data_1P4Y # _entry.id 1P4Y # _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 1P4Y pdb_00001p4y 10.2210/pdb1p4y/pdb NDB UD0028 ? ? RCSB RCSB019012 ? ? WWPDB D_1000019012 ? ? # 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 2003-09-02 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 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 4 'Structure model' 'Derived calculations' 6 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 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site 7 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' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 21 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 26 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 28 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 32 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 33 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 34 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 35 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1P4Y _pdbx_database_status.recvd_initial_deposition_date 2003-04-24 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1P4Z 'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' unspecified PDB 1P54 'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hays, F.A.' 1 'Vargason, J.M.' 2 'Ho, P.S.' 3 # _citation.id primary _citation.title 'Effect of Sequence on the Conformation of DNA Holliday Junctions' _citation.journal_abbrev Biochemistry _citation.journal_volume 42 _citation.page_first 9586 _citation.page_last 9597 _citation.year 2003 _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 12911300 _citation.pdbx_database_id_DOI 10.1021/bi0346603 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hays, F.A.' 1 ? primary 'Vargason, J.M.' 2 ? primary 'Ho, P.S.' 3 ? # 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*GP*CP*GP*CP*CP*GP*G)-3'" 3046.980 2 ? ? ? ? 2 non-polymer syn 'SODIUM ION' 22.990 4 ? ? ? ? 3 water nat water 18.015 108 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCGGCGCCGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SODIUM ION' NA 3 water 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 DG n 1 5 DC n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DG n 1 10 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details ;DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. ; # 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # 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 C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G 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 DC 7 7 7 DC C A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DC 1 11 11 DC C B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DG 4 14 14 DG G B . n B 1 5 DC 5 15 15 DC C B . n B 1 6 DG 6 16 16 DG G B . n B 1 7 DC 7 17 17 DC C B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DG 10 20 20 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 2 NA 1 21 21 NA N A . D 2 NA 1 36 36 NA N A . E 2 NA 1 49 49 NA N A . F 2 NA 1 55 55 NA N B . G 3 HOH 1 22 22 HOH W A . G 3 HOH 2 24 24 HOH W A . G 3 HOH 3 25 25 HOH W A . G 3 HOH 4 26 26 HOH W A . G 3 HOH 5 27 27 HOH W A . G 3 HOH 6 32 32 HOH W A . G 3 HOH 7 33 33 HOH W A . G 3 HOH 8 34 34 HOH W A . G 3 HOH 9 37 37 HOH W A . G 3 HOH 10 38 38 HOH W A . G 3 HOH 11 39 39 HOH W A . G 3 HOH 12 41 41 HOH W A . G 3 HOH 13 43 43 HOH W A . G 3 HOH 14 46 46 HOH W A . G 3 HOH 15 47 47 HOH W A . G 3 HOH 16 48 48 HOH W A . G 3 HOH 17 51 51 HOH W A . G 3 HOH 18 54 54 HOH W A . G 3 HOH 19 56 56 HOH W A . G 3 HOH 20 58 58 HOH W A . G 3 HOH 21 59 59 HOH W A . G 3 HOH 22 62 62 HOH W A . G 3 HOH 23 67 67 HOH W A . G 3 HOH 24 70 70 HOH W A . G 3 HOH 25 71 71 HOH W A . G 3 HOH 26 72 72 HOH W A . G 3 HOH 27 78 78 HOH W A . G 3 HOH 28 80 80 HOH W A . G 3 HOH 29 81 81 HOH W A . G 3 HOH 30 82 82 HOH W A . G 3 HOH 31 84 84 HOH W A . G 3 HOH 32 85 85 HOH W A . G 3 HOH 33 86 86 HOH W A . G 3 HOH 34 87 87 HOH W A . G 3 HOH 35 88 88 HOH W A . G 3 HOH 36 90 90 HOH W A . G 3 HOH 37 95 95 HOH W A . G 3 HOH 38 97 97 HOH W A . G 3 HOH 39 98 98 HOH W A . G 3 HOH 40 101 101 HOH W A . G 3 HOH 41 103 103 HOH W A . G 3 HOH 42 105 105 HOH W A . G 3 HOH 43 107 107 HOH W A . G 3 HOH 44 109 109 HOH W A . G 3 HOH 45 110 110 HOH W A . G 3 HOH 46 115 115 HOH W A . G 3 HOH 47 116 116 HOH W A . G 3 HOH 48 119 119 HOH W A . G 3 HOH 49 120 120 HOH W A . G 3 HOH 50 121 121 HOH W A . G 3 HOH 51 122 122 HOH W A . G 3 HOH 52 123 123 HOH W A . G 3 HOH 53 125 125 HOH W A . G 3 HOH 54 127 127 HOH W A . G 3 HOH 55 130 130 HOH W A . G 3 HOH 56 131 131 HOH W A . G 3 HOH 57 132 132 HOH W A . H 3 HOH 1 23 23 HOH W B . H 3 HOH 2 28 28 HOH W B . H 3 HOH 3 29 29 HOH W B . H 3 HOH 4 30 30 HOH W B . H 3 HOH 5 31 31 HOH W B . H 3 HOH 6 35 35 HOH W B . H 3 HOH 7 40 40 HOH W B . H 3 HOH 8 42 42 HOH W B . H 3 HOH 9 44 44 HOH W B . H 3 HOH 10 45 45 HOH W B . H 3 HOH 11 50 50 HOH W B . H 3 HOH 12 52 52 HOH W B . H 3 HOH 13 53 53 HOH W B . H 3 HOH 14 57 57 HOH W B . H 3 HOH 15 60 60 HOH W B . H 3 HOH 16 61 61 HOH W B . H 3 HOH 17 63 63 HOH W B . H 3 HOH 18 64 64 HOH W B . H 3 HOH 19 65 65 HOH W B . H 3 HOH 20 66 66 HOH W B . H 3 HOH 21 68 68 HOH W B . H 3 HOH 22 69 69 HOH W B . H 3 HOH 23 73 73 HOH W B . H 3 HOH 24 74 74 HOH W B . H 3 HOH 25 75 75 HOH W B . H 3 HOH 26 76 76 HOH W B . H 3 HOH 27 77 77 HOH W B . H 3 HOH 28 79 79 HOH W B . H 3 HOH 29 83 83 HOH W B . H 3 HOH 30 89 89 HOH W B . H 3 HOH 31 91 91 HOH W B . H 3 HOH 32 92 92 HOH W B . H 3 HOH 33 93 93 HOH W B . H 3 HOH 34 94 94 HOH W B . H 3 HOH 35 96 96 HOH W B . H 3 HOH 36 99 99 HOH W B . H 3 HOH 37 100 100 HOH W B . H 3 HOH 38 102 102 HOH W B . H 3 HOH 39 104 104 HOH W B . H 3 HOH 40 106 106 HOH W B . H 3 HOH 41 108 108 HOH W B . H 3 HOH 42 111 111 HOH W B . H 3 HOH 43 112 112 HOH W B . H 3 HOH 44 113 113 HOH W B . H 3 HOH 45 114 114 HOH W B . H 3 HOH 46 117 117 HOH W B . H 3 HOH 47 118 118 HOH W B . H 3 HOH 48 124 124 HOH W B . H 3 HOH 49 126 126 HOH W B . H 3 HOH 50 128 128 HOH W B . H 3 HOH 51 129 129 HOH W B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 EPMR phasing . ? 3 CNS refinement 1.0 ? 4 # _cell.entry_id 1P4Y _cell.length_a 66.513 _cell.length_b 24.179 _cell.length_c 37.004 _cell.angle_alpha 90.0 _cell.angle_beta 110.010 _cell.angle_gamma 90.0 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 # _symmetry.entry_id 1P4Y _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 5 _symmetry.cell_setting ? # _exptl.entry_id 1P4Y _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.94 _exptl_crystal.density_percent_sol 35.95 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details ;0.5mM DNA, 25mM sodium cacodylate, 7.5mM CaCl2, 0.1mM SPERMINE TETRAHYDROCHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00 ; _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 'sodium cacodylate' ? ? ? 1 2 1 CaCl2 ? ? ? 1 3 1 'SPERMINE TETRAHYDROCHLORIDE' ? ? ? 1 4 1 H2O ? ? ? 1 5 2 'sodium cacodylate' ? ? ? 1 6 2 CaCl2 ? ? ? 1 7 2 'SPERMINE TETRAHYDROCHLORIDE' ? ? ? 1 8 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 103.0 _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 2003-01-24 _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 'NI FILTER' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.542 _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 1.542 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1P4Y _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 22.550 _reflns.d_resolution_high 1.650 _reflns.number_obs 4940 _reflns.number_all ? _reflns.percent_possible_obs 74.0 _reflns.pdbx_Rmerge_I_obs 0.048 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 1.6 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.65 _reflns_shell.d_res_low 1.71 _reflns_shell.percent_possible_all 21.7 _reflns_shell.Rmerge_I_obs 0.279 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.140 _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 1P4Y _refine.ls_number_reflns_obs 4436 _refine.ls_number_reflns_all 4940 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 22.50 _refine.ls_d_res_high 1.70 _refine.ls_percent_reflns_obs 77.1 _refine.ls_R_factor_obs 0.229 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.229 _refine.ls_R_factor_R_free 0.26 _refine.ls_R_factor_R_free_error 0.012 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10 _refine.ls_number_reflns_R_free 490 _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 8.7 _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 ? _refine.pdbx_starting_model UD0008 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _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.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 1P4Y _refine_analyze.Luzzati_coordinate_error_obs 0.21 _refine_analyze.Luzzati_sigma_a_obs 0.03 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.26 _refine_analyze.Luzzati_sigma_a_free 0.10 _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_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 404 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.number_atoms_solvent 108 _refine_hist.number_atoms_total 516 _refine_hist.d_res_high 1.70 _refine_hist.d_res_low 22.50 # 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 0.007 ? ? ? '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 1.2 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 18.5 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.57 ? ? ? '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 1.7 _refine_ls_shell.d_res_low 1.81 _refine_ls_shell.number_reflns_R_work 374 _refine_ls_shell.R_factor_R_work 0.209 _refine_ls_shell.percent_reflns_obs 40.8 _refine_ls_shell.R_factor_R_free 0.285 _refine_ls_shell.R_factor_R_free_error 0.046 _refine_ls_shell.percent_reflns_R_free 9.4 _refine_ls_shell.number_reflns_R_free 39 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 1P4Y _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 1P4Y _struct.title 'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1P4Y _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Holliday Junction, DNA Four-Way 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 1 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 3 ? H N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1P4Y _struct_ref.pdbx_db_accession 1P4Y _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1P4Y A 1 ? 10 ? 1P4Y 1 ? 10 ? 1 10 2 1 1P4Y B 1 ? 10 ? 1P4Y 11 ? 20 ? 11 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 -12.6621821170 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 34.7701763015 # _struct_biol.id 1 _struct_biol.details ;THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHAINS A AND B. THE FULL FOUR STRANDED HOLLIDAY JUNCTION STRUCTURE CAN BE GENERATED BY THE FOLLOWING: matrix= ( -1.00000 -0.00046 -0.00015 ) ( -0.00046 1.00000 0.00072 ) ( 0.00015 0.00072 -1.00000 ) translation= (-12.65734 -0.02663 34.77174) ; _struct_biol.pdbx_parent_biol_id ? # 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 metalc1 metalc ? ? A DC 1 "O5'" ? ? ? 1_555 D NA . NA ? ? A DC 1 A NA 36 1_555 ? ? ? ? ? ? ? 2.475 ? ? metalc2 metalc ? ? A DG 10 N3 ? ? ? 1_555 E NA . NA ? ? A DG 10 A NA 49 1_555 ? ? ? ? ? ? ? 2.945 ? ? metalc3 metalc ? ? C NA . NA ? ? ? 1_555 G HOH . O ? ? A NA 21 A HOH 24 1_555 ? ? ? ? ? ? ? 2.810 ? ? metalc4 metalc ? ? C NA . NA ? ? ? 1_555 G HOH . O ? ? A NA 21 A HOH 25 1_555 ? ? ? ? ? ? ? 2.470 ? ? metalc5 metalc ? ? C NA . NA ? ? ? 1_555 G HOH . O ? ? A NA 21 A HOH 56 1_555 ? ? ? ? ? ? ? 2.716 ? ? metalc6 metalc ? ? C NA . NA ? ? ? 1_555 G HOH . O ? ? A NA 21 A HOH 109 1_555 ? ? ? ? ? ? ? 2.476 ? ? metalc7 metalc ? ? D NA . NA ? ? ? 1_555 G HOH . O ? ? A NA 36 A HOH 82 1_555 ? ? ? ? ? ? ? 2.638 ? ? metalc8 metalc ? ? E NA . NA ? ? ? 1_555 G HOH . O ? ? A NA 49 A HOH 56 1_555 ? ? ? ? ? ? ? 2.560 ? ? metalc9 metalc ? ? B DG 9 "O4'" ? ? ? 1_555 F NA . NA ? ? B DG 19 B NA 55 1_555 ? ? ? ? ? ? ? 2.634 ? ? metalc10 metalc ? ? F NA . NA ? ? ? 1_555 H HOH . O ? ? B NA 55 B HOH 75 1_555 ? ? ? ? ? ? ? 2.806 ? ? 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 DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 "O5'" ? A DC 1 ? A DC 1 ? 1_555 NA ? D NA . ? A NA 36 ? 1_555 O ? G HOH . ? A HOH 82 ? 1_555 121.7 ? 2 N3 ? A DG 10 ? A DG 10 ? 1_555 NA ? E NA . ? A NA 49 ? 1_555 O ? G HOH . ? A HOH 56 ? 1_555 101.5 ? 3 O ? G HOH . ? A HOH 24 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 25 ? 1_555 77.2 ? 4 O ? G HOH . ? A HOH 24 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 56 ? 1_555 83.5 ? 5 O ? G HOH . ? A HOH 25 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 56 ? 1_555 147.8 ? 6 O ? G HOH . ? A HOH 24 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 109 ? 1_555 134.8 ? 7 O ? G HOH . ? A HOH 25 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 109 ? 1_555 143.1 ? 8 O ? G HOH . ? A HOH 56 ? 1_555 NA ? C NA . ? A NA 21 ? 1_555 O ? G HOH . ? A HOH 109 ? 1_555 66.6 ? 9 "O4'" ? B DG 9 ? B DG 19 ? 1_555 NA ? F NA . ? B NA 55 ? 1_555 O ? H HOH . ? B HOH 75 ? 1_555 57.0 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A NA 21 ? 6 'BINDING SITE FOR RESIDUE NA A 21' AC2 Software A NA 36 ? 4 'BINDING SITE FOR RESIDUE NA A 36' AC3 Software A NA 49 ? 3 'BINDING SITE FOR RESIDUE NA A 49' AC4 Software B NA 55 ? 2 'BINDING SITE FOR RESIDUE NA B 55' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 HOH G . ? HOH A 24 . ? 1_555 ? 2 AC1 6 HOH G . ? HOH A 25 . ? 1_555 ? 3 AC1 6 NA E . ? NA A 49 . ? 1_555 ? 4 AC1 6 HOH G . ? HOH A 56 . ? 1_555 ? 5 AC1 6 HOH G . ? HOH A 109 . ? 1_555 ? 6 AC1 6 HOH H . ? HOH B 76 . ? 2_556 ? 7 AC2 4 DC A 1 ? DC A 1 . ? 1_555 ? 8 AC2 4 DC A 2 ? DC A 2 . ? 1_555 ? 9 AC2 4 HOH G . ? HOH A 82 . ? 1_555 ? 10 AC2 4 DG B 4 ? DG B 14 . ? 2_557 ? 11 AC3 3 DG A 10 ? DG A 10 . ? 1_555 ? 12 AC3 3 NA C . ? NA A 21 . ? 1_555 ? 13 AC3 3 HOH G . ? HOH A 56 . ? 1_555 ? 14 AC4 2 DG B 9 ? DG B 19 . ? 1_555 ? 15 AC4 2 HOH H . ? HOH B 75 . ? 1_555 ? # 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 HOH O O N N 72 HOH H1 H N N 73 HOH H2 H N N 74 NA NA NA N N 75 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 # _ndb_struct_conf_na.entry_id 1P4Y _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 0.293 -0.111 -0.028 -4.913 -7.931 0.007 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.116 0.100 -0.281 1.298 -1.726 5.301 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.399 -0.179 0.153 2.223 5.867 -0.414 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DG 4 1_555 B DC 7 1_555 -0.077 -0.140 0.368 -2.849 -25.438 -0.780 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 1 A DC 5 1_555 B DG 6 1_555 -0.436 0.049 0.938 -21.163 6.011 -6.733 5 A_DC5:DG16_B A 5 ? B 16 ? 19 1 1 A DG 6 1_555 B DC 5 1_555 -0.172 -0.138 0.100 -0.618 -11.453 -2.019 6 A_DG6:DC15_B A 6 ? B 15 ? 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 1 1_555 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.397 2.433 3.431 4.588 6.244 37.369 2.842 0.039 3.794 9.619 -7.068 38.136 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 -0.264 2.728 3.402 -3.669 -0.295 34.907 4.570 -0.135 3.389 -0.491 6.096 35.095 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 DG 4 1_555 B DC 7 1_555 -1.195 1.809 3.664 -3.205 0.345 40.411 2.567 1.319 3.759 0.499 4.631 40.534 3 AA_DG3DG4:DC17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DG 4 1_555 B DC 7 1_555 A DC 5 1_555 B DG 6 1_555 0.458 0.520 3.863 -5.310 -1.775 38.393 1.036 -1.447 3.742 -2.682 8.022 38.783 4 AA_DG4DC5:DG16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DC 5 1_555 B DG 6 1_555 A DG 6 1_555 B DC 5 1_555 0.017 0.408 3.035 3.273 4.789 29.483 -0.136 0.598 3.045 9.296 -6.354 30.035 5 AA_DC5DG6:DC15DG16_BB A 5 ? B 16 ? A 6 ? B 15 ? # _pdbx_initial_refinement_model.accession_code 1DCW _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details UD0008 # _atom_sites.entry_id 1P4Y _atom_sites.fract_transf_matrix[1][1] 0.015035 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005475 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.041358 _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] 0.028760 _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 NA O P # loop_