data_4NBP # _entry.id 4NBP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4NBP RCSB RCSB083000 WWPDB D_1000083000 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4LIF 'JCV OBD' unspecified PDB 4LMD 'JCV OBD' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4NBP _pdbx_database_status.recvd_initial_deposition_date 2013-10-23 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _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 'Meinke, G.' 1 'Bohm, A.' 2 'Bullock, P.' 3 # _citation.id primary _citation.title 'Insights into the Initiation of JC Virus DNA Replication Derived from the Crystal Structure of the T-Antigen Origin Binding Domain.' _citation.journal_abbrev 'Plos Pathog.' _citation.journal_volume 10 _citation.page_first e1003966 _citation.page_last e1003966 _citation.year 2014 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1553-7366 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24586168 _citation.pdbx_database_id_DOI 10.1371/journal.ppat.1003966 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Meinke, G.' 1 primary 'Phelan, P.J.' 2 primary 'Kalekar, R.' 3 primary 'Shin, J.' 4 primary 'Archambault, J.' 5 primary 'Bohm, A.' 6 primary 'Bullock, P.A.' 7 # _cell.entry_id 4NBP _cell.length_a 64.663 _cell.length_b 64.663 _cell.length_c 37.493 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4NBP _symmetry.space_group_name_H-M 'P 41' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _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 'Large T antigen' 15170.390 1 3.6.4.- ? 'Origin Binding Domain' ? 2 non-polymer syn 'L(+)-TARTARIC ACID' 150.087 2 ? ? ? ? 3 water nat water 18.015 222 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'LT, LT-AG' # _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 ;GSKVEDPKDFPVDLHAFLSQAVFSNRTVASFAVYTTKEKAQILYKKLMEKYSVTFISRHGFGGHNILFFLTPHRHRVSAI NNYCQKLCTFSFLICKGVNKEYLFYSALCRQPYAVVEESIQGGLKEHDFNPE ; _entity_poly.pdbx_seq_one_letter_code_can ;GSKVEDPKDFPVDLHAFLSQAVFSNRTVASFAVYTTKEKAQILYKKLMEKYSVTFISRHGFGGHNILFFLTPHRHRVSAI NNYCQKLCTFSFLICKGVNKEYLFYSALCRQPYAVVEESIQGGLKEHDFNPE ; _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 SER n 1 3 LYS n 1 4 VAL n 1 5 GLU n 1 6 ASP n 1 7 PRO n 1 8 LYS n 1 9 ASP n 1 10 PHE n 1 11 PRO n 1 12 VAL n 1 13 ASP n 1 14 LEU n 1 15 HIS n 1 16 ALA n 1 17 PHE n 1 18 LEU n 1 19 SER n 1 20 GLN n 1 21 ALA n 1 22 VAL n 1 23 PHE n 1 24 SER n 1 25 ASN n 1 26 ARG n 1 27 THR n 1 28 VAL n 1 29 ALA n 1 30 SER n 1 31 PHE n 1 32 ALA n 1 33 VAL n 1 34 TYR n 1 35 THR n 1 36 THR n 1 37 LYS n 1 38 GLU n 1 39 LYS n 1 40 ALA n 1 41 GLN n 1 42 ILE n 1 43 LEU n 1 44 TYR n 1 45 LYS n 1 46 LYS n 1 47 LEU n 1 48 MET n 1 49 GLU n 1 50 LYS n 1 51 TYR n 1 52 SER n 1 53 VAL n 1 54 THR n 1 55 PHE n 1 56 ILE n 1 57 SER n 1 58 ARG n 1 59 HIS n 1 60 GLY n 1 61 PHE n 1 62 GLY n 1 63 GLY n 1 64 HIS n 1 65 ASN n 1 66 ILE n 1 67 LEU n 1 68 PHE n 1 69 PHE n 1 70 LEU n 1 71 THR n 1 72 PRO n 1 73 HIS n 1 74 ARG n 1 75 HIS n 1 76 ARG n 1 77 VAL n 1 78 SER n 1 79 ALA n 1 80 ILE n 1 81 ASN n 1 82 ASN n 1 83 TYR n 1 84 CYS n 1 85 GLN n 1 86 LYS n 1 87 LEU n 1 88 CYS n 1 89 THR n 1 90 PHE n 1 91 SER n 1 92 PHE n 1 93 LEU n 1 94 ILE n 1 95 CYS n 1 96 LYS n 1 97 GLY n 1 98 VAL n 1 99 ASN n 1 100 LYS n 1 101 GLU n 1 102 TYR n 1 103 LEU n 1 104 PHE n 1 105 TYR n 1 106 SER n 1 107 ALA n 1 108 LEU n 1 109 CYS n 1 110 ARG n 1 111 GLN n 1 112 PRO n 1 113 TYR n 1 114 ALA n 1 115 VAL n 1 116 VAL n 1 117 GLU n 1 118 GLU n 1 119 SER n 1 120 ILE n 1 121 GLN n 1 122 GLY n 1 123 GLY n 1 124 LEU n 1 125 LYS n 1 126 GLU n 1 127 HIS n 1 128 ASP n 1 129 PHE n 1 130 ASN n 1 131 PRO n 1 132 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 ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name JCPyV _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'large T antigen' _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 'JC polyomavirus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10632 _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 511693 _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 Bl21 _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 pGEX _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code LT_POVJC _struct_ref.pdbx_db_accession P03072 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;KVEDPKDFPVDLHAFLSQAVFSNRTVASFAVYTTKEKAQILYKKLMEKYSVTFISRHGFGGHNILFFLTPHRHRVSAINN YCQKLCTFSFLICKGVNKEYLFYSALCRQPYAVVEESIQGGLKEHDFNPE ; _struct_ref.pdbx_align_begin 132 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4NBP _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 132 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P03072 _struct_ref_seq.db_align_beg 132 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 261 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 132 _struct_ref_seq.pdbx_auth_seq_align_end 261 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4NBP GLY A 1 ? UNP P03072 ? ? 'EXPRESSION TAG' 130 1 1 4NBP SER A 2 ? UNP P03072 ? ? 'EXPRESSION TAG' 131 2 # 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 TLA non-polymer . 'L(+)-TARTARIC ACID' ? 'C4 H6 O6' 150.087 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 4NBP _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.58 _exptl_crystal.density_percent_sol 52.39 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details '0.19 M sodium tartrate, 19 % Peg 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _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 315r' _diffrn_detector.pdbx_collection_date 2013-04-13 _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 'Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.075 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X29A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X29A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.075 # _reflns.entry_id 4NBP _reflns.observed_criterion_sigma_I 2 _reflns.observed_criterion_sigma_F 2 _reflns.d_resolution_low 45.7 _reflns.d_resolution_high 1.315 _reflns.number_obs 36181 _reflns.number_all 36965 _reflns.percent_possible_obs 97.8 _reflns.pdbx_Rmerge_I_obs 0.093 _reflns.pdbx_Rsym_value 0.093 _reflns.pdbx_netI_over_sigmaI 29.6 _reflns.B_iso_Wilson_estimate 16.04 _reflns.pdbx_redundancy 16 _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 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.32 1.37 99.4 .658 ? ? 12.5 ? ? ? ? ? ? 1 1 1.37 1.42 99.4 0.499 ? ? 13.8 ? ? ? ? ? ? 2 1 1.42 1.49 100.0 0.383 ? ? 14.0 ? ? ? ? ? ? 3 1 1.49 1.57 100 0.275 ? ? 14.1 ? ? ? ? ? ? 4 1 1.57 1.66 100 0.205 ? ? 14.2 ? ? ? ? ? ? 5 1 1.66 1.79 100 0.151 ? ? 14.3 ? ? ? ? ? ? 6 1 1.79 1.97 100 0.115 ? ? 14.4 ? ? ? ? ? ? 7 1 1.97 2.26 100 0.127 ? ? 20.6 ? ? ? ? ? ? 8 1 2.26 2.84 100 0.095 ? ? 21.4 ? ? ? ? ? ? 9 1 2.84 50 100 0.074 ? ? 20.2 ? ? ? ? ? ? 10 1 # _refine.entry_id 4NBP _refine.ls_number_reflns_obs 35098 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.43 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 45.7 _refine.ls_d_res_high 1.315 _refine.ls_percent_reflns_obs 99.73 _refine.ls_R_factor_obs 0.1554 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1542 _refine.ls_R_factor_R_free 0.1785 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.98 _refine.ls_number_reflns_R_free 1844 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 21.9 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model 'Isotropic + TLS' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.10 _refine.pdbx_overall_phase_error 18.11 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _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 1036 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 19 _refine_hist.number_atoms_solvent 222 _refine_hist.number_atoms_total 1277 _refine_hist.d_res_high 1.315 _refine_hist.d_res_low 45.7 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.017 ? ? 1137 ? 'X-RAY DIFFRACTION' f_angle_d 1.610 ? ? 1555 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 13.617 ? ? 416 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.107 ? ? 170 ? 'X-RAY DIFFRACTION' f_plane_restr 0.010 ? ? 203 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id . 1.3153 1.3326 2498 0.2759 93.00 0.2652 . . 129 . . . . 'X-RAY DIFFRACTION' . 1.3326 1.3509 2636 0.2374 100.00 0.2767 . . 136 . . . . 'X-RAY DIFFRACTION' . 1.3509 1.3702 2650 0.2166 100.00 0.2189 . . 122 . . . . 'X-RAY DIFFRACTION' . 1.3702 1.3906 2655 0.2188 100.00 0.2250 . . 147 . . . . 'X-RAY DIFFRACTION' . 1.3906 1.4124 2626 0.2010 100.00 0.1938 . . 109 . . . . 'X-RAY DIFFRACTION' . 1.4124 1.4355 2706 0.1994 100.00 0.2281 . . 117 . . . . 'X-RAY DIFFRACTION' . 1.4355 1.4603 2567 0.1954 100.00 0.2728 . . 170 . . . . 'X-RAY DIFFRACTION' . 1.4603 1.4868 2603 0.1917 100.00 0.1925 . . 133 . . . . 'X-RAY DIFFRACTION' . 1.4868 1.5154 2645 0.1737 100.00 0.1803 . . 152 . . . . 'X-RAY DIFFRACTION' . 1.5154 1.5464 2633 0.1726 100.00 0.1548 . . 139 . . . . 'X-RAY DIFFRACTION' . 1.5464 1.5800 2661 0.1644 100.00 0.1633 . . 123 . . . . 'X-RAY DIFFRACTION' . 1.5800 1.6167 2616 0.1625 100.00 0.2473 . . 169 . . . . 'X-RAY DIFFRACTION' . 1.6167 1.6572 2636 0.1521 100.00 0.1507 . . 139 . . . . 'X-RAY DIFFRACTION' . 1.6572 1.7020 2681 0.1550 100.00 0.1569 . . 156 . . . . 'X-RAY DIFFRACTION' . 1.7020 1.7521 2554 0.1528 100.00 0.1824 . . 149 . . . . 'X-RAY DIFFRACTION' . 1.7521 1.8086 2662 0.1648 100.00 0.1969 . . 126 . . . . 'X-RAY DIFFRACTION' . 1.8086 1.8733 2683 0.1622 100.00 0.2127 . . 125 . . . . 'X-RAY DIFFRACTION' . 1.8733 1.9483 2589 0.1596 100.00 0.1795 . . 143 . . . . 'X-RAY DIFFRACTION' . 1.9483 2.0369 2658 0.1462 100.00 0.1725 . . 139 . . . . 'X-RAY DIFFRACTION' . 2.0369 2.1443 2630 0.1404 100.00 0.1614 . . 134 . . . . 'X-RAY DIFFRACTION' . 2.1443 2.2787 2614 0.1451 100.00 0.1596 . . 122 . . . . 'X-RAY DIFFRACTION' . 2.2787 2.4546 2651 0.1592 100.00 0.1903 . . 149 . . . . 'X-RAY DIFFRACTION' . 2.4546 2.7016 2641 0.1710 100.00 0.1839 . . 148 . . . . 'X-RAY DIFFRACTION' . 2.7016 3.0924 2633 0.1618 100.00 0.2386 . . 130 . . . . 'X-RAY DIFFRACTION' . 3.0924 3.8958 2642 0.1328 100.00 0.1664 . . 137 . . . . 'X-RAY DIFFRACTION' . 3.8958 45.7513 2630 0.1279 100.00 0.1296 . . 144 . . . . 'X-RAY DIFFRACTION' # _struct.entry_id 4NBP _struct.title 'Crystal structure of the JCV large T-antigen origin binding domain' _struct.pdbx_descriptor 'Large T antigen (E.C.3.6.4.-)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4NBP _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'origin binding domain, DNA replication, binds DNA, 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 ? # _struct_biol.id 1 _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 PRO A 11 ? LEU A 18 ? PRO A 140 LEU A 147 5 ? 8 HELX_P HELX_P2 2 LYS A 37 ? TYR A 51 ? LYS A 166 TYR A 180 1 ? 15 HELX_P HELX_P3 3 ARG A 76 ? LYS A 86 ? ARG A 205 LYS A 215 1 ? 11 HELX_P HELX_P4 4 LYS A 100 ? LEU A 108 ? LYS A 229 LEU A 237 1 ? 9 HELX_P HELX_P5 5 LYS A 125 ? PHE A 129 ? LYS A 254 PHE A 258 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_conn.id covale1 _struct_conn.conn_type_id covale _struct_conn.pdbx_leaving_atom_flag ? _struct_conn.pdbx_PDB_id ? _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 39 _struct_conn.ptnr1_label_atom_id NZ _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 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_comp_id TLA _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_label_atom_id C1 _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 168 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id TLA _struct_conn.ptnr2_auth_seq_id 301 _struct_conn.ptnr2_symmetry 1_555 _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 1.323 _struct_conn.pdbx_value_order ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GLN _struct_mon_prot_cis.label_seq_id 111 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GLN _struct_mon_prot_cis.auth_seq_id 240 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 112 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 241 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 12.18 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 LEU A 93 ? GLY A 97 ? LEU A 222 GLY A 226 A 2 VAL A 28 ? THR A 36 ? VAL A 157 THR A 165 A 3 HIS A 64 ? HIS A 75 ? HIS A 193 HIS A 204 A 4 PHE A 55 ? PHE A 61 ? PHE A 184 PHE A 190 A 5 ALA A 114 ? GLU A 118 ? ALA A 243 GLU A 247 # 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 LYS A 96 ? O LYS A 225 N ALA A 32 ? N ALA A 161 A 2 3 N VAL A 28 ? N VAL A 157 O HIS A 75 ? O HIS A 204 A 3 4 O ILE A 66 ? O ILE A 195 N HIS A 59 ? N HIS A 188 A 4 5 N ARG A 58 ? N ARG A 187 O VAL A 116 ? O VAL A 245 # 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 ? ? ? ? 8 'BINDING SITE FOR RESIDUE TLA A 301' AC2 Software ? ? ? ? 8 'BINDING SITE FOR RESIDUE TLA A 302' # 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 8 GLU A 38 ? GLU A 167 . ? 1_555 ? 2 AC1 8 LYS A 39 ? LYS A 168 . ? 1_555 ? 3 AC1 8 LEU A 87 ? LEU A 216 . ? 1_555 ? 4 AC1 8 CYS A 88 ? CYS A 217 . ? 1_555 ? 5 AC1 8 THR A 89 ? THR A 218 . ? 1_555 ? 6 AC1 8 PHE A 90 ? PHE A 219 . ? 1_555 ? 7 AC1 8 SER A 91 ? SER A 220 . ? 1_555 ? 8 AC1 8 HOH D . ? HOH A 591 . ? 1_555 ? 9 AC2 8 HIS A 73 ? HIS A 202 . ? 3_655 ? 10 AC2 8 ARG A 74 ? ARG A 203 . ? 3_655 ? 11 AC2 8 HIS A 75 ? HIS A 204 . ? 1_555 ? 12 AC2 8 ALA A 79 ? ALA A 208 . ? 1_555 ? 13 AC2 8 HOH D . ? HOH A 409 . ? 1_555 ? 14 AC2 8 HOH D . ? HOH A 418 . ? 1_555 ? 15 AC2 8 HOH D . ? HOH A 437 . ? 1_555 ? 16 AC2 8 HOH D . ? HOH A 487 . ? 1_555 ? # _database_PDB_matrix.entry_id 4NBP _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 4NBP _atom_sites.fract_transf_matrix[1][1] 0.015465 _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] 0.015465 _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] 0.026672 _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 H 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 GLY 1 130 ? ? ? A . n A 1 2 SER 2 131 ? ? ? A . n A 1 3 LYS 3 132 ? ? ? A . n A 1 4 VAL 4 133 133 VAL VAL A . n A 1 5 GLU 5 134 134 GLU GLU A . n A 1 6 ASP 6 135 135 ASP ASP A . n A 1 7 PRO 7 136 136 PRO PRO A . n A 1 8 LYS 8 137 137 LYS LYS A . n A 1 9 ASP 9 138 138 ASP ASP A . n A 1 10 PHE 10 139 139 PHE PHE A . n A 1 11 PRO 11 140 140 PRO PRO A . n A 1 12 VAL 12 141 141 VAL VAL A . n A 1 13 ASP 13 142 142 ASP ASP A . n A 1 14 LEU 14 143 143 LEU LEU A . n A 1 15 HIS 15 144 144 HIS HIS A . n A 1 16 ALA 16 145 145 ALA ALA A . n A 1 17 PHE 17 146 146 PHE PHE A . n A 1 18 LEU 18 147 147 LEU LEU A . n A 1 19 SER 19 148 148 SER SER A . n A 1 20 GLN 20 149 149 GLN GLN A . n A 1 21 ALA 21 150 150 ALA ALA A . n A 1 22 VAL 22 151 151 VAL VAL A . n A 1 23 PHE 23 152 152 PHE PHE A . n A 1 24 SER 24 153 153 SER SER A . n A 1 25 ASN 25 154 154 ASN ASN A . n A 1 26 ARG 26 155 155 ARG ARG A . n A 1 27 THR 27 156 156 THR THR A . n A 1 28 VAL 28 157 157 VAL VAL A . n A 1 29 ALA 29 158 158 ALA ALA A . n A 1 30 SER 30 159 159 SER SER A . n A 1 31 PHE 31 160 160 PHE PHE A . n A 1 32 ALA 32 161 161 ALA ALA A . n A 1 33 VAL 33 162 162 VAL VAL A . n A 1 34 TYR 34 163 163 TYR TYR A . n A 1 35 THR 35 164 164 THR THR A . n A 1 36 THR 36 165 165 THR THR A . n A 1 37 LYS 37 166 166 LYS LYS A . n A 1 38 GLU 38 167 167 GLU GLU A . n A 1 39 LYS 39 168 168 LYS LYS A . n A 1 40 ALA 40 169 169 ALA ALA A . n A 1 41 GLN 41 170 170 GLN GLN A . n A 1 42 ILE 42 171 171 ILE ILE A . n A 1 43 LEU 43 172 172 LEU LEU A . n A 1 44 TYR 44 173 173 TYR TYR A . n A 1 45 LYS 45 174 174 LYS LYS A . n A 1 46 LYS 46 175 175 LYS LYS A . n A 1 47 LEU 47 176 176 LEU LEU A . n A 1 48 MET 48 177 177 MET MET A . n A 1 49 GLU 49 178 178 GLU GLU A . n A 1 50 LYS 50 179 179 LYS LYS A . n A 1 51 TYR 51 180 180 TYR TYR A . n A 1 52 SER 52 181 181 SER SER A . n A 1 53 VAL 53 182 182 VAL VAL A . n A 1 54 THR 54 183 183 THR THR A . n A 1 55 PHE 55 184 184 PHE PHE A . n A 1 56 ILE 56 185 185 ILE ILE A . n A 1 57 SER 57 186 186 SER SER A . n A 1 58 ARG 58 187 187 ARG ARG A . n A 1 59 HIS 59 188 188 HIS HIS A . n A 1 60 GLY 60 189 189 GLY GLY A . n A 1 61 PHE 61 190 190 PHE PHE A . n A 1 62 GLY 62 191 191 GLY GLY A . n A 1 63 GLY 63 192 192 GLY GLY A . n A 1 64 HIS 64 193 193 HIS HIS A . n A 1 65 ASN 65 194 194 ASN ASN A . n A 1 66 ILE 66 195 195 ILE ILE A . n A 1 67 LEU 67 196 196 LEU LEU A . n A 1 68 PHE 68 197 197 PHE PHE A . n A 1 69 PHE 69 198 198 PHE PHE A . n A 1 70 LEU 70 199 199 LEU LEU A . n A 1 71 THR 71 200 200 THR THR A . n A 1 72 PRO 72 201 201 PRO PRO A . n A 1 73 HIS 73 202 202 HIS HIS A . n A 1 74 ARG 74 203 203 ARG ARG A . n A 1 75 HIS 75 204 204 HIS HIS A . n A 1 76 ARG 76 205 205 ARG ARG A . n A 1 77 VAL 77 206 206 VAL VAL A . n A 1 78 SER 78 207 207 SER SER A . n A 1 79 ALA 79 208 208 ALA ALA A . n A 1 80 ILE 80 209 209 ILE ILE A . n A 1 81 ASN 81 210 210 ASN ASN A . n A 1 82 ASN 82 211 211 ASN ASN A . n A 1 83 TYR 83 212 212 TYR TYR A . n A 1 84 CYS 84 213 213 CYS CYS A . n A 1 85 GLN 85 214 214 GLN GLN A . n A 1 86 LYS 86 215 215 LYS LYS A . n A 1 87 LEU 87 216 216 LEU LEU A . n A 1 88 CYS 88 217 217 CYS CYS A . n A 1 89 THR 89 218 218 THR THR A . n A 1 90 PHE 90 219 219 PHE PHE A . n A 1 91 SER 91 220 220 SER SER A . n A 1 92 PHE 92 221 221 PHE PHE A . n A 1 93 LEU 93 222 222 LEU LEU A . n A 1 94 ILE 94 223 223 ILE ILE A . n A 1 95 CYS 95 224 224 CYS CYS A . n A 1 96 LYS 96 225 225 LYS LYS A . n A 1 97 GLY 97 226 226 GLY GLY A . n A 1 98 VAL 98 227 227 VAL VAL A . n A 1 99 ASN 99 228 228 ASN ASN A . n A 1 100 LYS 100 229 229 LYS LYS A . n A 1 101 GLU 101 230 230 GLU GLU A . n A 1 102 TYR 102 231 231 TYR TYR A . n A 1 103 LEU 103 232 232 LEU LEU A . n A 1 104 PHE 104 233 233 PHE PHE A . n A 1 105 TYR 105 234 234 TYR TYR A . n A 1 106 SER 106 235 235 SER SER A . n A 1 107 ALA 107 236 236 ALA ALA A . n A 1 108 LEU 108 237 237 LEU LEU A . n A 1 109 CYS 109 238 238 CYS CYS A . n A 1 110 ARG 110 239 239 ARG ARG A . n A 1 111 GLN 111 240 240 GLN GLN A . n A 1 112 PRO 112 241 241 PRO PRO A . n A 1 113 TYR 113 242 242 TYR TYR A . n A 1 114 ALA 114 243 243 ALA ALA A . n A 1 115 VAL 115 244 244 VAL VAL A . n A 1 116 VAL 116 245 245 VAL VAL A . n A 1 117 GLU 117 246 246 GLU GLU A . n A 1 118 GLU 118 247 247 GLU GLU A . n A 1 119 SER 119 248 248 SER SER A . n A 1 120 ILE 120 249 249 ILE ILE A . n A 1 121 GLN 121 250 250 GLN GLN A . n A 1 122 GLY 122 251 251 GLY GLY A . n A 1 123 GLY 123 252 252 GLY GLY A . n A 1 124 LEU 124 253 253 LEU LEU A . n A 1 125 LYS 125 254 254 LYS LYS A . n A 1 126 GLU 126 255 255 GLU GLU A . n A 1 127 HIS 127 256 256 HIS HIS A . n A 1 128 ASP 128 257 257 ASP ASP A . n A 1 129 PHE 129 258 258 PHE PHE A . n A 1 130 ASN 130 259 259 ASN ASN A . n A 1 131 PRO 131 260 260 PRO PRO A . n A 1 132 GLU 132 261 261 GLU GLU A . n # _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 # _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 2014-03-05 2 'Structure model' 1 1 2014-04-02 # _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 'Database references' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 12.8870 26.4594 1.6019 0.0937 0.1020 0.0919 0.0016 0.0058 0.0149 1.9808 1.9495 1.3481 -0.5550 0.3522 -0.1366 -0.0079 -0.0665 -0.0683 0.0984 -0.0002 0.0196 0.0505 0.0286 0.0136 'X-RAY DIFFRACTION' 2 ? refined 8.9566 25.4108 -3.1427 0.0797 0.0658 0.0916 -0.0001 0.0075 -0.0284 3.7235 3.0133 4.1910 -0.1882 1.1412 -1.2769 -0.0036 -0.0539 -0.0824 0.1283 -0.0372 0.0647 0.0459 0.0279 0.0350 'X-RAY DIFFRACTION' 3 ? refined 10.0057 38.1474 -9.9088 0.2276 0.1518 0.1276 0.0214 -0.0004 0.0185 5.0589 2.4928 6.3845 0.5806 -4.0521 -0.0939 0.1427 0.5660 0.1135 -0.4670 0.0583 0.0254 -0.4885 -0.4529 -0.2406 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? '(chain A and resid 134:214)' 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? '(chain A and resid 215:244)' 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? '(chain A and resid 245:261)' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 PHASER phasing . ? 2 PHENIX refinement '(phenix.refine: 1.8.4_1496)' ? 3 HKL-2000 'data reduction' . ? 4 SCALEPACK 'data scaling' . ? 5 # _pdbx_entry_details.entry_id 4NBP _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE PRESENCE OF TARTRATE IN THE INDICATED CRYSTALLIZATION CONDITIONS CAUSED THE SIDE CHAIN OF LYS A 168 TO COVALENTLY BOUND TO TLA A 301. SEE ALSO LINK REMARK ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? # _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_1 423 _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_2 489 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.18 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 ND2 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 ASN _pdbx_validate_symm_contact.auth_seq_id_1 154 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 B _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 OE2 _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 GLU _pdbx_validate_symm_contact.auth_seq_id_2 230 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 3_655 _pdbx_validate_symm_contact.dist 1.46 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id THR _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 218 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -122.57 _pdbx_validate_torsion.psi -61.12 # 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 VAL 133 ? CG1 ? A VAL 4 CG1 2 1 Y 1 A VAL 133 ? CG2 ? A VAL 4 CG2 3 1 Y 1 A GLU 134 ? CG ? A GLU 5 CG 4 1 Y 1 A GLU 134 ? CD ? A GLU 5 CD 5 1 Y 1 A GLU 134 ? OE1 ? A GLU 5 OE1 6 1 Y 1 A GLU 134 ? OE2 ? A GLU 5 OE2 7 1 Y 1 A LYS 137 ? CG ? A LYS 8 CG 8 1 Y 1 A LYS 137 ? CD ? A LYS 8 CD 9 1 Y 1 A LYS 137 ? CE ? A LYS 8 CE 10 1 Y 1 A LYS 137 ? NZ ? A LYS 8 NZ 11 1 Y 1 A ARG 155 ? CG ? A ARG 26 CG 12 1 Y 1 A ARG 155 ? CD ? A ARG 26 CD 13 1 Y 1 A ARG 155 ? NE ? A ARG 26 NE 14 1 Y 1 A ARG 155 ? CZ ? A ARG 26 CZ 15 1 Y 1 A ARG 155 ? NH1 ? A ARG 26 NH1 16 1 Y 1 A ARG 155 ? NH2 ? A ARG 26 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 GLY 130 ? A GLY 1 2 1 Y 1 A SER 131 ? A SER 2 3 1 Y 1 A LYS 132 ? A LYS 3 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'L(+)-TARTARIC ACID' TLA 3 water HOH # 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 TLA 1 301 168 TLA TLA A . C 2 TLA 1 302 1 TLA TLA A . D 3 HOH 1 401 1 HOH HOH A . D 3 HOH 2 402 2 HOH HOH A . D 3 HOH 3 403 3 HOH HOH A . D 3 HOH 4 404 4 HOH HOH A . D 3 HOH 5 405 5 HOH HOH A . D 3 HOH 6 406 6 HOH HOH A . D 3 HOH 7 407 7 HOH HOH A . D 3 HOH 8 408 8 HOH HOH A . D 3 HOH 9 409 9 HOH HOH A . D 3 HOH 10 410 10 HOH HOH A . D 3 HOH 11 411 11 HOH HOH A . D 3 HOH 12 412 12 HOH HOH A . D 3 HOH 13 413 13 HOH HOH A . D 3 HOH 14 414 14 HOH HOH A . D 3 HOH 15 415 15 HOH HOH A . D 3 HOH 16 416 16 HOH HOH A . D 3 HOH 17 417 17 HOH HOH A . D 3 HOH 18 418 18 HOH HOH A . D 3 HOH 19 419 19 HOH HOH A . D 3 HOH 20 420 20 HOH HOH A . D 3 HOH 21 421 21 HOH HOH A . D 3 HOH 22 422 22 HOH HOH A . D 3 HOH 23 423 23 HOH HOH A . D 3 HOH 24 424 24 HOH HOH A . D 3 HOH 25 425 25 HOH HOH A . D 3 HOH 26 426 26 HOH HOH A . D 3 HOH 27 427 27 HOH HOH A . D 3 HOH 28 428 28 HOH HOH A . D 3 HOH 29 429 29 HOH HOH A . D 3 HOH 30 430 30 HOH HOH A . D 3 HOH 31 431 31 HOH HOH A . D 3 HOH 32 432 32 HOH HOH A . D 3 HOH 33 433 33 HOH HOH A . D 3 HOH 34 434 34 HOH HOH A . D 3 HOH 35 435 35 HOH HOH A . D 3 HOH 36 436 36 HOH HOH A . D 3 HOH 37 437 37 HOH HOH A . D 3 HOH 38 438 38 HOH HOH A . D 3 HOH 39 439 39 HOH HOH A . D 3 HOH 40 440 40 HOH HOH A . D 3 HOH 41 441 41 HOH HOH A . D 3 HOH 42 442 42 HOH HOH A . D 3 HOH 43 443 43 HOH HOH A . D 3 HOH 44 444 44 HOH HOH A . D 3 HOH 45 445 45 HOH HOH A . D 3 HOH 46 446 46 HOH HOH A . D 3 HOH 47 447 47 HOH HOH A . D 3 HOH 48 448 48 HOH HOH A . D 3 HOH 49 449 49 HOH HOH A . D 3 HOH 50 450 50 HOH HOH A . D 3 HOH 51 451 51 HOH HOH A . D 3 HOH 52 452 52 HOH HOH A . D 3 HOH 53 453 53 HOH HOH A . D 3 HOH 54 454 54 HOH HOH A . D 3 HOH 55 455 55 HOH HOH A . D 3 HOH 56 456 56 HOH HOH A . D 3 HOH 57 457 57 HOH HOH A . D 3 HOH 58 458 58 HOH HOH A . D 3 HOH 59 459 59 HOH HOH A . D 3 HOH 60 460 60 HOH HOH A . D 3 HOH 61 461 61 HOH HOH A . D 3 HOH 62 462 62 HOH HOH A . D 3 HOH 63 463 63 HOH HOH A . D 3 HOH 64 464 64 HOH HOH A . D 3 HOH 65 465 65 HOH HOH A . D 3 HOH 66 466 66 HOH HOH A . D 3 HOH 67 467 67 HOH HOH A . D 3 HOH 68 468 68 HOH HOH A . D 3 HOH 69 469 69 HOH HOH A . D 3 HOH 70 470 70 HOH HOH A . D 3 HOH 71 471 71 HOH HOH A . D 3 HOH 72 472 72 HOH HOH A . D 3 HOH 73 473 73 HOH HOH A . D 3 HOH 74 474 74 HOH HOH A . D 3 HOH 75 475 75 HOH HOH A . D 3 HOH 76 476 76 HOH HOH A . D 3 HOH 77 477 77 HOH HOH A . D 3 HOH 78 478 78 HOH HOH A . D 3 HOH 79 479 79 HOH HOH A . D 3 HOH 80 480 80 HOH HOH A . D 3 HOH 81 481 81 HOH HOH A . D 3 HOH 82 482 82 HOH HOH A . D 3 HOH 83 483 83 HOH HOH A . D 3 HOH 84 484 84 HOH HOH A . D 3 HOH 85 485 85 HOH HOH A . D 3 HOH 86 486 86 HOH HOH A . D 3 HOH 87 487 87 HOH HOH A . D 3 HOH 88 488 88 HOH HOH A . D 3 HOH 89 489 89 HOH HOH A . D 3 HOH 90 490 90 HOH HOH A . D 3 HOH 91 491 91 HOH HOH A . D 3 HOH 92 492 92 HOH HOH A . D 3 HOH 93 493 93 HOH HOH A . D 3 HOH 94 494 94 HOH HOH A . D 3 HOH 95 495 95 HOH HOH A . D 3 HOH 96 496 96 HOH HOH A . D 3 HOH 97 497 97 HOH HOH A . D 3 HOH 98 498 98 HOH HOH A . D 3 HOH 99 499 99 HOH HOH A . D 3 HOH 100 500 100 HOH HOH A . D 3 HOH 101 501 101 HOH HOH A . D 3 HOH 102 502 102 HOH HOH A . D 3 HOH 103 503 103 HOH HOH A . D 3 HOH 104 504 104 HOH HOH A . D 3 HOH 105 505 105 HOH HOH A . D 3 HOH 106 506 106 HOH HOH A . D 3 HOH 107 507 107 HOH HOH A . D 3 HOH 108 508 108 HOH HOH A . D 3 HOH 109 509 109 HOH HOH A . D 3 HOH 110 510 110 HOH HOH A . D 3 HOH 111 511 111 HOH HOH A . D 3 HOH 112 512 112 HOH HOH A . D 3 HOH 113 513 113 HOH HOH A . D 3 HOH 114 514 114 HOH HOH A . D 3 HOH 115 515 115 HOH HOH A . D 3 HOH 116 516 116 HOH HOH A . D 3 HOH 117 517 117 HOH HOH A . D 3 HOH 118 518 118 HOH HOH A . D 3 HOH 119 519 119 HOH HOH A . D 3 HOH 120 520 120 HOH HOH A . D 3 HOH 121 521 121 HOH HOH A . D 3 HOH 122 522 122 HOH HOH A . D 3 HOH 123 523 123 HOH HOH A . D 3 HOH 124 524 125 HOH HOH A . D 3 HOH 125 525 126 HOH HOH A . D 3 HOH 126 526 127 HOH HOH A . D 3 HOH 127 527 128 HOH HOH A . D 3 HOH 128 528 129 HOH HOH A . D 3 HOH 129 529 130 HOH HOH A . D 3 HOH 130 530 131 HOH HOH A . D 3 HOH 131 531 132 HOH HOH A . D 3 HOH 132 532 133 HOH HOH A . D 3 HOH 133 533 134 HOH HOH A . D 3 HOH 134 534 135 HOH HOH A . D 3 HOH 135 535 136 HOH HOH A . D 3 HOH 136 536 137 HOH HOH A . D 3 HOH 137 537 138 HOH HOH A . D 3 HOH 138 538 139 HOH HOH A . D 3 HOH 139 539 140 HOH HOH A . D 3 HOH 140 540 141 HOH HOH A . D 3 HOH 141 541 142 HOH HOH A . D 3 HOH 142 542 143 HOH HOH A . D 3 HOH 143 543 144 HOH HOH A . D 3 HOH 144 544 145 HOH HOH A . D 3 HOH 145 545 146 HOH HOH A . D 3 HOH 146 546 147 HOH HOH A . D 3 HOH 147 547 148 HOH HOH A . D 3 HOH 148 548 149 HOH HOH A . D 3 HOH 149 549 150 HOH HOH A . D 3 HOH 150 550 151 HOH HOH A . D 3 HOH 151 551 152 HOH HOH A . D 3 HOH 152 552 153 HOH HOH A . D 3 HOH 153 553 154 HOH HOH A . D 3 HOH 154 554 155 HOH HOH A . D 3 HOH 155 555 156 HOH HOH A . D 3 HOH 156 556 157 HOH HOH A . D 3 HOH 157 557 158 HOH HOH A . D 3 HOH 158 558 159 HOH HOH A . D 3 HOH 159 559 160 HOH HOH A . D 3 HOH 160 560 161 HOH HOH A . D 3 HOH 161 561 162 HOH HOH A . D 3 HOH 162 562 163 HOH HOH A . D 3 HOH 163 563 164 HOH HOH A . D 3 HOH 164 564 165 HOH HOH A . D 3 HOH 165 565 166 HOH HOH A . D 3 HOH 166 566 167 HOH HOH A . D 3 HOH 167 567 168 HOH HOH A . D 3 HOH 168 568 169 HOH HOH A . D 3 HOH 169 569 170 HOH HOH A . D 3 HOH 170 570 171 HOH HOH A . D 3 HOH 171 571 172 HOH HOH A . D 3 HOH 172 572 173 HOH HOH A . D 3 HOH 173 573 174 HOH HOH A . D 3 HOH 174 574 175 HOH HOH A . D 3 HOH 175 575 176 HOH HOH A . D 3 HOH 176 576 177 HOH HOH A . D 3 HOH 177 577 178 HOH HOH A . D 3 HOH 178 578 179 HOH HOH A . D 3 HOH 179 579 180 HOH HOH A . D 3 HOH 180 580 181 HOH HOH A . D 3 HOH 181 581 182 HOH HOH A . D 3 HOH 182 582 183 HOH HOH A . D 3 HOH 183 583 184 HOH HOH A . D 3 HOH 184 584 185 HOH HOH A . D 3 HOH 185 585 186 HOH HOH A . D 3 HOH 186 586 187 HOH HOH A . D 3 HOH 187 587 188 HOH HOH A . D 3 HOH 188 588 189 HOH HOH A . D 3 HOH 189 589 190 HOH HOH A . D 3 HOH 190 590 191 HOH HOH A . D 3 HOH 191 591 192 HOH HOH A . D 3 HOH 192 592 193 HOH HOH A . D 3 HOH 193 593 194 HOH HOH A . D 3 HOH 194 594 195 HOH HOH A . D 3 HOH 195 595 196 HOH HOH A . D 3 HOH 196 596 197 HOH HOH A . D 3 HOH 197 597 199 HOH HOH A . D 3 HOH 198 598 200 HOH HOH A . D 3 HOH 199 599 201 HOH HOH A . D 3 HOH 200 600 202 HOH HOH A . D 3 HOH 201 601 203 HOH HOH A . D 3 HOH 202 602 204 HOH HOH A . D 3 HOH 203 603 205 HOH HOH A . D 3 HOH 204 604 206 HOH HOH A . D 3 HOH 205 605 207 HOH HOH A . D 3 HOH 206 606 208 HOH HOH A . D 3 HOH 207 607 209 HOH HOH A . D 3 HOH 208 608 210 HOH HOH A . D 3 HOH 209 609 211 HOH HOH A . D 3 HOH 210 610 212 HOH HOH A . D 3 HOH 211 611 213 HOH HOH A . D 3 HOH 212 612 214 HOH HOH A . D 3 HOH 213 613 215 HOH HOH A . D 3 HOH 214 614 216 HOH HOH A . D 3 HOH 215 615 217 HOH HOH A . D 3 HOH 216 616 218 HOH HOH A . D 3 HOH 217 617 219 HOH HOH A . D 3 HOH 218 618 220 HOH HOH A . D 3 HOH 219 619 221 HOH HOH A . D 3 HOH 220 620 222 HOH HOH A . D 3 HOH 221 621 223 HOH HOH A . D 3 HOH 222 622 224 HOH HOH A . #