data_1YD0 # _entry.id 1YD0 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1YD0 RCSB RCSB031390 WWPDB D_1000031390 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1LN0 'Endonuclease domain of I-TevI' unspecified PDB 1MK0 'Endonuclease domain of I-TevI' unspecified PDB 1KFT 'Solution Structure Of The C-Terminal Domain Of Uvrc From E- Coli' unspecified PDB 1D9X 'Crystal Structure of UvrB' unspecified PDB 1YCZ 'the same protein from Thermotoga maritima' unspecified PDB 1YD1 'the same protein from Thermotoga maritima bound to magnesium' unspecified PDB 1YD2 'the same protein from Thermotoga maritima Y19F mutant bound to manganese' unspecified PDB 1YD3 'the same protein from Thermotoga maritima Y43F mutant bound to manganese' unspecified PDB 1YD4 'the same protein from Thermotoga maritima Y29F mutant bound to manganese' unspecified PDB 1YD5 'the same protein from Thermotoga maritima N88A mutant bound to manganese' unspecified PDB 1YD6 'the same protein from Bacillus caldotenax' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YD0 _pdbx_database_status.recvd_initial_deposition_date 2004-12-23 _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 ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Truglio, J.J.' 1 'Rhau, B.' 2 'Croteau, D.L.' 3 'Wang, L.' 4 'Skorvaga, M.' 5 'Karakas, E.' 6 'DellaVecchia, M.J.' 7 'Wang, H.' 8 'Van Houten, B.' 9 'Kisker, C.' 10 # _citation.id primary _citation.title 'Structural insights into the first incision reaction during nucleotide excision repair' _citation.journal_abbrev 'Embo J.' _citation.journal_volume 24 _citation.page_first 885 _citation.page_last 894 _citation.year 2005 _citation.journal_id_ASTM EMJODG _citation.country UK _citation.journal_id_ISSN 0261-4189 _citation.journal_id_CSD 0897 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15692561 _citation.pdbx_database_id_DOI 10.1038/sj.emboj.7600568 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Truglio, J.J.' 1 primary 'Rhau, B.' 2 primary 'Croteau, D.L.' 3 primary 'Wang, L.' 4 primary 'Skorvaga, M.' 5 primary 'Karakas, E.' 6 primary 'Dellavecchia, M.J.' 7 primary 'Wang, H.' 8 primary 'Van Houten, B.' 9 primary 'Kisker, C.' 10 # _cell.entry_id 1YD0 _cell.length_a 55.009 _cell.length_b 55.009 _cell.length_c 109.025 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YD0 _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _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 'UvrABC system protein C' 11378.382 1 ? ? 'N-terminal domain' ? 2 non-polymer syn 'MANGANESE (II) ION' 54.938 4 ? ? ? ? 3 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 4 water nat water 18.015 132 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'UvrC protein, Excinuclease ABC subunit C' # _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 ;MKEKIRKKILLAPEEPGVYIFKNKGVPIYIGKAKRLSNRLRSYLNPQTEKVFRIGEEADELETIVVMNEREAFILEANLI KKYRPKYNVRLKDTDF ; _entity_poly.pdbx_seq_one_letter_code_can ;MKEKIRKKILLAPEEPGVYIFKNKGVPIYIGKAKRLSNRLRSYLNPQTEKVFRIGEEADELETIVVMNEREAFILEANLI KKYRPKYNVRLKDTDF ; _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 LYS n 1 3 GLU n 1 4 LYS n 1 5 ILE n 1 6 ARG n 1 7 LYS n 1 8 LYS n 1 9 ILE n 1 10 LEU n 1 11 LEU n 1 12 ALA n 1 13 PRO n 1 14 GLU n 1 15 GLU n 1 16 PRO n 1 17 GLY n 1 18 VAL n 1 19 TYR n 1 20 ILE n 1 21 PHE n 1 22 LYS n 1 23 ASN n 1 24 LYS n 1 25 GLY n 1 26 VAL n 1 27 PRO n 1 28 ILE n 1 29 TYR n 1 30 ILE n 1 31 GLY n 1 32 LYS n 1 33 ALA n 1 34 LYS n 1 35 ARG n 1 36 LEU n 1 37 SER n 1 38 ASN n 1 39 ARG n 1 40 LEU n 1 41 ARG n 1 42 SER n 1 43 TYR n 1 44 LEU n 1 45 ASN n 1 46 PRO n 1 47 GLN n 1 48 THR n 1 49 GLU n 1 50 LYS n 1 51 VAL n 1 52 PHE n 1 53 ARG n 1 54 ILE n 1 55 GLY n 1 56 GLU n 1 57 GLU n 1 58 ALA n 1 59 ASP n 1 60 GLU n 1 61 LEU n 1 62 GLU n 1 63 THR n 1 64 ILE n 1 65 VAL n 1 66 VAL n 1 67 MET n 1 68 ASN n 1 69 GLU n 1 70 ARG n 1 71 GLU n 1 72 ALA n 1 73 PHE n 1 74 ILE n 1 75 LEU n 1 76 GLU n 1 77 ALA n 1 78 ASN n 1 79 LEU n 1 80 ILE n 1 81 LYS n 1 82 LYS n 1 83 TYR n 1 84 ARG n 1 85 PRO n 1 86 LYS n 1 87 TYR n 1 88 ASN n 1 89 VAL n 1 90 ARG n 1 91 LEU n 1 92 LYS n 1 93 ASP n 1 94 THR n 1 95 ASP n 1 96 PHE 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 Thermotoga _entity_src_gen.pdbx_gene_src_gene ? _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 'Thermotoga maritima' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2336 _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 562 _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 ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _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 ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code UVRC_THEMA _struct_ref.pdbx_db_accession Q9WYA3 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MKEKIRKKILLAPEEPGVYIFKNKGVPIYIGKAKRLSNRLRSYLNPQTEKVFRIGEEADELETIVVMNEREAFILEANLI KKYRPKYNVRLKDTDF ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1YD0 _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 96 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9WYA3 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 96 _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 96 # 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 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 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 1YD0 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.7 _exptl_crystal.density_percent_sol 66 _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 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.pdbx_details 'PEG 8000, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 ? ? 1 3 ? ? 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2004-01-01 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.1 _diffrn_radiation_wavelength.wt 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'NSLS BEAMLINE X26C' NSLS X26C ? 1.1 2 SYNCHROTRON 'NSLS BEAMLINE X12B' NSLS X12B ? 1.1 3 SYNCHROTRON 'NSLS BEAMLINE X25' NSLS X25 ? 1.1 # _reflns.entry_id 1YD0 _reflns.observed_criterion_sigma_F 2 _reflns.observed_criterion_sigma_I 2 _reflns.d_resolution_high 1.5 _reflns.d_resolution_low 30 _reflns.number_all 50076 _reflns.number_obs 50076 _reflns.percent_possible_obs 98.4 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.5 _reflns_shell.d_res_low 1.54 _reflns_shell.percent_possible_all 99 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1YD0 _refine.ls_number_reflns_obs 25612 _refine.ls_number_reflns_all 25612 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 15.00 _refine.ls_d_res_high 1.50 _refine.ls_percent_reflns_obs 98.43 _refine.ls_R_factor_obs 0.16761 _refine.ls_R_factor_all 0.17 _refine.ls_R_factor_R_work 0.16672 _refine.ls_R_factor_R_free 0.18456 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 1358 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.960 _refine.correlation_coeff_Fo_to_Fc_free 0.953 _refine.B_iso_mean 24.806 _refine.aniso_B[1][1] 0.37 _refine.aniso_B[2][2] 0.37 _refine.aniso_B[3][3] -0.73 _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 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _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 0.057 _refine.pdbx_overall_ESU_R_Free 0.053 _refine.overall_SU_ML 0.026 _refine.overall_SU_B 1.454 _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 738 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 10 _refine_hist.number_atoms_solvent 132 _refine_hist.number_atoms_total 880 _refine_hist.d_res_high 1.50 _refine_hist.d_res_low 15.00 # 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 0.013 0.022 ? 755 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.456 2.013 ? 1009 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.028 5.000 ? 88 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 27.063 23.529 ? 34 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 12.365 15.000 ? 158 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 20.078 15.000 ? 7 'X-RAY DIFFRACTION' ? r_chiral_restr 0.091 0.200 ? 110 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.020 ? 544 'X-RAY DIFFRACTION' ? r_nbd_refined 0.198 0.200 ? 345 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.315 0.200 ? 534 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.161 0.200 ? 81 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.191 0.200 ? 19 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.162 0.200 ? 15 'X-RAY DIFFRACTION' ? r_mcbond_it 1.877 1.500 ? 463 'X-RAY DIFFRACTION' ? r_mcangle_it 2.574 2.000 ? 724 'X-RAY DIFFRACTION' ? r_scbond_it 4.082 3.000 ? 325 'X-RAY DIFFRACTION' ? r_scangle_it 5.941 4.500 ? 285 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 2.397 3.000 ? 788 'X-RAY DIFFRACTION' ? r_sphericity_free 7.469 3.000 ? 136 'X-RAY DIFFRACTION' ? r_sphericity_bonded 5.255 3.000 ? 744 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.503 _refine_ls_shell.d_res_low 1.542 _refine_ls_shell.number_reflns_R_work 1837 _refine_ls_shell.R_factor_R_work 0.14 _refine_ls_shell.percent_reflns_obs 98.93 _refine_ls_shell.R_factor_R_free 0.195 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 108 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # _struct.entry_id 1YD0 _struct.title ;Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima bound to its catalytic divalent cation: manganese ; _struct.pdbx_descriptor 'UvrABC system protein C' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YD0 _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN' _struct_keywords.text 'DNA BINDING PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 3 ? G N N 4 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 LYS A 2 ? ALA A 12 ? LYS A 2 ALA A 12 1 ? 11 HELX_P HELX_P2 2 ARG A 35 ? SER A 42 ? ARG A 35 SER A 42 1 ? 8 HELX_P HELX_P3 3 TYR A 43 ? ASN A 45 ? TYR A 43 ASN A 45 5 ? 3 HELX_P HELX_P4 4 THR A 48 ? ALA A 58 ? THR A 48 ALA A 58 1 ? 11 HELX_P HELX_P5 5 ASN A 68 ? ARG A 84 ? ASN A 68 ARG A 84 1 ? 17 # _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 ? ? B MN . MN ? ? ? 1_555 A GLU 76 OE2 ? ? A MN 2001 A GLU 76 1_555 ? ? ? ? ? ? ? 2.079 ? metalc2 metalc ? ? B MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2001 A HOH 2123 1_555 ? ? ? ? ? ? ? 2.152 ? metalc3 metalc ? ? B MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2001 A HOH 2026 1_555 ? ? ? ? ? ? ? 2.217 ? metalc4 metalc ? ? B MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2001 A HOH 2126 1_555 ? ? ? ? ? ? ? 2.137 ? metalc5 metalc ? ? B MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2001 A HOH 2007 1_555 ? ? ? ? ? ? ? 2.356 ? metalc6 metalc ? ? B MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2001 A HOH 2022 1_555 ? ? ? ? ? ? ? 2.178 ? metalc7 metalc ? ? D MN . MN ? ? ? 1_555 A GLU 49 OE2 ? ? A MN 2003 A GLU 49 1_555 ? ? ? ? ? ? ? 1.969 ? metalc8 metalc ? ? D MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2003 A HOH 2087 1_555 ? ? ? ? ? ? ? 2.140 ? metalc9 metalc ? ? D MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2003 A HOH 2128 1_555 ? ? ? ? ? ? ? 2.145 ? metalc10 metalc ? ? E MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2004 A HOH 2090 1_555 ? ? ? ? ? ? ? 2.033 ? metalc11 metalc ? ? E MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2004 A HOH 2110 1_555 ? ? ? ? ? ? ? 2.231 ? metalc12 metalc ? ? E MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2004 A HOH 2061 1_555 ? ? ? ? ? ? ? 2.296 ? metalc13 metalc ? ? E MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2004 A HOH 2107 1_555 ? ? ? ? ? ? ? 2.156 ? metalc14 metalc ? ? E MN . MN ? ? ? 1_555 A GLU 60 OE1 ? ? A MN 2004 A GLU 60 1_555 ? ? ? ? ? ? ? 1.990 ? metalc15 metalc ? ? E MN . MN ? ? ? 1_555 G HOH . O ? ? A MN 2004 A HOH 2101 1_555 ? ? ? ? ? ? ? 2.123 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 3 _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 # 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 VAL A 26 ? ALA A 33 ? VAL A 26 ALA A 33 A 2 GLY A 17 ? ASN A 23 ? GLY A 17 ASN A 23 A 3 GLU A 60 ? VAL A 65 ? GLU A 60 VAL A 65 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O ILE A 28 ? O ILE A 28 N PHE A 21 ? N PHE A 21 A 2 3 N ILE A 20 ? N ILE A 20 O GLU A 62 ? O GLU A 62 # 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 2001' AC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE MN A 2002' AC3 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE MN A 2003' AC4 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE MN A 2004' AC5 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE GOL A 1001' # 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 GLU A 76 ? GLU A 76 . ? 1_555 ? 2 AC1 6 HOH G . ? HOH A 2007 . ? 1_555 ? 3 AC1 6 HOH G . ? HOH A 2022 . ? 1_555 ? 4 AC1 6 HOH G . ? HOH A 2026 . ? 1_555 ? 5 AC1 6 HOH G . ? HOH A 2123 . ? 1_555 ? 6 AC1 6 HOH G . ? HOH A 2126 . ? 1_555 ? 7 AC2 3 MET A 1 ? MET A 1 . ? 3_644 ? 8 AC2 3 ARG A 6 ? ARG A 6 . ? 3_644 ? 9 AC2 3 ASN A 68 ? ASN A 68 . ? 1_555 ? 10 AC3 3 GLU A 49 ? GLU A 49 . ? 1_555 ? 11 AC3 3 HOH G . ? HOH A 2087 . ? 1_555 ? 12 AC3 3 HOH G . ? HOH A 2128 . ? 1_555 ? 13 AC4 6 GLU A 60 ? GLU A 60 . ? 1_555 ? 14 AC4 6 HOH G . ? HOH A 2061 . ? 1_555 ? 15 AC4 6 HOH G . ? HOH A 2090 . ? 1_555 ? 16 AC4 6 HOH G . ? HOH A 2101 . ? 1_555 ? 17 AC4 6 HOH G . ? HOH A 2107 . ? 1_555 ? 18 AC4 6 HOH G . ? HOH A 2110 . ? 1_555 ? 19 AC5 7 ILE A 20 ? ILE A 20 . ? 1_555 ? 20 AC5 7 LYS A 22 ? LYS A 22 . ? 1_555 ? 21 AC5 7 PRO A 27 ? PRO A 27 . ? 1_555 ? 22 AC5 7 GLU A 62 ? GLU A 62 . ? 1_555 ? 23 AC5 7 TYR A 83 ? TYR A 83 . ? 1_555 ? 24 AC5 7 HOH G . ? HOH A 2055 . ? 1_555 ? 25 AC5 7 HOH G . ? HOH A 2095 . ? 1_555 ? # _database_PDB_matrix.entry_id 1YD0 _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 1YD0 _atom_sites.fract_transf_matrix[1][1] 0.018179 _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] 0.018179 _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] 0.009172 _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 MN 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 MET 1 1 1 MET MET A . n A 1 2 LYS 2 2 2 LYS LYS A . n A 1 3 GLU 3 3 3 GLU GLU A . n A 1 4 LYS 4 4 4 LYS LYS A . n A 1 5 ILE 5 5 5 ILE ILE A . n A 1 6 ARG 6 6 6 ARG ARG A . n A 1 7 LYS 7 7 7 LYS LYS A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 ILE 9 9 9 ILE ILE A . n A 1 10 LEU 10 10 10 LEU LEU A . n A 1 11 LEU 11 11 11 LEU LEU A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 PRO 13 13 13 PRO PRO A . n A 1 14 GLU 14 14 14 GLU GLU A . n A 1 15 GLU 15 15 15 GLU GLU A . n A 1 16 PRO 16 16 16 PRO PRO A . n A 1 17 GLY 17 17 17 GLY GLY A . n A 1 18 VAL 18 18 18 VAL VAL A . n A 1 19 TYR 19 19 19 TYR TYR A . n A 1 20 ILE 20 20 20 ILE ILE A . n A 1 21 PHE 21 21 21 PHE PHE A . n A 1 22 LYS 22 22 22 LYS LYS A . n A 1 23 ASN 23 23 23 ASN ASN A . n A 1 24 LYS 24 24 24 LYS LYS A . n A 1 25 GLY 25 25 25 GLY GLY A . n A 1 26 VAL 26 26 26 VAL VAL A . n A 1 27 PRO 27 27 27 PRO PRO A . n A 1 28 ILE 28 28 28 ILE ILE A . n A 1 29 TYR 29 29 29 TYR TYR A . n A 1 30 ILE 30 30 30 ILE ILE A . n A 1 31 GLY 31 31 31 GLY GLY A . n A 1 32 LYS 32 32 32 LYS LYS A . n A 1 33 ALA 33 33 33 ALA ALA A . n A 1 34 LYS 34 34 34 LYS LYS A . n A 1 35 ARG 35 35 35 ARG ARG A . n A 1 36 LEU 36 36 36 LEU LEU A . n A 1 37 SER 37 37 37 SER SER A . n A 1 38 ASN 38 38 38 ASN ASN A . n A 1 39 ARG 39 39 39 ARG ARG A . n A 1 40 LEU 40 40 40 LEU LEU A . n A 1 41 ARG 41 41 41 ARG ARG A . n A 1 42 SER 42 42 42 SER SER A . n A 1 43 TYR 43 43 43 TYR TYR A . n A 1 44 LEU 44 44 44 LEU LEU A . n A 1 45 ASN 45 45 45 ASN ASN A . n A 1 46 PRO 46 46 46 PRO PRO A . n A 1 47 GLN 47 47 47 GLN GLN A . n A 1 48 THR 48 48 48 THR THR A . n A 1 49 GLU 49 49 49 GLU GLU A . n A 1 50 LYS 50 50 50 LYS LYS A . n A 1 51 VAL 51 51 51 VAL VAL A . n A 1 52 PHE 52 52 52 PHE PHE A . n A 1 53 ARG 53 53 53 ARG ARG A . n A 1 54 ILE 54 54 54 ILE ILE A . n A 1 55 GLY 55 55 55 GLY GLY A . n A 1 56 GLU 56 56 56 GLU GLU A . n A 1 57 GLU 57 57 57 GLU GLU A . n A 1 58 ALA 58 58 58 ALA ALA A . n A 1 59 ASP 59 59 59 ASP ASP A . n A 1 60 GLU 60 60 60 GLU GLU A . n A 1 61 LEU 61 61 61 LEU LEU A . n A 1 62 GLU 62 62 62 GLU GLU A . n A 1 63 THR 63 63 63 THR THR A . n A 1 64 ILE 64 64 64 ILE ILE A . n A 1 65 VAL 65 65 65 VAL VAL A . n A 1 66 VAL 66 66 66 VAL VAL A . n A 1 67 MET 67 67 67 MET MET A . n A 1 68 ASN 68 68 68 ASN ASN A . n A 1 69 GLU 69 69 69 GLU GLU A . n A 1 70 ARG 70 70 70 ARG ARG A . n A 1 71 GLU 71 71 71 GLU GLU A . n A 1 72 ALA 72 72 72 ALA ALA A . n A 1 73 PHE 73 73 73 PHE PHE A . n A 1 74 ILE 74 74 74 ILE ILE A . n A 1 75 LEU 75 75 75 LEU LEU A . n A 1 76 GLU 76 76 76 GLU GLU A . n A 1 77 ALA 77 77 77 ALA ALA A . n A 1 78 ASN 78 78 78 ASN ASN A . n A 1 79 LEU 79 79 79 LEU LEU A . n A 1 80 ILE 80 80 80 ILE ILE A . n A 1 81 LYS 81 81 81 LYS LYS A . n A 1 82 LYS 82 82 82 LYS LYS A . n A 1 83 TYR 83 83 83 TYR TYR A . n A 1 84 ARG 84 84 84 ARG ARG A . n A 1 85 PRO 85 85 85 PRO PRO A . n A 1 86 LYS 86 86 86 LYS LYS A . n A 1 87 TYR 87 87 87 TYR TYR A . n A 1 88 ASN 88 88 88 ASN ASN A . n A 1 89 VAL 89 89 89 VAL VAL A . n A 1 90 ARG 90 90 ? ? ? A . n A 1 91 LEU 91 91 ? ? ? A . n A 1 92 LYS 92 92 ? ? ? A . n A 1 93 ASP 93 93 ? ? ? A . n A 1 94 THR 94 94 ? ? ? A . n A 1 95 ASP 95 95 ? ? ? A . n A 1 96 PHE 96 96 ? ? ? 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 MN 1 2001 1 MN MN A . C 2 MN 1 2002 2 MN MN A . D 2 MN 1 2003 3 MN MN A . E 2 MN 1 2004 4 MN MN A . F 3 GOL 1 1001 1 GOL GOL A . G 4 HOH 1 2005 1 HOH HOH A . G 4 HOH 2 2006 2 HOH HOH A . G 4 HOH 3 2007 3 HOH HOH A . G 4 HOH 4 2008 4 HOH HOH A . G 4 HOH 5 2009 5 HOH HOH A . G 4 HOH 6 2010 6 HOH HOH A . G 4 HOH 7 2011 7 HOH HOH A . G 4 HOH 8 2012 8 HOH HOH A . G 4 HOH 9 2013 9 HOH HOH A . G 4 HOH 10 2014 10 HOH HOH A . G 4 HOH 11 2015 11 HOH HOH A . G 4 HOH 12 2016 12 HOH HOH A . G 4 HOH 13 2017 13 HOH HOH A . G 4 HOH 14 2018 14 HOH HOH A . G 4 HOH 15 2019 15 HOH HOH A . G 4 HOH 16 2020 16 HOH HOH A . G 4 HOH 17 2021 17 HOH HOH A . G 4 HOH 18 2022 18 HOH HOH A . G 4 HOH 19 2023 19 HOH HOH A . G 4 HOH 20 2024 20 HOH HOH A . G 4 HOH 21 2025 21 HOH HOH A . G 4 HOH 22 2026 22 HOH HOH A . G 4 HOH 23 2027 23 HOH HOH A . G 4 HOH 24 2028 24 HOH HOH A . G 4 HOH 25 2029 25 HOH HOH A . G 4 HOH 26 2030 26 HOH HOH A . G 4 HOH 27 2031 27 HOH HOH A . G 4 HOH 28 2032 28 HOH HOH A . G 4 HOH 29 2033 29 HOH HOH A . G 4 HOH 30 2034 30 HOH HOH A . G 4 HOH 31 2035 31 HOH HOH A . G 4 HOH 32 2036 32 HOH HOH A . G 4 HOH 33 2037 33 HOH HOH A . G 4 HOH 34 2038 34 HOH HOH A . G 4 HOH 35 2039 35 HOH HOH A . G 4 HOH 36 2040 36 HOH HOH A . G 4 HOH 37 2041 37 HOH HOH A . G 4 HOH 38 2042 38 HOH HOH A . G 4 HOH 39 2043 39 HOH HOH A . G 4 HOH 40 2044 40 HOH HOH A . G 4 HOH 41 2045 41 HOH HOH A . G 4 HOH 42 2046 42 HOH HOH A . G 4 HOH 43 2047 43 HOH HOH A . G 4 HOH 44 2048 44 HOH HOH A . G 4 HOH 45 2049 45 HOH HOH A . G 4 HOH 46 2050 46 HOH HOH A . G 4 HOH 47 2051 47 HOH HOH A . G 4 HOH 48 2052 48 HOH HOH A . G 4 HOH 49 2053 49 HOH HOH A . G 4 HOH 50 2054 50 HOH HOH A . G 4 HOH 51 2055 51 HOH HOH A . G 4 HOH 52 2056 52 HOH HOH A . G 4 HOH 53 2057 53 HOH HOH A . G 4 HOH 54 2058 54 HOH HOH A . G 4 HOH 55 2059 55 HOH HOH A . G 4 HOH 56 2060 56 HOH HOH A . G 4 HOH 57 2061 57 HOH HOH A . G 4 HOH 58 2062 58 HOH HOH A . G 4 HOH 59 2063 60 HOH HOH A . G 4 HOH 60 2064 61 HOH HOH A . G 4 HOH 61 2065 62 HOH HOH A . G 4 HOH 62 2066 63 HOH HOH A . G 4 HOH 63 2067 64 HOH HOH A . G 4 HOH 64 2068 65 HOH HOH A . G 4 HOH 65 2069 66 HOH HOH A . G 4 HOH 66 2070 67 HOH HOH A . G 4 HOH 67 2071 68 HOH HOH A . G 4 HOH 68 2072 69 HOH HOH A . G 4 HOH 69 2073 70 HOH HOH A . G 4 HOH 70 2074 71 HOH HOH A . G 4 HOH 71 2075 72 HOH HOH A . G 4 HOH 72 2076 73 HOH HOH A . G 4 HOH 73 2077 74 HOH HOH A . G 4 HOH 74 2078 75 HOH HOH A . G 4 HOH 75 2079 76 HOH HOH A . G 4 HOH 76 2080 77 HOH HOH A . G 4 HOH 77 2081 78 HOH HOH A . G 4 HOH 78 2082 79 HOH HOH A . G 4 HOH 79 2083 80 HOH HOH A . G 4 HOH 80 2084 81 HOH HOH A . G 4 HOH 81 2085 82 HOH HOH A . G 4 HOH 82 2086 83 HOH HOH A . G 4 HOH 83 2087 84 HOH HOH A . G 4 HOH 84 2088 85 HOH HOH A . G 4 HOH 85 2089 87 HOH HOH A . G 4 HOH 86 2090 88 HOH HOH A . G 4 HOH 87 2091 89 HOH HOH A . G 4 HOH 88 2092 90 HOH HOH A . G 4 HOH 89 2093 91 HOH HOH A . G 4 HOH 90 2094 92 HOH HOH A . G 4 HOH 91 2095 94 HOH HOH A . G 4 HOH 92 2096 95 HOH HOH A . G 4 HOH 93 2097 96 HOH HOH A . G 4 HOH 94 2098 97 HOH HOH A . G 4 HOH 95 2099 98 HOH HOH A . G 4 HOH 96 2100 99 HOH HOH A . G 4 HOH 97 2101 100 HOH HOH A . G 4 HOH 98 2102 101 HOH HOH A . G 4 HOH 99 2103 102 HOH HOH A . G 4 HOH 100 2104 103 HOH HOH A . G 4 HOH 101 2105 104 HOH HOH A . G 4 HOH 102 2106 105 HOH HOH A . G 4 HOH 103 2107 106 HOH HOH A . G 4 HOH 104 2108 107 HOH HOH A . G 4 HOH 105 2109 108 HOH HOH A . G 4 HOH 106 2110 110 HOH HOH A . G 4 HOH 107 2111 111 HOH HOH A . G 4 HOH 108 2112 114 HOH HOH A . G 4 HOH 109 2113 115 HOH HOH A . G 4 HOH 110 2114 117 HOH HOH A . G 4 HOH 111 2115 118 HOH HOH A . G 4 HOH 112 2116 119 HOH HOH A . G 4 HOH 113 2117 120 HOH HOH A . G 4 HOH 114 2118 121 HOH HOH A . G 4 HOH 115 2119 122 HOH HOH A . G 4 HOH 116 2120 124 HOH HOH A . G 4 HOH 117 2121 125 HOH HOH A . G 4 HOH 118 2122 126 HOH HOH A . G 4 HOH 119 2123 127 HOH HOH A . G 4 HOH 120 2124 129 HOH HOH A . G 4 HOH 121 2125 130 HOH HOH A . G 4 HOH 122 2126 131 HOH HOH A . G 4 HOH 123 2127 133 HOH HOH A . G 4 HOH 124 2128 134 HOH HOH A . G 4 HOH 125 2129 135 HOH HOH A . G 4 HOH 126 2130 137 HOH HOH A . G 4 HOH 127 2131 138 HOH HOH A . G 4 HOH 128 2132 139 HOH HOH A . G 4 HOH 129 2133 141 HOH HOH A . G 4 HOH 130 2134 144 HOH HOH A . G 4 HOH 131 2135 147 HOH HOH A . G 4 HOH 132 2136 148 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # _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 # _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 HOH _pdbx_struct_special_symmetry.auth_seq_id 2076 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id G _pdbx_struct_special_symmetry.label_comp_id HOH _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 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2123 ? 1_555 86.5 ? 2 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2026 ? 1_555 98.1 ? 3 O ? G HOH . ? A HOH 2123 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2026 ? 1_555 86.7 ? 4 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2126 ? 1_555 90.2 ? 5 O ? G HOH . ? A HOH 2123 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2126 ? 1_555 172.5 ? 6 O ? G HOH . ? A HOH 2026 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2126 ? 1_555 87.0 ? 7 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2007 ? 1_555 89.8 ? 8 O ? G HOH . ? A HOH 2123 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2007 ? 1_555 95.2 ? 9 O ? G HOH . ? A HOH 2026 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2007 ? 1_555 171.9 ? 10 O ? G HOH . ? A HOH 2126 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2007 ? 1_555 91.5 ? 11 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2022 ? 1_555 174.2 ? 12 O ? G HOH . ? A HOH 2123 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2022 ? 1_555 89.7 ? 13 O ? G HOH . ? A HOH 2026 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2022 ? 1_555 86.1 ? 14 O ? G HOH . ? A HOH 2126 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2022 ? 1_555 94.0 ? 15 O ? G HOH . ? A HOH 2007 ? 1_555 MN ? B MN . ? A MN 2001 ? 1_555 O ? G HOH . ? A HOH 2022 ? 1_555 86.1 ? 16 OE2 ? A GLU 49 ? A GLU 49 ? 1_555 MN ? D MN . ? A MN 2003 ? 1_555 O ? G HOH . ? A HOH 2087 ? 1_555 104.2 ? 17 OE2 ? A GLU 49 ? A GLU 49 ? 1_555 MN ? D MN . ? A MN 2003 ? 1_555 O ? G HOH . ? A HOH 2128 ? 1_555 102.4 ? 18 O ? G HOH . ? A HOH 2087 ? 1_555 MN ? D MN . ? A MN 2003 ? 1_555 O ? G HOH . ? A HOH 2128 ? 1_555 81.2 ? 19 O ? G HOH . ? A HOH 2090 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2110 ? 1_555 93.2 ? 20 O ? G HOH . ? A HOH 2090 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2061 ? 1_555 86.2 ? 21 O ? G HOH . ? A HOH 2110 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2061 ? 1_555 179.1 ? 22 O ? G HOH . ? A HOH 2090 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2107 ? 1_555 175.6 ? 23 O ? G HOH . ? A HOH 2110 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2107 ? 1_555 88.1 ? 24 O ? G HOH . ? A HOH 2061 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2107 ? 1_555 92.5 ? 25 O ? G HOH . ? A HOH 2090 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 OE1 ? A GLU 60 ? A GLU 60 ? 1_555 98.8 ? 26 O ? G HOH . ? A HOH 2110 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 OE1 ? A GLU 60 ? A GLU 60 ? 1_555 99.5 ? 27 O ? G HOH . ? A HOH 2061 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 OE1 ? A GLU 60 ? A GLU 60 ? 1_555 81.2 ? 28 O ? G HOH . ? A HOH 2107 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 OE1 ? A GLU 60 ? A GLU 60 ? 1_555 85.1 ? 29 O ? G HOH . ? A HOH 2090 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2101 ? 1_555 87.1 ? 30 O ? G HOH . ? A HOH 2110 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2101 ? 1_555 84.7 ? 31 O ? G HOH . ? A HOH 2061 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2101 ? 1_555 94.6 ? 32 O ? G HOH . ? A HOH 2107 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2101 ? 1_555 88.9 ? 33 OE1 ? A GLU 60 ? A GLU 60 ? 1_555 MN ? E MN . ? A MN 2004 ? 1_555 O ? G HOH . ? A HOH 2101 ? 1_555 172.5 ? # 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 2005-03-01 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 # _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' 'Version format compliance' 2 3 'Structure model' 'Non-polymer description' 3 3 'Structure model' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0005 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CNS phasing . ? 4 # 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 90 ? A ARG 90 2 1 Y 1 A LEU 91 ? A LEU 91 3 1 Y 1 A LYS 92 ? A LYS 92 4 1 Y 1 A ASP 93 ? A ASP 93 5 1 Y 1 A THR 94 ? A THR 94 6 1 Y 1 A ASP 95 ? A ASP 95 7 1 Y 1 A PHE 96 ? A PHE 96 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MANGANESE (II) ION' MN 3 GLYCEROL GOL 4 water HOH #