data_1J3E # _entry.id 1J3E # _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 1J3E NDB PD0390 RCSB RCSB005580 WWPDB D_1000005580 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1IU3 . unspecified TargetDB trt001000146.2 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1J3E _pdbx_database_status.recvd_initial_deposition_date 2003-01-24 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Fujikawa, N.' 1 'Kurumizaka, H.' 2 'Nureki, O.' 3 'Tanaka, Y.' 4 'Yamazoe, M.' 5 'Hiraga, S.' 6 'Yokoyama, S.' 7 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 8 # _citation.id primary _citation.title 'Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 32 _citation.page_first 82 _citation.page_last 92 _citation.year 2004 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 14704346 _citation.pdbx_database_id_DOI 10.1093/nar/gkh173 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Fujikawa, N.' 1 primary 'Kurumizaka, H.' 2 primary 'Nureki, O.' 3 primary 'Tanaka, Y.' 4 primary 'Yamazoe, M.' 5 primary 'Hiraga, S.' 6 primary 'Yokoyama, S.' 7 # _cell.entry_id 1J3E _cell.length_a 33.432 _cell.length_b 65.061 _cell.length_c 77.176 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1J3E _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # 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 syn "5'-D(*AP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*A)-3'" 3076.071 1 ? ? ? ? 2 polymer syn "5'-D(*TP*TP*GP*GP*AP*GP*CP*CP*TP*T)-3'" 3051.002 1 ? ? ? ? 3 polymer man 'SeqA protein' 12978.878 1 ? ? 'DNA binding domain' ? 4 water nat water 18.015 84 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes '(DA)(DA)(DG)(DG)(6MA)(DT)(DC)(DC)(DA)(DA)' AAGGATCCAA B ? 2 polydeoxyribonucleotide no no '(DT)(DT)(DG)(DG)(DA)(DG)(DC)(DC)(DT)(DT)' TTGGAGCCTT C ? 3 'polypeptide(L)' no no ;PLGSAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYW VITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI ; ;PLGSAMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYW VITNTNTGRKCSMIEHIMQSMQFPAELIEKVCGTI ; A trt001000146.2 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DA n 1 3 DG n 1 4 DG n 1 5 6MA n 1 6 DT n 1 7 DC n 1 8 DC n 1 9 DA n 1 10 DA n 2 1 DT n 2 2 DT n 2 3 DG n 2 4 DG n 2 5 DA n 2 6 DG n 2 7 DC n 2 8 DC n 2 9 DT n 2 10 DT n 3 1 PRO n 3 2 LEU n 3 3 GLY n 3 4 SER n 3 5 ALA n 3 6 MET n 3 7 ARG n 3 8 GLU n 3 9 LEU n 3 10 LEU n 3 11 LEU n 3 12 SER n 3 13 ASP n 3 14 GLU n 3 15 TYR n 3 16 ALA n 3 17 GLU n 3 18 GLN n 3 19 LYS n 3 20 ARG n 3 21 ALA n 3 22 VAL n 3 23 ASN n 3 24 ARG n 3 25 PHE n 3 26 MET n 3 27 LEU n 3 28 LEU n 3 29 LEU n 3 30 SER n 3 31 THR n 3 32 LEU n 3 33 TYR n 3 34 SER n 3 35 LEU n 3 36 ASP n 3 37 ALA n 3 38 GLN n 3 39 ALA n 3 40 PHE n 3 41 ALA n 3 42 GLU n 3 43 ALA n 3 44 THR n 3 45 GLU n 3 46 SER n 3 47 LEU n 3 48 HIS n 3 49 GLY n 3 50 ARG n 3 51 THR n 3 52 ARG n 3 53 VAL n 3 54 TYR n 3 55 PHE n 3 56 ALA n 3 57 ALA n 3 58 ASP n 3 59 GLU n 3 60 GLN n 3 61 THR n 3 62 LEU n 3 63 LEU n 3 64 LYS n 3 65 ASN n 3 66 GLY n 3 67 ASN n 3 68 GLN n 3 69 THR n 3 70 LYS n 3 71 PRO n 3 72 LYS n 3 73 HIS n 3 74 VAL n 3 75 PRO n 3 76 GLY n 3 77 THR n 3 78 PRO n 3 79 TYR n 3 80 TRP n 3 81 VAL n 3 82 ILE n 3 83 THR n 3 84 ASN n 3 85 THR n 3 86 ASN n 3 87 THR n 3 88 GLY n 3 89 ARG n 3 90 LYS n 3 91 CYS n 3 92 SER n 3 93 MET n 3 94 ILE n 3 95 GLU n 3 96 HIS n 3 97 ILE n 3 98 MET n 3 99 GLN n 3 100 SER n 3 101 MET n 3 102 GLN n 3 103 PHE n 3 104 PRO n 3 105 ALA n 3 106 GLU n 3 107 LEU n 3 108 ILE n 3 109 GLU n 3 110 LYS n 3 111 VAL n 3 112 CYS n 3 113 GLY n 3 114 THR n 3 115 ILE n # _entity_src_gen.entity_id 3 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus Escherichia _entity_src_gen.pdbx_gene_src_gene SeqA _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 'Escherichia coli' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 562 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain DH5a _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 pGEX6P-1 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 UNP SEQA_ECOLI 3 ;AMRELLLSDEYAEQKRAVNRFMLLLSTLYSLDAQAFAEATESLHGRTRVYFAADEQTLLKNGNQTKPKHVPGTPYWVITN TNTGRKCSMIEHIMQSMQFPAELIEKVCGTI ; ? P36658 ? 2 PDB 1J3E 1 ? ? 1J3E ? 3 PDB 1J3E 2 ? ? 1J3E ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1J3E A 5 ? 115 ? P36658 71 ? 181 ? 6 116 2 2 1J3E B 1 ? 10 ? 1J3E 201 ? 210 ? 201 210 3 3 1J3E C 1 ? 10 ? 1J3E 211 ? 220 ? 211 220 # 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 1J3E PRO A 1 ? UNP P36658 ? ? 'CLONING ARTIFACT' 2 1 1 1J3E LEU A 2 ? UNP P36658 ? ? 'CLONING ARTIFACT' 3 2 1 1J3E GLY A 3 ? UNP P36658 ? ? 'CLONING ARTIFACT' 4 3 1 1J3E SER A 4 ? UNP P36658 ? ? 'CLONING ARTIFACT' 5 4 # 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 6MA 'DNA linking' n "N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE" ? 'C11 H16 N5 O6 P' 345.248 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 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.entry_id 1J3E _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_percent_sol 43.06 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details 'Ca-acetate, Na-cacodylate, PEG8K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'PEG 8000' ? ? ? 1 2 1 Ca-acetate ? ? ? 1 3 1 Na-cacodylate ? ? ? 1 4 2 'PEG 8000' ? ? ? 1 5 2 Ca-acetate ? ? ? 1 6 2 Na-cacodylate ? ? ? # _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 MARRESEARCH _diffrn_detector.pdbx_collection_date 2002-10-26 _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 'rotated-inclined fixed exit double crystal' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9740 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL41XU' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL41XU _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9740 # _reflns.entry_id 1J3E _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 2.5 _reflns.d_resolution_low 50 _reflns.number_all 6296 _reflns.number_obs 6126 _reflns.percent_possible_obs 97.3 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.50 _reflns_shell.d_res_low 2.59 _reflns_shell.percent_possible_all 94.9 _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.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1J3E _refine.ls_d_res_high 2.5 _refine.ls_d_res_low 40 _refine.pdbx_ls_sigma_F 0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 6228 _refine.ls_number_reflns_obs 6094 _refine.ls_number_reflns_R_free 343 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2302 _refine.ls_R_factor_R_work 0.2302 _refine.ls_R_factor_R_free 0.296 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1J3E _refine_analyze.Luzzati_coordinate_error_obs 0.35 _refine_analyze.Luzzati_sigma_a_obs 0.44 _refine_analyze.Luzzati_d_res_low_obs 5 _refine_analyze.Luzzati_coordinate_error_free 0.50 _refine_analyze.Luzzati_sigma_a_free 0.52 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 908 _refine_hist.pdbx_number_atoms_nucleic_acid 407 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 84 _refine_hist.number_atoms_total 1399 _refine_hist.d_res_high 2.5 _refine_hist.d_res_low 40 # 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 c_angle_deg 1.40 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d 0.00983 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 19.7 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.41 ? ? ? '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.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 6 2.50 2.59 . 0.3552 . 0.415 . . 40 . 'X-RAY DIFFRACTION' . . 6 2.59 2.69 . 0.3257 . 0.3946 . . 33 . 'X-RAY DIFFRACTION' . . 6 2.69 2.82 . 0.3126 . 0.4517 . . 30 . 'X-RAY DIFFRACTION' . . 6 2.82 2.96 . 0.2962 . 0.4306 . . 26 . 'X-RAY DIFFRACTION' . . 6 2.96 3.15 . 0.2687 . 0.331 . . 33 . 'X-RAY DIFFRACTION' . . 6 3.15 3.39 . 0.2175 . 0.2335 . . 45 . 'X-RAY DIFFRACTION' . . # _struct.entry_id 1J3E _struct.title 'Crystal Structure of the E.coli SeqA protein complexed with N6-methyladenine- guanine mismatch DNA' _struct.pdbx_descriptor 'SeqA protein/DNA Complex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1J3E _struct_keywords.pdbx_keywords REPLICATION/DNA _struct_keywords.text ;Protein-DNA complex, Recognition of hemimethylated DNA, mismatched DNA, replication, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, REPLICATION-DNA COMPLEX ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 PRO C 1 ? SER C 12 ? PRO A 2 SER A 13 1 ? 12 HELX_P HELX_P2 2 SER C 12 ? GLN C 18 ? SER A 13 GLN A 19 1 ? 7 HELX_P HELX_P3 3 ARG C 20 ? ASP C 36 ? ARG A 21 ASP A 37 1 ? 17 HELX_P HELX_P4 4 ASP C 36 ? SER C 46 ? ASP A 37 SER A 47 1 ? 11 HELX_P HELX_P5 5 GLU C 59 ? ASN C 65 ? GLU A 60 ASN A 66 1 ? 7 HELX_P HELX_P6 6 ASN C 86 ? MET C 101 ? ASN A 87 MET A 102 1 ? 16 HELX_P HELX_P7 7 PRO C 104 ? GLY C 113 ? PRO A 105 GLY A 114 1 ? 10 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf1 disulf ? ? C CYS 91 SG ? ? ? 1_555 C CYS 112 SG ? ? A CYS 92 A CYS 113 1_555 ? ? ? ? ? ? ? 2.946 ? covale1 covale ? ? A DG 4 "O3'" ? ? ? 1_555 A 6MA 5 P ? ? B DG 204 B 6MA 205 1_555 ? ? ? ? ? ? ? 1.603 ? covale2 covale ? ? A 6MA 5 "O3'" ? ? ? 1_555 A DT 6 P ? ? B 6MA 205 B DT 206 1_555 ? ? ? ? ? ? ? 1.601 ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 10 N3 ? ? B DA 201 C DT 220 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 10 O4 ? ? B DA 201 C DT 220 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 9 N3 ? ? B DA 202 C DT 219 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 9 O4 ? ? B DA 202 C DT 219 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? B DG 203 C DC 218 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? B DG 203 C DC 218 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? B DG 203 C DC 218 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? B DG 204 C DC 217 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? B DG 204 C DC 217 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? B DG 204 C DC 217 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A 6MA 5 N1 ? ? ? 1_555 B DG 6 N1 ? ? B 6MA 205 C DG 216 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? hydrog12 hydrog ? ? A 6MA 5 N6 ? ? ? 1_555 B DG 6 O6 ? ? B 6MA 205 C DG 216 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? hydrog13 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? B DT 206 C DA 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? B DT 206 C DA 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 4 N1 ? ? B DC 207 C DG 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 4 O6 ? ? B DC 207 C DG 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 4 N2 ? ? B DC 207 C DG 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? B DC 208 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? B DC 208 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? B DC 208 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 2 N3 ? ? B DA 209 C DT 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 2 O4 ? ? B DA 209 C DT 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DT 1 N3 ? ? B DA 210 C DT 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 1 O4 ? ? B DA 210 C DT 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? hydrog ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 3 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 PHE C 55 ? ALA C 56 ? PHE A 56 ALA A 57 A 2 TRP C 80 ? VAL C 81 ? TRP A 81 VAL A 82 A 3 LYS C 72 ? HIS C 73 ? LYS A 73 HIS A 74 # 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 N ALA C 56 ? N ALA A 57 O TRP C 80 ? O TRP A 81 A 2 3 O VAL C 81 ? O VAL A 82 N LYS C 72 ? N LYS A 73 # _database_PDB_matrix.entry_id 1J3E _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 1J3E _atom_sites.fract_transf_matrix[1][1] 0.029911 _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] 0.015370 _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] 0.012957 _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 P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DA 1 201 201 DA A B . n A 1 2 DA 2 202 202 DA A B . n A 1 3 DG 3 203 203 DG G B . n A 1 4 DG 4 204 204 DG G B . n A 1 5 6MA 5 205 205 6MA 6MA B . n A 1 6 DT 6 206 206 DT T B . n A 1 7 DC 7 207 207 DC C B . n A 1 8 DC 8 208 208 DC C B . n A 1 9 DA 9 209 209 DA A B . n A 1 10 DA 10 210 210 DA A B . n B 2 1 DT 1 211 211 DT T C . n B 2 2 DT 2 212 212 DT T C . n B 2 3 DG 3 213 213 DG G C . n B 2 4 DG 4 214 214 DG G C . n B 2 5 DA 5 215 215 DA A C . n B 2 6 DG 6 216 216 DG G C . n B 2 7 DC 7 217 217 DC C C . n B 2 8 DC 8 218 218 DC C C . n B 2 9 DT 9 219 219 DT T C . n B 2 10 DT 10 220 220 DT T C . n C 3 1 PRO 1 2 2 PRO PRO A . n C 3 2 LEU 2 3 3 LEU LEU A . n C 3 3 GLY 3 4 4 GLY GLY A . n C 3 4 SER 4 5 5 SER SER A . n C 3 5 ALA 5 6 6 ALA ALA A . n C 3 6 MET 6 7 7 MET MET A . n C 3 7 ARG 7 8 8 ARG ARG A . n C 3 8 GLU 8 9 9 GLU GLU A . n C 3 9 LEU 9 10 10 LEU LEU A . n C 3 10 LEU 10 11 11 LEU LEU A . n C 3 11 LEU 11 12 12 LEU LEU A . n C 3 12 SER 12 13 13 SER SER A . n C 3 13 ASP 13 14 14 ASP ASP A . n C 3 14 GLU 14 15 15 GLU GLU A . n C 3 15 TYR 15 16 16 TYR TYR A . n C 3 16 ALA 16 17 17 ALA ALA A . n C 3 17 GLU 17 18 18 GLU GLU A . n C 3 18 GLN 18 19 19 GLN GLN A . n C 3 19 LYS 19 20 20 LYS LYS A . n C 3 20 ARG 20 21 21 ARG ARG A . n C 3 21 ALA 21 22 22 ALA ALA A . n C 3 22 VAL 22 23 23 VAL VAL A . n C 3 23 ASN 23 24 24 ASN ASN A . n C 3 24 ARG 24 25 25 ARG ARG A . n C 3 25 PHE 25 26 26 PHE PHE A . n C 3 26 MET 26 27 27 MET MET A . n C 3 27 LEU 27 28 28 LEU LEU A . n C 3 28 LEU 28 29 29 LEU LEU A . n C 3 29 LEU 29 30 30 LEU LEU A . n C 3 30 SER 30 31 31 SER SER A . n C 3 31 THR 31 32 32 THR THR A . n C 3 32 LEU 32 33 33 LEU LEU A . n C 3 33 TYR 33 34 34 TYR TYR A . n C 3 34 SER 34 35 35 SER SER A . n C 3 35 LEU 35 36 36 LEU LEU A . n C 3 36 ASP 36 37 37 ASP ASP A . n C 3 37 ALA 37 38 38 ALA ALA A . n C 3 38 GLN 38 39 39 GLN GLN A . n C 3 39 ALA 39 40 40 ALA ALA A . n C 3 40 PHE 40 41 41 PHE PHE A . n C 3 41 ALA 41 42 42 ALA ALA A . n C 3 42 GLU 42 43 43 GLU GLU A . n C 3 43 ALA 43 44 44 ALA ALA A . n C 3 44 THR 44 45 45 THR THR A . n C 3 45 GLU 45 46 46 GLU GLU A . n C 3 46 SER 46 47 47 SER SER A . n C 3 47 LEU 47 48 48 LEU LEU A . n C 3 48 HIS 48 49 49 HIS HIS A . n C 3 49 GLY 49 50 50 GLY GLY A . n C 3 50 ARG 50 51 51 ARG ARG A . n C 3 51 THR 51 52 52 THR THR A . n C 3 52 ARG 52 53 53 ARG ARG A . n C 3 53 VAL 53 54 54 VAL VAL A . n C 3 54 TYR 54 55 55 TYR TYR A . n C 3 55 PHE 55 56 56 PHE PHE A . n C 3 56 ALA 56 57 57 ALA ALA A . n C 3 57 ALA 57 58 58 ALA ALA A . n C 3 58 ASP 58 59 59 ASP ASP A . n C 3 59 GLU 59 60 60 GLU GLU A . n C 3 60 GLN 60 61 61 GLN GLN A . n C 3 61 THR 61 62 62 THR THR A . n C 3 62 LEU 62 63 63 LEU LEU A . n C 3 63 LEU 63 64 64 LEU LEU A . n C 3 64 LYS 64 65 65 LYS LYS A . n C 3 65 ASN 65 66 66 ASN ASN A . n C 3 66 GLY 66 67 67 GLY GLY A . n C 3 67 ASN 67 68 68 ASN ASN A . n C 3 68 GLN 68 69 69 GLN GLN A . n C 3 69 THR 69 70 70 THR THR A . n C 3 70 LYS 70 71 71 LYS LYS A . n C 3 71 PRO 71 72 72 PRO PRO A . n C 3 72 LYS 72 73 73 LYS LYS A . n C 3 73 HIS 73 74 74 HIS HIS A . n C 3 74 VAL 74 75 75 VAL VAL A . n C 3 75 PRO 75 76 76 PRO PRO A . n C 3 76 GLY 76 77 77 GLY GLY A . n C 3 77 THR 77 78 78 THR THR A . n C 3 78 PRO 78 79 79 PRO PRO A . n C 3 79 TYR 79 80 80 TYR TYR A . n C 3 80 TRP 80 81 81 TRP TRP A . n C 3 81 VAL 81 82 82 VAL VAL A . n C 3 82 ILE 82 83 83 ILE ILE A . n C 3 83 THR 83 84 84 THR THR A . n C 3 84 ASN 84 85 85 ASN ASN A . n C 3 85 THR 85 86 86 THR THR A . n C 3 86 ASN 86 87 87 ASN ASN A . n C 3 87 THR 87 88 88 THR THR A . n C 3 88 GLY 88 89 89 GLY GLY A . n C 3 89 ARG 89 90 90 ARG ARG A . n C 3 90 LYS 90 91 91 LYS LYS A . n C 3 91 CYS 91 92 92 CYS CYS A . n C 3 92 SER 92 93 93 SER SER A . n C 3 93 MET 93 94 94 MET MET A . n C 3 94 ILE 94 95 95 ILE ILE A . n C 3 95 GLU 95 96 96 GLU GLU A . n C 3 96 HIS 96 97 97 HIS HIS A . n C 3 97 ILE 97 98 98 ILE ILE A . n C 3 98 MET 98 99 99 MET MET A . n C 3 99 GLN 99 100 100 GLN GLN A . n C 3 100 SER 100 101 101 SER SER A . n C 3 101 MET 101 102 102 MET MET A . n C 3 102 GLN 102 103 103 GLN GLN A . n C 3 103 PHE 103 104 104 PHE PHE A . n C 3 104 PRO 104 105 105 PRO PRO A . n C 3 105 ALA 105 106 106 ALA ALA A . n C 3 106 GLU 106 107 107 GLU GLU A . n C 3 107 LEU 107 108 108 LEU LEU A . n C 3 108 ILE 108 109 109 ILE ILE A . n C 3 109 GLU 109 110 110 GLU GLU A . n C 3 110 LYS 110 111 111 LYS LYS A . n C 3 111 VAL 111 112 112 VAL VAL A . n C 3 112 CYS 112 113 113 CYS CYS A . n C 3 113 GLY 113 114 114 GLY GLY A . n C 3 114 THR 114 115 115 THR THR A . n C 3 115 ILE 115 116 116 ILE ILE A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name ? _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id 6MA _pdbx_struct_mod_residue.label_seq_id 5 _pdbx_struct_mod_residue.auth_asym_id B _pdbx_struct_mod_residue.auth_comp_id 6MA _pdbx_struct_mod_residue.auth_seq_id 205 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id A _pdbx_struct_mod_residue.details ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _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 2004-05-18 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 # _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 ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement 1.0 ? 4 # 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 13 ? ? -45.86 158.22 2 1 ASP A 37 ? ? -151.33 69.85 3 1 ALA A 38 ? ? -39.41 -28.07 4 1 THR A 52 ? ? -147.29 -25.85 5 1 MET A 102 ? ? -72.86 26.58 6 1 GLN A 103 ? ? 27.15 80.46 # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DG _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 203 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.058 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1J3E 'double helix' 1J3E 'b-form double helix' 1J3E 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DA 1 1_555 B DT 10 1_555 0.295 -0.445 -0.072 -4.878 -11.657 5.724 1 B_DA201:DT220_C B 201 ? C 220 ? 20 1 1 A DA 2 1_555 B DT 9 1_555 1.166 -0.218 0.333 1.309 -12.653 -3.728 2 B_DA202:DT219_C B 202 ? C 219 ? 20 1 1 A DG 3 1_555 B DC 8 1_555 -0.251 0.061 0.428 2.202 -3.340 -2.085 3 B_DG203:DC218_C B 203 ? C 218 ? 19 1 1 A DG 4 1_555 B DC 7 1_555 0.223 -0.018 0.263 11.284 -7.851 -3.518 4 B_DG204:DC217_C B 204 ? C 217 ? 19 1 1 A 6MA 5 1_555 B DG 6 1_555 -0.333 1.566 -0.295 4.301 -24.811 -6.368 5 B_6MA205:DG216_C B 205 ? C 216 ? 8 1 1 A DT 6 1_555 B DA 5 1_555 -0.470 -0.185 -0.281 1.902 -7.411 -4.404 6 B_DT206:DA215_C B 206 ? C 215 ? 20 1 1 A DC 7 1_555 B DG 4 1_555 0.212 -0.306 0.013 4.425 -4.724 -0.692 7 B_DC207:DG214_C B 207 ? C 214 ? 19 1 1 A DC 8 1_555 B DG 3 1_555 -0.075 -0.246 -0.266 6.521 -1.911 -3.264 8 B_DC208:DG213_C B 208 ? C 213 ? 19 1 1 A DA 9 1_555 B DT 2 1_555 0.656 -0.211 0.041 2.717 -7.823 -7.096 9 B_DA209:DT212_C B 209 ? C 212 ? 20 1 1 A DA 10 1_555 B DT 1 1_555 0.547 -0.307 -0.198 0.896 -2.822 -3.686 10 B_DA210:DT211_C B 210 ? C 211 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DA 1 1_555 B DT 10 1_555 A DA 2 1_555 B DT 9 1_555 -0.518 -0.111 3.145 -3.783 -2.918 43.358 0.122 0.345 3.178 -3.935 5.102 43.608 1 BB_DA201DA202:DT219DT220_CC B 201 ? C 220 ? B 202 ? C 219 ? 1 A DA 2 1_555 B DT 9 1_555 A DG 3 1_555 B DC 8 1_555 0.327 0.277 3.257 0.987 -3.020 31.789 1.046 -0.417 3.226 -5.496 -1.796 31.943 2 BB_DA202DG203:DC218DT219_CC B 202 ? C 219 ? B 203 ? C 218 ? 1 A DG 3 1_555 B DC 8 1_555 A DG 4 1_555 B DC 7 1_555 0.552 0.758 3.308 2.439 4.853 29.658 0.431 -0.547 3.420 9.381 -4.715 30.140 3 BB_DG203DG204:DC217DC218_CC B 203 ? C 218 ? B 204 ? C 217 ? 1 A DG 4 1_555 B DC 7 1_555 A 6MA 5 1_555 B DG 6 1_555 -1.037 0.773 3.418 3.794 -2.566 36.261 1.594 2.189 3.236 -4.102 -6.067 36.539 4 BB_DG2046MA205:DG216DC217_CC B 204 ? C 217 ? B 205 ? C 216 ? 1 A 6MA 5 1_555 B DG 6 1_555 A DT 6 1_555 B DA 5 1_555 1.119 1.044 3.247 1.889 -10.806 39.375 2.641 -1.405 2.921 -15.671 -2.739 40.816 5 BB_6MA205DT206:DA215DG216_CC B 205 ? C 216 ? B 206 ? C 215 ? 1 A DT 6 1_555 B DA 5 1_555 A DC 7 1_555 B DG 4 1_555 0.403 0.052 3.352 -0.501 7.047 29.563 -1.353 -0.872 3.269 13.567 0.965 30.377 6 BB_DT206DC207:DG214DA215_CC B 206 ? C 215 ? B 207 ? C 214 ? 1 A DC 7 1_555 B DG 4 1_555 A DC 8 1_555 B DG 3 1_555 0.342 -0.123 3.245 3.519 0.789 37.227 -0.295 -0.072 3.259 1.233 -5.496 37.395 7 BB_DC207DC208:DG213DG214_CC B 207 ? C 214 ? B 208 ? C 213 ? 1 A DC 8 1_555 B DG 3 1_555 A DA 9 1_555 B DT 2 1_555 -0.297 -0.391 3.434 -1.011 3.329 38.324 -1.026 0.319 3.396 5.058 1.536 38.476 8 BB_DC208DA209:DT212DG213_CC B 208 ? C 213 ? B 209 ? C 212 ? 1 A DA 9 1_555 B DT 2 1_555 A DA 10 1_555 B DT 1 1_555 0.509 0.121 3.353 2.950 0.900 39.165 0.069 -0.395 3.383 1.340 -4.393 39.282 9 BB_DA209DA210:DT211DT212_CC B 209 ? C 212 ? B 210 ? C 211 ? # _pdbx_entity_nonpoly.entity_id 4 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 D 4 HOH 1 3 3 HOH TIP B . D 4 HOH 2 4 4 HOH TIP B . D 4 HOH 3 5 5 HOH TIP B . D 4 HOH 4 14 14 HOH TIP B . D 4 HOH 5 21 21 HOH TIP B . D 4 HOH 6 22 22 HOH TIP B . D 4 HOH 7 29 29 HOH TIP B . D 4 HOH 8 30 30 HOH TIP B . D 4 HOH 9 43 43 HOH TIP B . D 4 HOH 10 54 54 HOH TIP B . D 4 HOH 11 56 56 HOH TIP B . D 4 HOH 12 67 67 HOH TIP B . D 4 HOH 13 73 73 HOH TIP B . D 4 HOH 14 79 79 HOH TIP B . D 4 HOH 15 80 80 HOH TIP B . E 4 HOH 1 6 6 HOH TIP C . E 4 HOH 2 11 11 HOH TIP C . E 4 HOH 3 12 12 HOH TIP C . E 4 HOH 4 16 16 HOH TIP C . E 4 HOH 5 33 33 HOH TIP C . E 4 HOH 6 37 37 HOH TIP C . E 4 HOH 7 40 40 HOH TIP C . E 4 HOH 8 44 44 HOH TIP C . E 4 HOH 9 52 52 HOH TIP C . E 4 HOH 10 57 57 HOH TIP C . E 4 HOH 11 58 58 HOH TIP C . E 4 HOH 12 69 69 HOH TIP C . E 4 HOH 13 76 76 HOH TIP C . E 4 HOH 14 77 77 HOH TIP C . E 4 HOH 15 83 83 HOH TIP C . F 4 HOH 1 117 1 HOH TIP A . F 4 HOH 2 118 2 HOH TIP A . F 4 HOH 3 119 7 HOH TIP A . F 4 HOH 4 120 8 HOH TIP A . F 4 HOH 5 121 9 HOH TIP A . F 4 HOH 6 122 10 HOH TIP A . F 4 HOH 7 123 13 HOH TIP A . F 4 HOH 8 124 15 HOH TIP A . F 4 HOH 9 125 17 HOH TIP A . F 4 HOH 10 126 18 HOH TIP A . F 4 HOH 11 127 19 HOH TIP A . F 4 HOH 12 128 20 HOH TIP A . F 4 HOH 13 129 23 HOH TIP A . F 4 HOH 14 130 24 HOH TIP A . F 4 HOH 15 131 25 HOH TIP A . F 4 HOH 16 132 26 HOH TIP A . F 4 HOH 17 133 27 HOH TIP A . F 4 HOH 18 134 28 HOH TIP A . F 4 HOH 19 135 31 HOH TIP A . F 4 HOH 20 136 32 HOH TIP A . F 4 HOH 21 137 34 HOH TIP A . F 4 HOH 22 138 35 HOH TIP A . F 4 HOH 23 139 36 HOH TIP A . F 4 HOH 24 140 38 HOH TIP A . F 4 HOH 25 141 39 HOH TIP A . F 4 HOH 26 142 41 HOH TIP A . F 4 HOH 27 143 42 HOH TIP A . F 4 HOH 28 144 45 HOH TIP A . F 4 HOH 29 145 46 HOH TIP A . F 4 HOH 30 146 47 HOH TIP A . F 4 HOH 31 147 48 HOH TIP A . F 4 HOH 32 148 49 HOH TIP A . F 4 HOH 33 149 50 HOH TIP A . F 4 HOH 34 150 51 HOH TIP A . F 4 HOH 35 151 53 HOH TIP A . F 4 HOH 36 152 55 HOH TIP A . F 4 HOH 37 153 59 HOH TIP A . F 4 HOH 38 154 60 HOH TIP A . F 4 HOH 39 155 61 HOH TIP A . F 4 HOH 40 156 62 HOH TIP A . F 4 HOH 41 157 63 HOH TIP A . F 4 HOH 42 158 64 HOH TIP A . F 4 HOH 43 159 65 HOH TIP A . F 4 HOH 44 160 66 HOH TIP A . F 4 HOH 45 161 68 HOH TIP A . F 4 HOH 46 162 70 HOH TIP A . F 4 HOH 47 163 71 HOH TIP A . F 4 HOH 48 164 72 HOH TIP A . F 4 HOH 49 165 74 HOH TIP A . F 4 HOH 50 166 75 HOH TIP A . F 4 HOH 51 167 78 HOH TIP A . F 4 HOH 52 168 81 HOH TIP A . F 4 HOH 53 169 82 HOH TIP A . F 4 HOH 54 170 84 HOH TIP A . #