data_1YD4 # _entry.id 1YD4 # _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 1YD4 pdb_00001yd4 10.2210/pdb1yd4/pdb RCSB RCSB031394 ? ? WWPDB D_1000031394 ? ? # 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 1YD0 'the same protein from Thermotoga maritima bound to manganese' 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 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 1YD4 _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 ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # 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 _citation_author.identifier_ORCID 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 1YD4 _cell.length_a 54.949 _cell.length_b 54.949 _cell.length_c 109.187 _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 1YD4 _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' 11362.382 1 ? Y29F 'N-terminal domain' ? 2 non-polymer syn 'MANGANESE (II) ION' 54.938 3 ? ? ? ? 3 water nat water 18.015 119 ? ? ? ? # _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 ;MKEKIRKKILLAPEEPGVYIFKNKGVPIFIGKAKRLSNRLRSYLNPQTEKVFRIGEEADELETIVVMNEREAFILEANLI KKYRPKYNVRLKDTDF ; _entity_poly.pdbx_seq_one_letter_code_can ;MKEKIRKKILLAPEEPGVYIFKNKGVPIFIGKAKRLSNRLRSYLNPQTEKVFRIGEEADELETIVVMNEREAFILEANLI 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 PHE 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 1YD4 _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 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 1YD4 _struct_ref_seq_dif.mon_id PHE _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 29 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q9WYA3 _struct_ref_seq_dif.db_mon_id TYR _struct_ref_seq_dif.pdbx_seq_db_seq_num 29 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 29 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 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 1YD4 _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 1YD4 _reflns.observed_criterion_sigma_F 2 _reflns.observed_criterion_sigma_I 2 _reflns.d_resolution_high 1.9 _reflns.d_resolution_low 30 _reflns.number_all 25177 _reflns.number_obs 25177 _reflns.percent_possible_obs 100 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.9 _reflns_shell.d_res_low 1.97 _reflns_shell.percent_possible_all 100 _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1YD4 _refine.ls_number_reflns_obs 13072 _refine.ls_number_reflns_all 13072 _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 1.90 _refine.ls_percent_reflns_obs 99.90 _refine.ls_R_factor_obs 0.17231 _refine.ls_R_factor_all 0.185 _refine.ls_R_factor_R_work 0.17064 _refine.ls_R_factor_R_free 0.20551 _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 693 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.959 _refine.correlation_coeff_Fo_to_Fc_free 0.948 _refine.B_iso_mean 21.860 _refine.aniso_B[1][1] 0.43 _refine.aniso_B[2][2] 0.43 _refine.aniso_B[3][3] -0.85 _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 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _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 0.099 _refine.pdbx_overall_ESU_R_Free 0.102 _refine.overall_SU_ML 0.060 _refine.overall_SU_B 3.786 _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 737 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 119 _refine_hist.number_atoms_total 859 _refine_hist.d_res_high 1.90 _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 0.018 0.022 ? 749 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 732 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.527 2.006 ? 1002 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.842 3.000 ? 1710 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.304 5.000 ? 88 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 28.275 23.529 ? 34 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 16.205 15.000 ? 158 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 21.767 15.000 ? 7 'X-RAY DIFFRACTION' ? r_chiral_restr 0.094 0.200 ? 110 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 792 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 147 'X-RAY DIFFRACTION' ? r_nbd_refined 0.232 0.200 ? 130 'X-RAY DIFFRACTION' ? r_nbd_other 0.183 0.200 ? 691 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.185 0.200 ? 365 'X-RAY DIFFRACTION' ? r_nbtor_other 0.089 0.200 ? 452 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.182 0.200 ? 66 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.223 0.200 ? 2 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.310 0.200 ? 34 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.161 0.200 ? 13 'X-RAY DIFFRACTION' ? r_mcbond_it 1.671 1.500 ? 588 'X-RAY DIFFRACTION' ? r_mcbond_other 0.290 1.500 ? 179 'X-RAY DIFFRACTION' ? r_mcangle_it 1.663 2.000 ? 724 'X-RAY DIFFRACTION' ? r_scbond_it 3.726 3.000 ? 356 'X-RAY DIFFRACTION' ? r_scangle_it 5.161 4.500 ? 278 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.901 _refine_ls_shell.d_res_low 1.949 _refine_ls_shell.number_reflns_R_work 925 _refine_ls_shell.R_factor_R_work 0.167 _refine_ls_shell.percent_reflns_obs 98.98 _refine_ls_shell.R_factor_R_free 0.218 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 48 _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 1YD4 _struct.title ;Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y29F bound to its catalytic divalent cation ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YD4 _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 3 ? # 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 _struct_conn.pdbx_role metalc1 metalc ? ? A GLU 60 OE1 ? ? ? 1_555 D MN . MN ? ? A GLU 60 A MN 1004 1_555 ? ? ? ? ? ? ? 2.190 ? ? metalc2 metalc ? ? A GLU 62 OE2 ? ? ? 1_555 D MN . MN ? ? A GLU 62 A MN 1004 1_555 ? ? ? ? ? ? ? 2.295 ? ? metalc3 metalc ? ? A GLU 76 OE2 ? ? ? 1_555 B MN . MN ? ? A GLU 76 A MN 1001 1_555 ? ? ? ? ? ? ? 2.069 ? ? metalc4 metalc ? ? B MN . MN ? ? ? 1_555 E HOH . O ? ? A MN 1001 A HOH 1022 1_555 ? ? ? ? ? ? ? 2.272 ? ? metalc5 metalc ? ? B MN . MN ? ? ? 1_555 E HOH . O ? ? A MN 1001 A HOH 1034 1_555 ? ? ? ? ? ? ? 2.138 ? ? metalc6 metalc ? ? B MN . MN ? ? ? 1_555 E HOH . O ? ? A MN 1001 A HOH 1058 1_555 ? ? ? ? ? ? ? 2.347 ? ? metalc7 metalc ? ? B MN . MN ? ? ? 1_555 E HOH . O ? ? A MN 1001 A HOH 1059 1_555 ? ? ? ? ? ? ? 2.308 ? ? metalc8 metalc ? ? B MN . MN ? ? ? 1_555 E HOH . O ? ? A MN 1001 A HOH 1123 1_555 ? ? ? ? ? ? ? 2.143 ? ? metalc9 metalc ? ? D MN . MN ? ? ? 1_555 E HOH . O ? ? A MN 1004 A HOH 1074 1_555 ? ? ? ? ? ? ? 2.639 ? ? # _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 VAL A 18 ? N VAL A 18 O ILE A 64 ? O ILE A 64 # 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 A MN 1001 ? 6 'BINDING SITE FOR RESIDUE MN A 1001' AC2 Software A MN 1002 ? 3 'BINDING SITE FOR RESIDUE MN A 1002' AC3 Software A MN 1004 ? 3 'BINDING SITE FOR RESIDUE MN A 1004' # 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 E . ? HOH A 1022 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH A 1034 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH A 1058 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH A 1059 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH A 1123 . ? 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 60 ? GLU A 60 . ? 1_555 ? 11 AC3 3 GLU A 62 ? GLU A 62 . ? 1_555 ? 12 AC3 3 HOH E . ? HOH A 1074 . ? 1_555 ? # _database_PDB_matrix.entry_id 1YD4 _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 1YD4 _atom_sites.fract_transf_matrix[1][1] 0.018199 _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] 0.018199 _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] 0.009159 _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 PHE 29 29 29 PHE PHE 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 1001 1 MN MN A . C 2 MN 1 1002 2 MN MN A . D 2 MN 1 1004 4 MN MN A . E 3 HOH 1 1005 1 HOH HOH A . E 3 HOH 2 1006 2 HOH HOH A . E 3 HOH 3 1007 3 HOH HOH A . E 3 HOH 4 1008 4 HOH HOH A . E 3 HOH 5 1009 5 HOH HOH A . E 3 HOH 6 1010 6 HOH HOH A . E 3 HOH 7 1011 7 HOH HOH A . E 3 HOH 8 1012 8 HOH HOH A . E 3 HOH 9 1013 9 HOH HOH A . E 3 HOH 10 1014 10 HOH HOH A . E 3 HOH 11 1015 11 HOH HOH A . E 3 HOH 12 1016 12 HOH HOH A . E 3 HOH 13 1017 13 HOH HOH A . E 3 HOH 14 1018 14 HOH HOH A . E 3 HOH 15 1019 15 HOH HOH A . E 3 HOH 16 1020 16 HOH HOH A . E 3 HOH 17 1021 17 HOH HOH A . E 3 HOH 18 1022 18 HOH HOH A . E 3 HOH 19 1023 19 HOH HOH A . E 3 HOH 20 1024 20 HOH HOH A . E 3 HOH 21 1025 21 HOH HOH A . E 3 HOH 22 1026 22 HOH HOH A . E 3 HOH 23 1027 23 HOH HOH A . E 3 HOH 24 1028 24 HOH HOH A . E 3 HOH 25 1029 25 HOH HOH A . E 3 HOH 26 1030 26 HOH HOH A . E 3 HOH 27 1031 27 HOH HOH A . E 3 HOH 28 1032 28 HOH HOH A . E 3 HOH 29 1033 29 HOH HOH A . E 3 HOH 30 1034 30 HOH HOH A . E 3 HOH 31 1035 31 HOH HOH A . E 3 HOH 32 1036 32 HOH HOH A . E 3 HOH 33 1037 33 HOH HOH A . E 3 HOH 34 1038 34 HOH HOH A . E 3 HOH 35 1039 35 HOH HOH A . E 3 HOH 36 1040 36 HOH HOH A . E 3 HOH 37 1041 37 HOH HOH A . E 3 HOH 38 1042 38 HOH HOH A . E 3 HOH 39 1043 39 HOH HOH A . E 3 HOH 40 1044 40 HOH HOH A . E 3 HOH 41 1045 41 HOH HOH A . E 3 HOH 42 1046 42 HOH HOH A . E 3 HOH 43 1047 43 HOH HOH A . E 3 HOH 44 1048 44 HOH HOH A . E 3 HOH 45 1049 45 HOH HOH A . E 3 HOH 46 1050 46 HOH HOH A . E 3 HOH 47 1051 47 HOH HOH A . E 3 HOH 48 1052 48 HOH HOH A . E 3 HOH 49 1053 49 HOH HOH A . E 3 HOH 50 1054 50 HOH HOH A . E 3 HOH 51 1055 51 HOH HOH A . E 3 HOH 52 1056 52 HOH HOH A . E 3 HOH 53 1057 53 HOH HOH A . E 3 HOH 54 1058 54 HOH HOH A . E 3 HOH 55 1059 55 HOH HOH A . E 3 HOH 56 1060 56 HOH HOH A . E 3 HOH 57 1061 57 HOH HOH A . E 3 HOH 58 1062 58 HOH HOH A . E 3 HOH 59 1063 59 HOH HOH A . E 3 HOH 60 1064 60 HOH HOH A . E 3 HOH 61 1065 61 HOH HOH A . E 3 HOH 62 1066 62 HOH HOH A . E 3 HOH 63 1067 63 HOH HOH A . E 3 HOH 64 1068 64 HOH HOH A . E 3 HOH 65 1069 65 HOH HOH A . E 3 HOH 66 1070 66 HOH HOH A . E 3 HOH 67 1071 67 HOH HOH A . E 3 HOH 68 1072 69 HOH HOH A . E 3 HOH 69 1073 72 HOH HOH A . E 3 HOH 70 1074 73 HOH HOH A . E 3 HOH 71 1075 74 HOH HOH A . E 3 HOH 72 1076 75 HOH HOH A . E 3 HOH 73 1077 76 HOH HOH A . E 3 HOH 74 1078 77 HOH HOH A . E 3 HOH 75 1079 78 HOH HOH A . E 3 HOH 76 1080 79 HOH HOH A . E 3 HOH 77 1081 80 HOH HOH A . E 3 HOH 78 1082 81 HOH HOH A . E 3 HOH 79 1083 82 HOH HOH A . E 3 HOH 80 1084 83 HOH HOH A . E 3 HOH 81 1085 85 HOH HOH A . E 3 HOH 82 1086 86 HOH HOH A . E 3 HOH 83 1087 87 HOH HOH A . E 3 HOH 84 1088 88 HOH HOH A . E 3 HOH 85 1089 89 HOH HOH A . E 3 HOH 86 1090 90 HOH HOH A . E 3 HOH 87 1091 91 HOH HOH A . E 3 HOH 88 1092 92 HOH HOH A . E 3 HOH 89 1093 93 HOH HOH A . E 3 HOH 90 1094 94 HOH HOH A . E 3 HOH 91 1095 95 HOH HOH A . E 3 HOH 92 1096 96 HOH HOH A . E 3 HOH 93 1097 97 HOH HOH A . E 3 HOH 94 1098 98 HOH HOH A . E 3 HOH 95 1099 99 HOH HOH A . E 3 HOH 96 1100 100 HOH HOH A . E 3 HOH 97 1101 101 HOH HOH A . E 3 HOH 98 1102 102 HOH HOH A . E 3 HOH 99 1103 103 HOH HOH A . E 3 HOH 100 1104 104 HOH HOH A . E 3 HOH 101 1105 106 HOH HOH A . E 3 HOH 102 1106 107 HOH HOH A . E 3 HOH 103 1107 108 HOH HOH A . E 3 HOH 104 1108 109 HOH HOH A . E 3 HOH 105 1109 110 HOH HOH A . E 3 HOH 106 1110 111 HOH HOH A . E 3 HOH 107 1111 112 HOH HOH A . E 3 HOH 108 1112 113 HOH HOH A . E 3 HOH 109 1113 114 HOH HOH A . E 3 HOH 110 1114 115 HOH HOH A . E 3 HOH 111 1115 116 HOH HOH A . E 3 HOH 112 1116 117 HOH HOH A . E 3 HOH 113 1117 118 HOH HOH A . E 3 HOH 114 1118 119 HOH HOH A . E 3 HOH 115 1119 121 HOH HOH A . E 3 HOH 116 1120 122 HOH HOH A . E 3 HOH 117 1121 124 HOH HOH A . E 3 HOH 118 1122 128 HOH HOH A . E 3 HOH 119 1123 143 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 # _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 1046 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _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 OE1 ? A GLU 60 ? A GLU 60 ? 1_555 MN ? D MN . ? A MN 1004 ? 1_555 OE2 ? A GLU 62 ? A GLU 62 ? 1_555 95.4 ? 2 OE1 ? A GLU 60 ? A GLU 60 ? 1_555 MN ? D MN . ? A MN 1004 ? 1_555 O ? E HOH . ? A HOH 1074 ? 1_555 88.7 ? 3 OE2 ? A GLU 62 ? A GLU 62 ? 1_555 MN ? D MN . ? A MN 1004 ? 1_555 O ? E HOH . ? A HOH 1074 ? 1_555 91.6 ? 4 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1022 ? 1_555 90.3 ? 5 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1034 ? 1_555 91.1 ? 6 O ? E HOH . ? A HOH 1022 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1034 ? 1_555 95.4 ? 7 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1058 ? 1_555 177.6 ? 8 O ? E HOH . ? A HOH 1022 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1058 ? 1_555 89.1 ? 9 O ? E HOH . ? A HOH 1034 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1058 ? 1_555 86.6 ? 10 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1059 ? 1_555 96.3 ? 11 O ? E HOH . ? A HOH 1022 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1059 ? 1_555 173.4 ? 12 O ? E HOH . ? A HOH 1034 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1059 ? 1_555 84.7 ? 13 O ? E HOH . ? A HOH 1058 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1059 ? 1_555 84.3 ? 14 OE2 ? A GLU 76 ? A GLU 76 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1123 ? 1_555 86.9 ? 15 O ? E HOH . ? A HOH 1022 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1123 ? 1_555 94.8 ? 16 O ? E HOH . ? A HOH 1034 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1123 ? 1_555 169.6 ? 17 O ? E HOH . ? A HOH 1058 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1123 ? 1_555 95.5 ? 18 O ? E HOH . ? A HOH 1059 ? 1_555 MN ? B MN . ? A MN 1001 ? 1_555 O ? E HOH . ? A HOH 1123 ? 1_555 85.5 ? # 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 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' 4 4 'Structure model' 'Derived calculations' # 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' pdbx_struct_conn_angle 3 4 'Structure model' struct_conn 4 4 'Structure model' struct_ref_seq_dif 5 4 'Structure model' struct_site # 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' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 26 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 31 4 'Structure model' '_struct_ref_seq_dif.details' 32 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 33 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 34 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 42.2752 _pdbx_refine_tls.origin_y 24.0460 _pdbx_refine_tls.origin_z 43.2070 _pdbx_refine_tls.T[1][1] -0.0031 _pdbx_refine_tls.T[2][2] -0.0564 _pdbx_refine_tls.T[3][3] -0.0181 _pdbx_refine_tls.T[1][2] -0.0190 _pdbx_refine_tls.T[1][3] 0.0144 _pdbx_refine_tls.T[2][3] -0.0021 _pdbx_refine_tls.L[1][1] 0.4052 _pdbx_refine_tls.L[2][2] 1.6039 _pdbx_refine_tls.L[3][3] 1.5110 _pdbx_refine_tls.L[1][2] -0.5045 _pdbx_refine_tls.L[1][3] -0.1748 _pdbx_refine_tls.L[2][3] 1.1009 _pdbx_refine_tls.S[1][1] 0.0055 _pdbx_refine_tls.S[1][2] 0.0261 _pdbx_refine_tls.S[1][3] -0.0171 _pdbx_refine_tls.S[2][1] 0.0943 _pdbx_refine_tls.S[2][2] -0.0516 _pdbx_refine_tls.S[2][3] 0.0159 _pdbx_refine_tls.S[3][1] 0.0735 _pdbx_refine_tls.S[3][2] -0.0221 _pdbx_refine_tls.S[3][3] 0.0461 _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 1 _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 89 _pdbx_refine_tls_group.end_auth_seq_id 89 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # 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 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CB _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 LYS _pdbx_validate_rmsd_bond.auth_seq_id_1 86 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 CG _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 LYS _pdbx_validate_rmsd_bond.auth_seq_id_2 86 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.345 _pdbx_validate_rmsd_bond.bond_target_value 1.521 _pdbx_validate_rmsd_bond.bond_deviation -0.176 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.027 _pdbx_validate_rmsd_bond.linker_flag N # 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 water HOH #