data_5DSA # _entry.id 5DSA # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 5DSA pdb_00005dsa 10.2210/pdb5dsa/pdb WWPDB D_1000213699 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5DSA _pdbx_database_status.recvd_initial_deposition_date 2015-09-17 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Vander Zanden, C.M.' 1 'Ho, P.S.' 2 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Biochemistry _citation.journal_id_ASTM BICHAW _citation.journal_id_CSD 0033 _citation.journal_id_ISSN 1520-4995 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 55 _citation.language ? _citation.page_first 5781 _citation.page_last 5789 _citation.title 'Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions.' _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.biochem.6b00801 _citation.pdbx_database_id_PubMed 27653243 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Vander Zanden, C.M.' 1 ? primary 'Rowe, R.K.' 2 ? primary 'Broad, A.J.' 3 ? primary 'Robertson, A.B.' 4 ? primary 'Ho, P.S.' 5 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 111.980 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 5DSA _cell.details ? _cell.formula_units_Z ? _cell.length_a 65.968 _cell.length_a_esd ? _cell.length_b 24.542 _cell.length_b_esd ? _cell.length_c 37.992 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DSA _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # 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*5CMP*CP*GP*G)-3'" 3061.008 2 ? ? ? ? 2 non-polymer syn 'CALCIUM ION' 40.078 2 ? ? ? ? 3 water nat water 18.015 87 ? ? ? ? # _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)(DG)(DG)(DC)(DG)(5CM)(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_ _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 5CM 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 10 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details synthetic # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5DSA _struct_ref.pdbx_db_accession 5DSA _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # 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 5DSA A 1 ? 10 ? 5DSA 1 ? 10 ? 1 10 2 1 5DSA B 1 ? 10 ? 5DSA 11 ? 20 ? 11 20 # 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 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 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 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5DSA _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.33 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 47.19 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 292 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.78 mM DNA, 1.0 mM Spermine, 3.5 mM CaCl2, 25 mM sodium cacodylate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 200K' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-10-08 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Rigaku collimator' _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source 'ROTATING ANODE' _diffrn_source.target ? _diffrn_source.type 'RIGAKU MICROMAX-003' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.54 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_synchrotron_site ? # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5DSA _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.680 _reflns.d_resolution_low 50.000 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 6159 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 91.800 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.000 _reflns.pdbx_Rmerge_I_obs 0.068 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 51.000 _reflns.pdbx_netI_over_sigmaI 20.700 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 3.208 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.072 _reflns.pdbx_Rpim_I_all 0.023 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 36747 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 1.680 1.710 ? ? ? ? ? 72 ? 23.200 ? ? ? ? 0.245 ? ? ? ? ? ? ? ? 2.100 ? 1.342 ? ? 0.302 0.173 0 1 1 0.952 ? 1.710 1.740 ? ? ? ? ? 273 ? 79.600 ? ? ? ? 0.205 ? ? ? ? ? ? ? ? 2.300 ? 2.378 ? ? 0.253 0.145 0 2 1 0.975 ? 1.740 1.770 ? ? ? ? ? 285 ? 85.300 ? ? ? ? 0.181 ? ? ? ? ? ? ? ? 2.600 ? 2.051 ? ? 0.219 0.121 0 3 1 0.988 ? 1.770 1.810 ? ? ? ? ? 271 ? 86.900 ? ? ? ? 0.227 ? ? ? ? ? ? ? ? 3.000 ? 1.831 ? ? 0.270 0.143 0 4 1 0.955 ? 1.810 1.850 ? ? ? ? ? 301 ? 88.800 ? ? ? ? 0.250 ? ? ? ? ? ? ? ? 3.100 ? 1.741 ? ? 0.298 0.159 0 5 1 0.956 ? 1.850 1.890 ? ? ? ? ? 315 ? 90.800 ? ? ? ? 0.287 ? ? ? ? ? ? ? ? 3.200 ? 1.945 ? ? 0.340 0.178 0 6 1 0.948 ? 1.890 1.940 ? ? ? ? ? 295 ? 91.900 ? ? ? ? 0.194 ? ? ? ? ? ? ? ? 3.300 ? 3.225 ? ? 0.227 0.116 0 7 1 0.953 ? 1.940 1.990 ? ? ? ? ? 312 ? 94.300 ? ? ? ? 0.200 ? ? ? ? ? ? ? ? 3.400 ? 2.025 ? ? 0.235 0.121 0 8 1 0.967 ? 1.990 2.050 ? ? ? ? ? 324 ? 95.000 ? ? ? ? 0.143 ? ? ? ? ? ? ? ? 3.500 ? 1.834 ? ? 0.167 0.085 0 9 1 0.976 ? 2.050 2.120 ? ? ? ? ? 312 ? 96.300 ? ? ? ? 0.121 ? ? ? ? ? ? ? ? 3.600 ? 1.620 ? ? 0.142 0.072 0 10 1 0.984 ? 2.120 2.190 ? ? ? ? ? 330 ? 97.900 ? ? ? ? 0.111 ? ? ? ? ? ? ? ? 3.800 ? 1.793 ? ? 0.128 0.062 0 11 1 0.988 ? 2.190 2.280 ? ? ? ? ? 333 ? 99.700 ? ? ? ? 0.158 ? ? ? ? ? ? ? ? 4.200 ? 5.010 ? ? 0.177 0.077 0 12 1 0.982 ? 2.280 2.380 ? ? ? ? ? 335 ? 100.000 ? ? ? ? 0.165 ? ? ? ? ? ? ? ? 6.400 ? 3.160 ? ? 0.179 0.068 0 13 1 0.993 ? 2.380 2.510 ? ? ? ? ? 342 ? 100.000 ? ? ? ? 0.150 ? ? ? ? ? ? ? ? 7.700 ? 3.018 ? ? 0.160 0.055 0 14 1 0.994 ? 2.510 2.670 ? ? ? ? ? 329 ? 100.000 ? ? ? ? 0.120 ? ? ? ? ? ? ? ? 8.500 ? 2.836 ? ? 0.127 0.042 0 15 1 0.995 ? 2.670 2.870 ? ? ? ? ? 339 ? 100.000 ? ? ? ? 0.098 ? ? ? ? ? ? ? ? 9.200 ? 2.810 ? ? 0.103 0.033 0 16 1 0.998 ? 2.870 3.160 ? ? ? ? ? 341 ? 100.000 ? ? ? ? 0.065 ? ? ? ? ? ? ? ? 10.200 ? 3.071 ? ? 0.069 0.020 0 17 1 0.999 ? 3.160 3.620 ? ? ? ? ? 337 ? 100.000 ? ? ? ? 0.058 ? ? ? ? ? ? ? ? 11.200 ? 3.785 ? ? 0.060 0.017 0 18 1 0.999 ? 3.620 4.560 ? ? ? ? ? 348 ? 100.000 ? ? ? ? 0.058 ? ? ? ? ? ? ? ? 11.800 ? 4.085 ? ? 0.061 0.017 0 19 1 0.998 ? 4.560 50.000 ? ? ? ? ? 365 ? 99.700 ? ? ? ? 0.060 ? ? ? ? ? ? ? ? 9.500 ? 4.456 ? ? 0.063 0.020 0 20 1 0.999 ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max 47.840 _refine.B_iso_mean 27.3150 _refine.B_iso_min 16.380 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 5DSA _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.6896 _refine.ls_d_res_low 30.5870 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 6116 _refine.ls_number_reflns_R_free 300 _refine.ls_number_reflns_R_work 5816 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 93.8200 _refine.ls_percent_reflns_R_free 4.9100 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2495 _refine.ls_R_factor_R_free 0.2775 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2480 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.340 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 1P4Y _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details 'random selection' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 36.1800 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.2100 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.6896 _refine_hist.d_res_low 30.5870 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 87 _refine_hist.number_atoms_total 495 _refine_hist.pdbx_number_residues_total 20 _refine_hist.pdbx_B_iso_mean_ligand 22.30 _refine_hist.pdbx_B_iso_mean_solvent 31.56 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 406 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.009 ? 454 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.187 ? 698 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.049 ? 76 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.010 ? 20 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 36.914 ? 180 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 1.6896 2.1287 2833 . 133 2700 88.0000 . . . 0.3685 . 0.3067 . . . . . . 2 . . . 'X-RAY DIFFRACTION' 2.1287 30.5915 3283 . 167 3116 99.0000 . . . 0.2575 . 0.2329 . . . . . . 2 . . . # _struct.entry_id 5DSA _struct.title 'Crystal structure of Holliday junctions stabilized by 5-methylcytosine in GCC junction core' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5DSA _struct_keywords.text 'Holliday junction, 5-methylcytosine, DNA' _struct_keywords.pdbx_keywords 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 3 ? F N N 3 ? # 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 DG 6 "O3'" ? ? ? 1_555 A 5CM 7 P ? ? A DG 6 A 5CM 7 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale both ? A 5CM 7 "O3'" ? ? ? 1_555 A DC 8 P ? ? A 5CM 7 A DC 8 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale3 covale both ? B DG 6 "O3'" ? ? ? 1_555 B 5CM 7 P ? ? B DG 16 B 5CM 17 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale4 covale both ? B 5CM 7 "O3'" ? ? ? 1_555 B DC 8 P ? ? B 5CM 17 B DC 18 1_555 ? ? ? ? ? ? ? 1.598 ? ? metalc1 metalc ? ? C CA . CA A ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 210 1_555 ? ? ? ? ? ? ? 2.524 ? ? metalc2 metalc ? ? C CA . CA A ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 221 1_555 ? ? ? ? ? ? ? 2.447 ? ? metalc3 metalc ? ? C CA . CA A ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 237 1_555 ? ? ? ? ? ? ? 2.225 ? ? metalc4 metalc ? ? C CA . CA A ? ? 1_555 F HOH . O ? ? A CA 101 B HOH 131 2_556 ? ? ? ? ? ? ? 2.355 ? ? metalc5 metalc ? ? D CA . CA B ? ? 1_555 E HOH . O ? ? A CA 102 A HOH 208 1_555 ? ? ? ? ? ? ? 2.738 ? ? metalc6 metalc ? ? D CA . CA B ? ? 1_555 E HOH . O ? ? A CA 102 A HOH 210 1_555 ? ? ? ? ? ? ? 2.472 ? ? metalc7 metalc ? ? D CA . CA B ? ? 1_555 E HOH . O ? ? A CA 102 A HOH 244 1_555 ? ? ? ? ? ? ? 2.517 ? ? hydrog1 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A 5CM 7 N3 ? ? ? 1_555 B DG 4 N1 ? ? A 5CM 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A 5CM 7 N4 ? ? ? 1_555 B DG 4 O6 ? ? A 5CM 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A 5CM 7 O2 ? ? ? 1_555 B DG 4 N2 ? ? A 5CM 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # 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 CA 101 ? 5 'binding site for residue CA A 101' AC2 Software A CA 102 ? 4 'binding site for residue CA A 102' AC3 Software B DG 16 ? 13 'binding site for Di-nucleotide DG B 16 and 5CM B 17' AC4 Software B 5CM 17 ? 13 'binding site for Di-nucleotide 5CM B 17 and DC B 18' # 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 5 CA D . ? CA A 102 . ? 1_555 ? 2 AC1 5 HOH E . ? HOH A 210 . ? 1_555 ? 3 AC1 5 HOH E . ? HOH A 221 . ? 1_555 ? 4 AC1 5 HOH E . ? HOH A 237 . ? 1_555 ? 5 AC1 5 HOH F . ? HOH B 131 . ? 2_556 ? 6 AC2 4 CA C . ? CA A 101 . ? 1_555 ? 7 AC2 4 HOH E . ? HOH A 208 . ? 1_555 ? 8 AC2 4 HOH E . ? HOH A 210 . ? 1_555 ? 9 AC2 4 HOH E . ? HOH A 244 . ? 1_555 ? 10 AC3 13 DG A 3 ? DG A 3 . ? 2_556 ? 11 AC3 13 DG A 4 ? DG A 4 . ? 1_555 ? 12 AC3 13 DG A 4 ? DG A 4 . ? 2_556 ? 13 AC3 13 DC A 5 ? DC A 5 . ? 1_555 ? 14 AC3 13 DG A 6 ? DG A 6 . ? 1_555 ? 15 AC3 13 DC B 5 ? DC B 15 . ? 1_555 ? 16 AC3 13 DC B 8 ? DC B 18 . ? 1_555 ? 17 AC3 13 HOH F . ? HOH B 106 . ? 1_555 ? 18 AC3 13 HOH F . ? HOH B 112 . ? 1_555 ? 19 AC3 13 HOH F . ? HOH B 113 . ? 1_555 ? 20 AC3 13 HOH F . ? HOH B 115 . ? 1_555 ? 21 AC3 13 HOH F . ? HOH B 118 . ? 1_555 ? 22 AC3 13 HOH F . ? HOH B 124 . ? 1_555 ? 23 AC4 13 DC A 2 ? DC A 2 . ? 2_556 ? 24 AC4 13 DG A 3 ? DG A 3 . ? 2_556 ? 25 AC4 13 DG A 4 ? DG A 4 . ? 2_556 ? 26 AC4 13 DG B 6 ? DG B 16 . ? 1_555 ? 27 AC4 13 DG B 6 ? DG B 16 . ? 2_556 ? 28 AC4 13 DG B 9 ? DG B 19 . ? 1_555 ? 29 AC4 13 HOH F . ? HOH B 105 . ? 1_555 ? 30 AC4 13 HOH F . ? HOH B 106 . ? 1_555 ? 31 AC4 13 HOH F . ? HOH B 107 . ? 1_555 ? 32 AC4 13 HOH F . ? HOH B 109 . ? 1_555 ? 33 AC4 13 HOH F . ? HOH B 111 . ? 1_555 ? 34 AC4 13 HOH F . ? HOH B 112 . ? 1_555 ? 35 AC4 13 HOH F . ? HOH B 115 . ? 1_555 ? # _atom_sites.entry_id 5DSA _atom_sites.fract_transf_matrix[1][1] 0.015159 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.006118 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.040746 _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] 0.028384 _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 CA N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 5CM 7 7 7 5CM 5CM A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DG 10 10 10 DG DG A . n B 1 1 DC 1 11 11 DC DC B . n B 1 2 DC 2 12 12 DC DC B . n B 1 3 DG 3 13 13 DG DG B . n B 1 4 DG 4 14 14 DG DG B . n B 1 5 DC 5 15 15 DC DC B . n B 1 6 DG 6 16 16 DG DG B . n B 1 7 5CM 7 17 17 5CM 5CM B . n B 1 8 DC 8 18 18 DC DC B . n B 1 9 DG 9 19 19 DG DG B . n B 1 10 DG 10 20 20 DG DG 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 CA 1 101 1 CA CA A . D 2 CA 1 102 2 CA CA A . E 3 HOH 1 201 76 HOH HOH A . E 3 HOH 2 202 74 HOH HOH A . E 3 HOH 3 203 83 HOH HOH A . E 3 HOH 4 204 11 HOH HOH A . E 3 HOH 5 205 49 HOH HOH A . E 3 HOH 6 206 9 HOH HOH A . E 3 HOH 7 207 30 HOH HOH A . E 3 HOH 8 208 3 HOH HOH A . E 3 HOH 9 209 44 HOH HOH A . E 3 HOH 10 210 34 HOH HOH A . E 3 HOH 11 211 77 HOH HOH A . E 3 HOH 12 212 62 HOH HOH A . E 3 HOH 13 213 14 HOH HOH A . E 3 HOH 14 214 45 HOH HOH A . E 3 HOH 15 215 2 HOH HOH A . E 3 HOH 16 216 85 HOH HOH A . E 3 HOH 17 217 61 HOH HOH A . E 3 HOH 18 218 52 HOH HOH A . E 3 HOH 19 219 7 HOH HOH A . E 3 HOH 20 220 4 HOH HOH A . E 3 HOH 21 221 24 HOH HOH A . E 3 HOH 22 222 50 HOH HOH A . E 3 HOH 23 223 47 HOH HOH A . E 3 HOH 24 224 66 HOH HOH A . E 3 HOH 25 225 18 HOH HOH A . E 3 HOH 26 226 56 HOH HOH A . E 3 HOH 27 227 69 HOH HOH A . E 3 HOH 28 228 84 HOH HOH A . E 3 HOH 29 229 63 HOH HOH A . E 3 HOH 30 230 51 HOH HOH A . E 3 HOH 31 231 79 HOH HOH A . E 3 HOH 32 232 36 HOH HOH A . E 3 HOH 33 233 75 HOH HOH A . E 3 HOH 34 234 53 HOH HOH A . E 3 HOH 35 235 43 HOH HOH A . E 3 HOH 36 236 33 HOH HOH A . E 3 HOH 37 237 54 HOH HOH A . E 3 HOH 38 238 42 HOH HOH A . E 3 HOH 39 239 41 HOH HOH A . E 3 HOH 40 240 22 HOH HOH A . E 3 HOH 41 241 72 HOH HOH A . E 3 HOH 42 242 19 HOH HOH A . E 3 HOH 43 243 12 HOH HOH A . E 3 HOH 44 244 31 HOH HOH A . E 3 HOH 45 245 39 HOH HOH A . E 3 HOH 46 246 59 HOH HOH A . F 3 HOH 1 101 87 HOH HOH B . F 3 HOH 2 102 58 HOH HOH B . F 3 HOH 3 103 68 HOH HOH B . F 3 HOH 4 104 23 HOH HOH B . F 3 HOH 5 105 71 HOH HOH B . F 3 HOH 6 106 48 HOH HOH B . F 3 HOH 7 107 38 HOH HOH B . F 3 HOH 8 108 1 HOH HOH B . F 3 HOH 9 109 60 HOH HOH B . F 3 HOH 10 110 8 HOH HOH B . F 3 HOH 11 111 20 HOH HOH B . F 3 HOH 12 112 10 HOH HOH B . F 3 HOH 13 113 13 HOH HOH B . F 3 HOH 14 114 32 HOH HOH B . F 3 HOH 15 115 28 HOH HOH B . F 3 HOH 16 116 6 HOH HOH B . F 3 HOH 17 117 86 HOH HOH B . F 3 HOH 18 118 29 HOH HOH B . F 3 HOH 19 119 81 HOH HOH B . F 3 HOH 20 120 46 HOH HOH B . F 3 HOH 21 121 67 HOH HOH B . F 3 HOH 22 122 26 HOH HOH B . F 3 HOH 23 123 27 HOH HOH B . F 3 HOH 24 124 37 HOH HOH B . F 3 HOH 25 125 17 HOH HOH B . F 3 HOH 26 126 21 HOH HOH B . F 3 HOH 27 127 82 HOH HOH B . F 3 HOH 28 128 25 HOH HOH B . F 3 HOH 29 129 73 HOH HOH B . F 3 HOH 30 130 40 HOH HOH B . F 3 HOH 31 131 64 HOH HOH B . F 3 HOH 32 132 35 HOH HOH B . F 3 HOH 33 133 16 HOH HOH B . F 3 HOH 34 134 80 HOH HOH B . F 3 HOH 35 135 57 HOH HOH B . F 3 HOH 36 136 78 HOH HOH B . F 3 HOH 37 137 65 HOH HOH B . F 3 HOH 38 138 5 HOH HOH B . F 3 HOH 39 139 55 HOH HOH B . F 3 HOH 40 140 15 HOH HOH B . F 3 HOH 41 141 70 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 5530 ? 1 MORE -22 ? 1 'SSA (A^2)' 6220 ? # 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 -14.2197567870 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 35.2305347805 # 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 O ? E HOH . ? A HOH 210 ? 1_555 CA A C CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 221 ? 1_555 72.0 ? 2 O ? E HOH . ? A HOH 210 ? 1_555 CA A C CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 237 ? 1_555 137.0 ? 3 O ? E HOH . ? A HOH 221 ? 1_555 CA A C CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 237 ? 1_555 71.7 ? 4 O ? E HOH . ? A HOH 210 ? 1_555 CA A C CA . ? A CA 101 ? 1_555 O ? F HOH . ? B HOH 131 ? 2_556 106.1 ? 5 O ? E HOH . ? A HOH 221 ? 1_555 CA A C CA . ? A CA 101 ? 1_555 O ? F HOH . ? B HOH 131 ? 2_556 74.7 ? 6 O ? E HOH . ? A HOH 237 ? 1_555 CA A C CA . ? A CA 101 ? 1_555 O ? F HOH . ? B HOH 131 ? 2_556 85.6 ? 7 O ? E HOH . ? A HOH 208 ? 1_555 CA B D CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 210 ? 1_555 73.4 ? 8 O ? E HOH . ? A HOH 208 ? 1_555 CA B D CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 244 ? 1_555 67.3 ? 9 O ? E HOH . ? A HOH 210 ? 1_555 CA B D CA . ? A CA 102 ? 1_555 O ? E HOH . ? A HOH 244 ? 1_555 90.2 ? # 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 2016-09-28 2 'Structure model' 1 1 2016-10-05 3 'Structure model' 1 2 2016-10-19 4 'Structure model' 1 3 2017-02-01 5 'Structure model' 1 4 2017-09-06 6 'Structure model' 1 5 2018-03-07 7 'Structure model' 1 6 2019-12-25 8 'Structure model' 1 7 2023-09-27 # _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' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Database references' 4 5 'Structure model' 'Author supporting evidence' 5 6 'Structure model' 'Data collection' 6 7 'Structure model' 'Author supporting evidence' 7 8 'Structure model' 'Data collection' 8 8 'Structure model' 'Database references' 9 8 'Structure model' 'Derived calculations' 10 8 '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 5 'Structure model' pdbx_audit_support 2 6 'Structure model' diffrn_source 3 7 'Structure model' pdbx_audit_support 4 8 'Structure model' chem_comp_atom 5 8 'Structure model' chem_comp_bond 6 8 'Structure model' database_2 7 8 'Structure model' pdbx_initial_refinement_model 8 8 'Structure model' pdbx_struct_conn_angle 9 8 'Structure model' struct_conn # 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' '_pdbx_audit_support.funding_organization' 2 6 'Structure model' '_diffrn_source.source' 3 7 'Structure model' '_pdbx_audit_support.funding_organization' 4 8 'Structure model' '_database_2.pdbx_DOI' 5 8 'Structure model' '_database_2.pdbx_database_accession' 6 8 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 8 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 8 'Structure model' '_pdbx_struct_conn_angle.value' 9 8 'Structure model' '_struct_conn.pdbx_dist_value' 10 8 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 11 8 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 12 8 'Structure model' '_struct_conn.ptnr1_label_asym_id' 13 8 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 8 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 8 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 8 'Structure model' '_struct_conn.ptnr2_symmetry' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.15 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 5 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O B HOH 119 ? ? O B HOH 127 ? ? 1.81 2 1 O B HOH 129 ? ? O B HOH 136 ? ? 1.92 3 1 O A HOH 207 ? ? O B HOH 118 ? ? 2.05 4 1 O A HOH 214 ? ? O A HOH 235 ? ? 2.07 5 1 OP1 B DC 12 ? ? O B HOH 101 ? ? 2.08 6 1 OP2 A DC 8 ? ? O A HOH 201 ? ? 2.17 7 1 O B HOH 112 ? ? O B HOH 130 ? ? 2.18 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 206 ? ? 1_555 O B HOH 115 ? ? 2_556 2.04 2 1 O A HOH 230 ? ? 1_555 O A HOH 234 ? ? 4_556 2.14 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 DC _pdbx_validate_rmsd_bond.auth_seq_id_1 5 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 DC _pdbx_validate_rmsd_bond.auth_seq_id_2 5 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.382 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.037 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag 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 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 CA CA CA N N 38 DC OP3 O N N 39 DC P P N N 40 DC OP1 O N N 41 DC OP2 O N N 42 DC "O5'" O N N 43 DC "C5'" C N N 44 DC "C4'" C N R 45 DC "O4'" O N N 46 DC "C3'" C N S 47 DC "O3'" O N N 48 DC "C2'" C N N 49 DC "C1'" C N R 50 DC N1 N N N 51 DC C2 C N N 52 DC O2 O N N 53 DC N3 N N N 54 DC C4 C N N 55 DC N4 N N N 56 DC C5 C N N 57 DC C6 C N N 58 DC HOP3 H N N 59 DC HOP2 H N N 60 DC "H5'" H N N 61 DC "H5''" H N N 62 DC "H4'" H N N 63 DC "H3'" H N N 64 DC "HO3'" H N N 65 DC "H2'" H N N 66 DC "H2''" H N N 67 DC "H1'" H N N 68 DC H41 H N N 69 DC H42 H N N 70 DC H5 H N N 71 DC H6 H N N 72 DG OP3 O N N 73 DG P P N N 74 DG OP1 O N N 75 DG OP2 O N N 76 DG "O5'" O N N 77 DG "C5'" C N N 78 DG "C4'" C N R 79 DG "O4'" O N N 80 DG "C3'" C N S 81 DG "O3'" O N N 82 DG "C2'" C N N 83 DG "C1'" C N R 84 DG N9 N Y N 85 DG C8 C Y N 86 DG N7 N Y N 87 DG C5 C Y N 88 DG C6 C N N 89 DG O6 O N N 90 DG N1 N N N 91 DG C2 C N N 92 DG N2 N N N 93 DG N3 N N N 94 DG C4 C Y N 95 DG HOP3 H N N 96 DG HOP2 H N N 97 DG "H5'" H N N 98 DG "H5''" H N N 99 DG "H4'" H N N 100 DG "H3'" H N N 101 DG "HO3'" H N N 102 DG "H2'" H N N 103 DG "H2''" H N N 104 DG "H1'" H N N 105 DG H8 H N N 106 DG H1 H N N 107 DG H21 H N N 108 DG H22 H N N 109 HOH O O N N 110 HOH H1 H N N 111 HOH H2 H N N 112 # 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 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 HOH O H1 sing N N 113 HOH O H2 sing N N 114 # _ndb_struct_conf_na.entry_id 5DSA _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 5 1_555 B DG 6 1_555 0.242 -0.139 0.346 -5.619 -8.353 -2.227 1 A_DC5:DG16_B A 5 ? B 16 ? 19 1 1 A DG 6 1_555 B DC 5 1_555 -0.049 -0.030 0.408 0.141 -14.149 -2.067 2 A_DG6:DC15_B A 6 ? B 15 ? 19 1 1 A 5CM 7 1_555 B DG 4 1_555 0.119 -0.046 0.789 -10.436 -14.650 -1.703 3 A_5CM7:DG14_B A 7 ? B 14 ? 19 1 1 A DC 8 1_555 B DG 3 1_555 0.084 -0.201 0.301 -3.489 -1.031 -2.129 4 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.253 -0.177 0.238 0.466 -4.174 -2.820 5 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DG 10 1_555 B DC 1 1_555 -0.094 -0.330 0.336 5.336 -12.608 -0.870 6 A_DG10:DC11_B A 10 ? 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 5 1_555 B DG 6 1_555 A DG 6 1_555 B DC 5 1_555 -0.482 0.844 3.193 -2.123 2.821 35.427 0.975 0.482 3.271 4.621 3.479 35.597 1 AA_DC5DG6:DC15DG16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DG 6 1_555 B DC 5 1_555 A 5CM 7 1_555 B DG 4 1_555 0.431 -0.083 3.702 -3.703 -3.666 35.283 0.463 -1.310 3.630 -6.008 6.068 35.653 2 AA_DG65CM7:DG14DC15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A 5CM 7 1_555 B DG 4 1_555 A DC 8 1_555 B DG 3 1_555 0.395 1.355 3.404 8.114 2.769 35.885 1.742 0.552 3.499 4.417 -12.943 36.862 3 AA_5CM7DC8:DG13DG14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.053 2.675 3.284 0.769 -2.978 38.091 4.451 0.175 3.073 -4.554 -1.176 38.210 4 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DG 10 1_555 B DC 1 1_555 -0.267 2.183 3.457 -6.027 3.660 40.725 2.666 -0.329 3.633 5.212 8.582 41.305 5 AA_DG9DG10:DC11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 1F31GM113580-01 _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 water HOH # _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.accession_code 1P4Y _pdbx_initial_refinement_model.details ? #