data_1Z4I # _entry.id 1Z4I # _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 1Z4I pdb_00001z4i 10.2210/pdb1z4i/pdb RCSB RCSB032287 ? ? WWPDB D_1000032287 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1Z4J ;the same protein complexed with uridine 2'-monophosphate ; unspecified PDB 1Z4K ;the same protein complexed with thymidine 3'-monophosphate ; unspecified PDB 1Z4L ;the same protein complexed with thymidine 5'-monophosphate ; unspecified PDB 1Z4M ;the same protein complexed with uridine 5'-monophosphate ; unspecified PDB 1Z4P ;the same protein complexed with deoxyriboguanosine 5'-monophosphate ; unspecified PDB 1Z4Q ;the same protein complexed with 3'-deoxy 2'3'-didehydrothymidine 5'-monophosphate (d4T-MP) ; unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Z4I _pdbx_database_status.recvd_initial_deposition_date 2005-03-16 _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 'Wallden, K.' 1 'Ruzzenente, B.' 2 'Rinaldo-Matthis, A.' 3 'Bianchi, V.' 4 'Nordlund, P.' 5 # _citation.id primary _citation.title 'Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase' _citation.journal_abbrev STRUCTURE _citation.journal_volume 13 _citation.page_first 1081 _citation.page_last 1088 _citation.year 2005 _citation.journal_id_ASTM STRUE6 _citation.country UK _citation.journal_id_ISSN 0969-2126 _citation.journal_id_CSD 2005 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16004879 _citation.pdbx_database_id_DOI 10.1016/j.str.2005.04.023 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wallden, K.' 1 ? primary 'Ruzzenente, B.' 2 ? primary 'Rinaldo-Matthis, A.' 3 ? primary 'Bianchi, V.' 4 ? primary 'Nordlund, P.' 5 ? # _cell.entry_id 1Z4I _cell.length_a 73.700 _cell.length_b 73.700 _cell.length_c 106.420 _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 1Z4I _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 "5'(3')-deoxyribonucleotidase" 22840.135 1 3.1.3.- D41N ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; 308.182 1 ? ? ? ? 4 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 5 water nat water 18.015 194 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;Mitochondrial deoxyribonucleotidase, 5',3'-nucleotidase, mitochondrial, Deoxy-5'-nucleotidase 2, dNT-2 ; # _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 ;GGRALRVLVNMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGA VEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEH VLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRPC ; _entity_poly.pdbx_seq_one_letter_code_can ;GGRALRVLVNMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGA VEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEH VLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRPC ; _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 GLY n 1 2 GLY n 1 3 ARG n 1 4 ALA n 1 5 LEU n 1 6 ARG n 1 7 VAL n 1 8 LEU n 1 9 VAL n 1 10 ASN n 1 11 MET n 1 12 ASP n 1 13 GLY n 1 14 VAL n 1 15 LEU n 1 16 ALA n 1 17 ASP n 1 18 PHE n 1 19 GLU n 1 20 GLY n 1 21 GLY n 1 22 PHE n 1 23 LEU n 1 24 ARG n 1 25 LYS n 1 26 PHE n 1 27 ARG n 1 28 ALA n 1 29 ARG n 1 30 PHE n 1 31 PRO n 1 32 ASP n 1 33 GLN n 1 34 PRO n 1 35 PHE n 1 36 ILE n 1 37 ALA n 1 38 LEU n 1 39 GLU n 1 40 ASP n 1 41 ARG n 1 42 ARG n 1 43 GLY n 1 44 PHE n 1 45 TRP n 1 46 VAL n 1 47 SER n 1 48 GLU n 1 49 GLN n 1 50 TYR n 1 51 GLY n 1 52 ARG n 1 53 LEU n 1 54 ARG n 1 55 PRO n 1 56 GLY n 1 57 LEU n 1 58 SER n 1 59 GLU n 1 60 LYS n 1 61 ALA n 1 62 ILE n 1 63 SER n 1 64 ILE n 1 65 TRP n 1 66 GLU n 1 67 SER n 1 68 LYS n 1 69 ASN n 1 70 PHE n 1 71 PHE n 1 72 PHE n 1 73 GLU n 1 74 LEU n 1 75 GLU n 1 76 PRO n 1 77 LEU n 1 78 PRO n 1 79 GLY n 1 80 ALA n 1 81 VAL n 1 82 GLU n 1 83 ALA n 1 84 VAL n 1 85 LYS n 1 86 GLU n 1 87 MET n 1 88 ALA n 1 89 SER n 1 90 LEU n 1 91 GLN n 1 92 ASN n 1 93 THR n 1 94 ASP n 1 95 VAL n 1 96 PHE n 1 97 ILE n 1 98 CYS n 1 99 THR n 1 100 SER n 1 101 PRO n 1 102 ILE n 1 103 LYS n 1 104 MET n 1 105 PHE n 1 106 LYS n 1 107 TYR n 1 108 CYS n 1 109 PRO n 1 110 TYR n 1 111 GLU n 1 112 LYS n 1 113 TYR n 1 114 ALA n 1 115 TRP n 1 116 VAL n 1 117 GLU n 1 118 LYS n 1 119 TYR n 1 120 PHE n 1 121 GLY n 1 122 PRO n 1 123 ASP n 1 124 PHE n 1 125 LEU n 1 126 GLU n 1 127 GLN n 1 128 ILE n 1 129 VAL n 1 130 LEU n 1 131 THR n 1 132 ARG n 1 133 ASP n 1 134 LYS n 1 135 THR n 1 136 VAL n 1 137 VAL n 1 138 SER n 1 139 ALA n 1 140 ASP n 1 141 LEU n 1 142 LEU n 1 143 ILE n 1 144 ASP n 1 145 ASP n 1 146 ARG n 1 147 PRO n 1 148 ASP n 1 149 ILE n 1 150 THR n 1 151 GLY n 1 152 ALA n 1 153 GLU n 1 154 PRO n 1 155 THR n 1 156 PRO n 1 157 SER n 1 158 TRP n 1 159 GLU n 1 160 HIS n 1 161 VAL n 1 162 LEU n 1 163 PHE n 1 164 THR n 1 165 ALA n 1 166 CYS n 1 167 HIS n 1 168 ASN n 1 169 GLN n 1 170 HIS n 1 171 LEU n 1 172 GLN n 1 173 LEU n 1 174 GLN n 1 175 PRO n 1 176 PRO n 1 177 ARG n 1 178 ARG n 1 179 ARG n 1 180 LEU n 1 181 HIS n 1 182 SER n 1 183 TRP n 1 184 ALA n 1 185 ASP n 1 186 ASP n 1 187 TRP n 1 188 LYS n 1 189 ALA n 1 190 ILE n 1 191 LEU n 1 192 ASP n 1 193 SER n 1 194 LYS n 1 195 ARG n 1 196 PRO n 1 197 CYS 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 human _entity_src_gen.gene_src_genus Homo _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli BL21(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 plysS _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code NT5M_HUMAN _struct_ref.pdbx_db_accession Q9NPB1 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;GGRALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGA VEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEH VLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRPC ; _struct_ref.pdbx_align_begin 32 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1Z4I _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 197 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9NPB1 _struct_ref_seq.db_align_beg 32 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 228 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 32 _struct_ref_seq.pdbx_auth_seq_align_end 228 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 1Z4I _struct_ref_seq_dif.mon_id ASN _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 10 _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 Q9NPB1 _struct_ref_seq_dif.db_mon_id ASP _struct_ref_seq_dif.pdbx_seq_db_seq_num 41 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 41 _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 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 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 UMP non-polymer . ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; DUMP 'C9 H13 N2 O8 P' 308.182 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 1Z4I _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.8 _exptl_crystal.density_percent_sol 55 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.5 _exptl_crystal_grow.pdbx_details 'PEG8000, potassium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _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 4' _diffrn_detector.pdbx_collection_date 2003-11-07 _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 Si111 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID14-3' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID14-3 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1Z4I _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 1.98 _reflns.d_resolution_low 20 _reflns.number_all 21094 _reflns.number_obs 21057 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.08 _reflns.pdbx_netI_over_sigmaI 23.6 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 15.1 _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 1.98 _reflns_shell.d_res_low 2.1 _reflns_shell.percent_possible_all 98.8 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.36 _reflns_shell.meanI_over_sigI_obs 7.8 _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 1Z4I _refine.ls_number_reflns_obs 19972 _refine.ls_number_reflns_all 21094 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.00 _refine.ls_d_res_high 1.98 _refine.ls_percent_reflns_obs 99.98 _refine.ls_R_factor_obs 0.16564 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.16355 _refine.ls_R_factor_R_free 0.20608 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 1082 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.961 _refine.correlation_coeff_Fo_to_Fc_free 0.937 _refine.B_iso_mean 26.509 _refine.aniso_B[1][1] -0.43 _refine.aniso_B[2][2] -0.43 _refine.aniso_B[3][3] 0.86 _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 1.40 _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 'MOLECULAR REPLACEMENT' _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 0.126 _refine.pdbx_overall_ESU_R_Free 0.126 _refine.overall_SU_ML 0.075 _refine.overall_SU_B 2.632 _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 1597 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 27 _refine_hist.number_atoms_solvent 194 _refine_hist.number_atoms_total 1818 _refine_hist.d_res_high 1.98 _refine_hist.d_res_low 20.00 # 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 0.019 0.021 ? 1697 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 1513 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.690 1.974 ? 2303 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.933 3.000 ? 3519 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.245 5.000 ? 193 'X-RAY DIFFRACTION' ? r_chiral_restr 0.104 0.200 ? 239 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.010 0.020 ? 1836 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.011 0.020 ? 367 'X-RAY DIFFRACTION' ? r_nbd_refined 0.211 0.200 ? 324 'X-RAY DIFFRACTION' ? r_nbd_other 0.254 0.200 ? 1677 'X-RAY DIFFRACTION' ? r_nbtor_other 0.086 0.200 ? 950 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.145 0.200 ? 136 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.088 0.200 ? 4 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.314 0.200 ? 50 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.159 0.200 ? 14 'X-RAY DIFFRACTION' ? r_mcbond_it 1.116 1.500 ? 973 'X-RAY DIFFRACTION' ? r_mcangle_it 2.107 2.000 ? 1578 'X-RAY DIFFRACTION' ? r_scbond_it 2.921 3.000 ? 724 'X-RAY DIFFRACTION' ? r_scangle_it 4.702 4.500 ? 725 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.980 _refine_ls_shell.d_res_low 2.031 _refine_ls_shell.number_reflns_R_work 1420 _refine_ls_shell.R_factor_R_work 0.184 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.268 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 85 _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 1Z4I _struct.title ;Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with deoxyribouridine 5'-monophosphate ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Z4I _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'alfa beta fold, Hydrolase' # 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 ? E N N 5 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # 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 ASP A 17 ? PHE A 30 ? ASP A 48 PHE A 61 1 ? 14 HELX_P HELX_P2 2 ALA A 37 ? ARG A 41 ? ALA A 68 ARG A 72 5 ? 5 HELX_P HELX_P3 3 TRP A 45 ? ARG A 54 ? TRP A 76 ARG A 85 1 ? 10 HELX_P HELX_P4 4 GLY A 56 ? GLU A 66 ? GLY A 87 GLU A 97 1 ? 11 HELX_P HELX_P5 5 GLY A 79 ? LEU A 90 ? GLY A 110 LEU A 121 1 ? 12 HELX_P HELX_P6 6 TYR A 107 ? GLY A 121 ? TYR A 138 GLY A 152 1 ? 15 HELX_P HELX_P7 7 PRO A 122 ? GLU A 126 ? PRO A 153 GLU A 157 5 ? 5 HELX_P HELX_P8 8 ALA A 165 ? GLN A 169 ? ALA A 196 GLN A 200 5 ? 5 HELX_P HELX_P9 9 ASP A 186 ? SER A 193 ? ASP A 217 SER A 224 1 ? 8 # _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 ASN 10 OD1 ? ? ? 1_555 B MG . MG ? ? A ASN 41 A MG 1228 1_555 ? ? ? ? ? ? ? 2.044 ? ? metalc2 metalc ? ? A ASP 12 O ? ? ? 1_555 B MG . MG ? ? A ASP 43 A MG 1228 1_555 ? ? ? ? ? ? ? 2.083 ? ? metalc3 metalc ? ? A ASP 145 OD1 ? ? ? 1_555 B MG . MG ? ? A ASP 176 A MG 1228 1_555 ? ? ? ? ? ? ? 2.159 ? ? metalc4 metalc ? ? C UMP . OP1 B ? ? 1_555 B MG . MG ? ? A UMP 1001 A MG 1228 1_555 ? ? ? ? ? ? ? 2.019 ? ? metalc5 metalc ? ? C UMP . OP3 A ? ? 1_555 B MG . MG ? ? A UMP 1001 A MG 1228 1_555 ? ? ? ? ? ? ? 2.131 ? ? metalc6 metalc ? ? B MG . MG ? ? ? 1_555 D GOL . O1 ? ? A MG 1228 A GOL 2001 1_555 ? ? ? ? ? ? ? 2.173 ? ? metalc7 metalc ? ? B MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 1228 A HOH 2096 1_555 ? ? ? ? ? ? ? 2.152 ? ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 6 _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 ? parallel A 2 3 ? parallel A 3 4 ? parallel A 4 5 ? parallel A 5 6 ? 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 ILE A 128 ? LEU A 130 ? ILE A 159 LEU A 161 A 2 THR A 93 ? THR A 99 ? THR A 124 THR A 130 A 3 LEU A 5 ? ASN A 10 ? LEU A 36 ASN A 41 A 4 LEU A 141 ? ASP A 144 ? LEU A 172 ASP A 175 A 5 GLU A 159 ? PHE A 163 ? GLU A 190 PHE A 194 A 6 ARG A 178 ? LEU A 180 ? ARG A 209 LEU A 211 # 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 VAL A 129 ? O VAL A 160 N ILE A 97 ? N ILE A 128 A 2 3 O PHE A 96 ? O PHE A 127 N VAL A 9 ? N VAL A 40 A 3 4 N LEU A 8 ? N LEU A 39 O LEU A 141 ? O LEU A 172 A 4 5 N LEU A 142 ? N LEU A 173 O VAL A 161 ? O VAL A 192 A 5 6 N LEU A 162 ? N LEU A 193 O ARG A 178 ? O ARG A 209 # 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 MG 1228 ? 6 'BINDING SITE FOR RESIDUE MG A 1228' AC2 Software A UMP 1001 ? 25 'BINDING SITE FOR RESIDUE UMP A 1001' AC3 Software A GOL 2001 ? 7 'BINDING SITE FOR RESIDUE GOL A 2001' # 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 ASN A 10 ? ASN A 41 . ? 1_555 ? 2 AC1 6 ASP A 12 ? ASP A 43 . ? 1_555 ? 3 AC1 6 ASP A 145 ? ASP A 176 . ? 1_555 ? 4 AC1 6 UMP C . ? UMP A 1001 . ? 1_555 ? 5 AC1 6 GOL D . ? GOL A 2001 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH A 2096 . ? 1_555 ? 7 AC2 25 ASN A 10 ? ASN A 41 . ? 1_555 ? 8 AC2 25 MET A 11 ? MET A 42 . ? 1_555 ? 9 AC2 25 ASP A 12 ? ASP A 43 . ? 1_555 ? 10 AC2 25 PHE A 18 ? PHE A 49 . ? 1_555 ? 11 AC2 25 PHE A 44 ? PHE A 75 . ? 1_555 ? 12 AC2 25 TRP A 45 ? TRP A 76 . ? 1_555 ? 13 AC2 25 VAL A 46 ? VAL A 77 . ? 1_555 ? 14 AC2 25 SER A 47 ? SER A 78 . ? 1_555 ? 15 AC2 25 TRP A 65 ? TRP A 96 . ? 1_555 ? 16 AC2 25 PHE A 71 ? PHE A 102 . ? 1_555 ? 17 AC2 25 THR A 99 ? THR A 130 . ? 1_555 ? 18 AC2 25 SER A 100 ? SER A 131 . ? 1_555 ? 19 AC2 25 PRO A 101 ? PRO A 132 . ? 1_555 ? 20 AC2 25 ILE A 102 ? ILE A 133 . ? 1_555 ? 21 AC2 25 LYS A 112 ? LYS A 143 . ? 1_555 ? 22 AC2 25 LYS A 134 ? LYS A 165 . ? 1_555 ? 23 AC2 25 MG B . ? MG A 1228 . ? 1_555 ? 24 AC2 25 GOL D . ? GOL A 2001 . ? 1_555 ? 25 AC2 25 HOH E . ? HOH A 2012 . ? 1_555 ? 26 AC2 25 HOH E . ? HOH A 2058 . ? 1_555 ? 27 AC2 25 HOH E . ? HOH A 2096 . ? 1_555 ? 28 AC2 25 HOH E . ? HOH A 2112 . ? 1_555 ? 29 AC2 25 HOH E . ? HOH A 2186 . ? 1_555 ? 30 AC2 25 HOH E . ? HOH A 2187 . ? 1_555 ? 31 AC2 25 HOH E . ? HOH A 2188 . ? 1_555 ? 32 AC3 7 ASP A 12 ? ASP A 43 . ? 1_555 ? 33 AC3 7 PHE A 18 ? PHE A 49 . ? 1_555 ? 34 AC3 7 GLU A 19 ? GLU A 50 . ? 1_555 ? 35 AC3 7 PHE A 44 ? PHE A 75 . ? 1_555 ? 36 AC3 7 ASP A 145 ? ASP A 176 . ? 1_555 ? 37 AC3 7 UMP C . ? UMP A 1001 . ? 1_555 ? 38 AC3 7 MG B . ? MG A 1228 . ? 1_555 ? # _database_PDB_matrix.entry_id 1Z4I _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 1Z4I _atom_sites.fract_transf_matrix[1][1] 0.013569 _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] 0.013569 _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] 0.009397 _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 MG N O P 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 GLY 1 32 ? ? ? A . n A 1 2 GLY 2 33 ? ? ? A . n A 1 3 ARG 3 34 34 ARG ARG A . n A 1 4 ALA 4 35 35 ALA ALA A . n A 1 5 LEU 5 36 36 LEU LEU A . n A 1 6 ARG 6 37 37 ARG ARG A . n A 1 7 VAL 7 38 38 VAL VAL A . n A 1 8 LEU 8 39 39 LEU LEU A . n A 1 9 VAL 9 40 40 VAL VAL A . n A 1 10 ASN 10 41 41 ASN ASN A . n A 1 11 MET 11 42 42 MET MET A . n A 1 12 ASP 12 43 43 ASP ASP A . n A 1 13 GLY 13 44 44 GLY GLY A . n A 1 14 VAL 14 45 45 VAL VAL A . n A 1 15 LEU 15 46 46 LEU LEU A . n A 1 16 ALA 16 47 47 ALA ALA A . n A 1 17 ASP 17 48 48 ASP ASP A . n A 1 18 PHE 18 49 49 PHE PHE A . n A 1 19 GLU 19 50 50 GLU GLU A . n A 1 20 GLY 20 51 51 GLY GLY A . n A 1 21 GLY 21 52 52 GLY GLY A . n A 1 22 PHE 22 53 53 PHE PHE A . n A 1 23 LEU 23 54 54 LEU LEU A . n A 1 24 ARG 24 55 55 ARG ARG A . n A 1 25 LYS 25 56 56 LYS LYS A . n A 1 26 PHE 26 57 57 PHE PHE A . n A 1 27 ARG 27 58 58 ARG ARG A . n A 1 28 ALA 28 59 59 ALA ALA A . n A 1 29 ARG 29 60 60 ARG ARG A . n A 1 30 PHE 30 61 61 PHE PHE A . n A 1 31 PRO 31 62 62 PRO PRO A . n A 1 32 ASP 32 63 63 ASP ASP A . n A 1 33 GLN 33 64 64 GLN GLN A . n A 1 34 PRO 34 65 65 PRO PRO A . n A 1 35 PHE 35 66 66 PHE PHE A . n A 1 36 ILE 36 67 67 ILE ILE A . n A 1 37 ALA 37 68 68 ALA ALA A . n A 1 38 LEU 38 69 69 LEU LEU A . n A 1 39 GLU 39 70 70 GLU GLU A . n A 1 40 ASP 40 71 71 ASP ASP A . n A 1 41 ARG 41 72 72 ARG ARG A . n A 1 42 ARG 42 73 73 ARG ARG A . n A 1 43 GLY 43 74 74 GLY GLY A . n A 1 44 PHE 44 75 75 PHE PHE A . n A 1 45 TRP 45 76 76 TRP TRP A . n A 1 46 VAL 46 77 77 VAL VAL A . n A 1 47 SER 47 78 78 SER SER A . n A 1 48 GLU 48 79 79 GLU GLU A . n A 1 49 GLN 49 80 80 GLN GLN A . n A 1 50 TYR 50 81 81 TYR TYR A . n A 1 51 GLY 51 82 82 GLY GLY A . n A 1 52 ARG 52 83 83 ARG ARG A . n A 1 53 LEU 53 84 84 LEU LEU A . n A 1 54 ARG 54 85 85 ARG ARG A . n A 1 55 PRO 55 86 86 PRO PRO A . n A 1 56 GLY 56 87 87 GLY GLY A . n A 1 57 LEU 57 88 88 LEU LEU A . n A 1 58 SER 58 89 89 SER SER A . n A 1 59 GLU 59 90 90 GLU GLU A . n A 1 60 LYS 60 91 91 LYS LYS A . n A 1 61 ALA 61 92 92 ALA ALA A . n A 1 62 ILE 62 93 93 ILE ILE A . n A 1 63 SER 63 94 94 SER SER A . n A 1 64 ILE 64 95 95 ILE ILE A . n A 1 65 TRP 65 96 96 TRP TRP A . n A 1 66 GLU 66 97 97 GLU GLU A . n A 1 67 SER 67 98 98 SER SER A . n A 1 68 LYS 68 99 99 LYS LYS A . n A 1 69 ASN 69 100 100 ASN ASN A . n A 1 70 PHE 70 101 101 PHE PHE A . n A 1 71 PHE 71 102 102 PHE PHE A . n A 1 72 PHE 72 103 103 PHE PHE A . n A 1 73 GLU 73 104 104 GLU GLU A . n A 1 74 LEU 74 105 105 LEU LEU A . n A 1 75 GLU 75 106 106 GLU GLU A . n A 1 76 PRO 76 107 107 PRO PRO A . n A 1 77 LEU 77 108 108 LEU LEU A . n A 1 78 PRO 78 109 109 PRO PRO A . n A 1 79 GLY 79 110 110 GLY GLY A . n A 1 80 ALA 80 111 111 ALA ALA A . n A 1 81 VAL 81 112 112 VAL VAL A . n A 1 82 GLU 82 113 113 GLU GLU A . n A 1 83 ALA 83 114 114 ALA ALA A . n A 1 84 VAL 84 115 115 VAL VAL A . n A 1 85 LYS 85 116 116 LYS LYS A . n A 1 86 GLU 86 117 117 GLU GLU A . n A 1 87 MET 87 118 118 MET MET A . n A 1 88 ALA 88 119 119 ALA ALA A . n A 1 89 SER 89 120 120 SER SER A . n A 1 90 LEU 90 121 121 LEU LEU A . n A 1 91 GLN 91 122 122 GLN GLN A . n A 1 92 ASN 92 123 123 ASN ASN A . n A 1 93 THR 93 124 124 THR THR A . n A 1 94 ASP 94 125 125 ASP ASP A . n A 1 95 VAL 95 126 126 VAL VAL A . n A 1 96 PHE 96 127 127 PHE PHE A . n A 1 97 ILE 97 128 128 ILE ILE A . n A 1 98 CYS 98 129 129 CYS CYS A . n A 1 99 THR 99 130 130 THR THR A . n A 1 100 SER 100 131 131 SER SER A . n A 1 101 PRO 101 132 132 PRO PRO A . n A 1 102 ILE 102 133 133 ILE ILE A . n A 1 103 LYS 103 134 134 LYS LYS A . n A 1 104 MET 104 135 135 MET MET A . n A 1 105 PHE 105 136 136 PHE PHE A . n A 1 106 LYS 106 137 137 LYS LYS A . n A 1 107 TYR 107 138 138 TYR TYR A . n A 1 108 CYS 108 139 139 CYS CYS A . n A 1 109 PRO 109 140 140 PRO PRO A . n A 1 110 TYR 110 141 141 TYR TYR A . n A 1 111 GLU 111 142 142 GLU GLU A . n A 1 112 LYS 112 143 143 LYS LYS A . n A 1 113 TYR 113 144 144 TYR TYR A . n A 1 114 ALA 114 145 145 ALA ALA A . n A 1 115 TRP 115 146 146 TRP TRP A . n A 1 116 VAL 116 147 147 VAL VAL A . n A 1 117 GLU 117 148 148 GLU GLU A . n A 1 118 LYS 118 149 149 LYS LYS A . n A 1 119 TYR 119 150 150 TYR TYR A . n A 1 120 PHE 120 151 151 PHE PHE A . n A 1 121 GLY 121 152 152 GLY GLY A . n A 1 122 PRO 122 153 153 PRO PRO A . n A 1 123 ASP 123 154 154 ASP ASP A . n A 1 124 PHE 124 155 155 PHE PHE A . n A 1 125 LEU 125 156 156 LEU LEU A . n A 1 126 GLU 126 157 157 GLU GLU A . n A 1 127 GLN 127 158 158 GLN GLN A . n A 1 128 ILE 128 159 159 ILE ILE A . n A 1 129 VAL 129 160 160 VAL VAL A . n A 1 130 LEU 130 161 161 LEU LEU A . n A 1 131 THR 131 162 162 THR THR A . n A 1 132 ARG 132 163 163 ARG ARG A . n A 1 133 ASP 133 164 164 ASP ASP A . n A 1 134 LYS 134 165 165 LYS LYS A . n A 1 135 THR 135 166 166 THR THR A . n A 1 136 VAL 136 167 167 VAL VAL A . n A 1 137 VAL 137 168 168 VAL VAL A . n A 1 138 SER 138 169 169 SER SER A . n A 1 139 ALA 139 170 170 ALA ALA A . n A 1 140 ASP 140 171 171 ASP ASP A . n A 1 141 LEU 141 172 172 LEU LEU A . n A 1 142 LEU 142 173 173 LEU LEU A . n A 1 143 ILE 143 174 174 ILE ILE A . n A 1 144 ASP 144 175 175 ASP ASP A . n A 1 145 ASP 145 176 176 ASP ASP A . n A 1 146 ARG 146 177 177 ARG ARG A . n A 1 147 PRO 147 178 178 PRO PRO A . n A 1 148 ASP 148 179 179 ASP ASP A . n A 1 149 ILE 149 180 180 ILE ILE A . n A 1 150 THR 150 181 181 THR THR A . n A 1 151 GLY 151 182 182 GLY GLY A . n A 1 152 ALA 152 183 183 ALA ALA A . n A 1 153 GLU 153 184 184 GLU GLU A . n A 1 154 PRO 154 185 185 PRO PRO A . n A 1 155 THR 155 186 186 THR THR A . n A 1 156 PRO 156 187 187 PRO PRO A . n A 1 157 SER 157 188 188 SER SER A . n A 1 158 TRP 158 189 189 TRP TRP A . n A 1 159 GLU 159 190 190 GLU GLU A . n A 1 160 HIS 160 191 191 HIS HIS A . n A 1 161 VAL 161 192 192 VAL VAL A . n A 1 162 LEU 162 193 193 LEU LEU A . n A 1 163 PHE 163 194 194 PHE PHE A . n A 1 164 THR 164 195 195 THR THR A . n A 1 165 ALA 165 196 196 ALA ALA A . n A 1 166 CYS 166 197 197 CYS CYS A . n A 1 167 HIS 167 198 198 HIS HIS A . n A 1 168 ASN 168 199 199 ASN ASN A . n A 1 169 GLN 169 200 200 GLN GLN A . n A 1 170 HIS 170 201 201 HIS HIS A . n A 1 171 LEU 171 202 202 LEU LEU A . n A 1 172 GLN 172 203 203 GLN GLN A . n A 1 173 LEU 173 204 204 LEU LEU A . n A 1 174 GLN 174 205 205 GLN GLN A . n A 1 175 PRO 175 206 206 PRO PRO A . n A 1 176 PRO 176 207 207 PRO PRO A . n A 1 177 ARG 177 208 208 ARG ARG A . n A 1 178 ARG 178 209 209 ARG ARG A . n A 1 179 ARG 179 210 210 ARG ARG A . n A 1 180 LEU 180 211 211 LEU LEU A . n A 1 181 HIS 181 212 212 HIS HIS A . n A 1 182 SER 182 213 213 SER SER A . n A 1 183 TRP 183 214 214 TRP TRP A . n A 1 184 ALA 184 215 215 ALA ALA A . n A 1 185 ASP 185 216 216 ASP ASP A . n A 1 186 ASP 186 217 217 ASP ASP A . n A 1 187 TRP 187 218 218 TRP TRP A . n A 1 188 LYS 188 219 219 LYS LYS A . n A 1 189 ALA 189 220 220 ALA ALA A . n A 1 190 ILE 190 221 221 ILE ILE A . n A 1 191 LEU 191 222 222 LEU LEU A . n A 1 192 ASP 192 223 223 ASP ASP A . n A 1 193 SER 193 224 224 SER SER A . n A 1 194 LYS 194 225 225 LYS LYS A . n A 1 195 ARG 195 226 226 ARG ARG A . n A 1 196 PRO 196 227 227 PRO PRO A . n A 1 197 CYS 197 228 ? ? ? 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 MG 1 1228 228 MG MG A . C 3 UMP 1 1001 1 UMP UMP A . D 4 GOL 1 2001 1 GOL GLC A . E 5 HOH 1 2002 1 HOH HOH A . E 5 HOH 2 2003 2 HOH HOH A . E 5 HOH 3 2004 3 HOH HOH A . E 5 HOH 4 2005 4 HOH HOH A . E 5 HOH 5 2006 5 HOH HOH A . E 5 HOH 6 2007 6 HOH HOH A . E 5 HOH 7 2008 7 HOH HOH A . E 5 HOH 8 2009 8 HOH HOH A . E 5 HOH 9 2010 9 HOH HOH A . E 5 HOH 10 2011 10 HOH HOH A . E 5 HOH 11 2012 11 HOH HOH A . E 5 HOH 12 2013 12 HOH HOH A . E 5 HOH 13 2014 13 HOH HOH A . E 5 HOH 14 2015 14 HOH HOH A . E 5 HOH 15 2016 15 HOH HOH A . E 5 HOH 16 2017 16 HOH HOH A . E 5 HOH 17 2018 17 HOH HOH A . E 5 HOH 18 2019 18 HOH HOH A . E 5 HOH 19 2020 19 HOH HOH A . E 5 HOH 20 2021 20 HOH HOH A . E 5 HOH 21 2022 21 HOH HOH A . E 5 HOH 22 2023 22 HOH HOH A . E 5 HOH 23 2024 23 HOH HOH A . E 5 HOH 24 2025 24 HOH HOH A . E 5 HOH 25 2026 25 HOH HOH A . E 5 HOH 26 2027 27 HOH HOH A . E 5 HOH 27 2028 28 HOH HOH A . E 5 HOH 28 2029 29 HOH HOH A . E 5 HOH 29 2030 30 HOH HOH A . E 5 HOH 30 2031 31 HOH HOH A . E 5 HOH 31 2032 32 HOH HOH A . E 5 HOH 32 2033 33 HOH HOH A . E 5 HOH 33 2034 34 HOH HOH A . E 5 HOH 34 2035 35 HOH HOH A . E 5 HOH 35 2036 36 HOH HOH A . E 5 HOH 36 2037 37 HOH HOH A . E 5 HOH 37 2038 38 HOH HOH A . E 5 HOH 38 2039 39 HOH HOH A . E 5 HOH 39 2040 40 HOH HOH A . E 5 HOH 40 2041 41 HOH HOH A . E 5 HOH 41 2042 42 HOH HOH A . E 5 HOH 42 2043 43 HOH HOH A . E 5 HOH 43 2044 44 HOH HOH A . E 5 HOH 44 2045 45 HOH HOH A . E 5 HOH 45 2046 46 HOH HOH A . E 5 HOH 46 2047 47 HOH HOH A . E 5 HOH 47 2048 48 HOH HOH A . E 5 HOH 48 2049 49 HOH HOH A . E 5 HOH 49 2050 50 HOH HOH A . E 5 HOH 50 2051 51 HOH HOH A . E 5 HOH 51 2052 52 HOH HOH A . E 5 HOH 52 2053 53 HOH HOH A . E 5 HOH 53 2054 54 HOH HOH A . E 5 HOH 54 2055 56 HOH HOH A . E 5 HOH 55 2056 57 HOH HOH A . E 5 HOH 56 2057 58 HOH HOH A . E 5 HOH 57 2058 59 HOH HOH A . E 5 HOH 58 2059 60 HOH HOH A . E 5 HOH 59 2060 61 HOH HOH A . E 5 HOH 60 2061 62 HOH HOH A . E 5 HOH 61 2062 63 HOH HOH A . E 5 HOH 62 2063 64 HOH HOH A . E 5 HOH 63 2064 65 HOH HOH A . E 5 HOH 64 2065 66 HOH HOH A . E 5 HOH 65 2066 67 HOH HOH A . E 5 HOH 66 2067 68 HOH HOH A . E 5 HOH 67 2068 69 HOH HOH A . E 5 HOH 68 2069 70 HOH HOH A . E 5 HOH 69 2070 71 HOH HOH A . E 5 HOH 70 2071 72 HOH HOH A . E 5 HOH 71 2072 73 HOH HOH A . E 5 HOH 72 2073 74 HOH HOH A . E 5 HOH 73 2074 75 HOH HOH A . E 5 HOH 74 2075 76 HOH HOH A . E 5 HOH 75 2076 77 HOH HOH A . E 5 HOH 76 2077 78 HOH HOH A . E 5 HOH 77 2078 79 HOH HOH A . E 5 HOH 78 2079 80 HOH HOH A . E 5 HOH 79 2080 81 HOH HOH A . E 5 HOH 80 2081 82 HOH HOH A . E 5 HOH 81 2082 83 HOH HOH A . E 5 HOH 82 2083 84 HOH HOH A . E 5 HOH 83 2084 85 HOH HOH A . E 5 HOH 84 2085 86 HOH HOH A . E 5 HOH 85 2086 87 HOH HOH A . E 5 HOH 86 2087 88 HOH HOH A . E 5 HOH 87 2088 89 HOH HOH A . E 5 HOH 88 2089 90 HOH HOH A . E 5 HOH 89 2090 91 HOH HOH A . E 5 HOH 90 2091 92 HOH HOH A . E 5 HOH 91 2092 93 HOH HOH A . E 5 HOH 92 2093 94 HOH HOH A . E 5 HOH 93 2094 95 HOH HOH A . E 5 HOH 94 2095 96 HOH HOH A . E 5 HOH 95 2096 98 HOH HOH A . E 5 HOH 96 2097 99 HOH HOH A . E 5 HOH 97 2098 100 HOH HOH A . E 5 HOH 98 2099 101 HOH HOH A . E 5 HOH 99 2100 102 HOH HOH A . E 5 HOH 100 2101 103 HOH HOH A . E 5 HOH 101 2102 104 HOH HOH A . E 5 HOH 102 2103 105 HOH HOH A . E 5 HOH 103 2104 106 HOH HOH A . E 5 HOH 104 2105 107 HOH HOH A . E 5 HOH 105 2106 108 HOH HOH A . E 5 HOH 106 2107 109 HOH HOH A . E 5 HOH 107 2108 110 HOH HOH A . E 5 HOH 108 2109 111 HOH HOH A . E 5 HOH 109 2110 112 HOH HOH A . E 5 HOH 110 2111 113 HOH HOH A . E 5 HOH 111 2112 114 HOH HOH A . E 5 HOH 112 2113 115 HOH HOH A . E 5 HOH 113 2114 116 HOH HOH A . E 5 HOH 114 2115 117 HOH HOH A . E 5 HOH 115 2116 118 HOH HOH A . E 5 HOH 116 2117 120 HOH HOH A . E 5 HOH 117 2118 121 HOH HOH A . E 5 HOH 118 2119 122 HOH HOH A . E 5 HOH 119 2120 123 HOH HOH A . E 5 HOH 120 2121 124 HOH HOH A . E 5 HOH 121 2122 125 HOH HOH A . E 5 HOH 122 2123 126 HOH HOH A . E 5 HOH 123 2124 127 HOH HOH A . E 5 HOH 124 2125 129 HOH HOH A . E 5 HOH 125 2126 130 HOH HOH A . E 5 HOH 126 2127 131 HOH HOH A . E 5 HOH 127 2128 133 HOH HOH A . E 5 HOH 128 2129 134 HOH HOH A . E 5 HOH 129 2130 135 HOH HOH A . E 5 HOH 130 2131 136 HOH HOH A . E 5 HOH 131 2132 137 HOH HOH A . E 5 HOH 132 2133 138 HOH HOH A . E 5 HOH 133 2134 139 HOH HOH A . E 5 HOH 134 2135 141 HOH HOH A . E 5 HOH 135 2136 142 HOH HOH A . E 5 HOH 136 2137 144 HOH HOH A . E 5 HOH 137 2138 145 HOH HOH A . E 5 HOH 138 2139 146 HOH HOH A . E 5 HOH 139 2140 147 HOH HOH A . E 5 HOH 140 2141 148 HOH HOH A . E 5 HOH 141 2142 149 HOH HOH A . E 5 HOH 142 2143 150 HOH HOH A . E 5 HOH 143 2144 151 HOH HOH A . E 5 HOH 144 2145 152 HOH HOH A . E 5 HOH 145 2146 153 HOH HOH A . E 5 HOH 146 2147 154 HOH HOH A . E 5 HOH 147 2148 155 HOH HOH A . E 5 HOH 148 2149 156 HOH HOH A . E 5 HOH 149 2150 157 HOH HOH A . E 5 HOH 150 2151 158 HOH HOH A . E 5 HOH 151 2152 159 HOH HOH A . E 5 HOH 152 2153 160 HOH HOH A . E 5 HOH 153 2154 161 HOH HOH A . E 5 HOH 154 2155 162 HOH HOH A . E 5 HOH 155 2156 163 HOH HOH A . E 5 HOH 156 2157 164 HOH HOH A . E 5 HOH 157 2158 165 HOH HOH A . E 5 HOH 158 2159 166 HOH HOH A . E 5 HOH 159 2160 167 HOH HOH A . E 5 HOH 160 2161 168 HOH HOH A . E 5 HOH 161 2162 169 HOH HOH A . E 5 HOH 162 2163 170 HOH HOH A . E 5 HOH 163 2164 171 HOH HOH A . E 5 HOH 164 2165 172 HOH HOH A . E 5 HOH 165 2166 173 HOH HOH A . E 5 HOH 166 2167 174 HOH HOH A . E 5 HOH 167 2168 175 HOH HOH A . E 5 HOH 168 2169 176 HOH HOH A . E 5 HOH 169 2170 177 HOH HOH A . E 5 HOH 170 2171 178 HOH HOH A . E 5 HOH 171 2172 179 HOH HOH A . E 5 HOH 172 2173 180 HOH HOH A . E 5 HOH 173 2174 181 HOH HOH A . E 5 HOH 174 2175 182 HOH HOH A . E 5 HOH 175 2176 183 HOH HOH A . E 5 HOH 176 2177 184 HOH HOH A . E 5 HOH 177 2178 185 HOH HOH A . E 5 HOH 178 2179 186 HOH HOH A . E 5 HOH 179 2180 187 HOH HOH A . E 5 HOH 180 2181 188 HOH HOH A . E 5 HOH 181 2182 189 HOH HOH A . E 5 HOH 182 2183 190 HOH HOH A . E 5 HOH 183 2184 191 HOH HOH A . E 5 HOH 184 2185 192 HOH HOH A . E 5 HOH 185 2186 193 HOH HOH A . E 5 HOH 186 2187 194 HOH HOH A . E 5 HOH 187 2188 195 HOH HOH A . E 5 HOH 188 2189 196 HOH HOH A . E 5 HOH 189 2190 197 HOH HOH A . E 5 HOH 190 2191 198 HOH HOH A . E 5 HOH 191 2192 199 HOH HOH A . E 5 HOH 192 2193 200 HOH HOH A . E 5 HOH 193 2194 201 HOH HOH A . E 5 HOH 194 2195 202 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 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,E # 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' 8_665 -y+1,-x+1,-z+1/2 0.0000000000 -1.0000000000 0.0000000000 73.7000000000 -1.0000000000 0.0000000000 0.0000000000 73.7000000000 0.0000000000 0.0000000000 -1.0000000000 53.2100000000 # 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 OD1 ? A ASN 10 ? A ASN 41 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O ? A ASP 12 ? A ASP 43 ? 1_555 91.4 ? 2 OD1 ? A ASN 10 ? A ASN 41 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 OD1 ? A ASP 145 ? A ASP 176 ? 1_555 91.5 ? 3 O ? A ASP 12 ? A ASP 43 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 OD1 ? A ASP 145 ? A ASP 176 ? 1_555 91.5 ? 4 OD1 ? A ASN 10 ? A ASN 41 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 OP1 B C UMP . ? A UMP 1001 ? 1_555 97.3 ? 5 O ? A ASP 12 ? A ASP 43 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 OP1 B C UMP . ? A UMP 1001 ? 1_555 105.8 ? 6 OD1 ? A ASP 145 ? A ASP 176 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 OP1 B C UMP . ? A UMP 1001 ? 1_555 160.3 ? 7 OD1 ? A ASN 10 ? A ASN 41 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 OP3 A C UMP . ? A UMP 1001 ? 1_555 90.3 ? 8 O ? A ASP 12 ? A ASP 43 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 OP3 A C UMP . ? A UMP 1001 ? 1_555 85.3 ? 9 OD1 ? A ASP 145 ? A ASP 176 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 OP3 A C UMP . ? A UMP 1001 ? 1_555 176.3 ? 10 OP1 B C UMP . ? A UMP 1001 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 OP3 A C UMP . ? A UMP 1001 ? 1_555 21.9 ? 11 OD1 ? A ASN 10 ? A ASN 41 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O1 ? D GOL . ? A GOL 2001 ? 1_555 174.9 ? 12 O ? A ASP 12 ? A ASP 43 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O1 ? D GOL . ? A GOL 2001 ? 1_555 84.6 ? 13 OD1 ? A ASP 145 ? A ASP 176 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O1 ? D GOL . ? A GOL 2001 ? 1_555 85.5 ? 14 OP1 B C UMP . ? A UMP 1001 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O1 ? D GOL . ? A GOL 2001 ? 1_555 86.8 ? 15 OP3 A C UMP . ? A UMP 1001 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O1 ? D GOL . ? A GOL 2001 ? 1_555 92.4 ? 16 OD1 ? A ASN 10 ? A ASN 41 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O ? E HOH . ? A HOH 2096 ? 1_555 91.2 ? 17 O ? A ASP 12 ? A ASP 43 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O ? E HOH . ? A HOH 2096 ? 1_555 175.5 ? 18 OD1 ? A ASP 145 ? A ASP 176 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O ? E HOH . ? A HOH 2096 ? 1_555 84.8 ? 19 OP1 B C UMP . ? A UMP 1001 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O ? E HOH . ? A HOH 2096 ? 1_555 77.4 ? 20 OP3 A C UMP . ? A UMP 1001 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O ? E HOH . ? A HOH 2096 ? 1_555 98.3 ? 21 O1 ? D GOL . ? A GOL 2001 ? 1_555 MG ? B MG . ? A MG 1228 ? 1_555 O ? E HOH . ? A HOH 2096 ? 1_555 92.6 ? # 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 2005-07-26 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' 'Non-polymer description' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Database references' 5 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_alt_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id' 20 4 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 21 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 22 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 26 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 28 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 32 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 33 4 'Structure model' '_struct_ref_seq_dif.details' 34 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 35 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 36 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.24 ? 1 MOSFLM 'data reduction' . ? 2 XDS 'data scaling' . ? 3 CNS phasing . ? 4 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 125.81 120.30 5.51 0.50 N 2 1 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH2 A ARG 37 ? ? 113.12 120.30 -7.18 0.50 N 3 1 CB A ASP 63 ? ? CG A ASP 63 ? ? OD2 A ASP 63 ? ? 124.75 118.30 6.45 0.90 N 4 1 CB A ASP 71 ? ? CG A ASP 71 ? ? OD2 A ASP 71 ? ? 124.57 118.30 6.27 0.90 N 5 1 NE A ARG 210 ? ? CZ A ARG 210 ? ? NH2 A ARG 210 ? ? 117.27 120.30 -3.03 0.50 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 MET A 42 ? ? -96.07 -69.27 2 1 VAL A 45 ? ? -128.42 -56.44 3 1 ARG A 85 ? ? 176.47 130.81 4 1 ASN A 100 ? ? 72.40 -0.33 5 1 SER A 213 ? ? 179.95 174.11 # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag Y _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id A _pdbx_unobs_or_zero_occ_atoms.auth_comp_id PRO _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 227 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id O _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id A _pdbx_unobs_or_zero_occ_atoms.label_comp_id PRO _pdbx_unobs_or_zero_occ_atoms.label_seq_id 196 _pdbx_unobs_or_zero_occ_atoms.label_atom_id O # 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 GLY 32 ? A GLY 1 2 1 Y 1 A GLY 33 ? A GLY 2 3 1 Y 1 A CYS 228 ? A CYS 197 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; UMP 4 GLYCEROL GOL 5 water HOH #