data_1XJY # _entry.id 1XJY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 1XJY pdb_00001xjy 10.2210/pdb1xjy/pdb NDB AD0033 ? ? RCSB RCSB030440 ? ? WWPDB D_1000030440 ? ? # 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 2005-03-15 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-03-13 5 'Structure model' 1 4 2024-04-03 # _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' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 5 'Structure model' 'Refinement description' # 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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 5 'Structure model' pdbx_initial_refinement_model # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1XJY _pdbx_database_status.recvd_initial_deposition_date 2004-09-26 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1XJX _pdbx_database_related.details 'the same nucleic acid at 1.7 angstrom' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kitayner, M.' 1 'Rozenberg, H.' 2 'Rabinovich, D.' 3 'Shakked, Z.' 4 # _citation.id primary _citation.title 'Structures of the DNA-binding site of Runt-domain transcription regulators.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 61 _citation.page_first 236 _citation.page_last 246 _citation.year 2005 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15735333 _citation.pdbx_database_id_DOI 10.1107/S0907444904032378 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kitayner, M.' 1 ? primary 'Rozenberg, H.' 2 ? primary 'Rabinovich, D.' 3 ? primary 'Shakked, Z.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3'" 2722.784 1 ? ? ? ? 2 polymer syn "5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3'" 2740.812 1 ? ? ? ? 3 water nat water 18.015 90 ? ? ? ? # 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 '(DT)(DC)(DT)(DG)(DC)(DG)(DG)(DT)(DC)' TCTGCGGTC A ? 2 polydeoxyribonucleotide no no '(DT)(DG)(DA)(DC)(DC)(DG)(DC)(DA)(DG)' TGACCGCAG B ? # _pdbx_entity_nonpoly.entity_id 3 _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 DT n 1 2 DC n 1 3 DT n 1 4 DG n 1 5 DC n 1 6 DG n 1 7 DG n 1 8 DT n 1 9 DC n 2 1 DT n 2 2 DG n 2 3 DA n 2 4 DC n 2 5 DC n 2 6 DG n 2 7 DC n 2 8 DA n 2 9 DG 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 DT 1 1 1 DT T A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n B 2 1 DT 1 10 10 DT T B . n B 2 2 DG 2 11 11 DG G B . n B 2 3 DA 3 12 12 DA A B . n B 2 4 DC 4 13 13 DC C B . n B 2 5 DC 5 14 14 DC C B . n B 2 6 DG 6 15 15 DG G B . n B 2 7 DC 7 16 16 DC C B . n B 2 8 DA 8 17 17 DA A B . n B 2 9 DG 9 18 18 DG G B . 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 C 3 HOH 1 20 20 HOH HOH A . C 3 HOH 2 21 21 HOH HOH A . C 3 HOH 3 23 23 HOH HOH A . C 3 HOH 4 25 25 HOH HOH A . C 3 HOH 5 27 27 HOH HOH A . C 3 HOH 6 28 28 HOH HOH A . C 3 HOH 7 29 29 HOH HOH A . C 3 HOH 8 32 32 HOH HOH A . C 3 HOH 9 33 33 HOH HOH A . C 3 HOH 10 37 37 HOH HOH A . C 3 HOH 11 40 40 HOH HOH A . C 3 HOH 12 42 42 HOH HOH A . C 3 HOH 13 43 43 HOH HOH A . C 3 HOH 14 45 45 HOH HOH A . C 3 HOH 15 46 46 HOH HOH A . C 3 HOH 16 50 50 HOH HOH A . C 3 HOH 17 51 51 HOH HOH A . C 3 HOH 18 55 55 HOH HOH A . C 3 HOH 19 57 57 HOH HOH A . C 3 HOH 20 58 58 HOH HOH A . C 3 HOH 21 61 61 HOH HOH A . C 3 HOH 22 62 62 HOH HOH A . C 3 HOH 23 63 63 HOH HOH A . C 3 HOH 24 66 66 HOH HOH A . C 3 HOH 25 69 69 HOH HOH A . C 3 HOH 26 71 71 HOH HOH A . C 3 HOH 27 72 72 HOH HOH A . C 3 HOH 28 76 76 HOH HOH A . C 3 HOH 29 77 77 HOH HOH A . C 3 HOH 30 82 82 HOH HOH A . C 3 HOH 31 83 83 HOH HOH A . C 3 HOH 32 86 86 HOH HOH A . C 3 HOH 33 88 88 HOH HOH A . C 3 HOH 34 89 89 HOH HOH A . C 3 HOH 35 90 90 HOH HOH A . C 3 HOH 36 91 91 HOH HOH A . C 3 HOH 37 92 92 HOH HOH A . C 3 HOH 38 95 95 HOH HOH A . C 3 HOH 39 96 96 HOH HOH A . C 3 HOH 40 99 99 HOH HOH A . C 3 HOH 41 101 101 HOH HOH A . C 3 HOH 42 102 102 HOH HOH A . C 3 HOH 43 103 103 HOH HOH A . C 3 HOH 44 104 104 HOH HOH A . C 3 HOH 45 106 106 HOH HOH A . D 3 HOH 1 19 19 HOH HOH B . D 3 HOH 2 22 22 HOH HOH B . D 3 HOH 3 24 24 HOH HOH B . D 3 HOH 4 26 26 HOH HOH B . D 3 HOH 5 30 30 HOH HOH B . D 3 HOH 6 31 31 HOH HOH B . D 3 HOH 7 34 34 HOH HOH B . D 3 HOH 8 35 35 HOH HOH B . D 3 HOH 9 36 36 HOH HOH B . D 3 HOH 10 38 38 HOH HOH B . D 3 HOH 11 39 39 HOH HOH B . D 3 HOH 12 41 41 HOH HOH B . D 3 HOH 13 44 44 HOH HOH B . D 3 HOH 14 47 47 HOH HOH B . D 3 HOH 15 48 48 HOH HOH B . D 3 HOH 16 49 49 HOH HOH B . D 3 HOH 17 52 52 HOH HOH B . D 3 HOH 18 53 53 HOH HOH B . D 3 HOH 19 54 54 HOH HOH B . D 3 HOH 20 56 56 HOH HOH B . D 3 HOH 21 59 59 HOH HOH B . D 3 HOH 22 60 60 HOH HOH B . D 3 HOH 23 64 64 HOH HOH B . D 3 HOH 24 65 65 HOH HOH B . D 3 HOH 25 67 67 HOH HOH B . D 3 HOH 26 68 68 HOH HOH B . D 3 HOH 27 70 70 HOH HOH B . D 3 HOH 28 73 73 HOH HOH B . D 3 HOH 29 74 74 HOH HOH B . D 3 HOH 30 75 75 HOH HOH B . D 3 HOH 31 78 78 HOH HOH B . D 3 HOH 32 79 79 HOH HOH B . D 3 HOH 33 80 80 HOH HOH B . D 3 HOH 34 81 81 HOH HOH B . D 3 HOH 35 84 84 HOH HOH B . D 3 HOH 36 85 85 HOH HOH B . D 3 HOH 37 87 87 HOH HOH B . D 3 HOH 38 93 93 HOH HOH B . D 3 HOH 39 94 94 HOH HOH B . D 3 HOH 40 97 97 HOH HOH B . D 3 HOH 41 98 98 HOH HOH B . D 3 HOH 42 100 100 HOH HOH B . D 3 HOH 43 105 105 HOH HOH B . D 3 HOH 44 107 107 HOH HOH B . D 3 HOH 45 108 108 HOH HOH B . # 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 DT 1 ? "O5'" ? A DT 1 "O5'" 2 1 Y 1 A DT 1 ? "C5'" ? A DT 1 "C5'" 3 1 Y 1 A DT 1 ? "C4'" ? A DT 1 "C4'" 4 1 Y 1 A DT 1 ? "O4'" ? A DT 1 "O4'" 5 1 Y 1 A DT 1 ? "C3'" ? A DT 1 "C3'" 6 1 Y 1 A DT 1 ? "C2'" ? A DT 1 "C2'" 7 1 Y 1 A DT 1 ? "C1'" ? A DT 1 "C1'" 8 1 Y 1 A DT 1 ? N1 ? A DT 1 N1 9 1 Y 1 A DT 1 ? C2 ? A DT 1 C2 10 1 Y 1 A DT 1 ? O2 ? A DT 1 O2 11 1 Y 1 A DT 1 ? N3 ? A DT 1 N3 12 1 Y 1 A DT 1 ? C4 ? A DT 1 C4 13 1 Y 1 A DT 1 ? O4 ? A DT 1 O4 14 1 Y 1 A DT 1 ? C5 ? A DT 1 C5 15 1 Y 1 A DT 1 ? C7 ? A DT 1 C7 16 1 Y 1 A DT 1 ? C6 ? A DT 1 C6 17 1 Y 1 B DT 10 ? "O5'" ? B DT 1 "O5'" 18 1 Y 1 B DT 10 ? "C5'" ? B DT 1 "C5'" 19 1 Y 1 B DT 10 ? "C4'" ? B DT 1 "C4'" 20 1 Y 1 B DT 10 ? "O4'" ? B DT 1 "O4'" 21 1 Y 1 B DT 10 ? "C3'" ? B DT 1 "C3'" 22 1 Y 1 B DT 10 ? "C2'" ? B DT 1 "C2'" 23 1 Y 1 B DT 10 ? "C1'" ? B DT 1 "C1'" 24 1 Y 1 B DT 10 ? N1 ? B DT 1 N1 25 1 Y 1 B DT 10 ? C2 ? B DT 1 C2 26 1 Y 1 B DT 10 ? O2 ? B DT 1 O2 27 1 Y 1 B DT 10 ? N3 ? B DT 1 N3 28 1 Y 1 B DT 10 ? C4 ? B DT 1 C4 29 1 Y 1 B DT 10 ? O4 ? B DT 1 O4 30 1 Y 1 B DT 10 ? C5 ? B DT 1 C5 31 1 Y 1 B DT 10 ? C7 ? B DT 1 C7 32 1 Y 1 B DT 10 ? C6 ? B DT 1 C6 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 ULTIMA 'model building' . ? 3 SHELXL-97 refinement . ? 4 ULTIMA phasing . ? 5 # _cell.entry_id 1XJY _cell.length_a 42.295 _cell.length_b 42.295 _cell.length_c 24.333 _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 1XJY _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1XJY _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.99 _exptl_crystal.density_percent_sol 38.24 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _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 'pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _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 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV++' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details 'OSMIC CONFOCAL MIRROR' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.54 1.0 2 1.5418 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RUH3R' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.54 _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 1XJY _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 19.0 _reflns.d_resolution_high 2.0 _reflns.number_obs 2975 _reflns.number_all ? _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.042 _reflns.pdbx_netI_over_sigmaI 52.4 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.1 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.00 _reflns_shell.d_res_low 2.03 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.261 _reflns_shell.meanI_over_sigI_obs 8.9 _reflns_shell.pdbx_redundancy 6.6 _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1XJY _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 2931 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 15.00 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 97.2 _refine.ls_R_factor_obs 0.1418 _refine.ls_R_factor_all 0.1418 _refine.ls_R_factor_R_work 0.1407 _refine.ls_R_factor_R_free 0.1884 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 146 _refine.ls_number_parameters 1696 _refine.ls_number_restraints 5755 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _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 ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _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 'ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56' _refine.pdbx_starting_model 'FIBER A-DNA' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ;L.CLOWNEY ET AL.,J.AM.CHEM.SOC.118(1996)509-518, A.GELBIN ET AL.,J.AM.CHEM.SOC.118(1996)519-529, G.PARKINSON ET AL.,ACTA CRYST.D52(1996)57-64 ; _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.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.B_iso_min ? _refine.B_iso_max ? _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 1XJY _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 0.00 _refine_analyze.occupancy_sum_non_hydrogen 420.00 _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 330 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 90 _refine_hist.number_atoms_total 420 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 15.00 # 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 s_bond_d 0.007 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.024 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.021 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.0005 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.006 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.007 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.112 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.000 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1XJY _pdbx_refine.R_factor_all_no_cutoff 0.1418 _pdbx_refine.R_factor_obs_no_cutoff 0.1407 _pdbx_refine.free_R_factor_no_cutoff 0.1884 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5.0 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 146 _pdbx_refine.R_factor_all_4sig_cutoff 0.1383 _pdbx_refine.R_factor_obs_4sig_cutoff 0.1372 _pdbx_refine.free_R_factor_4sig_cutoff 0.1833 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 4.8 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 133 _pdbx_refine.number_reflns_obs_4sig_cutoff 2758 _pdbx_refine.number_reflns_obs_no_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 1XJY _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 1XJY _struct.title 'The crystal structures of the DNA binding sites of the RUNX1 transcription factor' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1XJY _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'A-DNA, DOUBLE HELIX, OVERHANGING BASES, RUNX1, 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 3 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1XJY 1XJY ? ? ? 2 2 PDB 1XJY 1XJY ? ? ? # 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 1XJY A 1 ? 9 ? 1XJY 1 ? 9 ? 1 9 2 2 1XJY B 1 ? 9 ? 1XJY 10 ? 18 ? 10 18 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 8 N1 ? ? A DT 3 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 8 N6 ? ? A DT 3 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 4 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 5 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 5 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 5 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 6 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 6 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 6 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 7 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 7 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 7 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 8 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 8 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 9 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 9 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 9 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A DC 2 ? ? "O3'" A DC 2 ? ? P A DT 3 ? ? 127.04 119.70 7.34 1.20 Y 2 1 "C3'" A DT 3 ? ? "O3'" A DT 3 ? ? P A DG 4 ? ? 127.53 119.70 7.83 1.20 Y 3 1 N1 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 113.31 118.90 -5.59 0.60 N 4 1 N3 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 126.49 121.90 4.59 0.70 N 5 1 C6 B DC 13 ? ? N1 B DC 13 ? ? C2 B DC 13 ? ? 124.04 120.30 3.74 0.40 N 6 1 N3 B DC 13 ? ? C2 B DC 13 ? ? O2 B DC 13 ? ? 127.12 121.90 5.22 0.70 N 7 1 C2 B DC 13 ? ? N1 B DC 13 ? ? "C1'" B DC 13 ? ? 112.02 118.80 -6.78 1.10 N 8 1 "C3'" B DC 13 ? ? "O3'" B DC 13 ? ? P B DC 14 ? ? 134.19 119.70 14.49 1.20 Y 9 1 "O4'" B DG 15 ? ? "C1'" B DG 15 ? ? N9 B DG 15 ? ? 110.14 108.30 1.84 0.30 N 10 1 C6 B DC 16 ? ? N1 B DC 16 ? ? C2 B DC 16 ? ? 122.73 120.30 2.43 0.40 N 11 1 N1 B DG 18 ? ? C6 B DG 18 ? ? O6 B DG 18 ? ? 123.91 119.90 4.01 0.60 N # 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 1XJY _ndb_struct_conf_na.feature 'a-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 2 1_555 B DG 9 1_555 -0.505 -0.387 0.077 -13.094 -11.574 -4.761 1 A_DC2:DG18_B A 2 ? B 18 ? 19 1 1 A DT 3 1_555 B DA 8 1_555 -0.530 -0.232 0.388 2.555 -8.620 5.148 2 A_DT3:DA17_B A 3 ? B 17 ? 20 1 1 A DG 4 1_555 B DC 7 1_555 -0.124 -0.408 -0.204 -7.557 -16.261 -3.088 3 A_DG4:DC16_B A 4 ? B 16 ? 19 1 1 A DC 5 1_555 B DG 6 1_555 0.082 -0.106 0.359 -0.581 -6.419 -0.508 4 A_DC5:DG15_B A 5 ? B 15 ? 19 1 1 A DG 6 1_555 B DC 5 1_555 -0.124 -0.379 -0.142 4.201 -4.869 -1.449 5 A_DG6:DC14_B A 6 ? B 14 ? 19 1 1 A DG 7 1_555 B DC 4 1_555 -0.143 -0.290 -0.277 -12.342 -12.712 -0.871 6 A_DG7:DC13_B A 7 ? B 13 ? 19 1 1 A DT 8 1_555 B DA 3 1_555 -0.010 -0.079 -0.015 -2.863 -17.561 5.900 7 A_DT8:DA12_B A 8 ? B 12 ? 20 1 1 A DC 9 1_555 B DG 2 1_555 1.116 -0.621 -0.216 10.997 -10.132 -5.736 8 A_DC9:DG11_B A 9 ? B 11 ? 19 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 2 1_555 B DG 9 1_555 A DT 3 1_555 B DA 8 1_555 1.111 -1.105 3.019 -3.019 6.108 33.253 -2.755 -2.330 2.671 10.536 5.208 33.925 1 AA_DC2DT3:DA17DG18_BB A 2 ? B 18 ? A 3 ? B 17 ? 1 A DT 3 1_555 B DA 8 1_555 A DG 4 1_555 B DC 7 1_555 -0.331 -1.366 3.365 3.859 15.534 34.044 -4.035 0.989 2.482 24.898 -6.184 37.518 2 AA_DT3DG4:DC16DA17_BB A 3 ? B 17 ? A 4 ? B 16 ? 1 A DG 4 1_555 B DC 7 1_555 A DC 5 1_555 B DG 6 1_555 0.306 -1.550 3.066 -4.668 0.569 36.398 -2.534 -1.080 2.981 0.906 7.434 36.690 3 AA_DG4DC5:DG15DC16_BB A 4 ? B 16 ? A 5 ? B 15 ? 1 A DC 5 1_555 B DG 6 1_555 A DG 6 1_555 B DC 5 1_555 -0.215 -2.078 3.153 1.913 4.890 20.584 -7.434 1.287 2.565 13.405 -5.245 21.236 4 AA_DC5DG6:DC14DG15_BB A 5 ? B 15 ? A 6 ? B 14 ? 1 A DG 6 1_555 B DC 5 1_555 A DG 7 1_555 B DC 4 1_555 -0.337 -1.512 3.829 -0.499 5.399 36.549 -3.217 0.456 3.581 8.551 0.791 36.936 5 AA_DG6DG7:DC13DC14_BB A 6 ? B 14 ? A 7 ? B 13 ? 1 A DG 7 1_555 B DC 4 1_555 A DT 8 1_555 B DA 3 1_555 0.203 -1.028 3.002 -2.703 8.273 32.156 -3.007 -0.750 2.638 14.604 4.772 33.283 6 AA_DG7DT8:DA12DC13_BB A 7 ? B 13 ? A 8 ? B 12 ? 1 A DT 8 1_555 B DA 3 1_555 A DC 9 1_555 B DG 2 1_555 -0.674 -1.072 2.897 -1.238 8.677 35.022 -2.779 0.939 2.588 14.147 2.018 36.069 7 AA_DT8DC9:DG11DA12_BB A 8 ? B 12 ? A 9 ? B 11 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type other _pdbx_initial_refinement_model.source_name ? _pdbx_initial_refinement_model.details 'FIBER A-DNA' # _atom_sites.entry_id 1XJY _atom_sites.fract_transf_matrix[1][1] 0.023643 _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] 0.023643 _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] 0.041096 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O P # loop_