 49 49 GLY GLY A . n A 1 53 MSE 53 50 50 MSE MSE A . n A 1 54 CYS 54 51 51 CYS CYS A . n A 1 55 ILE 55 52 52 ILE ILE A . n A 1 56 SER 56 53 53 SER SER A . n A 1 57 TYR 57 54 54 TYR TYR A . n A 1 58 PHE 58 55 55 PHE PHE A . n A 1 59 GLY 59 56 56 GLY GLY A . n A 1 60 ARG 60 57 57 ARG ARG A . n A 1 61 ILE 61 58 58 ILE ILE A . n A 1 62 PRO 62 59 59 PRO PRO A . n A 1 63 HIS 63 60 60 HIS HIS A . n A 1 64 VAL 64 61 61 VAL VAL A . n A 1 65 GLY 65 62 62 GLY GLY A . n A 1 66 GLU 66 63 63 GLU GLU A . n A 1 67 TYR 67 64 64 TYR TYR A . n A 1 68 PHE 68 65 65 PHE PHE A . n A 1 69 ASP 69 66 66 ASP ASP A . n A 1 70 TRP 70 67 67 TRP TRP A . n A 1 71 ALA 71 68 68 ALA ALA A . n A 1 72 GLY 72 69 69 GLY GLY A . n A 1 73 TRP 73 70 70 TRP TRP A . n A 1 74 ARG 74 71 71 ARG ARG A . n A 1 75 ILE 75 72 72 ILE ILE A . n A 1 76 GLU 76 73 73 GLU GLU A . n A 1 77 ILE 77 74 74 ILE ILE A . n A 1 78 VAL 78 75 75 VAL VAL A . n A 1 79 ASP 79 76 76 ASP ASP A . n A 1 80 LEU 80 77 77 LEU LEU A . n A 1 81 ASP 81 78 78 ASP ASP A . n A 1 82 GLY 82 79 79 GLY GLY A . n A 1 83 ALA 83 80 80 ALA ALA A . n A 1 84 ARG 84 81 81 ARG ARG A . n A 1 85 ILE 85 82 82 ILE ILE A . n A 1 86 ASP 86 83 83 ASP ASP A . n A 1 87 MLY 87 84 84 MLY MLY A . n A 1 88 LEU 88 85 85 LEU LEU A . n A 1 89 LEU 89 86 86 LEU LEU A . n A 1 90 LEU 90 87 87 LEU LEU A . n A 1 91 GLN 91 88 88 GLN GLN A . n A 1 92 ARG 92 89 89 ARG ARG A . n A 1 93 LEU 93 90 90 LEU LEU A . n A 1 94 ASN 94 91 91 ASN ASN A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Midwest Center for Structural Genomics' _pdbx_SG_project.initial_of_center MCSG # 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 MN 1 92 1 MN MN A . C 3 MG 1 93 1 MG MG A . D 4 HOH 1 94 1 HOH HOH A . D 4 HOH 2 95 2 HOH HOH A . D 4 HOH 3 96 3 HOH HOH A . D 4 HOH 4 97 4 HOH HOH A . D 4 HOH 5 98 5 HOH HOH A . D 4 HOH 6 99 6 HOH HOH A . D 4 HOH 7 100 7 HOH HOH A . D 4 HOH 8 101 8 HOH HOH A . D 4 HOH 9 102 9 HOH HOH A . D 4 HOH 10 103 10 HOH HOH A . D 4 HOH 11 104 11 HOH HOH A . D 4 HOH 12 105 12 HOH HOH A . D 4 HOH 13 106 13 HOH HOH A . D 4 HOH 14 107 14 HOH HOH A . D 4 HOH 15 108 15 HOH HOH A . D 4 HOH 16 109 16 HOH HOH A . D 4 HOH 17 110 17 HOH HOH A . D 4 HOH 18 111 18 HOH HOH A . D 4 HOH 19 112 19 HOH HOH A . D 4 HOH 20 113 20 HOH HOH A . D 4 HOH 21 114 21 HOH HOH A . D 4 HOH 22 115 22 HOH HOH A . D 4 HOH 23 116 23 HOH HOH A . D 4 HOH 24 117 24 HOH HOH A . D 4 HOH 25 118 25 HOH HOH A . D 4 HOH 26 119 26 HOH HOH A . D 4 HOH 27 120 27 HOH HOH A . D 4 HOH 28 121 28 HOH HOH A . D 4 HOH 29 122 29 HOH HOH A . D 4 HOH 30 123 30 HOH HOH A . D 4 HOH 31 124 31 HOH HOH A . D 4 HOH 32 125 32 HOH HOH A . D 4 HOH 33 126 33 HOH HOH A . D 4 HOH 34 127 34 HOH HOH A . D 4 HOH 35 128 35 HOH HOH A . D 4 HOH 36 129 36 HOH HOH A . D 4 HOH 37 130 37 HOH HOH A . D 4 HOH 38 131 38 HOH HOH A . D 4 HOH 39 132 39 HOH HOH A . D 4 HOH 40 133 40 HOH HOH A . D 4 HOH 41 134 41 HOH HOH A . D 4 HOH 42 135 42 HOH HOH A . D 4 HOH 43 136 43 HOH HOH A . D 4 HOH 44 137 44 HOH HOH A . D 4 HOH 45 138 45 HOH HOH A . D 4 HOH 46 139 46 HOH HOH A . D 4 HOH 47 140 47 HOH HOH A . D 4 HOH 48 141 48 HOH HOH A . D 4 HOH 49 142 49 HOH HOH A . D 4 HOH 50 143 50 HOH HOH A . D 4 HOH 51 144 51 HOH HOH A . D 4 HOH 52 145 52 HOH HOH A . D 4 HOH 53 146 53 HOH HOH A . D 4 HOH 54 147 54 HOH HOH A . D 4 HOH 55 148 55 HOH HOH A . D 4 HOH 56 149 56 HOH HOH A . D 4 HOH 57 150 57 HOH HOH A . D 4 HOH 58 151 58 HOH HOH A . D 4 HOH 59 152 59 HOH HOH A . D 4 HOH 60 153 60 HOH HOH A . D 4 HOH 61 154 61 HOH HOH A . D 4 HOH 62 155 62 HOH HOH A . D 4 HOH 63 156 63 HOH HOH A . D 4 HOH 64 157 64 HOH HOH A . D 4 HOH 65 158 65 HOH HOH A . D 4 HOH 66 159 66 HOH HOH A . D 4 HOH 67 160 67 HOH HOH A . D 4 HOH 68 161 68 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 12 A MSE 9 ? MET SELENOMETHIONINE 2 A MSE 53 A MSE 50 ? MET SELENOMETHIONINE 3 A MLY 87 A MLY 84 ? LYS N-DIMETHYL-LYSINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_assembly_prop.biol_id 1 _pdbx_struct_assembly_prop.type 'ABSA (A^2)' _pdbx_struct_assembly_prop.value 1640 _pdbx_struct_assembly_prop.details ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 4_565 x,-y+1,-z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 88.0610000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id MN _pdbx_struct_special_symmetry.auth_seq_id 92 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id MN _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OD2 ? A ASP 79 ? A ASP 76 ? 1_555 MN ? B MN . ? A MN 92 ? 1_555 OD2 ? A ASP 81 ? A ASP 78 ? 1_555 87.6 ? 2 OD2 ? A ASP 79 ? A ASP 76 ? 1_555 MN ? B MN . ? A MN 92 ? 1_555 OD2 ? A ASP 86 ? A ASP 83 ? 1_555 88.7 ? 3 OD2 ? A ASP 81 ? A ASP 78 ? 1_555 MN ? B MN . ? A MN 92 ? 1_555 OD2 ? A ASP 86 ? A ASP 83 ? 1_555 87.8 ? 4 OD2 ? A ASP 86 ? A ASP 83 ? 1_555 MG ? C MG . ? A MG 93 ? 1_555 O ? D HOH . ? A HOH 104 ? 1_555 84.2 ? 5 OD2 ? A ASP 86 ? A ASP 83 ? 1_555 MG ? C MG . ? A MG 93 ? 1_555 O ? D HOH . ? A HOH 96 ? 1_555 85.1 ? 6 O ? D HOH . ? A HOH 104 ? 1_555 MG ? C MG . ? A MG 93 ? 1_555 O ? D HOH . ? A HOH 96 ? 1_555 86.2 ? 7 OD2 ? A ASP 86 ? A ASP 83 ? 1_555 MG ? C MG . ? A MG 93 ? 1_555 O ? D HOH . ? A HOH 133 ? 1_555 171.4 ? 8 O ? D HOH . ? A HOH 104 ? 1_555 MG ? C MG . ? A MG 93 ? 1_555 O ? D HOH . ? A HOH 133 ? 1_555 87.2 ? 9 O ? D HOH . ? A HOH 96 ? 1_555 MG ? C MG . ? A MG 93 ? 1_555 O ? D HOH . ? A HOH 133 ? 1_555 93.8 ? # 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 2007-11-13 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 # _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 ? # 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' Advisory 2 2 'Structure model' 'Source and taxonomy' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 3 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # _diffrn_reflns.diffrn_id 1 _diffrn_reflns.pdbx_d_res_high 2.000 _diffrn_reflns.pdbx_d_res_low 50.000 _diffrn_reflns.pdbx_number_obs 7134 _diffrn_reflns.pdbx_Rmerge_I_obs 0.075 _diffrn_reflns.pdbx_Rsym_value ? _diffrn_reflns.pdbx_chi_squared 1.90 _diffrn_reflns.av_sigmaI_over_netI 9.90 _diffrn_reflns.pdbx_redundancy 4.70 _diffrn_reflns.pdbx_percent_possible_obs 91.20 _diffrn_reflns.number 33510 _diffrn_reflns.pdbx_observed_criterion ? _diffrn_reflns.limit_h_max ? _diffrn_reflns.limit_h_min ? _diffrn_reflns.limit_k_max ? _diffrn_reflns.limit_k_min ? _diffrn_reflns.limit_l_max ? _diffrn_reflns.limit_l_min ? # loop_ _pdbx_diffrn_reflns_shell.diffrn_id _pdbx_diffrn_reflns_shell.d_res_high _pdbx_diffrn_reflns_shell.d_res_low _pdbx_diffrn_reflns_shell.number_obs _pdbx_diffrn_reflns_shell.rejects _pdbx_diffrn_reflns_shell.Rmerge_I_obs _pdbx_diffrn_reflns_shell.Rsym_value _pdbx_diffrn_reflns_shell.chi_squared _pdbx_diffrn_reflns_shell.redundancy _pdbx_diffrn_reflns_shell.percent_possible_obs 1 4.93 50.00 ? ? 0.069 ? 7.141 5.00 99.30 1 3.91 4.93 ? ? 0.062 ? 3.995 5.30 100.00 1 3.42 3.91 ? ? 0.063 ? 2.727 5.40 100.00 1 3.11 3.42 ? ? 0.060 ? 1.566 5.50 100.00 1 2.88 3.11 ? ? 0.072 ? 1.161 5.50 100.00 1 2.71 2.88 ? ? 0.095 ? 1.022 5.50 100.00 1 2.58 2.71 ? ? 0.122 ? 0.895 5.50 100.00 1 2.47 2.58 ? ? 0.148 ? 0.814 5.40 100.00 1 2.37 2.47 ? ? 0.198 ? 0.779 5.30 99.60 1 2.29 2.37 ? ? 0.238 ? 0.697 5.00 99.00 1 2.22 2.29 ? ? 0.287 ? 0.705 4.20 99.00 1 2.15 2.22 ? ? 0.353 ? 0.723 3.20 95.00 1 2.10 2.15 ? ? 0.368 ? 0.674 2.30 81.60 1 2.05 2.10 ? ? 0.459 ? 0.811 1.60 60.30 1 2.00 2.05 ? ? 0.356 ? 0.575 1.30 30.70 # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 23.6435 _pdbx_refine_tls.origin_y 41.4612 _pdbx_refine_tls.origin_z 10.5886 _pdbx_refine_tls.T[1][1] -0.3476 _pdbx_refine_tls.T[2][2] -0.2472 _pdbx_refine_tls.T[3][3] -0.3122 _pdbx_refine_tls.T[1][2] 0.0340 _pdbx_refine_tls.T[1][3] -0.0018 _pdbx_refine_tls.T[2][3] 0.0519 _pdbx_refine_tls.L[1][1] 3.2223 _pdbx_refine_tls.L[2][2] 5.4709 _pdbx_refine_tls.L[3][3] 3.7470 _pdbx_refine_tls.L[1][2] -1.1919 _pdbx_refine_tls.L[1][3] -1.4603 _pdbx_refine_tls.L[2][3] 0.0242 _pdbx_refine_tls.S[1][1] 0.0269 _pdbx_refine_tls.S[2][2] 0.3394 _pdbx_refine_tls.S[3][3] -0.3662 _pdbx_refine_tls.S[1][2] -0.5916 _pdbx_refine_tls.S[1][3] 0.0936 _pdbx_refine_tls.S[2][3] -0.0143 _pdbx_refine_tls.S[2][1] 0.6604 _pdbx_refine_tls.S[3][1] 0.0107 _pdbx_refine_tls.S[3][2] -0.0750 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 10 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 94 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 7 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 91 _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # _pdbx_phasing_MAD_set.id 1 _pdbx_phasing_MAD_set.d_res_high 2.00 _pdbx_phasing_MAD_set.d_res_low 50.00 _pdbx_phasing_MAD_set.reflns_acentric 6470 _pdbx_phasing_MAD_set.loc_acentric 0.100 _pdbx_phasing_MAD_set.power_acentric 0.000 _pdbx_phasing_MAD_set.R_cullis_acentric 1.410 _pdbx_phasing_MAD_set.reflns_centric 664 _pdbx_phasing_MAD_set.loc_centric 0.100 _pdbx_phasing_MAD_set.power_centric 0.000 _pdbx_phasing_MAD_set.R_cullis_centric 1.000 # loop_ _pdbx_phasing_MAD_set_shell.id _pdbx_phasing_MAD_set_shell.d_res_high _pdbx_phasing_MAD_set_shell.d_res_low _pdbx_phasing_MAD_set_shell.reflns_acentric _pdbx_phasing_MAD_set_shell.loc_acentric _pdbx_phasing_MAD_set_shell.power_acentric _pdbx_phasing_MAD_set_shell.R_cullis_acentric _pdbx_phasing_MAD_set_shell.reflns_centric _pdbx_phasing_MAD_set_shell.loc_centric _pdbx_phasing_MAD_set_shell.power_centric _pdbx_phasing_MAD_set_shell.R_cullis_centric 1 12.50 50.00 21 1.100 0.000 1.580 14 0.800 0.000 1.000 1 7.14 12.50 115 0.800 0.000 1.280 42 0.600 0.000 1.000 1 5.00 7.14 286 0.600 0.000 1.550 62 0.300 0.000 1.000 1 3.85 5.00 527 0.400 0.000 1.180 85 0.300 0.000 1.000 1 3.13 3.85 849 0.200 0.000 1.200 102 0.100 0.000 1.000 1 2.63 3.13 1261 0.100 0.000 3.280 130 0.000 0.000 1.000 1 2.27 2.63 1731 0.100 0.000 1.970 146 0.000 0.000 1.000 1 2.00 2.27 1680 0.000 0.000 1.130 83 0.000 0.000 1.000 # loop_ _pdbx_phasing_MAD_set_site.id _pdbx_phasing_MAD_set_site.atom_type_symbol _pdbx_phasing_MAD_set_site.fract_x _pdbx_phasing_MAD_set_site.fract_y _pdbx_phasing_MAD_set_site.fract_z _pdbx_phasing_MAD_set_site.b_iso _pdbx_phasing_MAD_set_site.occupancy 1 Se -0.265 -0.533 -0.201 62.92737 0.000 2 Se -0.274 -0.633 -0.082 98.77704 0.000 # loop_ _pdbx_phasing_MAD_shell.d_res_high _pdbx_phasing_MAD_shell.d_res_low _pdbx_phasing_MAD_shell.reflns _pdbx_phasing_MAD_shell.fom _pdbx_phasing_MAD_shell.reflns_centric _pdbx_phasing_MAD_shell.fom_centric _pdbx_phasing_MAD_shell.reflns_acentric _pdbx_phasing_MAD_shell.fom_acentric 12.50 50.00 35 0.291 14 0.000 21 0.485 7.14 12.50 157 0.442 42 0.000 115 0.604 5.00 7.14 348 0.439 62 0.000 286 0.535 3.85 5.00 612 0.381 85 0.000 527 0.443 3.13 3.85 951 0.349 102 0.000 849 0.391 2.63 3.13 1391 0.219 130 0.000 1261 0.241 2.27 2.63 1877 0.080 146 0.000 1731 0.087 2.00 2.27 1763 0.015 83 0.000 1680 0.016 # _pdbx_phasing_dm.entry_id 2R8D _pdbx_phasing_dm.method 'Solvent flattening and Histogram matching' _pdbx_phasing_dm.reflns 7134 # loop_ _pdbx_phasing_dm_shell.d_res_high _pdbx_phasing_dm_shell.d_res_low _pdbx_phasing_dm_shell.delta_phi_final _pdbx_phasing_dm_shell.delta_phi_initial _pdbx_phasing_dm_shell.fom_acentric _pdbx_phasing_dm_shell.fom_centric _pdbx_phasing_dm_shell.fom _pdbx_phasing_dm_shell.reflns_acentric _pdbx_phasing_dm_shell.reflns_centric _pdbx_phasing_dm_shell.reflns 5.130 100.000 57.500 ? ? ? 0.846 ? ? 501 4.040 5.130 58.300 ? ? ? 0.925 ? ? 501 3.510 4.040 58.900 ? ? ? 0.896 ? ? 502 3.170 3.510 59.800 ? ? ? 0.883 ? ? 516 2.940 3.170 61.500 ? ? ? 0.854 ? ? 507 2.760 2.940 60.000 ? ? ? 0.874 ? ? 501 2.620 2.760 70.600 ? ? ? 0.878 ? ? 502 2.510 2.620 70.400 ? ? ? 0.868 ? ? 507 2.410 2.510 78.600 ? ? ? 0.868 ? ? 502 2.320 2.410 76.700 ? ? ? 0.882 ? ? 502 2.250 2.320 81.800 ? ? ? 0.850 ? ? 502 2.180 2.250 89.200 ? ? ? 0.840 ? ? 530 2.110 2.180 85.600 ? ? ? 0.819 ? ? 503 2.000 2.110 89.700 ? ? ? 0.624 ? ? 558 # _phasing.method SAD # _phasing_MAD.entry_id 2R8D _phasing_MAD.pdbx_d_res_high 2.00 _phasing_MAD.pdbx_d_res_low 50.00 _phasing_MAD.pdbx_reflns 7134 _phasing_MAD.pdbx_fom 0.179 _phasing_MAD.pdbx_reflns_centric 664 _phasing_MAD.pdbx_fom_centric 0.000 _phasing_MAD.pdbx_reflns_acentric 6470 _phasing_MAD.pdbx_fom_acentric 0.198 # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal DENZO . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data reduction' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 2 MLPHARE . ? other 'Z.Otwinowski or E.Dodson' 'ccp4@dl.ac.uk, ccp4@yorvic.york.ac.uk' phasing http://www.ccp4.ac.uk/main.html Fortran_77 ? 3 DM 5.0 ? program 'K. Cowtan' ccp4@dl.ac.uk phasing http://www.ccp4.ac.uk/main.html Fortran_77 ? 4 REFMAC . ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 5 PDB_EXTRACT 3.000 'July 2, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 6 SBC-Collect . ? ? ? ? 'data collection' ? ? ? 7 HKL-3000 . ? ? ? ? 'data reduction' ? ? ? 8 HKL-3000 . ? ? ? ? 'data scaling' ? ? ? 9 HKL-3000 . ? ? ? ? phasing ? ? ? 10 SHELXD . ? ? ? ? phasing ? ? ? 11 SHELXE . ? ? ? ? 'model building' ? ? ? 12 SOLVE . ? ? ? ? phasing ? ? ? 13 RESOLVE . ? ? ? ? phasing ? ? ? 14 ARP/wARP . ? ? ? ? 'model building' ? ? ? 15 CCP4 . ? ? ? ? phasing ? ? ? 16 O . ? ? ? ? 'model building' ? ? ? 17 Coot . ? ? ? ? 'model building' ? ? ? 18 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id HIS _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 45 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -141.27 _pdbx_validate_torsion.psi -6.76 # 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 SER -2 ? A SER 1 2 1 Y 1 A ASN -1 ? A ASN 2 3 1 Y 1 A ALA 0 ? A ALA 3 4 1 Y 1 A GLU 1 ? A GLU 4 5 1 Y 1 A ASN 2 ? A ASN 5 6 1 Y 1 A THR 3 ? A THR 6 7 1 Y 1 A ASP 4 ? A ASP 7 8 1 Y 1 A GLU 5 ? A GLU 8 9 1 Y 1 A ASP 6 ? A ASP 9 10 1 Y 1 A LEU 36 ? A LEU 39 11 1 Y 1 A PRO 37 ? A PRO 40 12 1 Y 1 A ASP 38 ? A ASP 41 13 1 Y 1 A GLY 39 ? A GLY 42 14 1 Y 1 A GLU 40 ? A GLU 43 15 1 Y 1 A GLU 41 ? A GLU 44 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MANGANESE (II) ION' MN 3 'MAGNESIUM ION' MG 4 water HOH #