data_1S1L # _entry.id 1S1L # _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 1S1L pdb_00001s1l 10.2210/pdb1s1l/pdb NDB UD0052 ? ? RCSB RCSB021251 ? ? WWPDB D_1000021251 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2004-08-31 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-11 5 'Structure model' 1 4 2024-02-14 6 'Structure model' 1 5 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' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 6 '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' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' struct_conn 6 6 '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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1S1L _pdbx_database_status.recvd_initial_deposition_date 2004-01-06 _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type NDB UD0006 'DNA Holliday Junction' unspecified NDB UD0008 'DNA Holliday Junction' unspecified NDB UD0019 'DNA Holliday Junction' unspecified NDB UD0028 'DNA Holliday Junction' unspecified NDB UD0030 'DNA Holliday Junction' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hays, F.A.' 1 'Jones, Z.J.' 2 'Ho, P.S.' 3 # _citation.id primary _citation.title 'Influence of minor groove substituents on the structure of DNA holliday junctions.' _citation.journal_abbrev Biochemistry _citation.journal_volume 43 _citation.page_first 9813 _citation.page_last 9822 _citation.year 2004 _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 15274635 _citation.pdbx_database_id_DOI 10.1021/bi049461d # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hays, F.A.' 1 ? primary 'Jones, Z.J.' 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*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'" 3045.006 2 ? ? ? ? 2 water nat water 18.015 62 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DC)(DI)(DG)(DT)(DA)(DC)(5CM)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCIGTACCGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _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 DI n 1 4 DG n 1 5 DT n 1 6 DA n 1 7 DC n 1 8 5CM n 1 9 DG n 1 10 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 5CM 'DNA linking' n "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 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 DI 'DNA linking' y "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" ? 'C10 H13 N4 O7 P' 332.207 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 C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DI 3 3 3 DI DI A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 5CM 8 8 8 5CM 5CM 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 1 11 DC C B . n B 1 2 DC 2 2 12 DC C B . n B 1 3 DI 3 3 13 DI DI B . n B 1 4 DG 4 4 14 DG G B . n B 1 5 DT 5 5 15 DT T B . n B 1 6 DA 6 6 16 DA A B . n B 1 7 DC 7 7 17 DC C B . n B 1 8 5CM 8 8 18 5CM 5CM B . n B 1 9 DG 9 9 19 DG G B . n B 1 10 DG 10 10 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 HOH 1 21 21 HOH WAT A . C 2 HOH 2 22 22 HOH WAT A . C 2 HOH 3 23 23 HOH WAT A . C 2 HOH 4 24 24 HOH WAT A . C 2 HOH 5 25 25 HOH WAT A . C 2 HOH 6 28 28 HOH WAT A . C 2 HOH 7 29 29 HOH WAT A . C 2 HOH 8 33 33 HOH WAT A . C 2 HOH 9 34 34 HOH WAT A . C 2 HOH 10 35 35 HOH WAT A . C 2 HOH 11 36 36 HOH WAT A . C 2 HOH 12 37 37 HOH WAT A . C 2 HOH 13 38 38 HOH WAT A . C 2 HOH 14 39 39 HOH WAT A . C 2 HOH 15 41 41 HOH WAT A . C 2 HOH 16 43 43 HOH WAT A . C 2 HOH 17 44 44 HOH WAT A . C 2 HOH 18 45 45 HOH WAT A . C 2 HOH 19 47 47 HOH WAT A . C 2 HOH 20 50 50 HOH WAT A . C 2 HOH 21 54 54 HOH WAT A . C 2 HOH 22 55 55 HOH WAT A . C 2 HOH 23 56 56 HOH WAT A . C 2 HOH 24 58 58 HOH WAT A . C 2 HOH 25 59 59 HOH WAT A . C 2 HOH 26 62 62 HOH WAT A . C 2 HOH 27 64 64 HOH WAT A . C 2 HOH 28 67 67 HOH WAT A . C 2 HOH 29 68 68 HOH WAT A . C 2 HOH 30 70 70 HOH WAT A . C 2 HOH 31 73 73 HOH WAT A . C 2 HOH 32 74 74 HOH WAT A . C 2 HOH 33 76 76 HOH WAT A . C 2 HOH 34 77 77 HOH WAT A . C 2 HOH 35 79 79 HOH WAT A . C 2 HOH 36 80 80 HOH WAT A . C 2 HOH 37 81 81 HOH WAT A . C 2 HOH 38 82 82 HOH WAT A . D 2 HOH 1 26 26 HOH WAT B . D 2 HOH 2 27 27 HOH WAT B . D 2 HOH 3 30 30 HOH WAT B . D 2 HOH 4 31 31 HOH WAT B . D 2 HOH 5 32 32 HOH WAT B . D 2 HOH 6 40 40 HOH WAT B . D 2 HOH 7 42 42 HOH WAT B . D 2 HOH 8 46 46 HOH WAT B . D 2 HOH 9 48 48 HOH WAT B . D 2 HOH 10 49 49 HOH WAT B . D 2 HOH 11 51 51 HOH WAT B . D 2 HOH 12 52 52 HOH WAT B . D 2 HOH 13 53 53 HOH WAT B . D 2 HOH 14 57 57 HOH WAT B . D 2 HOH 15 60 60 HOH WAT B . D 2 HOH 16 61 61 HOH WAT B . D 2 HOH 17 63 63 HOH WAT B . D 2 HOH 18 65 65 HOH WAT B . D 2 HOH 19 66 66 HOH WAT B . D 2 HOH 20 69 69 HOH WAT B . D 2 HOH 21 71 71 HOH WAT B . D 2 HOH 22 72 72 HOH WAT B . D 2 HOH 23 75 75 HOH WAT B . D 2 HOH 24 78 78 HOH WAT B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 SCALEPACK 'data scaling' . ? 2 EPMR phasing . ? 3 # _cell.entry_id 1S1L _cell.length_a 64.923 _cell.length_b 24.869 _cell.length_c 37.095 _cell.angle_alpha 90.00 _cell.angle_beta 109.22 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1S1L _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1S1L _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 42.8 _exptl_crystal.description ? _exptl_crystal.density_Matthews 2.17 _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 ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details '25mM Na Cacodylate, .5mM DNA, 180mM CaCl2, 2.4mM spermine against 20% resevoir MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP' _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 'Na Cacodylate' ? ? ? 1 2 1 '.5mM DNA' ? ? ? 1 3 1 CaCl2 ? ? ? 1 4 1 spermine ? ? ? 1 5 2 MPD ? ? ? 1 6 2 'Na Cacodylate' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 103 _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 2003-11-08 _diffrn_detector.details 'osmic mirrors' # _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 # _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 _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.542 # _reflns.entry_id 1S1L _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 18.2 _reflns.d_resolution_high 2.0 _reflns.number_obs 3492 _reflns.number_all 3492 _reflns.percent_possible_obs 93.4 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 11.2 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.00 _reflns_shell.d_res_low 2.07 _reflns_shell.percent_possible_all 61.8 _reflns_shell.Rmerge_I_obs 0.291 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.4 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1S1L _refine.ls_number_reflns_obs 2852 _refine.ls_number_reflns_all 3492 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 44978.75 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF 44978.75 _refine.ls_d_res_low 18.2 _refine.ls_d_res_high 2.20 _refine.ls_percent_reflns_obs 96.2 _refine.ls_R_factor_obs 0.236 _refine.ls_R_factor_all 0.266 _refine.ls_R_factor_R_work 0.236 _refine.ls_R_factor_R_free 0.258 _refine.ls_R_factor_R_free_error 0.015 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 286 _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 11.2 _refine.aniso_B[1][1] 2.08 _refine.aniso_B[2][2] 2.33 _refine.aniso_B[3][3] -4.41 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] -1.93 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.360393 _refine.solvent_model_param_bsol 50.3728 _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 'ndb id UD0019' _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.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_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 1S1L _refine_analyze.Luzzati_coordinate_error_obs 0.28 _refine_analyze.Luzzati_sigma_a_obs 0.16 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.29 _refine_analyze.Luzzati_sigma_a_free 0.37 _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 0 _refine_hist.number_atoms_solvent 62 _refine_hist.number_atoms_total 466 _refine_hist.d_res_high 2.20 _refine_hist.d_res_low 18.2 # 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 0.003 ? ? ? '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 18.4 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.28 ? ? ? '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 2.20 _refine_ls_shell.d_res_low 2.34 _refine_ls_shell.number_reflns_R_work 391 _refine_ls_shell.R_factor_R_work 0.267 _refine_ls_shell.percent_reflns_obs 88.0 _refine_ls_shell.R_factor_R_free 0.334 _refine_ls_shell.R_factor_R_free_error 0.053 _refine_ls_shell.percent_reflns_R_free 9.3 _refine_ls_shell.number_reflns_R_free 40 _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 ? # 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.PARAM DNA-RNA.TOP 'X-RAY DIFFRACTION' 2 ION.PARAM ION.TOP 'X-RAY DIFFRACTION' 3 WATER_REP.PARAM WATER.TOP 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1S1L _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 1S1L _struct.title 'Influence of Groove Interactions on the Formation of DNA Holliday Junctions' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1S1L _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Holliday Junction, DNA Four-Way Junction, major groove, Inosine, minor groove, 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1S1L _struct_ref.pdbx_db_accession 1S1L _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 1S1L A 1 ? 10 ? 1S1L 1 ? 10 ? 1 10 2 1 1S1L B 1 ? 10 ? 1S1L 1 ? 10 ? 1 10 # _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 # 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_656 -x+1,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 52.7114641330 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 35.0273809579 # _struct_biol.id 1 _struct_biol.details 'Full four stranded Holliday junction structure is generated by a 2-fold symmetry axis.' _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 covale1 covale both ? A DC 7 "O3'" ? ? ? 1_555 A 5CM 8 P ? ? A DC 7 A 5CM 8 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale2 covale both ? A 5CM 8 "O3'" ? ? ? 1_555 A DG 9 P ? ? A 5CM 8 A DG 9 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale3 covale both ? B DC 7 "O3'" ? ? ? 1_555 B 5CM 8 P ? ? B DC 7 B 5CM 8 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? B 5CM 8 "O3'" ? ? ? 1_555 B DG 9 P ? ? B 5CM 8 B DG 9 1_555 ? ? ? ? ? ? ? 1.604 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 7 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog8 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 5 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 5 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 6 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 6 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 B _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 42 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 42 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 2_655 _pdbx_validate_symm_contact.dist 1.47 # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 5CM 8 A 5CM 8 ? DC ? 2 B 5CM 8 B 5CM 8 ? DC ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 49 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_database_remark.id 300 _pdbx_database_remark.text ;BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE FULL BIOLOGICAL UNIT CONSISTS OF A FOUR STRANDED DNA HOLLIDAY JUNCTION. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ; # 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 5CM N1 N N N 1 5CM C2 C N N 2 5CM N3 N N N 3 5CM C4 C N N 4 5CM C5 C N N 5 5CM C5A C N N 6 5CM C6 C N N 7 5CM O2 O N N 8 5CM N4 N N N 9 5CM "C1'" C N R 10 5CM "C2'" C N N 11 5CM "C3'" C N S 12 5CM "C4'" C N R 13 5CM "O4'" O N N 14 5CM "O3'" O N N 15 5CM "C5'" C N N 16 5CM "O5'" O N N 17 5CM P P N N 18 5CM OP1 O N N 19 5CM OP2 O N N 20 5CM OP3 O N N 21 5CM H5A1 H N N 22 5CM H5A2 H N N 23 5CM H5A3 H N N 24 5CM H6 H N N 25 5CM HN41 H N N 26 5CM HN42 H N N 27 5CM "H1'" H N N 28 5CM "H2'" H N N 29 5CM "H2''" H N N 30 5CM "H3'" H N N 31 5CM "H4'" H N N 32 5CM "HO3'" H N N 33 5CM "H5'" H N N 34 5CM "H5''" H N N 35 5CM HOP2 H N N 36 5CM HOP3 H N N 37 DA OP3 O N N 38 DA P P N N 39 DA OP1 O N N 40 DA OP2 O N N 41 DA "O5'" O N N 42 DA "C5'" C N N 43 DA "C4'" C N R 44 DA "O4'" O N N 45 DA "C3'" C N S 46 DA "O3'" O N N 47 DA "C2'" C N N 48 DA "C1'" C N R 49 DA N9 N Y N 50 DA C8 C Y N 51 DA N7 N Y N 52 DA C5 C Y N 53 DA C6 C Y N 54 DA N6 N N N 55 DA N1 N Y N 56 DA C2 C Y N 57 DA N3 N Y N 58 DA C4 C Y N 59 DA HOP3 H N N 60 DA HOP2 H N N 61 DA "H5'" H N N 62 DA "H5''" H N N 63 DA "H4'" H N N 64 DA "H3'" H N N 65 DA "HO3'" H N N 66 DA "H2'" H N N 67 DA "H2''" H N N 68 DA "H1'" H N N 69 DA H8 H N N 70 DA H61 H N N 71 DA H62 H N N 72 DA H2 H N N 73 DC OP3 O N N 74 DC P P N N 75 DC OP1 O N N 76 DC OP2 O N N 77 DC "O5'" O N N 78 DC "C5'" C N N 79 DC "C4'" C N R 80 DC "O4'" O N N 81 DC "C3'" C N S 82 DC "O3'" O N N 83 DC "C2'" C N N 84 DC "C1'" C N R 85 DC N1 N N N 86 DC C2 C N N 87 DC O2 O N N 88 DC N3 N N N 89 DC C4 C N N 90 DC N4 N N N 91 DC C5 C N N 92 DC C6 C N N 93 DC HOP3 H N N 94 DC HOP2 H N N 95 DC "H5'" H N N 96 DC "H5''" H N N 97 DC "H4'" H N N 98 DC "H3'" H N N 99 DC "HO3'" H N N 100 DC "H2'" H N N 101 DC "H2''" H N N 102 DC "H1'" H N N 103 DC H41 H N N 104 DC H42 H N N 105 DC H5 H N N 106 DC H6 H N N 107 DG OP3 O N N 108 DG P P N N 109 DG OP1 O N N 110 DG OP2 O N N 111 DG "O5'" O N N 112 DG "C5'" C N N 113 DG "C4'" C N R 114 DG "O4'" O N N 115 DG "C3'" C N S 116 DG "O3'" O N N 117 DG "C2'" C N N 118 DG "C1'" C N R 119 DG N9 N Y N 120 DG C8 C Y N 121 DG N7 N Y N 122 DG C5 C Y N 123 DG C6 C N N 124 DG O6 O N N 125 DG N1 N N N 126 DG C2 C N N 127 DG N2 N N N 128 DG N3 N N N 129 DG C4 C Y N 130 DG HOP3 H N N 131 DG HOP2 H N N 132 DG "H5'" H N N 133 DG "H5''" H N N 134 DG "H4'" H N N 135 DG "H3'" H N N 136 DG "HO3'" H N N 137 DG "H2'" H N N 138 DG "H2''" H N N 139 DG "H1'" H N N 140 DG H8 H N N 141 DG H1 H N N 142 DG H21 H N N 143 DG H22 H N N 144 DI OP3 O N N 145 DI P P N N 146 DI OP1 O N N 147 DI OP2 O N N 148 DI "O5'" O N N 149 DI "C5'" C N N 150 DI "C4'" C N R 151 DI "O4'" O N N 152 DI "C3'" C N S 153 DI "O3'" O N N 154 DI "C2'" C N N 155 DI "C1'" C N R 156 DI N9 N Y N 157 DI C8 C Y N 158 DI N7 N Y N 159 DI C5 C Y N 160 DI C6 C N N 161 DI O6 O N N 162 DI N1 N N N 163 DI C2 C N N 164 DI N3 N N N 165 DI C4 C Y N 166 DI HOP3 H N N 167 DI HOP2 H N N 168 DI "H5'" H N N 169 DI "H5''" H N N 170 DI "H4'" H N N 171 DI "H3'" H N N 172 DI "HO3'" H N N 173 DI "H2'" H N N 174 DI "H2''" H N N 175 DI "H1'" H N N 176 DI H8 H N N 177 DI H1 H N N 178 DI H2 H N N 179 DT OP3 O N N 180 DT P P N N 181 DT OP1 O N N 182 DT OP2 O N N 183 DT "O5'" O N N 184 DT "C5'" C N N 185 DT "C4'" C N R 186 DT "O4'" O N N 187 DT "C3'" C N S 188 DT "O3'" O N N 189 DT "C2'" C N N 190 DT "C1'" C N R 191 DT N1 N N N 192 DT C2 C N N 193 DT O2 O N N 194 DT N3 N N N 195 DT C4 C N N 196 DT O4 O N N 197 DT C5 C N N 198 DT C7 C N N 199 DT C6 C N N 200 DT HOP3 H N N 201 DT HOP2 H N N 202 DT "H5'" H N N 203 DT "H5''" H N N 204 DT "H4'" H N N 205 DT "H3'" H N N 206 DT "HO3'" H N N 207 DT "H2'" H N N 208 DT "H2''" H N N 209 DT "H1'" H N N 210 DT H3 H N N 211 DT H71 H N N 212 DT H72 H N N 213 DT H73 H N N 214 DT H6 H N N 215 HOH O O N N 216 HOH H1 H N N 217 HOH H2 H N N 218 # 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 5CM N1 C2 sing N N 1 5CM N1 C6 sing N N 2 5CM N1 "C1'" sing N N 3 5CM C2 N3 sing N N 4 5CM C2 O2 doub N N 5 5CM N3 C4 doub N N 6 5CM C4 C5 sing N N 7 5CM C4 N4 sing N N 8 5CM C5 C5A sing N N 9 5CM C5 C6 doub N N 10 5CM C5A H5A1 sing N N 11 5CM C5A H5A2 sing N N 12 5CM C5A H5A3 sing N N 13 5CM C6 H6 sing N N 14 5CM N4 HN41 sing N N 15 5CM N4 HN42 sing N N 16 5CM "C1'" "C2'" sing N N 17 5CM "C1'" "O4'" sing N N 18 5CM "C1'" "H1'" sing N N 19 5CM "C2'" "C3'" sing N N 20 5CM "C2'" "H2'" sing N N 21 5CM "C2'" "H2''" sing N N 22 5CM "C3'" "C4'" sing N N 23 5CM "C3'" "O3'" sing N N 24 5CM "C3'" "H3'" sing N N 25 5CM "C4'" "O4'" sing N N 26 5CM "C4'" "C5'" sing N N 27 5CM "C4'" "H4'" sing N N 28 5CM "O3'" "HO3'" sing N N 29 5CM "C5'" "O5'" sing N N 30 5CM "C5'" "H5'" sing N N 31 5CM "C5'" "H5''" sing N N 32 5CM "O5'" P sing N N 33 5CM P OP1 doub N N 34 5CM P OP2 sing N N 35 5CM P OP3 sing N N 36 5CM OP2 HOP2 sing N N 37 5CM OP3 HOP3 sing N N 38 DA OP3 P sing N N 39 DA OP3 HOP3 sing N N 40 DA P OP1 doub N N 41 DA P OP2 sing N N 42 DA P "O5'" sing N N 43 DA OP2 HOP2 sing N N 44 DA "O5'" "C5'" sing N N 45 DA "C5'" "C4'" sing N N 46 DA "C5'" "H5'" sing N N 47 DA "C5'" "H5''" sing N N 48 DA "C4'" "O4'" sing N N 49 DA "C4'" "C3'" sing N N 50 DA "C4'" "H4'" sing N N 51 DA "O4'" "C1'" sing N N 52 DA "C3'" "O3'" sing N N 53 DA "C3'" "C2'" sing N N 54 DA "C3'" "H3'" sing N N 55 DA "O3'" "HO3'" sing N N 56 DA "C2'" "C1'" sing N N 57 DA "C2'" "H2'" sing N N 58 DA "C2'" "H2''" sing N N 59 DA "C1'" N9 sing N N 60 DA "C1'" "H1'" sing N N 61 DA N9 C8 sing Y N 62 DA N9 C4 sing Y N 63 DA C8 N7 doub Y N 64 DA C8 H8 sing N N 65 DA N7 C5 sing Y N 66 DA C5 C6 sing Y N 67 DA C5 C4 doub Y N 68 DA C6 N6 sing N N 69 DA C6 N1 doub Y N 70 DA N6 H61 sing N N 71 DA N6 H62 sing N N 72 DA N1 C2 sing Y N 73 DA C2 N3 doub Y N 74 DA C2 H2 sing N N 75 DA N3 C4 sing Y N 76 DC OP3 P sing N N 77 DC OP3 HOP3 sing N N 78 DC P OP1 doub N N 79 DC P OP2 sing N N 80 DC P "O5'" sing N N 81 DC OP2 HOP2 sing N N 82 DC "O5'" "C5'" sing N N 83 DC "C5'" "C4'" sing N N 84 DC "C5'" "H5'" sing N N 85 DC "C5'" "H5''" sing N N 86 DC "C4'" "O4'" sing N N 87 DC "C4'" "C3'" sing N N 88 DC "C4'" "H4'" sing N N 89 DC "O4'" "C1'" sing N N 90 DC "C3'" "O3'" sing N N 91 DC "C3'" "C2'" sing N N 92 DC "C3'" "H3'" sing N N 93 DC "O3'" "HO3'" sing N N 94 DC "C2'" "C1'" sing N N 95 DC "C2'" "H2'" sing N N 96 DC "C2'" "H2''" sing N N 97 DC "C1'" N1 sing N N 98 DC "C1'" "H1'" sing N N 99 DC N1 C2 sing N N 100 DC N1 C6 sing N N 101 DC C2 O2 doub N N 102 DC C2 N3 sing N N 103 DC N3 C4 doub N N 104 DC C4 N4 sing N N 105 DC C4 C5 sing N N 106 DC N4 H41 sing N N 107 DC N4 H42 sing N N 108 DC C5 C6 doub N N 109 DC C5 H5 sing N N 110 DC C6 H6 sing N N 111 DG OP3 P sing N N 112 DG OP3 HOP3 sing N N 113 DG P OP1 doub N N 114 DG P OP2 sing N N 115 DG P "O5'" sing N N 116 DG OP2 HOP2 sing N N 117 DG "O5'" "C5'" sing N N 118 DG "C5'" "C4'" sing N N 119 DG "C5'" "H5'" sing N N 120 DG "C5'" "H5''" sing N N 121 DG "C4'" "O4'" sing N N 122 DG "C4'" "C3'" sing N N 123 DG "C4'" "H4'" sing N N 124 DG "O4'" "C1'" sing N N 125 DG "C3'" "O3'" sing N N 126 DG "C3'" "C2'" sing N N 127 DG "C3'" "H3'" sing N N 128 DG "O3'" "HO3'" sing N N 129 DG "C2'" "C1'" sing N N 130 DG "C2'" "H2'" sing N N 131 DG "C2'" "H2''" sing N N 132 DG "C1'" N9 sing N N 133 DG "C1'" "H1'" sing N N 134 DG N9 C8 sing Y N 135 DG N9 C4 sing Y N 136 DG C8 N7 doub Y N 137 DG C8 H8 sing N N 138 DG N7 C5 sing Y N 139 DG C5 C6 sing N N 140 DG C5 C4 doub Y N 141 DG C6 O6 doub N N 142 DG C6 N1 sing N N 143 DG N1 C2 sing N N 144 DG N1 H1 sing N N 145 DG C2 N2 sing N N 146 DG C2 N3 doub N N 147 DG N2 H21 sing N N 148 DG N2 H22 sing N N 149 DG N3 C4 sing N N 150 DI OP3 P sing N N 151 DI OP3 HOP3 sing N N 152 DI P OP1 doub N N 153 DI P OP2 sing N N 154 DI P "O5'" sing N N 155 DI OP2 HOP2 sing N N 156 DI "O5'" "C5'" sing N N 157 DI "C5'" "C4'" sing N N 158 DI "C5'" "H5'" sing N N 159 DI "C5'" "H5''" sing N N 160 DI "C4'" "O4'" sing N N 161 DI "C4'" "C3'" sing N N 162 DI "C4'" "H4'" sing N N 163 DI "O4'" "C1'" sing N N 164 DI "C3'" "O3'" sing N N 165 DI "C3'" "C2'" sing N N 166 DI "C3'" "H3'" sing N N 167 DI "O3'" "HO3'" sing N N 168 DI "C2'" "C1'" sing N N 169 DI "C2'" "H2'" sing N N 170 DI "C2'" "H2''" sing N N 171 DI "C1'" N9 sing N N 172 DI "C1'" "H1'" sing N N 173 DI N9 C8 sing Y N 174 DI N9 C4 sing Y N 175 DI C8 N7 doub Y N 176 DI C8 H8 sing N N 177 DI N7 C5 sing Y N 178 DI C5 C6 sing N N 179 DI C5 C4 doub Y N 180 DI C6 O6 doub N N 181 DI C6 N1 sing N N 182 DI N1 C2 sing N N 183 DI N1 H1 sing N N 184 DI C2 N3 doub N N 185 DI C2 H2 sing N N 186 DI N3 C4 sing N N 187 DT OP3 P sing N N 188 DT OP3 HOP3 sing N N 189 DT P OP1 doub N N 190 DT P OP2 sing N N 191 DT P "O5'" sing N N 192 DT OP2 HOP2 sing N N 193 DT "O5'" "C5'" sing N N 194 DT "C5'" "C4'" sing N N 195 DT "C5'" "H5'" sing N N 196 DT "C5'" "H5''" sing N N 197 DT "C4'" "O4'" sing N N 198 DT "C4'" "C3'" sing N N 199 DT "C4'" "H4'" sing N N 200 DT "O4'" "C1'" sing N N 201 DT "C3'" "O3'" sing N N 202 DT "C3'" "C2'" sing N N 203 DT "C3'" "H3'" sing N N 204 DT "O3'" "HO3'" sing N N 205 DT "C2'" "C1'" sing N N 206 DT "C2'" "H2'" sing N N 207 DT "C2'" "H2''" sing N N 208 DT "C1'" N1 sing N N 209 DT "C1'" "H1'" sing N N 210 DT N1 C2 sing N N 211 DT N1 C6 sing N N 212 DT C2 O2 doub N N 213 DT C2 N3 sing N N 214 DT N3 C4 sing N N 215 DT N3 H3 sing N N 216 DT C4 O4 doub N N 217 DT C4 C5 sing N N 218 DT C5 C7 sing N N 219 DT C5 C6 doub N N 220 DT C7 H71 sing N N 221 DT C7 H72 sing N N 222 DT C7 H73 sing N N 223 DT C6 H6 sing N N 224 HOH O H1 sing N N 225 HOH O H2 sing N N 226 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1S1L 'b-form double helix' 1S1L 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 10 1_555 0.616 -0.432 -0.114 2.947 -24.710 1.658 1 A_DC1:DG10_B A 1 ? B 10 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.974 -0.090 0.644 -6.868 -5.580 11.520 2 A_DC2:DG9_B A 2 ? B 9 ? 19 1 1 A DG 4 1_555 B DC 7 1_555 -1.617 -0.356 -0.660 -5.017 -38.558 4.531 3 A_DG4:DC7_B A 4 ? B 7 ? ? 1 1 A DT 5 1_555 B DA 6 1_555 0.025 0.083 0.219 -7.572 -26.722 -7.003 4 A_DT5:DA6_B A 5 ? B 6 ? 20 1 1 A DA 6 1_555 B DT 5 1_555 -0.054 -0.122 0.079 -9.693 -17.070 7.074 5 A_DA6:DT5_B A 6 ? B 5 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.736 2.554 3.895 -1.865 4.206 43.094 2.958 -1.219 4.081 5.706 2.530 43.327 1 AA_DC1DC2:DG9DG10_BB A 1 ? B 10 ? A 2 ? B 9 ? 1 A DG 4 1_555 B DC 7 1_555 A DT 5 1_555 B DA 6 1_555 -0.493 0.451 3.367 -12.660 3.124 40.938 0.287 -0.660 3.392 4.336 17.572 42.879 2 AA_DG4DT5:DA6DC7_BB A 4 ? B 7 ? A 5 ? B 6 ? 1 A DT 5 1_555 B DA 6 1_555 A DA 6 1_555 B DT 5 1_555 1.321 1.115 3.404 6.372 3.415 42.057 1.160 -1.122 3.633 4.716 -8.801 42.646 3 AA_DT5DA6:DT5DA6_BB A 5 ? B 6 ? A 6 ? B 5 ? # _pdbx_initial_refinement_model.accession_code 1L6B _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 'ndb id UD0019' # _atom_sites.entry_id 1S1L _atom_sites.fract_transf_matrix[1][1] 0.015403 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005370 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.040211 _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] 0.028549 _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_