data_3IGT # _entry.id 3IGT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3IGT pdb_00003igt 10.2210/pdb3igt/pdb NDB NA0108 ? ? RCSB RCSB054392 ? ? WWPDB D_1000054392 ? ? # 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 2009-08-18 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' # 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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3IGT _pdbx_database_status.recvd_initial_deposition_date 2009-07-28 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Khuu, P.' 1 'Ho, P.S.' 2 # _citation.id primary _citation.title 'A rare nucleotide base tautomer in the structure of an asymmetric DNA junction.' _citation.journal_abbrev Biochemistry _citation.journal_volume 48 _citation.page_first 7824 _citation.page_last 7832 _citation.year 2009 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19580331 _citation.pdbx_database_id_DOI 10.1021/bi900829b # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Khuu, P.' 1 ? primary 'Ho, P.S.' 2 ? # 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(*CP*CP*GP*AP*GP*TP*CP*CP*TP*A)-3'" 3004.980 1 ? ? ? 'DNA HOLLIDAY JUNCTION STRAND 1' 2 polymer syn "5'-D(*CP*TP*CP*AP*AP*CP*TP*CP*GP*G)-3'" 3004.980 1 ? ? ? 'DNA HOLLIDAY JUNCTION STRAND 2' 3 polymer syn "5'-D(*TP*CP*GP*GP*CP*CP*TP*GP*AP*G)-3'" 3061.003 1 ? ? ? 'DNA HOLLIDAY JUNCTION STRAND 3' 4 polymer syn "5'-D(*TP*AP*GP*GP*GP*GP*CP*CP*GP*A)-3'" 3110.041 1 ? ? ? 'DNA HOLLIDAY JUNCTION STRAND 4' 5 water nat water 18.015 114 ? ? ? ? # 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 no '(DC)(DC)(DG)(DA)(DG)(DT)(DC)(DC)(DT)(DA)' CCGAGTCCTA A ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DC)(DA)(DA)(DC)(DT)(DC)(DG)(DG)' CTCAACTCGG B ? 3 polydeoxyribonucleotide no no '(DT)(DC)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG)' TCGGCCTGAG C ? 4 polydeoxyribonucleotide no no '(DT)(DA)(DG)(DG)(DG)(DG)(DC)(DC)(DG)(DA)' TAGGGGCCGA D ? # _pdbx_entity_nonpoly.entity_id 5 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DG n 1 4 DA n 1 5 DG n 1 6 DT n 1 7 DC n 1 8 DC n 1 9 DT n 1 10 DA n 2 1 DC n 2 2 DT n 2 3 DC n 2 4 DA n 2 5 DA n 2 6 DC n 2 7 DT n 2 8 DC n 2 9 DG n 2 10 DG n 3 1 DT n 3 2 DC n 3 3 DG n 3 4 DG n 3 5 DC n 3 6 DC n 3 7 DT n 3 8 DG n 3 9 DA n 3 10 DG n 4 1 DT n 4 2 DA n 4 3 DG n 4 4 DG n 4 5 DG n 4 6 DG n 4 7 DC n 4 8 DC n 4 9 DG n 4 10 DA n # 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 DC 1 1 1 DC DC A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DT 9 9 9 DT DT A . n A 1 10 DA 10 10 10 DA DA A . n B 2 1 DC 1 11 11 DC DC B . n B 2 2 DT 2 12 12 DT DT B . n B 2 3 DC 3 13 13 DC DC B . n B 2 4 DA 4 14 14 DA DA B . n B 2 5 DA 5 15 15 DA DA B . n B 2 6 DC 6 16 16 DC DC B . n B 2 7 DT 7 17 17 DT DT B . n B 2 8 DC 8 18 18 DC DC B . n B 2 9 DG 9 19 19 DG DG B . n B 2 10 DG 10 20 20 DG DG B . n C 3 1 DT 1 21 21 DT DT C . n C 3 2 DC 2 22 22 DC DC C . n C 3 3 DG 3 23 23 DG DG C . n C 3 4 DG 4 24 24 DG DG C . n C 3 5 DC 5 25 25 DC DC C . n C 3 6 DC 6 26 26 DC DC C . n C 3 7 DT 7 27 27 DT DT C . n C 3 8 DG 8 28 28 DG DG C . n C 3 9 DA 9 29 29 DA DA C . n C 3 10 DG 10 30 30 DG DG C . n D 4 1 DT 1 31 31 DT DT D . n D 4 2 DA 2 32 32 DA DA D . n D 4 3 DG 3 33 33 DG DG D . n D 4 4 DG 4 34 34 DG DG D . n D 4 5 DG 5 35 35 DG DG D . n D 4 6 DG 6 36 36 DG DG D . n D 4 7 DC 7 37 37 DC DC D . n D 4 8 DC 8 38 38 DC DC D . n D 4 9 DG 9 39 39 DG DG D . n D 4 10 DA 10 40 40 DA DA D . 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 E 5 HOH 1 41 41 HOH HOH A . E 5 HOH 2 46 46 HOH HOH A . E 5 HOH 3 48 48 HOH HOH A . E 5 HOH 4 50 50 HOH HOH A . E 5 HOH 5 52 52 HOH HOH A . E 5 HOH 6 53 53 HOH HOH A . E 5 HOH 7 54 54 HOH HOH A . E 5 HOH 8 55 55 HOH HOH A . E 5 HOH 9 56 56 HOH HOH A . E 5 HOH 10 60 60 HOH HOH A . E 5 HOH 11 61 61 HOH HOH A . E 5 HOH 12 62 62 HOH HOH A . E 5 HOH 13 63 63 HOH HOH A . E 5 HOH 14 65 65 HOH HOH A . E 5 HOH 15 66 66 HOH HOH A . E 5 HOH 16 70 70 HOH HOH A . E 5 HOH 17 77 77 HOH HOH A . E 5 HOH 18 80 80 HOH HOH A . E 5 HOH 19 87 87 HOH HOH A . E 5 HOH 20 88 88 HOH HOH A . E 5 HOH 21 94 94 HOH HOH A . E 5 HOH 22 96 96 HOH HOH A . E 5 HOH 23 98 98 HOH HOH A . E 5 HOH 24 103 103 HOH HOH A . E 5 HOH 25 104 104 HOH HOH A . E 5 HOH 26 115 115 HOH HOH A . E 5 HOH 27 116 116 HOH HOH A . E 5 HOH 28 117 117 HOH HOH A . E 5 HOH 29 118 118 HOH HOH A . E 5 HOH 30 133 133 HOH HOH A . E 5 HOH 31 136 136 HOH HOH A . E 5 HOH 32 138 138 HOH HOH A . E 5 HOH 33 139 139 HOH HOH A . E 5 HOH 34 140 140 HOH HOH A . E 5 HOH 35 146 146 HOH HOH A . E 5 HOH 36 149 149 HOH HOH A . F 5 HOH 1 47 47 HOH HOH B . F 5 HOH 2 58 58 HOH HOH B . F 5 HOH 3 64 64 HOH HOH B . F 5 HOH 4 69 69 HOH HOH B . F 5 HOH 5 75 75 HOH HOH B . F 5 HOH 6 76 76 HOH HOH B . F 5 HOH 7 78 78 HOH HOH B . F 5 HOH 8 79 79 HOH HOH B . F 5 HOH 9 81 81 HOH HOH B . F 5 HOH 10 84 84 HOH HOH B . F 5 HOH 11 85 85 HOH HOH B . F 5 HOH 12 86 86 HOH HOH B . F 5 HOH 13 89 89 HOH HOH B . F 5 HOH 14 91 91 HOH HOH B . F 5 HOH 15 100 100 HOH HOH B . F 5 HOH 16 105 105 HOH HOH B . F 5 HOH 17 110 110 HOH HOH B . F 5 HOH 18 112 112 HOH HOH B . F 5 HOH 19 114 114 HOH HOH B . F 5 HOH 20 120 120 HOH HOH B . F 5 HOH 21 122 122 HOH HOH B . F 5 HOH 22 123 123 HOH HOH B . F 5 HOH 23 127 127 HOH HOH B . F 5 HOH 24 129 129 HOH HOH B . F 5 HOH 25 142 142 HOH HOH B . F 5 HOH 26 143 143 HOH HOH B . F 5 HOH 27 144 144 HOH HOH B . F 5 HOH 28 152 152 HOH HOH B . G 5 HOH 1 43 43 HOH HOH C . G 5 HOH 2 44 44 HOH HOH C . G 5 HOH 3 49 49 HOH HOH C . G 5 HOH 4 51 51 HOH HOH C . G 5 HOH 5 57 57 HOH HOH C . G 5 HOH 6 59 59 HOH HOH C . G 5 HOH 7 71 71 HOH HOH C . G 5 HOH 8 73 73 HOH HOH C . G 5 HOH 9 83 83 HOH HOH C . G 5 HOH 10 90 90 HOH HOH C . G 5 HOH 11 107 107 HOH HOH C . G 5 HOH 12 119 119 HOH HOH C . G 5 HOH 13 121 121 HOH HOH C . G 5 HOH 14 131 131 HOH HOH C . G 5 HOH 15 132 132 HOH HOH C . G 5 HOH 16 134 134 HOH HOH C . G 5 HOH 17 141 141 HOH HOH C . G 5 HOH 18 145 145 HOH HOH C . G 5 HOH 19 147 147 HOH HOH C . G 5 HOH 20 148 148 HOH HOH C . G 5 HOH 21 151 151 HOH HOH C . G 5 HOH 22 153 153 HOH HOH C . G 5 HOH 23 154 154 HOH HOH C . H 5 HOH 1 42 42 HOH HOH D . H 5 HOH 2 45 45 HOH HOH D . H 5 HOH 3 67 67 HOH HOH D . H 5 HOH 4 68 68 HOH HOH D . H 5 HOH 5 72 72 HOH HOH D . H 5 HOH 6 74 74 HOH HOH D . H 5 HOH 7 82 82 HOH HOH D . H 5 HOH 8 92 92 HOH HOH D . H 5 HOH 9 93 93 HOH HOH D . H 5 HOH 10 95 95 HOH HOH D . H 5 HOH 11 97 97 HOH HOH D . H 5 HOH 12 99 99 HOH HOH D . H 5 HOH 13 101 101 HOH HOH D . H 5 HOH 14 102 102 HOH HOH D . H 5 HOH 15 106 106 HOH HOH D . H 5 HOH 16 108 108 HOH HOH D . H 5 HOH 17 109 109 HOH HOH D . H 5 HOH 18 111 111 HOH HOH D . H 5 HOH 19 113 113 HOH HOH D . H 5 HOH 20 124 124 HOH HOH D . H 5 HOH 21 125 125 HOH HOH D . H 5 HOH 22 126 126 HOH HOH D . H 5 HOH 23 128 128 HOH HOH D . H 5 HOH 24 130 130 HOH HOH D . H 5 HOH 25 135 135 HOH HOH D . H 5 HOH 26 137 137 HOH HOH D . H 5 HOH 27 150 150 HOH HOH D . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.2 ? 1 HKL-2000 'data reduction' . ? 2 SCALA 'data scaling' . ? 3 # _cell.entry_id 3IGT _cell.length_a 22.344 _cell.length_b 34.554 _cell.length_c 37.631 _cell.angle_alpha 109.92 _cell.angle_beta 90.03 _cell.angle_gamma 109.02 _cell.Z_PDB 1 _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 3IGT _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3IGT _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.10 _exptl_crystal.density_percent_sol 41.52 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;0.8 mM DNA; 25 mM sodium cacodylate buffer; 100 mM calcium chloride; equilibrated against a reservoir of 35% aqueous 2-methyl-2,4-dimethylpentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2005 _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 MIRRORS _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU300' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.54 # _reflns.entry_id 3IGT _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.9 _reflns.number_obs 6797 _reflns.number_all 3048 _reflns.percent_possible_obs 89.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.068 _reflns.pdbx_netI_over_sigmaI 15.5 _reflns.B_iso_Wilson_estimate 10.3 _reflns.pdbx_redundancy ? _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.9 _reflns_shell.d_res_low 2.02 _reflns_shell.percent_possible_all 62.9 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.289 _reflns_shell.meanI_over_sigI_obs 2.8 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 719 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3IGT _refine.ls_number_reflns_obs 6797 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 57338.16 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.0 _refine.ls_d_res_high 1.90 _refine.ls_percent_reflns_obs 86.8 _refine.ls_R_factor_obs 0.224 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.224 _refine.ls_R_factor_R_free 0.265 _refine.ls_R_factor_R_free_error 0.010 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.9 _refine.ls_number_reflns_R_free 740 _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 17.9 _refine.aniso_B[1][1] 3.73 _refine.aniso_B[2][2] 0.15 _refine.aniso_B[3][3] -3.88 _refine.aniso_B[1][2] 0.12 _refine.aniso_B[1][3] -0.11 _refine.aniso_B[2][3] 0.38 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.35 _refine.solvent_model_param_bsol 71.3963 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'BULK SOLVENT MODEL USED' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _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 ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _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_analyze.entry_id 3IGT _refine_analyze.Luzzati_coordinate_error_obs 0.25 _refine_analyze.Luzzati_sigma_a_obs 0.28 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.32 _refine_analyze.Luzzati_sigma_a_free 0.43 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _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 0 _refine_hist.pdbx_number_atoms_nucleic_acid 808 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 114 _refine_hist.number_atoms_total 922 _refine_hist.d_res_high 1.90 _refine_hist.d_res_low 8.0 # 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_bond_d 0.004 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.8 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 17.4 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.36 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.90 _refine_ls_shell.d_res_low 2.02 _refine_ls_shell.number_reflns_R_work 719 _refine_ls_shell.R_factor_R_work 0.341 _refine_ls_shell.percent_reflns_obs 61.1 _refine_ls_shell.R_factor_R_free 0.404 _refine_ls_shell.R_factor_R_free_error 0.043 _refine_ls_shell.percent_reflns_R_free 11.1 _refine_ls_shell.number_reflns_R_free 90 _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 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 dna-rna_rep.par dna-rna.top 'X-RAY DIFFRACTION' 2 ? ? 'X-RAY DIFFRACTION' 3 &_1_PARAMETER_INFILE_3 ? 'X-RAY DIFFRACTION' # _struct_ncs_dom.id 1 _struct_ncs_dom.details ? _struct_ncs_dom.pdbx_ens_id 1 # _struct_ncs_ens.id 1 _struct_ncs_ens.details ? # _database_PDB_matrix.entry_id 3IGT _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 # _struct.entry_id 3IGT _struct.title 'A rare nucleotide base tautomer in the structure of an asymmetric DNA junction' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3IGT _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA FOUR-STRANDED JUNCTION, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 5 ? G N N 5 ? H N N 5 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 3IGT 3IGT 1 1 CCGAGTCCTA ? 2 PDB 3IGT 3IGT 2 1 CTCAACTCGG ? 3 PDB 3IGT 3IGT 3 1 TCGGCCTGAG ? 4 PDB 3IGT 3IGT 4 1 TAGGGGCCGA ? # 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 3IGT A 1 ? 10 ? 3IGT 1 ? 10 ? 1 10 2 2 3IGT B 1 ? 10 ? 3IGT 11 ? 20 ? 11 20 3 3 3IGT C 1 ? 10 ? 3IGT 21 ? 30 ? 21 30 4 4 3IGT D 1 ? 10 ? 3IGT 31 ? 40 ? 31 40 # _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2710 ? 1 MORE -13 ? 1 'SSA (A^2)' 6930 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _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 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 4 B DT 17 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 O2 ? ? ? 1_555 D DG 4 N2 ? ? A DC 7 D DG 34 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog17 hydrog ? ? A DC 8 N3 ? ? ? 1_555 D DG 3 N1 ? ? A DC 8 D DG 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N4 ? ? ? 1_555 D DG 3 O6 ? ? A DC 8 D DG 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 O2 ? ? ? 1_555 D DG 3 N2 ? ? A DC 8 D DG 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 9 N3 ? ? ? 1_555 D DA 2 N1 ? ? A DT 9 D DA 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 9 O4 ? ? ? 1_555 D DA 2 N6 ? ? A DT 9 D DA 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 10 N1 ? ? ? 1_555 D DT 1 N3 ? ? A DA 10 D DT 31 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog23 hydrog ? ? B DC 1 N3 ? ? ? 1_555 C DG 10 N1 ? ? B DC 11 C DG 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B DC 1 N4 ? ? ? 1_555 C DG 10 O6 ? ? B DC 11 C DG 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B DC 1 O2 ? ? ? 1_555 C DG 10 N2 ? ? B DC 11 C DG 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B DT 2 N3 ? ? ? 1_555 C DA 9 N1 ? ? B DT 12 C DA 29 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog27 hydrog ? ? B DC 3 N3 ? ? ? 1_555 C DG 8 N1 ? ? B DC 13 C DG 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B DC 3 N4 ? ? ? 1_555 C DG 8 O6 ? ? B DC 13 C DG 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B DC 3 O2 ? ? ? 1_555 C DG 8 N2 ? ? B DC 13 C DG 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B DA 4 N1 ? ? ? 1_555 C DT 7 N3 ? ? B DA 14 C DT 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B DA 4 N6 ? ? ? 1_555 C DT 7 O4 ? ? B DA 14 C DT 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DT 1 N3 ? ? ? 1_555 D DA 10 N1 ? ? C DT 21 D DA 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C DT 1 O4 ? ? ? 1_555 D DA 10 N6 ? ? C DT 21 D DA 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C DC 2 N3 ? ? ? 1_555 D DG 9 N1 ? ? C DC 22 D DG 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C DC 2 N4 ? ? ? 1_555 D DG 9 O6 ? ? C DC 22 D DG 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C DC 2 O2 ? ? ? 1_555 D DG 9 N2 ? ? C DC 22 D DG 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C DG 3 N1 ? ? ? 1_555 D DC 8 N3 ? ? C DG 23 D DC 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C DG 3 N2 ? ? ? 1_555 D DC 8 O2 ? ? C DG 23 D DC 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C DG 3 O6 ? ? ? 1_555 D DC 8 N4 ? ? C DG 23 D DC 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C DG 4 N2 ? ? ? 1_555 D DC 7 N3 ? ? C DG 24 D DC 37 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog41 hydrog ? ? C DC 5 N3 ? ? ? 1_555 D DG 6 N1 ? ? C DC 25 D DG 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C DC 5 N4 ? ? ? 1_555 D DG 6 O6 ? ? C DC 25 D DG 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C DC 5 O2 ? ? ? 1_555 D DG 6 N2 ? ? C DC 25 D DG 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C DC 6 N3 ? ? ? 1_555 D DG 5 N1 ? ? C DC 26 D DG 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C DC 6 N4 ? ? ? 1_555 D DG 5 O6 ? ? C DC 26 D DG 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C DC 6 O2 ? ? ? 1_555 D DG 5 N2 ? ? C DC 26 D DG 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _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 19 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.090 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # _ndb_struct_conf_na.entry_id 3IGT _ndb_struct_conf_na.feature 'b-form double helix' # 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 DC 1 1_555 B DG 10 1_555 0.256 0.111 -0.480 -2.022 -28.498 9.961 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 -0.415 -0.057 0.813 8.166 -6.591 9.348 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.278 -0.097 1.123 -1.554 -0.606 10.220 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DA 4 1_555 B DT 7 1_555 0.306 0.416 -0.095 -10.854 -25.291 3.698 4 A_DA4:DT17_B A 4 ? B 17 ? ? ? 1 A DG 5 1_555 B DC 6 1_555 0.077 0.061 0.202 -1.851 -10.077 7.223 5 A_DG5:DC16_B A 5 ? B 16 ? 19 1 1 A DT 6 1_555 B DA 5 1_555 0.193 0.070 0.755 -5.917 -3.491 -4.415 6 A_DT6:DA15_B A 6 ? B 15 ? 20 1 1 C DT 7 1_555 B DA 4 1_555 0.641 0.151 -0.012 3.319 -16.967 0.016 7 C_DT27:DA14_B C 27 ? B 14 ? 20 1 1 C DG 8 1_555 B DC 3 1_555 0.075 0.333 0.562 0.765 -11.532 0.761 8 C_DG28:DC13_B C 28 ? B 13 ? 19 1 1 C DA 9 1_555 B DT 2 1_555 0.793 0.275 0.728 -12.056 -12.957 -0.744 9 C_DA29:DT12_B C 29 ? B 12 ? ? ? 1 C DG 10 1_555 B DC 1 1_555 0.303 -0.308 0.195 13.765 -13.654 -0.312 10 C_DG30:DC11_B C 30 ? B 11 ? 19 1 1 C DT 1 1_555 D DA 10 1_555 -0.202 -0.305 0.190 -9.038 -13.783 -4.085 11 C_DT21:DA40_D C 21 ? D 40 ? 20 1 1 C DC 2 1_555 D DG 9 1_555 -0.108 -0.087 0.357 6.112 -16.202 3.594 12 C_DC22:DG39_D C 22 ? D 39 ? 19 1 1 C DG 3 1_555 D DC 8 1_555 -0.331 -0.431 -0.655 3.781 2.966 0.303 13 C_DG23:DC38_D C 23 ? D 38 ? 19 1 1 C DG 4 1_555 D DC 7 1_555 1.345 0.348 0.789 6.893 -24.213 -3.383 14 C_DG24:DC37_D C 24 ? D 37 ? ? ? 1 C DC 5 1_555 D DG 6 1_555 -0.439 0.312 0.099 3.826 -23.181 -1.101 15 C_DC25:DG36_D C 25 ? D 36 ? 19 1 1 C DC 6 1_555 D DG 5 1_555 -0.431 -0.267 0.792 -14.152 10.083 -7.278 16 C_DC26:DG35_D C 26 ? D 35 ? 19 1 1 A DC 7 1_555 D DG 4 1_555 -1.096 0.346 0.457 -3.318 -28.872 11.199 17 A_DC7:DG34_D A 7 ? D 34 ? ? 1 1 A DC 8 1_555 D DG 3 1_555 -0.094 -0.051 0.483 -7.712 2.654 -0.373 18 A_DC8:DG33_D A 8 ? D 33 ? 19 1 1 A DT 9 1_555 D DA 2 1_555 -1.465 -0.110 -0.712 -9.528 -33.166 8.333 19 A_DT9:DA32_D A 9 ? D 32 ? 20 1 1 A DA 10 1_555 D DT 1 1_555 0.161 0.095 -0.077 -4.121 -14.701 13.905 20 A_DA10:DT31_D A 10 ? D 31 ? ? 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 DC 1 1_555 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.442 2.386 3.281 -5.071 6.920 34.633 2.829 -1.506 3.579 11.408 8.360 35.648 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.093 2.367 3.673 -1.592 -9.876 42.952 4.128 -0.281 3.077 -13.274 2.140 44.048 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DA 4 1_555 B DT 7 1_555 -1.487 1.147 3.734 3.968 2.724 43.833 1.238 2.404 3.654 3.636 -5.296 44.084 3 AA_DG3DA4:DT17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DA 4 1_555 B DT 7 1_555 A DG 5 1_555 B DC 6 1_555 0.972 0.389 3.162 0.608 -4.414 35.287 1.257 -1.507 3.107 -7.246 -0.998 35.558 4 AA_DA4DG5:DC16DT17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DG 5 1_555 B DC 6 1_555 A DT 6 1_555 B DA 5 1_555 -0.465 -0.418 3.571 -2.246 7.076 33.717 -1.894 0.406 3.438 12.019 3.814 34.501 5 AA_DG5DT6:DA15DC16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DT 6 1_555 B DA 5 1_555 C DT 7 1_555 B DA 4 1_555 1.000 -0.687 2.743 9.618 -2.666 30.669 -0.813 -0.268 2.962 -4.882 -17.608 32.215 6 AC_DT6DT27:DA14DA15_BB A 6 ? B 15 ? C 27 ? B 14 ? 1 C DT 7 1_555 B DA 4 1_555 C DG 8 1_555 B DC 3 1_555 0.449 2.115 3.611 2.253 -1.428 41.401 3.152 -0.371 3.558 -2.018 -3.183 41.483 7 CC_DT27DG28:DC13DA14_BB C 27 ? B 14 ? C 28 ? B 13 ? 1 C DG 8 1_555 B DC 3 1_555 C DA 9 1_555 B DT 2 1_555 -0.707 1.184 3.845 -6.562 5.360 39.444 0.982 0.123 4.028 7.832 9.588 40.309 8 CC_DG28DA29:DT12DC13_BB C 28 ? B 13 ? C 29 ? B 12 ? 1 C DA 9 1_555 B DT 2 1_555 C DG 10 1_555 B DC 1 1_555 0.082 -0.110 2.980 2.416 -3.346 33.760 0.300 0.212 2.975 -5.735 -4.141 34.004 9 CC_DA29DG30:DC11DT12_BB C 29 ? B 12 ? C 30 ? B 11 ? 1 C DT 1 1_555 D DA 10 1_555 C DC 2 1_555 D DG 9 1_555 0.292 1.687 3.263 3.286 6.346 35.418 1.782 0.015 3.515 10.302 -5.335 36.109 10 CC_DT21DC22:DG39DA40_DD C 21 ? D 40 ? C 22 ? D 39 ? 1 C DC 2 1_555 D DG 9 1_555 C DG 3 1_555 D DC 8 1_555 -0.039 2.724 3.625 0.207 0.177 42.053 3.775 0.079 3.636 0.247 -0.288 42.054 11 CC_DC22DG23:DC38DG39_DD C 22 ? D 39 ? C 23 ? D 38 ? 1 C DG 3 1_555 D DC 8 1_555 C DG 4 1_555 D DC 7 1_555 -0.701 1.318 3.510 -7.787 -1.745 38.550 2.183 0.038 3.519 -2.609 11.643 39.337 12 CC_DG23DG24:DC37DC38_DD C 23 ? D 38 ? C 24 ? D 37 ? 1 C DG 4 1_555 D DC 7 1_555 C DC 5 1_555 D DG 6 1_555 0.127 0.254 3.026 4.934 -5.843 34.141 1.237 0.476 2.933 -9.801 -8.275 34.962 13 CC_DG24DC25:DG36DC37_DD C 24 ? D 37 ? C 25 ? D 36 ? 1 C DC 5 1_555 D DG 6 1_555 C DC 6 1_555 D DG 5 1_555 0.365 0.429 3.715 -2.963 6.675 40.094 -0.227 -0.900 3.701 9.639 4.279 40.727 14 CC_DC25DC26:DG35DG36_DD C 25 ? D 36 ? C 26 ? D 35 ? 1 C DC 6 1_555 D DG 5 1_555 A DC 7 1_555 D DG 4 1_555 1.187 -0.584 2.798 8.398 5.326 26.228 -2.334 -0.674 2.863 11.236 -17.718 28.019 15 CA_DC26DC7:DG34DG35_DD C 26 ? D 35 ? A 7 ? D 34 ? 1 A DC 7 1_555 D DG 4 1_555 A DC 8 1_555 D DG 3 1_555 -0.221 1.794 3.793 0.256 -5.195 46.154 2.771 0.305 3.580 -6.601 -0.325 46.431 16 AA_DC7DC8:DG33DG34_DD A 7 ? D 34 ? A 8 ? D 33 ? 1 A DC 8 1_555 D DG 3 1_555 A DT 9 1_555 D DA 2 1_555 0.057 1.350 3.243 9.794 10.146 29.914 0.544 1.667 3.369 18.423 -17.782 33.003 17 AA_DC8DT9:DA32DG33_DD A 8 ? D 33 ? A 9 ? D 32 ? 1 A DT 9 1_555 D DA 2 1_555 A DA 10 1_555 D DT 1 1_555 0.150 1.726 3.362 -13.159 10.444 44.610 1.230 -1.336 3.488 13.216 16.652 47.517 18 AA_DT9DA10:DT31DA32_DD A 9 ? D 32 ? A 10 ? D 31 ? # _atom_sites.entry_id 3IGT _atom_sites.fract_transf_matrix[1][1] 0.044755 _atom_sites.fract_transf_matrix[1][2] 0.015424 _atom_sites.fract_transf_matrix[1][3] 0.005986 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.030611 _atom_sites.fract_transf_matrix[2][3] 0.011833 _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] 0.028490 _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 # loop_ #