data_5QOH # _entry.id 5QOH # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.318 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5QOH WWPDB D_1001402206 # _pdbx_database_status.entry_id 5QOH _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.recvd_initial_deposition_date 2019-02-22 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Nelson, E.R.' 1 ? 'Velupillai, S.' 2 ? 'Talon, R.' 3 ? 'Collins, P.M.' 4 ? 'Krojer, T.' 5 ? 'Wang, D.' 6 ? 'Brandao-Neto, J.' 7 ? 'Douangamath, A.' 8 ? 'Burgess-Brown, N.' 9 ? 'Arrowsmith, C.H.' 10 ? 'Bountra, C.' 11 ? 'Huber, K.' 12 ? 'von Delft, F.' 13 ? # _citation.id primary _citation.title 'PanDDA analysis group deposition' _citation.journal_abbrev 'To Be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.identifier_ORCID _citation_author.ordinal primary 'Nelson, E.R.' ? 1 primary 'Velupillai, S.' ? 2 primary 'Talon, R.' ? 3 primary 'Collins, P.M.' ? 4 primary 'Krojer, T.' ? 5 primary 'Wang, D.' ? 6 primary 'Brandao-Neto, J.' ? 7 primary 'Douangamath, A.' ? 8 primary 'Burgess-Brown, N.' ? 9 primary 'Arrowsmith, C.H.' ? 10 primary 'Bountra, C.' ? 11 primary 'Huber, K.' ? 12 primary 'von Delft, F.' ? 13 # _cell.entry_id 5QOH _cell.length_a 48.760 _cell.length_b 61.370 _cell.length_c 66.400 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QOH _symmetry.Int_Tables_number 19 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? # 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 'DCP2 (NUDT20)' 19073.738 1 3.6.1.62 ? 'UNP residues 95-260' ? 2 non-polymer syn 1,2-ETHANEDIOL 62.068 2 ? ? ? ? 3 non-polymer syn 'DIMETHYL SULFOXIDE' 78.133 1 ? ? ? ? 4 non-polymer syn 'ACETATE ION' 59.044 2 ? ? ? ? 5 non-polymer syn 'DI(HYDROXYETHYL)ETHER' 106.120 1 ? ? ? ? 6 non-polymer syn N,N-dimethylpyridin-4-amine 122.168 1 ? ? ? ? 7 water nat water 18.015 91 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Nucleoside diphosphate-linked moiety X motif 20, Nudix motif 20, mRNA-decapping enzyme 2, hDpc, m7GpppN-mRNA hydrolase' # _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 ;SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLAR LYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGF SSTGSTP ; _entity_poly.pdbx_seq_one_letter_code_can ;SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLAR LYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGF SSTGSTP ; _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 SER n 1 2 MET n 1 3 GLY n 1 4 VAL n 1 5 PRO n 1 6 THR n 1 7 TYR n 1 8 GLY n 1 9 ALA n 1 10 ILE n 1 11 ILE n 1 12 LEU n 1 13 ASP n 1 14 GLU n 1 15 THR n 1 16 LEU n 1 17 GLU n 1 18 ASN n 1 19 VAL n 1 20 LEU n 1 21 LEU n 1 22 VAL n 1 23 GLN n 1 24 GLY n 1 25 TYR n 1 26 LEU n 1 27 ALA n 1 28 LYS n 1 29 SER n 1 30 GLY n 1 31 TRP n 1 32 GLY n 1 33 PHE n 1 34 PRO n 1 35 LYS n 1 36 GLY n 1 37 LYS n 1 38 VAL n 1 39 ASN n 1 40 LYS n 1 41 GLU n 1 42 GLU n 1 43 ALA n 1 44 PRO n 1 45 HIS n 1 46 ASP n 1 47 CYS n 1 48 ALA n 1 49 ALA n 1 50 ARG n 1 51 GLU n 1 52 VAL n 1 53 PHE n 1 54 GLU n 1 55 GLU n 1 56 THR n 1 57 GLY n 1 58 PHE n 1 59 ASP n 1 60 ILE n 1 61 LYS n 1 62 ASP n 1 63 TYR n 1 64 ILE n 1 65 CYS n 1 66 LYS n 1 67 ASP n 1 68 ASP n 1 69 TYR n 1 70 ILE n 1 71 GLU n 1 72 LEU n 1 73 ARG n 1 74 ILE n 1 75 ASN n 1 76 ASP n 1 77 GLN n 1 78 LEU n 1 79 ALA n 1 80 ARG n 1 81 LEU n 1 82 TYR n 1 83 ILE n 1 84 ILE n 1 85 PRO n 1 86 GLY n 1 87 ILE n 1 88 PRO n 1 89 LYS n 1 90 ASP n 1 91 THR n 1 92 LYS n 1 93 PHE n 1 94 ASN n 1 95 PRO n 1 96 LYS n 1 97 THR n 1 98 ARG n 1 99 ARG n 1 100 GLU n 1 101 ILE n 1 102 ARG n 1 103 ASN n 1 104 ILE n 1 105 GLU n 1 106 TRP n 1 107 PHE n 1 108 SER n 1 109 ILE n 1 110 GLU n 1 111 LYS n 1 112 LEU n 1 113 PRO n 1 114 CYS n 1 115 HIS n 1 116 ARG n 1 117 ASN n 1 118 ASP n 1 119 MET n 1 120 THR n 1 121 PRO n 1 122 LYS n 1 123 SER n 1 124 LYS n 1 125 LEU n 1 126 GLY n 1 127 LEU n 1 128 ALA n 1 129 PRO n 1 130 ASN n 1 131 LYS n 1 132 PHE n 1 133 PHE n 1 134 MET n 1 135 ALA n 1 136 ILE n 1 137 PRO n 1 138 PHE n 1 139 ILE n 1 140 ARG n 1 141 PRO n 1 142 LEU n 1 143 ARG n 1 144 ASP n 1 145 TRP n 1 146 LEU n 1 147 SER n 1 148 ARG n 1 149 ARG n 1 150 PHE n 1 151 GLY n 1 152 ASP n 1 153 SER n 1 154 SER n 1 155 ASP n 1 156 SER n 1 157 ASP n 1 158 ASN n 1 159 GLY n 1 160 PHE n 1 161 SER n 1 162 SER n 1 163 THR n 1 164 GLY n 1 165 SER n 1 166 THR n 1 167 PRO 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 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 167 _entity_src_gen.gene_src_common_name Human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'DCP2, NUDT20' _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' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _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 DCP2_HUMAN _struct_ref.pdbx_db_accession Q8IU60 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARL YIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFS STGSTP ; _struct_ref.pdbx_align_begin 95 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5QOH _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 167 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q8IU60 _struct_ref_seq.db_align_beg 95 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 260 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 95 _struct_ref_seq.pdbx_auth_seq_align_end 260 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 5QOH _struct_ref_seq_dif.mon_id SER _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _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 Q8IU60 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 94 _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 ACT non-polymer . 'ACETATE ION' ? 'C2 H3 O2 -1' 59.044 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 DMS non-polymer . 'DIMETHYL SULFOXIDE' ? 'C2 H6 O S' 78.133 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 JGD non-polymer . N,N-dimethylpyridin-4-amine ? 'C7 H10 N2' 122.168 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 PEG non-polymer . 'DI(HYDROXYETHYL)ETHER' ? 'C4 H10 O3' 106.120 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 5QOH _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity 0.000 _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 2.60 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 52.77 _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.description ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 4.5 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '0.1 M acetate, pH 4.5, 5-25% PEG3350' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.crystal_id 1 _diffrn.ambient_temp_details ? _diffrn.pdbx_serial_crystal_experiment ? # _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 2M' _diffrn_detector.pdbx_collection_date 2016-12-05 _diffrn_detector.diffrn_id 1 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.92819 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I04-1' _diffrn_source.pdbx_wavelength_list 0.92819 _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I04-1 _diffrn_source.pdbx_wavelength ? # _reflns.entry_id 5QOH _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 39.300 _reflns.d_resolution_high 1.930 _reflns.number_obs 15554 _reflns.number_all ? _reflns.percent_possible_obs 99.900 _reflns.pdbx_Rmerge_I_obs 0.074 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 15.600 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.500 _reflns.pdbx_Rrim_I_all 0.080 _reflns.pdbx_Rpim_I_all 0.031 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_number_measured_all 100412 _reflns.pdbx_scaling_rejects 0 _reflns.pdbx_chi_squared ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.details ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_CC_half 1 1 1.930 1.980 ? 7576 ? ? 0.812 ? ? ? 6.700 ? 2.400 ? 1125 ? ? ? ? 100.000 0.880 0.337 0.724 1 2 8.630 39.300 ? 1176 ? ? 0.022 ? ? ? 5.500 ? 53.600 ? 215 ? ? ? ? 99.400 0.024 0.010 1.000 # _refine.entry_id 5QOH _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 1.9300 _refine.ls_d_res_low 45.1100 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.8100 _refine.ls_number_reflns_obs 14769 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1883 _refine.ls_R_factor_R_work 0.1856 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2459 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.8000 _refine.ls_number_reflns_R_free 742 _refine.ls_number_reflns_R_work ? _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 37.3800 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 2.4500 _refine.aniso_B[2][2] -2.5900 _refine.aniso_B[3][3] 0.1400 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9630 _refine.correlation_coeff_Fo_to_Fc_free 0.9230 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.1530 _refine.pdbx_overall_ESU_R_Free 0.1550 _refine.overall_SU_ML 0.1200 _refine.overall_SU_B 4.3070 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 'PDB entry 5MP0' _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 98.340 _refine.B_iso_min 18.520 _refine.pdbx_overall_phase_error ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_R_factor_R_free_error_details ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.9300 _refine_hist.d_res_low 45.1100 _refine_hist.pdbx_number_atoms_ligand 36 _refine_hist.number_atoms_solvent 91 _refine_hist.number_atoms_total 1322 _refine_hist.pdbx_number_residues_total 149 _refine_hist.pdbx_B_iso_mean_ligand 62.19 _refine_hist.pdbx_B_iso_mean_solvent 46.64 _refine_hist.pdbx_number_atoms_protein 1195 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' r_bond_refined_d 1642 0.018 0.019 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 1384 0.002 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 2022 1.876 1.961 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 3193 1.087 2.980 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 187 7.185 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 73 32.513 21.781 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 247 16.413 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 19 23.959 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 202 0.120 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 1763 0.009 0.021 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 364 0.003 0.020 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 760 2.994 3.487 ? ? 'X-RAY DIFFRACTION' r_mcbond_other 756 2.987 3.477 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 901 4.488 5.131 ? ? # _refine_ls_shell.d_res_high 1.9300 _refine_ls_shell.d_res_low 1.9800 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.8200 _refine_ls_shell.number_reflns_R_work 1063 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2730 _refine_ls_shell.R_factor_R_free 0.2900 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 59 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1122 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_obs ? # _struct.entry_id 5QOH _struct.title 'PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with XST00000847b' _struct.pdbx_descriptor 'DCP2 (NUDT20) (E.C.3.6.1.62)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 5QOH _struct_keywords.text 'SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE' _struct_keywords.pdbx_keywords 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 2 ? D N N 3 ? E N N 4 ? F N N 4 ? G N N 5 ? H N N 6 ? I N N 7 ? # 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 AA1 TYR A 25 ? SER A 29 ? TYR A 118 SER A 122 5 ? 5 HELX_P HELX_P2 AA2 ALA A 43 ? GLY A 57 ? ALA A 136 GLY A 150 1 ? 15 HELX_P HELX_P3 AA3 GLU A 110 ? LEU A 112 ? GLU A 203 LEU A 205 5 ? 3 HELX_P HELX_P4 AA4 MET A 119 ? SER A 123 ? MET A 212 SER A 216 5 ? 5 HELX_P HELX_P5 AA5 ALA A 135 ? PRO A 137 ? ALA A 228 PRO A 230 5 ? 3 HELX_P HELX_P6 AA6 PHE A 138 ? PHE A 150 ? PHE A 231 PHE A 243 1 ? 13 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 4 ? AA2 ? 3 ? # 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 AA1 1 2 ? anti-parallel AA1 2 3 ? parallel AA1 3 4 ? anti-parallel AA2 1 2 ? anti-parallel AA2 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 AA1 1 LYS A 35 ? LYS A 37 ? LYS A 128 LYS A 130 AA1 2 THR A 6 ? ILE A 11 ? THR A 99 ILE A 104 AA1 3 GLN A 77 ? ILE A 84 ? GLN A 170 ILE A 177 AA1 4 TYR A 69 ? ILE A 74 ? TYR A 162 ILE A 167 AA2 1 TRP A 31 ? GLY A 32 ? TRP A 124 GLY A 125 AA2 2 ASN A 18 ? GLN A 23 ? ASN A 111 GLN A 116 AA2 3 ASN A 103 ? SER A 108 ? ASN A 196 SER A 201 # 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 AA1 1 2 O GLY A 36 ? O GLY A 129 N TYR A 7 ? N TYR A 100 AA1 2 3 N ILE A 10 ? N ILE A 103 O ILE A 84 ? O ILE A 177 AA1 3 4 O GLN A 77 ? O GLN A 170 N ILE A 74 ? N ILE A 167 AA2 1 2 O GLY A 32 ? O GLY A 125 N VAL A 22 ? N VAL A 115 AA2 2 3 N GLN A 23 ? N GLN A 116 O ASN A 103 ? O ASN A 196 # 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 EDO 301 ? 4 'binding site for residue EDO A 301' AC2 Software A EDO 302 ? 6 'binding site for residue EDO A 302' AC3 Software A DMS 303 ? 2 'binding site for residue DMS A 303' AC4 Software A ACT 304 ? 3 'binding site for residue ACT A 304' AC5 Software A ACT 305 ? 5 'binding site for residue ACT A 305' AC6 Software A PEG 306 ? 8 'binding site for residue PEG A 306' AC7 Software A JGD 307 ? 3 'binding site for residue JGD A 307' # 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 4 ALA A 49 ? ALA A 142 . ? 1_555 ? 2 AC1 4 ASP A 59 ? ASP A 152 . ? 1_555 ? 3 AC1 4 HOH I . ? HOH A 440 . ? 1_555 ? 4 AC1 4 HOH I . ? HOH A 448 . ? 1_555 ? 5 AC2 6 PRO A 129 ? PRO A 222 . ? 1_555 ? 6 AC2 6 ASN A 130 ? ASN A 223 . ? 1_555 ? 7 AC2 6 LYS A 131 ? LYS A 224 . ? 1_555 ? 8 AC2 6 ACT F . ? ACT A 305 . ? 1_555 ? 9 AC2 6 HOH I . ? HOH A 404 . ? 1_555 ? 10 AC2 6 HOH I . ? HOH A 449 . ? 3_357 ? 11 AC3 2 ASN A 18 ? ASN A 111 . ? 1_555 ? 12 AC3 2 TRP A 106 ? TRP A 199 . ? 1_555 ? 13 AC4 3 SER A 29 ? SER A 122 . ? 1_555 ? 14 AC4 3 TYR A 63 ? TYR A 156 . ? 3_357 ? 15 AC4 3 HOH I . ? HOH A 414 . ? 1_555 ? 16 AC5 5 ARG A 116 ? ARG A 209 . ? 1_555 ? 17 AC5 5 PRO A 129 ? PRO A 222 . ? 1_555 ? 18 AC5 5 ASN A 130 ? ASN A 223 . ? 1_555 ? 19 AC5 5 PHE A 133 ? PHE A 226 . ? 1_555 ? 20 AC5 5 EDO C . ? EDO A 302 . ? 1_555 ? 21 AC6 8 VAL A 22 ? VAL A 115 . ? 1_555 ? 22 AC6 8 GLY A 24 ? GLY A 117 . ? 1_555 ? 23 AC6 8 LYS A 28 ? LYS A 121 . ? 1_555 ? 24 AC6 8 GLY A 30 ? GLY A 123 . ? 1_555 ? 25 AC6 8 GLY A 32 ? GLY A 125 . ? 1_555 ? 26 AC6 8 LYS A 35 ? LYS A 128 . ? 1_555 ? 27 AC6 8 GLU A 55 ? GLU A 148 . ? 1_555 ? 28 AC6 8 MET A 134 ? MET A 227 . ? 1_555 ? 29 AC7 3 PHE A 93 ? PHE A 186 . ? 1_555 ? 30 AC7 3 ASN A 103 ? ASN A 196 . ? 1_555 ? 31 AC7 3 ILE A 104 ? ILE A 197 . ? 1_555 ? # _atom_sites.entry_id 5QOH _atom_sites.fract_transf_matrix[1][1] 0.020509 _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] 0.016295 _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] 0.015060 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C 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 SER 1 94 ? ? ? A . n A 1 2 MET 2 95 ? ? ? A . n A 1 3 GLY 3 96 96 GLY GLY A . n A 1 4 VAL 4 97 97 VAL VAL A . n A 1 5 PRO 5 98 98 PRO PRO A . n A 1 6 THR 6 99 99 THR THR A . n A 1 7 TYR 7 100 100 TYR TYR A . n A 1 8 GLY 8 101 101 GLY GLY A . n A 1 9 ALA 9 102 102 ALA ALA A . n A 1 10 ILE 10 103 103 ILE ILE A . n A 1 11 ILE 11 104 104 ILE ILE A . n A 1 12 LEU 12 105 105 LEU LEU A . n A 1 13 ASP 13 106 106 ASP ASP A . n A 1 14 GLU 14 107 107 GLU GLU A . n A 1 15 THR 15 108 108 THR THR A . n A 1 16 LEU 16 109 109 LEU LEU A . n A 1 17 GLU 17 110 110 GLU GLU A . n A 1 18 ASN 18 111 111 ASN ASN A . n A 1 19 VAL 19 112 112 VAL VAL A . n A 1 20 LEU 20 113 113 LEU LEU A . n A 1 21 LEU 21 114 114 LEU LEU A . n A 1 22 VAL 22 115 115 VAL VAL A . n A 1 23 GLN 23 116 116 GLN GLN A . n A 1 24 GLY 24 117 117 GLY GLY A . n A 1 25 TYR 25 118 118 TYR TYR A . n A 1 26 LEU 26 119 119 LEU LEU A . n A 1 27 ALA 27 120 120 ALA ALA A . n A 1 28 LYS 28 121 121 LYS LYS A . n A 1 29 SER 29 122 122 SER SER A . n A 1 30 GLY 30 123 123 GLY GLY A . n A 1 31 TRP 31 124 124 TRP TRP A . n A 1 32 GLY 32 125 125 GLY GLY A . n A 1 33 PHE 33 126 126 PHE PHE A . n A 1 34 PRO 34 127 127 PRO PRO A . n A 1 35 LYS 35 128 128 LYS LYS A . n A 1 36 GLY 36 129 129 GLY GLY A . n A 1 37 LYS 37 130 130 LYS LYS A . n A 1 38 VAL 38 131 131 VAL VAL A . n A 1 39 ASN 39 132 132 ASN ASN A . n A 1 40 LYS 40 133 133 LYS LYS A . n A 1 41 GLU 41 134 134 GLU GLU A . n A 1 42 GLU 42 135 135 GLU GLU A . n A 1 43 ALA 43 136 136 ALA ALA A . n A 1 44 PRO 44 137 137 PRO PRO A . n A 1 45 HIS 45 138 138 HIS HIS A . n A 1 46 ASP 46 139 139 ASP ASP A . n A 1 47 CYS 47 140 140 CYS CYS A . n A 1 48 ALA 48 141 141 ALA ALA A . n A 1 49 ALA 49 142 142 ALA ALA A . n A 1 50 ARG 50 143 143 ARG ARG A . n A 1 51 GLU 51 144 144 GLU GLU A . n A 1 52 VAL 52 145 145 VAL VAL A . n A 1 53 PHE 53 146 146 PHE PHE A . n A 1 54 GLU 54 147 147 GLU GLU A . n A 1 55 GLU 55 148 148 GLU GLU A . n A 1 56 THR 56 149 149 THR THR A . n A 1 57 GLY 57 150 150 GLY GLY A . n A 1 58 PHE 58 151 151 PHE PHE A . n A 1 59 ASP 59 152 152 ASP ASP A . n A 1 60 ILE 60 153 153 ILE ILE A . n A 1 61 LYS 61 154 154 LYS LYS A . n A 1 62 ASP 62 155 155 ASP ASP A . n A 1 63 TYR 63 156 156 TYR TYR A . n A 1 64 ILE 64 157 157 ILE ILE A . n A 1 65 CYS 65 158 158 CYS CYS A . n A 1 66 LYS 66 159 159 LYS LYS A . n A 1 67 ASP 67 160 160 ASP ASP A . n A 1 68 ASP 68 161 161 ASP ASP A . n A 1 69 TYR 69 162 162 TYR TYR A . n A 1 70 ILE 70 163 163 ILE ILE A . n A 1 71 GLU 71 164 164 GLU GLU A . n A 1 72 LEU 72 165 165 LEU LEU A . n A 1 73 ARG 73 166 166 ARG ARG A . n A 1 74 ILE 74 167 167 ILE ILE A . n A 1 75 ASN 75 168 168 ASN ASN A . n A 1 76 ASP 76 169 169 ASP ASP A . n A 1 77 GLN 77 170 170 GLN GLN A . n A 1 78 LEU 78 171 171 LEU LEU A . n A 1 79 ALA 79 172 172 ALA ALA A . n A 1 80 ARG 80 173 173 ARG ARG A . n A 1 81 LEU 81 174 174 LEU LEU A . n A 1 82 TYR 82 175 175 TYR TYR A . n A 1 83 ILE 83 176 176 ILE ILE A . n A 1 84 ILE 84 177 177 ILE ILE A . n A 1 85 PRO 85 178 178 PRO PRO A . n A 1 86 GLY 86 179 179 GLY GLY A . n A 1 87 ILE 87 180 180 ILE ILE A . n A 1 88 PRO 88 181 181 PRO PRO A . n A 1 89 LYS 89 182 182 LYS LYS A . n A 1 90 ASP 90 183 183 ASP ASP A . n A 1 91 THR 91 184 184 THR THR A . n A 1 92 LYS 92 185 185 LYS LYS A . n A 1 93 PHE 93 186 186 PHE PHE A . n A 1 94 ASN 94 187 187 ASN ASN A . n A 1 95 PRO 95 188 188 PRO PRO A . n A 1 96 LYS 96 189 189 LYS LYS A . n A 1 97 THR 97 190 190 THR THR A . n A 1 98 ARG 98 191 191 ARG ARG A . n A 1 99 ARG 99 192 192 ARG ARG A . n A 1 100 GLU 100 193 193 GLU GLU A . n A 1 101 ILE 101 194 194 ILE ILE A . n A 1 102 ARG 102 195 195 ARG ARG A . n A 1 103 ASN 103 196 196 ASN ASN A . n A 1 104 ILE 104 197 197 ILE ILE A . n A 1 105 GLU 105 198 198 GLU GLU A . n A 1 106 TRP 106 199 199 TRP TRP A . n A 1 107 PHE 107 200 200 PHE PHE A . n A 1 108 SER 108 201 201 SER SER A . n A 1 109 ILE 109 202 202 ILE ILE A . n A 1 110 GLU 110 203 203 GLU GLU A . n A 1 111 LYS 111 204 204 LYS LYS A . n A 1 112 LEU 112 205 205 LEU LEU A . n A 1 113 PRO 113 206 206 PRO PRO A . n A 1 114 CYS 114 207 207 CYS CYS A . n A 1 115 HIS 115 208 208 HIS HIS A . n A 1 116 ARG 116 209 209 ARG ARG A . n A 1 117 ASN 117 210 210 ASN ASN A . n A 1 118 ASP 118 211 211 ASP ASP A . n A 1 119 MET 119 212 212 MET MET A . n A 1 120 THR 120 213 213 THR THR A . n A 1 121 PRO 121 214 214 PRO PRO A . n A 1 122 LYS 122 215 215 LYS LYS A . n A 1 123 SER 123 216 216 SER SER A . n A 1 124 LYS 124 217 217 LYS LYS A . n A 1 125 LEU 125 218 218 LEU LEU A . n A 1 126 GLY 126 219 219 GLY GLY A . n A 1 127 LEU 127 220 220 LEU LEU A . n A 1 128 ALA 128 221 221 ALA ALA A . n A 1 129 PRO 129 222 222 PRO PRO A . n A 1 130 ASN 130 223 223 ASN ASN A . n A 1 131 LYS 131 224 224 LYS LYS A . n A 1 132 PHE 132 225 225 PHE PHE A . n A 1 133 PHE 133 226 226 PHE PHE A . n A 1 134 MET 134 227 227 MET MET A . n A 1 135 ALA 135 228 228 ALA ALA A . n A 1 136 ILE 136 229 229 ILE ILE A . n A 1 137 PRO 137 230 230 PRO PRO A . n A 1 138 PHE 138 231 231 PHE PHE A . n A 1 139 ILE 139 232 232 ILE ILE A . n A 1 140 ARG 140 233 233 ARG ARG A . n A 1 141 PRO 141 234 234 PRO PRO A . n A 1 142 LEU 142 235 235 LEU LEU A . n A 1 143 ARG 143 236 236 ARG ARG A . n A 1 144 ASP 144 237 237 ASP ASP A . n A 1 145 TRP 145 238 238 TRP TRP A . n A 1 146 LEU 146 239 239 LEU LEU A . n A 1 147 SER 147 240 240 SER SER A . n A 1 148 ARG 148 241 241 ARG ARG A . n A 1 149 ARG 149 242 242 ARG ARG A . n A 1 150 PHE 150 243 243 PHE PHE A . n A 1 151 GLY 151 244 244 GLY GLY A . n A 1 152 ASP 152 245 ? ? ? A . n A 1 153 SER 153 246 ? ? ? A . n A 1 154 SER 154 247 ? ? ? A . n A 1 155 ASP 155 248 ? ? ? A . n A 1 156 SER 156 249 ? ? ? A . n A 1 157 ASP 157 250 ? ? ? A . n A 1 158 ASN 158 251 ? ? ? A . n A 1 159 GLY 159 252 ? ? ? A . n A 1 160 PHE 160 253 ? ? ? A . n A 1 161 SER 161 254 ? ? ? A . n A 1 162 SER 162 255 ? ? ? A . n A 1 163 THR 163 256 ? ? ? A . n A 1 164 GLY 164 257 ? ? ? A . n A 1 165 SER 165 258 ? ? ? A . n A 1 166 THR 166 259 ? ? ? A . n A 1 167 PRO 167 260 ? ? ? 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 EDO 1 301 2 EDO EDO A . C 2 EDO 1 302 3 EDO EDO A . D 3 DMS 1 303 1 DMS DMS A . E 4 ACT 1 304 1 ACT ACT A . F 4 ACT 1 305 2 ACT ACT A . G 5 PEG 1 306 1 PEG PEG A . H 6 JGD 1 307 1 JGD LIG A . I 7 HOH 1 401 104 HOH HOH A . I 7 HOH 2 402 17 HOH HOH A . I 7 HOH 3 403 12 HOH HOH A . I 7 HOH 4 404 19 HOH HOH A . I 7 HOH 5 405 29 HOH HOH A . I 7 HOH 6 406 8 HOH HOH A . I 7 HOH 7 407 39 HOH HOH A . I 7 HOH 8 408 15 HOH HOH A . I 7 HOH 9 409 96 HOH HOH A . I 7 HOH 10 410 1 HOH HOH A . I 7 HOH 11 411 60 HOH HOH A . I 7 HOH 12 412 66 HOH HOH A . I 7 HOH 13 413 10 HOH HOH A . I 7 HOH 14 414 68 HOH HOH A . I 7 HOH 15 415 83 HOH HOH A . I 7 HOH 16 416 35 HOH HOH A . I 7 HOH 17 417 13 HOH HOH A . I 7 HOH 18 418 67 HOH HOH A . I 7 HOH 19 419 90 HOH HOH A . I 7 HOH 20 420 102 HOH HOH A . I 7 HOH 21 421 59 HOH HOH A . I 7 HOH 22 422 88 HOH HOH A . I 7 HOH 23 423 55 HOH HOH A . I 7 HOH 24 424 80 HOH HOH A . I 7 HOH 25 425 31 HOH HOH A . I 7 HOH 26 426 38 HOH HOH A . I 7 HOH 27 427 32 HOH HOH A . I 7 HOH 28 428 7 HOH HOH A . I 7 HOH 29 429 79 HOH HOH A . I 7 HOH 30 430 85 HOH HOH A . I 7 HOH 31 431 5 HOH HOH A . I 7 HOH 32 432 14 HOH HOH A . I 7 HOH 33 433 23 HOH HOH A . I 7 HOH 34 434 62 HOH HOH A . I 7 HOH 35 435 71 HOH HOH A . I 7 HOH 36 436 76 HOH HOH A . I 7 HOH 37 437 100 HOH HOH A . I 7 HOH 38 438 36 HOH HOH A . I 7 HOH 39 439 43 HOH HOH A . I 7 HOH 40 440 97 HOH HOH A . I 7 HOH 41 441 4 HOH HOH A . I 7 HOH 42 442 95 HOH HOH A . I 7 HOH 43 443 78 HOH HOH A . I 7 HOH 44 444 33 HOH HOH A . I 7 HOH 45 445 18 HOH HOH A . I 7 HOH 46 446 107 HOH HOH A . I 7 HOH 47 447 2 HOH HOH A . I 7 HOH 48 448 46 HOH HOH A . I 7 HOH 49 449 16 HOH HOH A . I 7 HOH 50 450 65 HOH HOH A . I 7 HOH 51 451 28 HOH HOH A . I 7 HOH 52 452 9 HOH HOH A . I 7 HOH 53 453 6 HOH HOH A . I 7 HOH 54 454 24 HOH HOH A . I 7 HOH 55 455 27 HOH HOH A . I 7 HOH 56 456 11 HOH HOH A . I 7 HOH 57 457 25 HOH HOH A . I 7 HOH 58 458 50 HOH HOH A . I 7 HOH 59 459 57 HOH HOH A . I 7 HOH 60 460 22 HOH HOH A . I 7 HOH 61 461 87 HOH HOH A . I 7 HOH 62 462 81 HOH HOH A . I 7 HOH 63 463 52 HOH HOH A . I 7 HOH 64 464 84 HOH HOH A . I 7 HOH 65 465 3 HOH HOH A . I 7 HOH 66 466 72 HOH HOH A . I 7 HOH 67 467 74 HOH HOH A . I 7 HOH 68 468 69 HOH HOH A . I 7 HOH 69 469 30 HOH HOH A . I 7 HOH 70 470 92 HOH HOH A . I 7 HOH 71 471 42 HOH HOH A . I 7 HOH 72 472 47 HOH HOH A . I 7 HOH 73 473 103 HOH HOH A . I 7 HOH 74 474 40 HOH HOH A . I 7 HOH 75 475 106 HOH HOH A . I 7 HOH 76 476 105 HOH HOH A . I 7 HOH 77 477 21 HOH HOH A . I 7 HOH 78 478 94 HOH HOH A . I 7 HOH 79 479 64 HOH HOH A . I 7 HOH 80 480 109 HOH HOH A . I 7 HOH 81 481 91 HOH HOH A . I 7 HOH 82 482 86 HOH HOH A . I 7 HOH 83 483 26 HOH HOH A . I 7 HOH 84 484 75 HOH HOH A . I 7 HOH 85 485 101 HOH HOH A . I 7 HOH 86 486 98 HOH HOH A . I 7 HOH 87 487 51 HOH HOH A . I 7 HOH 88 488 56 HOH HOH A . I 7 HOH 89 489 20 HOH HOH A . I 7 HOH 90 490 93 HOH HOH A . I 7 HOH 91 491 41 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1200 ? 1 MORE 9 ? 1 'SSA (A^2)' 8830 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2019-05-08 2 'Structure model' 1 1 2019-11-20 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Data collection' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category diffrn_source # 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 2 'Structure model' '_diffrn_source.pdbx_synchrotron_beamline' 2 2 'Structure model' '_diffrn_source.type' # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 REFMAC 5.8.0189 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 2 Aimless 0.5.29 17/10/16 program 'Phil Evans' ? 'data scaling' http://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.html ? ? 3 PDB_EXTRACT 3.23 'SEP. 23, 2016' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 4 XDS . ? program ? ? 'data reduction' ? ? ? 5 REFMAC . ? program ? ? phasing ? ? ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 CB _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 ASP _pdbx_validate_rmsd_angle.auth_seq_id_1 106 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CG _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 ASP _pdbx_validate_rmsd_angle.auth_seq_id_2 106 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 OD1 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 ASP _pdbx_validate_rmsd_angle.auth_seq_id_3 106 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 124.20 _pdbx_validate_rmsd_angle.angle_target_value 118.30 _pdbx_validate_rmsd_angle.angle_deviation 5.90 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.90 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 LEU A 119 ? ? 59.83 -115.75 2 1 PHE A 243 ? ? -126.53 -55.86 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LYS 130 ? CE ? A LYS 37 CE 2 1 Y 1 A LYS 130 ? NZ ? A LYS 37 NZ 3 1 Y 1 A LYS 133 ? CG ? A LYS 40 CG 4 1 Y 1 A LYS 133 ? CD ? A LYS 40 CD 5 1 Y 1 A LYS 133 ? CE ? A LYS 40 CE 6 1 Y 1 A LYS 133 ? NZ ? A LYS 40 NZ 7 1 Y 1 A GLU 134 ? CG ? A GLU 41 CG 8 1 Y 1 A GLU 134 ? CD ? A GLU 41 CD 9 1 Y 1 A GLU 134 ? OE1 ? A GLU 41 OE1 10 1 Y 1 A GLU 134 ? OE2 ? A GLU 41 OE2 11 1 Y 1 A LYS 159 ? CD ? A LYS 66 CD 12 1 Y 1 A LYS 159 ? CE ? A LYS 66 CE 13 1 Y 1 A LYS 159 ? NZ ? A LYS 66 NZ 14 1 Y 1 A LYS 185 ? CE ? A LYS 92 CE 15 1 Y 1 A LYS 185 ? NZ ? A LYS 92 NZ 16 1 Y 1 A LYS 215 ? CD ? A LYS 122 CD 17 1 Y 1 A LYS 215 ? CE ? A LYS 122 CE 18 1 Y 1 A LYS 215 ? NZ ? A LYS 122 NZ 19 1 Y 1 A LYS 217 ? CE ? A LYS 124 CE 20 1 Y 1 A LYS 217 ? NZ ? A LYS 124 NZ 21 1 Y 1 A ARG 241 ? CD ? A ARG 148 CD 22 1 Y 1 A ARG 241 ? NE ? A ARG 148 NE 23 1 Y 1 A ARG 241 ? CZ ? A ARG 148 CZ 24 1 Y 1 A ARG 241 ? NH1 ? A ARG 148 NH1 25 1 Y 1 A ARG 241 ? NH2 ? A ARG 148 NH2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A SER 94 ? A SER 1 2 1 Y 1 A MET 95 ? A MET 2 3 1 Y 1 A ASP 245 ? A ASP 152 4 1 Y 1 A SER 246 ? A SER 153 5 1 Y 1 A SER 247 ? A SER 154 6 1 Y 1 A ASP 248 ? A ASP 155 7 1 Y 1 A SER 249 ? A SER 156 8 1 Y 1 A ASP 250 ? A ASP 157 9 1 Y 1 A ASN 251 ? A ASN 158 10 1 Y 1 A GLY 252 ? A GLY 159 11 1 Y 1 A PHE 253 ? A PHE 160 12 1 Y 1 A SER 254 ? A SER 161 13 1 Y 1 A SER 255 ? A SER 162 14 1 Y 1 A THR 256 ? A THR 163 15 1 Y 1 A GLY 257 ? A GLY 164 16 1 Y 1 A SER 258 ? A SER 165 17 1 Y 1 A THR 259 ? A THR 166 18 1 Y 1 A PRO 260 ? A PRO 167 # _pdbx_deposit_group.group_id G_1002061 _pdbx_deposit_group.group_description ;XDomainX of XOrganismX DCP2 (NUDT20) screened against the XXX Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 ; _pdbx_deposit_group.group_title 'PanDDA analysis group deposition' _pdbx_deposit_group.group_type 'changed state' # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 1,2-ETHANEDIOL EDO 3 'DIMETHYL SULFOXIDE' DMS 4 'ACETATE ION' ACT 5 'DI(HYDROXYETHYL)ETHER' PEG 6 N,N-dimethylpyridin-4-amine JGD 7 water HOH # _pdbx_related_exp_data_set.ordinal 1 _pdbx_related_exp_data_set.data_reference 10.5281/zenodo.1437589 _pdbx_related_exp_data_set.metadata_reference 10.5281/zenodo.1437589 _pdbx_related_exp_data_set.data_set_type 'other data' _pdbx_related_exp_data_set.details 'Complete PanDDA analysis' #