data_5W09 # _entry.id 5W09 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.289 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5W09 WWPDB D_1000228229 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2018-02-07 _pdbx_database_PDB_obs_spr.pdb_id NONE _pdbx_database_PDB_obs_spr.replace_pdb_id 5W09 _pdbx_database_PDB_obs_spr.details 'THIS ENTRY WAS OBSOLETED DUE TO AN ERROR DISCOVERED BY THE AUTHORS' # _pdbx_database_status.status_code OBS _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5W09 _pdbx_database_status.recvd_initial_deposition_date 2017-05-30 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Lee, S.' 1 ? 'Wang, Y.' 2 ? 'Dai, S.' 3 ? 'Zhang, G.' 4 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Acta Crystallogr D Struct Biol' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2059-7983 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 73 _citation.language ? _citation.page_first 955 _citation.page_last 969 _citation.title 'Hydrogen bonds are a primary driving force for de novo protein folding.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1107/S2059798317015303 _citation.pdbx_database_id_PubMed 29199976 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Lee, S.' 1 primary 'Wang, C.' 2 primary 'Liu, H.' 3 primary 'Xiong, J.' 4 primary 'Jiji, R.' 5 primary 'Hong, X.' 6 primary 'Yan, X.' 7 primary 'Chen, Z.' 8 primary 'Hammel, M.' 9 primary 'Wang, Y.' 10 primary 'Dai, S.' 11 primary 'Wang, J.' 12 primary 'Jiang, C.' 13 primary 'Zhang, G.' 14 # _cell.entry_id 5W09 _cell.length_a 61.458 _cell.length_b 28.359 _cell.length_c 61.512 _cell.angle_alpha 90.00 _cell.angle_beta 119.99 _cell.angle_gamma 90.00 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W09 _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 # 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 'Single-stranded DNA cytosine deaminase' 18565.398 1 3.5.4.38 ? 'UNP residues 1-153' ? 2 water nat water 18.015 152 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Activation-induced cytidine deaminase,AID,Cytidine aminohydrolase' # _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 ;MDSLLMNRRKFLYQFKNVRWAKGRRETYLCYVVKRRDSATSFSLDFGYLRNKNGCHVELLFLRYISDWDLDPGRCYRVTW FTSWSPCYDCARHVADFLRGNPNLSLRIFTARLYFCEDRKAEPEGLRRLHRAGVQIAIMTFKDYFYCWNTFVE ; _entity_poly.pdbx_seq_one_letter_code_can ;MDSLLMNRRKFLYQFKNVRWAKGRRETYLCYVVKRRDSATSFSLDFGYLRNKNGCHVELLFLRYISDWDLDPGRCYRVTW FTSWSPCYDCARHVADFLRGNPNLSLRIFTARLYFCEDRKAEPEGLRRLHRAGVQIAIMTFKDYFYCWNTFVE ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 ASP n 1 3 SER n 1 4 LEU n 1 5 LEU n 1 6 MET n 1 7 ASN n 1 8 ARG n 1 9 ARG n 1 10 LYS n 1 11 PHE n 1 12 LEU n 1 13 TYR n 1 14 GLN n 1 15 PHE n 1 16 LYS n 1 17 ASN n 1 18 VAL n 1 19 ARG n 1 20 TRP n 1 21 ALA n 1 22 LYS n 1 23 GLY n 1 24 ARG n 1 25 ARG n 1 26 GLU n 1 27 THR n 1 28 TYR n 1 29 LEU n 1 30 CYS n 1 31 TYR n 1 32 VAL n 1 33 VAL n 1 34 LYS n 1 35 ARG n 1 36 ARG n 1 37 ASP n 1 38 SER n 1 39 ALA n 1 40 THR n 1 41 SER n 1 42 PHE n 1 43 SER n 1 44 LEU n 1 45 ASP n 1 46 PHE n 1 47 GLY n 1 48 TYR n 1 49 LEU n 1 50 ARG n 1 51 ASN n 1 52 LYS n 1 53 ASN n 1 54 GLY n 1 55 CYS n 1 56 HIS n 1 57 VAL n 1 58 GLU n 1 59 LEU n 1 60 LEU n 1 61 PHE n 1 62 LEU n 1 63 ARG n 1 64 TYR n 1 65 ILE n 1 66 SER n 1 67 ASP n 1 68 TRP n 1 69 ASP n 1 70 LEU n 1 71 ASP n 1 72 PRO n 1 73 GLY n 1 74 ARG n 1 75 CYS n 1 76 TYR n 1 77 ARG n 1 78 VAL n 1 79 THR n 1 80 TRP n 1 81 PHE n 1 82 THR n 1 83 SER n 1 84 TRP n 1 85 SER n 1 86 PRO n 1 87 CYS n 1 88 TYR n 1 89 ASP n 1 90 CYS n 1 91 ALA n 1 92 ARG n 1 93 HIS n 1 94 VAL n 1 95 ALA n 1 96 ASP n 1 97 PHE n 1 98 LEU n 1 99 ARG n 1 100 GLY n 1 101 ASN n 1 102 PRO n 1 103 ASN n 1 104 LEU n 1 105 SER n 1 106 LEU n 1 107 ARG n 1 108 ILE n 1 109 PHE n 1 110 THR n 1 111 ALA n 1 112 ARG n 1 113 LEU n 1 114 TYR n 1 115 PHE n 1 116 CYS n 1 117 GLU n 1 118 ASP n 1 119 ARG n 1 120 LYS n 1 121 ALA n 1 122 GLU n 1 123 PRO n 1 124 GLU n 1 125 GLY n 1 126 LEU n 1 127 ARG n 1 128 ARG n 1 129 LEU n 1 130 HIS n 1 131 ARG n 1 132 ALA n 1 133 GLY n 1 134 VAL n 1 135 GLN n 1 136 ILE n 1 137 ALA n 1 138 ILE n 1 139 MET n 1 140 THR n 1 141 PHE n 1 142 LYS n 1 143 ASP n 1 144 TYR n 1 145 PHE n 1 146 TYR n 1 147 CYS n 1 148 TRP n 1 149 ASN n 1 150 THR n 1 151 PHE n 1 152 VAL n 1 153 GLU 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 153 _entity_src_gen.gene_src_common_name Human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'AICDA, AID' _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-Gold(DE3)pLysS AG' ; _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 866768 _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 AICDA_HUMAN _struct_ref.pdbx_db_accession Q9GZX7 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MDSLLMNRRKFLYQFKNVRWAKGRRETYLCYVVKRRDSATSFSLDFGYLRNKNGCHVELLFLRYISDWDLDPGRCYRVTW FTSWSPCYDCARHVADFLRGNPNLSLRIFTARLYFCEDRKAEPEGLRRLHRAGVQIAIMTFKDYFYCWNTFVE ; _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5W09 _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 153 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9GZX7 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 153 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 153 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 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 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.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5W09 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.50 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 50.81 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 9.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '4M potassium formate, 0.1M BIS-Tris propane, 2% (w/v) PEG monomethyl ether 2000' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-08-02 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 24-ID-E' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9795 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 24-ID-E _diffrn_source.pdbx_synchrotron_site APS # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 5W09 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 53.280 _reflns.d_resolution_high 2.000 _reflns.number_obs 12225 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 23.6000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.700 _reflns.pdbx_CC_half ? _reflns.pdbx_Rpim_I_all 0.104 _reflns.pdbx_Rrim_I_all ? # _reflns_shell.d_res_high 1.999 _reflns_shell.d_res_low 2.051 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 1002 _reflns_shell.percent_possible_all ? _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all 0.417 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5W09 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 12225 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 53.28 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 99.9 _refine.ls_R_factor_obs 0.268 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.267 _refine.ls_R_factor_R_free 0.291 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.500 _refine.ls_number_reflns_R_free 582 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.874 _refine.correlation_coeff_Fo_to_Fc_free 0.843 _refine.B_iso_mean 31.52 _refine.aniso_B[1][1] -15.30000 _refine.aniso_B[2][2] 24.39000 _refine.aniso_B[3][3] -9.09000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] -11.13000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ; _refine.pdbx_starting_model 5JJ4 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.055 _refine.pdbx_overall_ESU_R_Free 0.043 _refine.overall_SU_ML 0.174 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 5.752 _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1302 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 152 _refine_hist.number_atoms_total 1454 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 53.28 # 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 0.016 0.019 ? 1340 'X-RAY DIFFRACTION' ? r_bond_other_d 0.004 0.020 ? 1212 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.028 1.927 ? 1808 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.319 3.000 ? 2771 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 10.674 5.000 ? 152 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 32.285 20.811 ? 74 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 19.239 15.000 ? 223 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 16.576 15.000 ? 19 'X-RAY DIFFRACTION' ? r_chiral_restr 0.122 0.200 ? 180 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 1495 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.003 0.020 ? 360 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 3.405 3.334 ? 611 'X-RAY DIFFRACTION' ? r_mcbond_other 3.365 3.335 ? 610 'X-RAY DIFFRACTION' ? r_mcangle_it 4.862 5.005 ? 762 'X-RAY DIFFRACTION' ? r_mcangle_other 4.860 5.005 ? 763 'X-RAY DIFFRACTION' ? r_scbond_it 3.098 3.297 ? 729 'X-RAY DIFFRACTION' ? r_scbond_other 3.091 3.295 ? 727 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other 4.440 4.956 ? 1046 'X-RAY DIFFRACTION' ? r_long_range_B_refined 8.522 ? ? 19308 'X-RAY DIFFRACTION' ? r_long_range_B_other 8.510 ? ? 19270 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.00 _refine_ls_shell.d_res_low 2.05 _refine_ls_shell.number_reflns_R_work 888 _refine_ls_shell.R_factor_R_work 0.2850 _refine_ls_shell.percent_reflns_obs 98.75 _refine_ls_shell.R_factor_R_free 0.3440 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 60 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 5W09 _struct.title 'Crystal Structure of a twinned Human Activation-induced Cytidine Deaminase catalytic core (1-153) at 2.0A resolution' _struct.pdbx_descriptor 'Single-stranded DNA cytosine deaminase (E.C.3.5.4.38)' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 5W09 _struct_keywords.text 'B-cells, SHM, CSR, antibody, 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 ? # 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 HIS A 56 ? ASP A 67 ? HIS A 56 ASP A 67 1 ? 12 HELX_P HELX_P2 AA2 CYS A 87 ? ARG A 99 ? CYS A 87 ARG A 99 1 ? 13 HELX_P HELX_P3 AA3 ALA A 121 ? ARG A 128 ? ALA A 121 ARG A 128 5 ? 8 HELX_P HELX_P4 AA4 LEU A 129 ? GLY A 133 ? LEU A 129 GLY A 133 5 ? 5 HELX_P HELX_P5 AA5 THR A 140 ? THR A 150 ? THR A 140 THR A 150 1 ? 11 # _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 ? 2 ? AA2 ? 3 ? AA3 ? 2 ? # 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 AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA3 1 2 ? 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 TYR A 28 ? TYR A 31 ? TYR A 28 TYR A 31 AA1 2 GLY A 47 ? ARG A 50 ? GLY A 47 ARG A 50 AA2 1 SER A 41 ? SER A 43 ? SER A 41 SER A 43 AA2 2 LYS A 34 ? ARG A 36 ? LYS A 34 ARG A 36 AA2 3 TYR A 76 ? ARG A 77 ? TYR A 76 ARG A 77 AA3 1 PHE A 109 ? THR A 110 ? PHE A 109 THR A 110 AA3 2 ALA A 137 ? ILE A 138 ? ALA A 137 ILE A 138 # 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 N LEU A 29 ? N LEU A 29 O LEU A 49 ? O LEU A 49 AA2 1 2 O PHE A 42 ? O PHE A 42 N ARG A 35 ? N ARG A 35 AA2 2 3 N LYS A 34 ? N LYS A 34 O ARG A 77 ? O ARG A 77 AA3 1 2 N THR A 110 ? N THR A 110 O ALA A 137 ? O ALA A 137 # _atom_sites.entry_id 5W09 _atom_sites.fract_transf_matrix[1][1] 0.016271 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009390 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.035262 _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] 0.018770 _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 N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 1 1 MET MET A . n A 1 2 ASP 2 2 2 ASP ASP A . n A 1 3 SER 3 3 3 SER SER A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 MET 6 6 6 MET MET A . n A 1 7 ASN 7 7 7 ASN ASN A . n A 1 8 ARG 8 8 8 ARG ARG A . n A 1 9 ARG 9 9 9 ARG ARG A . n A 1 10 LYS 10 10 10 LYS LYS A . n A 1 11 PHE 11 11 11 PHE PHE A . n A 1 12 LEU 12 12 12 LEU LEU A . n A 1 13 TYR 13 13 13 TYR TYR A . n A 1 14 GLN 14 14 14 GLN GLN A . n A 1 15 PHE 15 15 15 PHE PHE A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 ASN 17 17 17 ASN ASN A . n A 1 18 VAL 18 18 18 VAL VAL A . n A 1 19 ARG 19 19 19 ARG ARG A . n A 1 20 TRP 20 20 20 TRP TRP A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 LYS 22 22 22 LYS LYS A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 ARG 24 24 24 ARG ARG A . n A 1 25 ARG 25 25 25 ARG ARG A . n A 1 26 GLU 26 26 26 GLU GLU A . n A 1 27 THR 27 27 27 THR THR A . n A 1 28 TYR 28 28 28 TYR TYR A . n A 1 29 LEU 29 29 29 LEU LEU A . n A 1 30 CYS 30 30 30 CYS CYS A . n A 1 31 TYR 31 31 31 TYR TYR A . n A 1 32 VAL 32 32 32 VAL VAL A . n A 1 33 VAL 33 33 33 VAL VAL A . n A 1 34 LYS 34 34 34 LYS LYS A . n A 1 35 ARG 35 35 35 ARG ARG A . n A 1 36 ARG 36 36 36 ARG ARG A . n A 1 37 ASP 37 37 37 ASP ASP A . n A 1 38 SER 38 38 38 SER SER A . n A 1 39 ALA 39 39 39 ALA ALA A . n A 1 40 THR 40 40 40 THR THR A . n A 1 41 SER 41 41 41 SER SER A . n A 1 42 PHE 42 42 42 PHE PHE A . n A 1 43 SER 43 43 43 SER SER A . n A 1 44 LEU 44 44 44 LEU LEU A . n A 1 45 ASP 45 45 45 ASP ASP A . n A 1 46 PHE 46 46 46 PHE PHE A . n A 1 47 GLY 47 47 47 GLY GLY A . n A 1 48 TYR 48 48 48 TYR TYR A . n A 1 49 LEU 49 49 49 LEU LEU A . n A 1 50 ARG 50 50 50 ARG ARG A . n A 1 51 ASN 51 51 51 ASN ASN A . n A 1 52 LYS 52 52 52 LYS LYS A . n A 1 53 ASN 53 53 53 ASN ASN A . n A 1 54 GLY 54 54 54 GLY GLY A . n A 1 55 CYS 55 55 55 CYS CYS A . n A 1 56 HIS 56 56 56 HIS HIS A . n A 1 57 VAL 57 57 57 VAL VAL A . n A 1 58 GLU 58 58 58 GLU GLU A . n A 1 59 LEU 59 59 59 LEU LEU A . n A 1 60 LEU 60 60 60 LEU LEU A . n A 1 61 PHE 61 61 61 PHE PHE A . n A 1 62 LEU 62 62 62 LEU LEU A . n A 1 63 ARG 63 63 63 ARG ARG A . n A 1 64 TYR 64 64 64 TYR TYR A . n A 1 65 ILE 65 65 65 ILE ILE A . n A 1 66 SER 66 66 66 SER SER A . n A 1 67 ASP 67 67 67 ASP ASP A . n A 1 68 TRP 68 68 68 TRP TRP A . n A 1 69 ASP 69 69 69 ASP ASP A . n A 1 70 LEU 70 70 70 LEU LEU A . n A 1 71 ASP 71 71 71 ASP ASP A . n A 1 72 PRO 72 72 72 PRO PRO A . n A 1 73 GLY 73 73 73 GLY GLY A . n A 1 74 ARG 74 74 74 ARG ARG A . n A 1 75 CYS 75 75 75 CYS CYS A . n A 1 76 TYR 76 76 76 TYR TYR A . n A 1 77 ARG 77 77 77 ARG ARG A . n A 1 78 VAL 78 78 78 VAL VAL A . n A 1 79 THR 79 79 79 THR THR A . n A 1 80 TRP 80 80 80 TRP TRP A . n A 1 81 PHE 81 81 81 PHE PHE A . n A 1 82 THR 82 82 82 THR THR A . n A 1 83 SER 83 83 83 SER SER A . n A 1 84 TRP 84 84 84 TRP TRP A . n A 1 85 SER 85 85 85 SER SER A . n A 1 86 PRO 86 86 86 PRO PRO A . n A 1 87 CYS 87 87 87 CYS CYS A . n A 1 88 TYR 88 88 88 TYR TYR A . n A 1 89 ASP 89 89 89 ASP ASP A . n A 1 90 CYS 90 90 90 CYS CYS A . n A 1 91 ALA 91 91 91 ALA ALA A . n A 1 92 ARG 92 92 92 ARG ARG A . n A 1 93 HIS 93 93 93 HIS HIS A . n A 1 94 VAL 94 94 94 VAL VAL A . n A 1 95 ALA 95 95 95 ALA ALA A . n A 1 96 ASP 96 96 96 ASP ASP A . n A 1 97 PHE 97 97 97 PHE PHE A . n A 1 98 LEU 98 98 98 LEU LEU A . n A 1 99 ARG 99 99 99 ARG ARG A . n A 1 100 GLY 100 100 100 GLY GLY A . n A 1 101 ASN 101 101 101 ASN ASN A . n A 1 102 PRO 102 102 102 PRO PRO A . n A 1 103 ASN 103 103 103 ASN ASN A . n A 1 104 LEU 104 104 104 LEU LEU A . n A 1 105 SER 105 105 105 SER SER A . n A 1 106 LEU 106 106 106 LEU LEU A . n A 1 107 ARG 107 107 107 ARG ARG A . n A 1 108 ILE 108 108 108 ILE ILE A . n A 1 109 PHE 109 109 109 PHE PHE A . n A 1 110 THR 110 110 110 THR THR A . n A 1 111 ALA 111 111 111 ALA ALA A . n A 1 112 ARG 112 112 112 ARG ARG A . n A 1 113 LEU 113 113 113 LEU LEU A . n A 1 114 TYR 114 114 114 TYR TYR A . n A 1 115 PHE 115 115 115 PHE PHE A . n A 1 116 CYS 116 116 116 CYS CYS A . n A 1 117 GLU 117 117 117 GLU GLU A . n A 1 118 ASP 118 118 118 ASP ASP A . n A 1 119 ARG 119 119 119 ARG ARG A . n A 1 120 LYS 120 120 120 LYS LYS A . n A 1 121 ALA 121 121 121 ALA ALA A . n A 1 122 GLU 122 122 122 GLU GLU A . n A 1 123 PRO 123 123 123 PRO PRO A . n A 1 124 GLU 124 124 124 GLU GLU A . n A 1 125 GLY 125 125 125 GLY GLY A . n A 1 126 LEU 126 126 126 LEU LEU A . n A 1 127 ARG 127 127 127 ARG ARG A . n A 1 128 ARG 128 128 128 ARG ARG A . n A 1 129 LEU 129 129 129 LEU LEU A . n A 1 130 HIS 130 130 130 HIS HIS A . n A 1 131 ARG 131 131 131 ARG ARG A . n A 1 132 ALA 132 132 132 ALA ALA A . n A 1 133 GLY 133 133 133 GLY GLY A . n A 1 134 VAL 134 134 134 VAL VAL A . n A 1 135 GLN 135 135 135 GLN GLN A . n A 1 136 ILE 136 136 136 ILE ILE A . n A 1 137 ALA 137 137 137 ALA ALA A . n A 1 138 ILE 138 138 138 ILE ILE A . n A 1 139 MET 139 139 139 MET MET A . n A 1 140 THR 140 140 140 THR THR A . n A 1 141 PHE 141 141 141 PHE PHE A . n A 1 142 LYS 142 142 142 LYS LYS A . n A 1 143 ASP 143 143 143 ASP ASP A . n A 1 144 TYR 144 144 144 TYR TYR A . n A 1 145 PHE 145 145 145 PHE PHE A . n A 1 146 TYR 146 146 146 TYR TYR A . n A 1 147 CYS 147 147 147 CYS CYS A . n A 1 148 TRP 148 148 148 TRP TRP A . n A 1 149 ASN 149 149 149 ASN ASN A . n A 1 150 THR 150 150 150 THR THR A . n A 1 151 PHE 151 151 151 PHE PHE A . n A 1 152 VAL 152 152 152 VAL VAL A . n A 1 153 GLU 153 153 153 GLU GLU 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 HOH 1 201 205 HOH HOH A . B 2 HOH 2 202 207 HOH HOH A . B 2 HOH 3 203 209 HOH HOH A . B 2 HOH 4 204 210 HOH HOH A . B 2 HOH 5 205 36 HOH HOH A . B 2 HOH 6 206 211 HOH HOH A . B 2 HOH 7 207 212 HOH HOH A . B 2 HOH 8 208 213 HOH HOH A . B 2 HOH 9 209 214 HOH HOH A . B 2 HOH 10 210 215 HOH HOH A . B 2 HOH 11 211 216 HOH HOH A . B 2 HOH 12 212 217 HOH HOH A . B 2 HOH 13 213 8 HOH HOH A . B 2 HOH 14 214 43 HOH HOH A . B 2 HOH 15 215 50 HOH HOH A . B 2 HOH 16 216 10 HOH HOH A . B 2 HOH 17 217 219 HOH HOH A . B 2 HOH 18 218 220 HOH HOH A . B 2 HOH 19 219 222 HOH HOH A . B 2 HOH 20 220 223 HOH HOH A . B 2 HOH 21 221 224 HOH HOH A . B 2 HOH 22 222 9 HOH HOH A . B 2 HOH 23 223 21 HOH HOH A . B 2 HOH 24 224 24 HOH HOH A . B 2 HOH 25 225 225 HOH HOH A . B 2 HOH 26 226 48 HOH HOH A . B 2 HOH 27 227 226 HOH HOH A . B 2 HOH 28 228 227 HOH HOH A . B 2 HOH 29 229 228 HOH HOH A . B 2 HOH 30 230 229 HOH HOH A . B 2 HOH 31 231 230 HOH HOH A . B 2 HOH 32 232 231 HOH HOH A . B 2 HOH 33 233 18 HOH HOH A . B 2 HOH 34 234 12 HOH HOH A . B 2 HOH 35 235 232 HOH HOH A . B 2 HOH 36 236 233 HOH HOH A . B 2 HOH 37 237 234 HOH HOH A . B 2 HOH 38 238 236 HOH HOH A . B 2 HOH 39 239 238 HOH HOH A . B 2 HOH 40 240 239 HOH HOH A . B 2 HOH 41 241 240 HOH HOH A . B 2 HOH 42 242 49 HOH HOH A . B 2 HOH 43 243 2 HOH HOH A . B 2 HOH 44 244 20 HOH HOH A . B 2 HOH 45 245 41 HOH HOH A . B 2 HOH 46 246 242 HOH HOH A . B 2 HOH 47 247 3 HOH HOH A . B 2 HOH 48 248 243 HOH HOH A . B 2 HOH 49 249 6 HOH HOH A . B 2 HOH 50 250 248 HOH HOH A . B 2 HOH 51 251 46 HOH HOH A . B 2 HOH 52 252 244 HOH HOH A . B 2 HOH 53 253 245 HOH HOH A . B 2 HOH 54 254 16 HOH HOH A . B 2 HOH 55 255 246 HOH HOH A . B 2 HOH 56 256 272 HOH HOH A . B 2 HOH 57 257 250 HOH HOH A . B 2 HOH 58 258 28 HOH HOH A . B 2 HOH 59 259 30 HOH HOH A . B 2 HOH 60 260 14 HOH HOH A . B 2 HOH 61 261 251 HOH HOH A . B 2 HOH 62 262 47 HOH HOH A . B 2 HOH 63 263 252 HOH HOH A . B 2 HOH 64 264 253 HOH HOH A . B 2 HOH 65 265 5 HOH HOH A . B 2 HOH 66 266 254 HOH HOH A . B 2 HOH 67 267 25 HOH HOH A . B 2 HOH 68 268 255 HOH HOH A . B 2 HOH 69 269 256 HOH HOH A . B 2 HOH 70 270 257 HOH HOH A . B 2 HOH 71 271 258 HOH HOH A . B 2 HOH 72 272 259 HOH HOH A . B 2 HOH 73 273 27 HOH HOH A . B 2 HOH 74 274 260 HOH HOH A . B 2 HOH 75 275 261 HOH HOH A . B 2 HOH 76 276 262 HOH HOH A . B 2 HOH 77 277 29 HOH HOH A . B 2 HOH 78 278 264 HOH HOH A . B 2 HOH 79 279 17 HOH HOH A . B 2 HOH 80 280 265 HOH HOH A . B 2 HOH 81 281 266 HOH HOH A . B 2 HOH 82 282 267 HOH HOH A . B 2 HOH 83 283 38 HOH HOH A . B 2 HOH 84 284 269 HOH HOH A . B 2 HOH 85 285 1 HOH HOH A . B 2 HOH 86 286 270 HOH HOH A . B 2 HOH 87 287 26 HOH HOH A . B 2 HOH 88 288 274 HOH HOH A . B 2 HOH 89 289 39 HOH HOH A . B 2 HOH 90 290 34 HOH HOH A . B 2 HOH 91 291 275 HOH HOH A . B 2 HOH 92 292 276 HOH HOH A . B 2 HOH 93 293 277 HOH HOH A . B 2 HOH 94 294 279 HOH HOH A . B 2 HOH 95 295 51 HOH HOH A . B 2 HOH 96 296 280 HOH HOH A . B 2 HOH 97 297 281 HOH HOH A . B 2 HOH 98 298 282 HOH HOH A . B 2 HOH 99 299 52 HOH HOH A . B 2 HOH 100 300 33 HOH HOH A . B 2 HOH 101 301 283 HOH HOH A . B 2 HOH 102 302 284 HOH HOH A . B 2 HOH 103 303 285 HOH HOH A . B 2 HOH 104 304 286 HOH HOH A . B 2 HOH 105 305 287 HOH HOH A . B 2 HOH 106 306 35 HOH HOH A . B 2 HOH 107 307 45 HOH HOH A . B 2 HOH 108 308 22 HOH HOH A . B 2 HOH 109 309 44 HOH HOH A . B 2 HOH 110 310 288 HOH HOH A . B 2 HOH 111 311 289 HOH HOH A . B 2 HOH 112 312 290 HOH HOH A . B 2 HOH 113 313 291 HOH HOH A . B 2 HOH 114 314 292 HOH HOH A . B 2 HOH 115 315 23 HOH HOH A . B 2 HOH 116 316 7 HOH HOH A . B 2 HOH 117 317 293 HOH HOH A . B 2 HOH 118 318 294 HOH HOH A . B 2 HOH 119 319 19 HOH HOH A . B 2 HOH 120 320 37 HOH HOH A . B 2 HOH 121 321 309 HOH HOH A . B 2 HOH 122 322 295 HOH HOH A . B 2 HOH 123 323 32 HOH HOH A . B 2 HOH 124 324 31 HOH HOH A . B 2 HOH 125 325 296 HOH HOH A . B 2 HOH 126 326 15 HOH HOH A . B 2 HOH 127 327 297 HOH HOH A . B 2 HOH 128 328 298 HOH HOH A . B 2 HOH 129 329 300 HOH HOH A . B 2 HOH 130 330 301 HOH HOH A . B 2 HOH 131 331 13 HOH HOH A . B 2 HOH 132 332 302 HOH HOH A . B 2 HOH 133 333 303 HOH HOH A . B 2 HOH 134 334 310 HOH HOH A . B 2 HOH 135 335 304 HOH HOH A . B 2 HOH 136 336 305 HOH HOH A . B 2 HOH 137 337 313 HOH HOH A . B 2 HOH 138 338 42 HOH HOH A . B 2 HOH 139 339 311 HOH HOH A . B 2 HOH 140 340 306 HOH HOH A . B 2 HOH 141 341 307 HOH HOH A . B 2 HOH 142 342 308 HOH HOH A . B 2 HOH 143 343 312 HOH HOH A . B 2 HOH 144 344 314 HOH HOH A . B 2 HOH 145 345 315 HOH HOH A . B 2 HOH 146 346 316 HOH HOH A . B 2 HOH 147 347 317 HOH HOH A . B 2 HOH 148 348 318 HOH HOH A . B 2 HOH 149 349 319 HOH HOH A . B 2 HOH 150 350 320 HOH HOH A . B 2 HOH 151 351 40 HOH HOH A . B 2 HOH 152 352 11 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 # _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 2017-12-20 2 'Structure model' 1 1 2018-02-07 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 2 'Structure model' repository Obsolete ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' Advisory 2 2 'Structure model' Other # 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 2 'Structure model' pdbx_database_PDB_obs_spr 2 2 'Structure model' pdbx_database_status # 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' '_pdbx_database_status.status_code' 2 2 'Structure model' '_pdbx_database_status.status_code_sf' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0158 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 242 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 320 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.11 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 209 ? ? 1_555 O A HOH 252 ? ? 1_545 2.04 2 1 O A ASP 96 ? ? 1_555 NH1 A ARG 127 ? ? 2_646 2.08 3 1 OD2 A ASP 96 ? ? 1_555 NH2 A ARG 131 ? ? 2_646 2.14 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CB _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 TRP _pdbx_validate_rmsd_bond.auth_seq_id_1 20 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 CG _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 TRP _pdbx_validate_rmsd_bond.auth_seq_id_2 20 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.363 _pdbx_validate_rmsd_bond.bond_target_value 1.498 _pdbx_validate_rmsd_bond.bond_deviation -0.135 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.018 _pdbx_validate_rmsd_bond.linker_flag N # 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 CA A LEU 49 ? ? CB A LEU 49 ? ? CG A LEU 49 ? ? 135.27 115.30 19.97 2.30 N 2 1 NE A ARG 50 ? ? CZ A ARG 50 ? ? NH2 A ARG 50 ? ? 123.82 120.30 3.52 0.50 N 3 1 NE A ARG 119 ? ? CZ A ARG 119 ? ? NH1 A ARG 119 ? ? 123.36 120.30 3.06 0.50 N 4 1 NE A ARG 128 ? ? CZ A ARG 128 ? ? NH2 A ARG 128 ? ? 117.14 120.30 -3.16 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 SER A 3 ? ? -153.32 -151.26 2 1 LEU A 5 ? ? 73.13 107.85 3 1 ASN A 7 ? ? 85.66 21.52 4 1 ARG A 8 ? ? 48.56 -95.78 5 1 LYS A 10 ? ? -68.37 -74.97 6 1 ASN A 17 ? ? -86.58 49.46 7 1 VAL A 18 ? ? 70.00 -15.72 8 1 TRP A 20 ? ? -131.15 -70.60 9 1 ALA A 21 ? ? -49.63 156.13 10 1 LYS A 22 ? ? 105.38 -65.04 11 1 ASP A 37 ? ? -79.88 -77.74 12 1 SER A 38 ? ? -155.18 68.73 13 1 ALA A 39 ? ? 85.51 -37.91 14 1 LEU A 44 ? ? -118.71 -72.73 15 1 ASP A 69 ? ? 51.26 78.31 16 1 SER A 83 ? ? -57.09 -71.67 17 1 ASP A 118 ? ? -57.90 -2.50 18 1 ALA A 137 ? ? -102.52 -155.59 # loop_ _pdbx_validate_peptide_omega.id _pdbx_validate_peptide_omega.PDB_model_num _pdbx_validate_peptide_omega.auth_comp_id_1 _pdbx_validate_peptide_omega.auth_asym_id_1 _pdbx_validate_peptide_omega.auth_seq_id_1 _pdbx_validate_peptide_omega.PDB_ins_code_1 _pdbx_validate_peptide_omega.label_alt_id_1 _pdbx_validate_peptide_omega.auth_comp_id_2 _pdbx_validate_peptide_omega.auth_asym_id_2 _pdbx_validate_peptide_omega.auth_seq_id_2 _pdbx_validate_peptide_omega.PDB_ins_code_2 _pdbx_validate_peptide_omega.label_alt_id_2 _pdbx_validate_peptide_omega.omega 1 1 LEU A 5 ? ? MET A 6 ? ? -119.35 2 1 LEU A 12 ? ? TYR A 13 ? ? -147.56 3 1 TRP A 20 ? ? ALA A 21 ? ? -138.89 4 1 ARG A 25 ? ? GLU A 26 ? ? -145.97 # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 351 ? 6.84 . 2 1 O ? A HOH 352 ? 7.10 . # 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 22 ? CB ? A LYS 22 CB 2 1 Y 1 A LYS 22 ? CG ? A LYS 22 CG 3 1 Y 1 A LYS 22 ? CD ? A LYS 22 CD 4 1 Y 1 A LYS 22 ? CE ? A LYS 22 CE 5 1 Y 1 A LYS 22 ? NZ ? A LYS 22 NZ # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute Of Allergy and Infectious Diseases' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 'T32 AI 7405-26' _pdbx_audit_support.ordinal 1 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _pdbx_reflns_twin.domain_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.type _pdbx_reflns_twin.operator _pdbx_reflns_twin.fraction 1 1 1 ? 'H, K, L' 0.228 2 1 1 ? '-H, -K, H+L' 0.118 3 1 1 ? 'H+L, -K, -L' 0.175 4 1 1 ? '-H-L, K, H' 0.182 5 1 1 ? 'L, K, -H-L' 0.155 6 1 1 ? 'L, -K, H' 0.142 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _pdbx_struct_assembly_auth_evidence.details ? #