data_3EY0 # _entry.id 3EY0 # _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 3EY0 pdb_00003ey0 10.2210/pdb3ey0/pdb NDB DD0102 ? ? RCSB RCSB049908 ? ? WWPDB D_1000049908 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2009-10-27 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-12-27 4 'Structure model' 1 3 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' Advisory 2 2 'Structure model' 'Refinement description' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' 6 3 'Structure model' 'Derived calculations' 7 4 '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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site 7 4 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.value' 10 3 'Structure model' '_struct_conn.pdbx_dist_value' 11 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 12 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 13 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 14 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 15 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 16 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 17 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 18 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 19 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 20 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 21 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 22 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 23 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 24 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 25 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3EY0 _pdbx_database_status.recvd_initial_deposition_date 2008-10-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Pous, J.' 1 'Moreno, T.' 2 'Subirana, J.A.' 3 'Campos, J.L.' 4 # _citation.id primary _citation.title 'Coiled-coil conformation of a pentamidine-DNA complex' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 66 _citation.page_first 251 _citation.page_last 257 _citation.year 2010 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20179336 _citation.pdbx_database_id_DOI 10.1107/S0907444909055693 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Moreno, T.' 1 ? primary 'Pous, J.' 2 ? primary 'Subirana, J.A.' 3 ? primary 'Campos, J.L.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DT)-3'" 3042.041 2 ? ? ? ? 2 non-polymer syn '1,5-BIS(4-AMIDINOPHENOXY)PENTANE' 340.419 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 51 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)' _entity_poly.pdbx_seq_one_letter_code_can ATATATATAT _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '1,5-BIS(4-AMIDINOPHENOXY)PENTANE' PNT 3 'MAGNESIUM ION' MG 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DT n 1 3 DA n 1 4 DT n 1 5 DA n 1 6 DT n 1 7 DA n 1 8 DT n 1 9 DA n 1 10 DT n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Synthesized by using phosphoramiditine method' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 PNT non-polymer . '1,5-BIS(4-AMIDINOPHENOXY)PENTANE' ? 'C19 H24 N4 O2' 340.419 # 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 DA 1 1 1 DA A A . n A 1 2 DT 2 2 2 DT T A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DT 6 6 6 DT T A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DA 9 9 9 DA A A . n A 1 10 DT 10 10 10 DT T A . n B 1 1 DA 1 1 1 DA A B . n B 1 2 DT 2 2 2 DT T B . n B 1 3 DA 3 3 3 DA A B . n B 1 4 DT 4 4 4 DT T B . n B 1 5 DA 5 5 5 DA A B . n B 1 6 DT 6 6 6 DT T B . n B 1 7 DA 7 7 7 DA A B . n B 1 8 DT 8 8 8 DT T B . n B 1 9 DA 9 9 9 DA A B . n B 1 10 DT 10 10 10 DT T 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 PNT 1 11 1 PNT PNT A . D 3 MG 1 11 1 MG MG B . E 4 HOH 1 12 4 HOH HOH A . E 4 HOH 2 13 5 HOH HOH A . E 4 HOH 3 14 9 HOH HOH A . E 4 HOH 4 15 11 HOH HOH A . E 4 HOH 5 16 13 HOH HOH A . E 4 HOH 6 17 15 HOH HOH A . E 4 HOH 7 18 17 HOH HOH A . E 4 HOH 8 19 18 HOH HOH A . E 4 HOH 9 20 19 HOH HOH A . E 4 HOH 10 21 29 HOH HOH A . E 4 HOH 11 22 35 HOH HOH A . E 4 HOH 12 23 41 HOH HOH A . E 4 HOH 13 24 43 HOH HOH A . E 4 HOH 14 25 57 HOH HOH A . E 4 HOH 15 26 58 HOH HOH A . E 4 HOH 16 27 66 HOH HOH A . E 4 HOH 17 28 67 HOH HOH A . E 4 HOH 18 29 68 HOH HOH A . E 4 HOH 19 30 70 HOH HOH A . E 4 HOH 20 32 79 HOH HOH A . E 4 HOH 21 33 80 HOH HOH A . E 4 HOH 22 34 81 HOH HOH A . E 4 HOH 23 35 82 HOH HOH A . E 4 HOH 24 36 83 HOH HOH A . E 4 HOH 25 37 84 HOH HOH A . E 4 HOH 26 38 86 HOH HOH A . E 4 HOH 27 39 87 HOH HOH A . F 4 HOH 1 31 77 HOH HOH B . F 4 HOH 2 32 1 HOH HOH B . F 4 HOH 3 33 2 HOH HOH B . F 4 HOH 4 34 3 HOH HOH B . F 4 HOH 5 35 7 HOH HOH B . F 4 HOH 6 36 12 HOH HOH B . F 4 HOH 7 37 14 HOH HOH B . F 4 HOH 8 38 22 HOH HOH B . F 4 HOH 9 39 25 HOH HOH B . F 4 HOH 10 40 27 HOH HOH B . F 4 HOH 11 41 28 HOH HOH B . F 4 HOH 12 42 30 HOH HOH B . F 4 HOH 13 43 31 HOH HOH B . F 4 HOH 14 44 59 HOH HOH B . F 4 HOH 15 45 60 HOH HOH B . F 4 HOH 16 46 61 HOH HOH B . F 4 HOH 17 47 63 HOH HOH B . F 4 HOH 18 48 64 HOH HOH B . F 4 HOH 19 49 71 HOH HOH B . F 4 HOH 20 50 72 HOH HOH B . F 4 HOH 21 51 73 HOH HOH B . F 4 HOH 22 52 74 HOH HOH B . F 4 HOH 23 53 78 HOH HOH B . F 4 HOH 24 54 88 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 AMoRE phasing . ? 2 REFMAC refinement 5.4.0069 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _cell.entry_id 3EY0 _cell.length_a 27.789 _cell.length_b 27.789 _cell.length_c 311.950 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3EY0 _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3EY0 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.86 _exptl_crystal.density_percent_sol 56.95 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 278.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details '20 mM MgCl2, 50 mM MES, 15% Isopropanol, 3.62 mM ds-DNA, 16.86 mM PNT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278.15K' _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 MgCl2 ? ? ? 1 2 1 MES ? ? ? 1 3 1 Isopropanol ? ? ? 1 4 1 ds-DNA ? ? ? 1 5 1 PNT ? ? ? 1 6 2 MgCl2 ? ? ? 1 7 2 MES ? ? ? 1 8 2 Isopropanol ? ? ? 1 9 2 PNT ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 104 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2008-04-24 _diffrn_detector.details Mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97950 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM16' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM16 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97950 # _reflns.entry_id 3EY0 _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.0 _reflns.d_resolution_high 2.52 _reflns.number_obs 2899 _reflns.number_all 2899 _reflns.percent_possible_obs 94.7 _reflns.pdbx_Rmerge_I_obs 0.098 _reflns.pdbx_Rsym_value 0.098 _reflns.pdbx_netI_over_sigmaI 37.625 _reflns.B_iso_Wilson_estimate 56.01 _reflns.pdbx_redundancy 15.8 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.52 _reflns_shell.d_res_low 2.56 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.212 _reflns_shell.pdbx_Rsym_value 0.212 _reflns_shell.meanI_over_sigI_obs 15.750 _reflns_shell.pdbx_redundancy 18.4 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 128 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3EY0 _refine.ls_number_reflns_obs 2511 _refine.ls_number_reflns_all 2782 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 50.0 _refine.ls_d_res_high 2.52 _refine.ls_percent_reflns_obs 93.62 _refine.ls_R_factor_obs 0.22193 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21572 _refine.ls_R_factor_R_free 0.27715 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.4 _refine.ls_number_reflns_R_free 262 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.936 _refine.correlation_coeff_Fo_to_Fc_free 0.885 _refine.B_iso_mean 43.499 _refine.aniso_B[1][1] 0.22 _refine.aniso_B[2][2] 0.22 _refine.aniso_B[3][3] -0.34 _refine.aniso_B[1][2] 0.11 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'standard watson-crick DNA' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.520 _refine.pdbx_overall_ESU_R_Free 0.323 _refine.overall_SU_ML 0.238 _refine.overall_SU_B 25.145 _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _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 26 _refine_hist.number_atoms_solvent 51 _refine_hist.number_atoms_total 481 _refine_hist.d_res_high 2.52 _refine_hist.d_res_low 50.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.018 0.021 ? 480 'X-RAY DIFFRACTION' ? r_bond_other_d 0.003 0.020 ? 236 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.644 3.000 ? 727 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.224 3.000 ? 571 'X-RAY DIFFRACTION' ? r_chiral_restr 0.052 0.200 ? 78 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 0.020 ? 238 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.002 0.020 ? 58 'X-RAY DIFFRACTION' ? r_scbond_it 1.028 3.000 ? 200 'X-RAY DIFFRACTION' ? r_scangle_it 1.577 4.500 ? 311 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.52 _refine_ls_shell.d_res_low 2.59 _refine_ls_shell.number_reflns_R_work 162 _refine_ls_shell.R_factor_R_work 0.248 _refine_ls_shell.percent_reflns_obs 95.19 _refine_ls_shell.R_factor_R_free 0.411 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 16 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3EY0 _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 3EY0 _struct.title 'A new form of DNA-drug interaction in the minor groove of a coiled coil' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3EY0 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA drug pentamidine coiled-coil all-AT, 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 3 ? E N N 4 ? F N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3EY0 _struct_ref.pdbx_db_accession 3EY0 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code ATATATATAT _struct_ref.pdbx_db_isoform ? # 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 3EY0 A 1 ? 10 ? 3EY0 1 ? 10 ? 1 10 2 1 3EY0 B 1 ? 10 ? 3EY0 1 ? 10 ? 1 10 # _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # 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)' 1070 ? 1 MORE -8.5 ? 1 'SSA (A^2)' 4410 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details 'Double stranded ATATATATAT' # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 27 B MG 11 1_555 ? ? ? ? ? ? ? 2.188 ? ? metalc2 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 28 B MG 11 1_555 ? ? ? ? ? ? ? 2.712 ? ? metalc3 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 29 B MG 11 1_555 ? ? ? ? ? ? ? 2.264 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 11 B HOH 33 1_555 ? ? ? ? ? ? ? 1.910 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 11 B HOH 53 1_555 ? ? ? ? ? ? ? 2.050 ? ? metalc6 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 11 B HOH 54 1_555 ? ? ? ? ? ? ? 2.472 ? ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 10 N3 ? ? A DA 1 B DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 10 O4 ? ? A DA 1 B DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B DA 9 N1 ? ? A DT 2 B DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B DA 9 N6 ? ? A DT 2 B DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 3 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 3 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 5 B DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 5 B DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 6 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 6 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 8 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 8 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 9 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 9 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 1 N7 ? ? A DT 10 B DA 1 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog20 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 10 B DA 1 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? A HOH 27 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? E HOH . ? A HOH 28 ? 1_555 99.7 ? 2 O ? E HOH . ? A HOH 27 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 75.0 ? 3 O ? E HOH . ? A HOH 28 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 74.3 ? 4 O ? E HOH . ? A HOH 27 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 33 ? 1_555 95.0 ? 5 O ? E HOH . ? A HOH 28 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 33 ? 1_555 113.2 ? 6 O ? E HOH . ? A HOH 29 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 33 ? 1_555 168.7 ? 7 O ? E HOH . ? A HOH 27 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 53 ? 1_555 85.1 ? 8 O ? E HOH . ? A HOH 28 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 53 ? 1_555 159.9 ? 9 O ? E HOH . ? A HOH 29 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 53 ? 1_555 88.3 ? 10 O ? F HOH . ? B HOH 33 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 53 ? 1_555 85.6 ? 11 O ? E HOH . ? A HOH 27 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 54 ? 1_555 165.2 ? 12 O ? E HOH . ? A HOH 28 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 54 ? 1_555 95.0 ? 13 O ? E HOH . ? A HOH 29 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 54 ? 1_555 107.2 ? 14 O ? F HOH . ? B HOH 33 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 54 ? 1_555 81.1 ? 15 O ? F HOH . ? B HOH 53 ? 1_555 MG ? D MG . ? B MG 11 ? 1_555 O ? F HOH . ? B HOH 54 ? 1_555 80.4 ? # 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 PNT 11 ? 14 'BINDING SITE FOR RESIDUE PNT A 11' AC2 Software B MG 11 ? 6 'BINDING SITE FOR RESIDUE MG B 11' # 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 14 DA A 5 ? DA A 5 . ? 1_555 ? 2 AC1 14 DT A 6 ? DT A 6 . ? 1_555 ? 3 AC1 14 DA A 7 ? DA A 7 . ? 1_555 ? 4 AC1 14 DT A 8 ? DT A 8 . ? 1_555 ? 5 AC1 14 DA A 9 ? DA A 9 . ? 1_555 ? 6 AC1 14 DT A 10 ? DT A 10 . ? 1_555 ? 7 AC1 14 HOH E . ? HOH A 32 . ? 1_555 ? 8 AC1 14 DA B 5 ? DA B 5 . ? 1_555 ? 9 AC1 14 DT B 6 ? DT B 6 . ? 1_555 ? 10 AC1 14 DA B 7 ? DA B 7 . ? 1_555 ? 11 AC1 14 DT B 8 ? DT B 8 . ? 1_555 ? 12 AC1 14 DT B 10 ? DT B 10 . ? 1_555 ? 13 AC1 14 HOH F . ? HOH B 32 . ? 1_555 ? 14 AC1 14 HOH F . ? HOH B 35 . ? 1_555 ? 15 AC2 6 HOH E . ? HOH A 27 . ? 1_555 ? 16 AC2 6 HOH E . ? HOH A 28 . ? 1_555 ? 17 AC2 6 HOH E . ? HOH A 29 . ? 1_555 ? 18 AC2 6 HOH F . ? HOH B 33 . ? 1_555 ? 19 AC2 6 HOH F . ? HOH B 53 . ? 1_555 ? 20 AC2 6 HOH F . ? HOH B 54 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A DT 4 ? ? "C2'" A DT 4 ? ? "C1'" A DT 4 ? ? 96.89 102.40 -5.51 0.80 N 2 1 "O4'" B DA 1 ? ? "C1'" B DA 1 ? ? N9 B DA 1 ? ? 110.80 108.30 2.50 0.30 N 3 1 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 111.25 108.30 2.95 0.30 N 4 1 "O4'" B DT 10 ? ? "C1'" B DT 10 ? ? N1 B DT 10 ? ? 111.47 108.30 3.17 0.30 N # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 16.2235 _pdbx_refine_tls.origin_y 10.8519 _pdbx_refine_tls.origin_z 90.3531 _pdbx_refine_tls.T[1][1] -0.0827 _pdbx_refine_tls.T[2][2] 0.1452 _pdbx_refine_tls.T[3][3] -0.0839 _pdbx_refine_tls.T[1][2] 0.0185 _pdbx_refine_tls.T[1][3] 0.0070 _pdbx_refine_tls.T[2][3] 0.0225 _pdbx_refine_tls.L[1][1] 5.9764 _pdbx_refine_tls.L[2][2] 1.5319 _pdbx_refine_tls.L[3][3] 3.9536 _pdbx_refine_tls.L[1][2] 0.6693 _pdbx_refine_tls.L[1][3] -3.1111 _pdbx_refine_tls.L[2][3] -0.8875 _pdbx_refine_tls.S[1][1] -0.3623 _pdbx_refine_tls.S[2][2] 0.1994 _pdbx_refine_tls.S[3][3] 0.1629 _pdbx_refine_tls.S[1][2] 0.3347 _pdbx_refine_tls.S[1][3] 0.0450 _pdbx_refine_tls.S[2][3] -0.1417 _pdbx_refine_tls.S[2][1] -0.0277 _pdbx_refine_tls.S[3][1] 0.2706 _pdbx_refine_tls.S[3][2] 0.0280 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 10 _pdbx_refine_tls_group.selection_details ? _pdbx_refine_tls_group.beg_label_asym_id . _pdbx_refine_tls_group.beg_label_seq_id . _pdbx_refine_tls_group.end_label_asym_id . _pdbx_refine_tls_group.end_label_seq_id . _pdbx_refine_tls_group.selection ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DT OP3 O N N 37 DT P P N N 38 DT OP1 O N N 39 DT OP2 O N N 40 DT "O5'" O N N 41 DT "C5'" C N N 42 DT "C4'" C N R 43 DT "O4'" O N N 44 DT "C3'" C N S 45 DT "O3'" O N N 46 DT "C2'" C N N 47 DT "C1'" C N R 48 DT N1 N N N 49 DT C2 C N N 50 DT O2 O N N 51 DT N3 N N N 52 DT C4 C N N 53 DT O4 O N N 54 DT C5 C N N 55 DT C7 C N N 56 DT C6 C N N 57 DT HOP3 H N N 58 DT HOP2 H N N 59 DT "H5'" H N N 60 DT "H5''" H N N 61 DT "H4'" H N N 62 DT "H3'" H N N 63 DT "HO3'" H N N 64 DT "H2'" H N N 65 DT "H2''" H N N 66 DT "H1'" H N N 67 DT H3 H N N 68 DT H71 H N N 69 DT H72 H N N 70 DT H73 H N N 71 DT H6 H N N 72 HOH O O N N 73 HOH H1 H N N 74 HOH H2 H N N 75 MG MG MG N N 76 PNT C1 C Y N 77 PNT C2 C Y N 78 PNT C3 C Y N 79 PNT C4 C Y N 80 PNT C5 C Y N 81 PNT C6 C Y N 82 PNT C7 C N N 83 PNT C8 C N N 84 PNT C9 C N N 85 PNT C10 C N N 86 PNT "C1'" C Y N 87 PNT "C2'" C Y N 88 PNT "C3'" C Y N 89 PNT "C4'" C Y N 90 PNT "C5'" C Y N 91 PNT "C6'" C Y N 92 PNT "C7'" C N N 93 PNT "C8'" C N N 94 PNT "C9'" C N N 95 PNT O1 O N N 96 PNT "O1'" O N N 97 PNT N1 N N N 98 PNT N2 N N N 99 PNT "N1'" N N N 100 PNT "N2'" N N N 101 PNT H2 H N N 102 PNT H3 H N N 103 PNT H5 H N N 104 PNT H6 H N N 105 PNT H71 H N N 106 PNT H72 H N N 107 PNT H81 H N N 108 PNT H82 H N N 109 PNT H101 H N N 110 PNT H102 H N N 111 PNT "H2'" H N N 112 PNT "H3'" H N N 113 PNT "H5'" H N N 114 PNT "H6'" H N N 115 PNT "H7'1" H N N 116 PNT "H7'2" H N N 117 PNT "H8'1" H N N 118 PNT "H8'2" H N N 119 PNT HN1 H N N 120 PNT HN2 H N N 121 PNT HN3 H N N 122 PNT "HN'1" H N N 123 PNT "HN'2" H N N 124 PNT "HN'3" H N N 125 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DT OP3 P sing N N 39 DT OP3 HOP3 sing N N 40 DT P OP1 doub N N 41 DT P OP2 sing N N 42 DT P "O5'" sing N N 43 DT OP2 HOP2 sing N N 44 DT "O5'" "C5'" sing N N 45 DT "C5'" "C4'" sing N N 46 DT "C5'" "H5'" sing N N 47 DT "C5'" "H5''" sing N N 48 DT "C4'" "O4'" sing N N 49 DT "C4'" "C3'" sing N N 50 DT "C4'" "H4'" sing N N 51 DT "O4'" "C1'" sing N N 52 DT "C3'" "O3'" sing N N 53 DT "C3'" "C2'" sing N N 54 DT "C3'" "H3'" sing N N 55 DT "O3'" "HO3'" sing N N 56 DT "C2'" "C1'" sing N N 57 DT "C2'" "H2'" sing N N 58 DT "C2'" "H2''" sing N N 59 DT "C1'" N1 sing N N 60 DT "C1'" "H1'" sing N N 61 DT N1 C2 sing N N 62 DT N1 C6 sing N N 63 DT C2 O2 doub N N 64 DT C2 N3 sing N N 65 DT N3 C4 sing N N 66 DT N3 H3 sing N N 67 DT C4 O4 doub N N 68 DT C4 C5 sing N N 69 DT C5 C7 sing N N 70 DT C5 C6 doub N N 71 DT C7 H71 sing N N 72 DT C7 H72 sing N N 73 DT C7 H73 sing N N 74 DT C6 H6 sing N N 75 HOH O H1 sing N N 76 HOH O H2 sing N N 77 PNT C1 C2 doub Y N 78 PNT C1 C6 sing Y N 79 PNT C1 O1 sing N N 80 PNT C2 C3 sing Y N 81 PNT C2 H2 sing N N 82 PNT C3 C4 doub Y N 83 PNT C3 H3 sing N N 84 PNT C4 C5 sing Y N 85 PNT C4 C9 sing N N 86 PNT C5 C6 doub Y N 87 PNT C5 H5 sing N N 88 PNT C6 H6 sing N N 89 PNT C7 C8 sing N N 90 PNT C7 O1 sing N N 91 PNT C7 H71 sing N N 92 PNT C7 H72 sing N N 93 PNT C8 C10 sing N N 94 PNT C8 H81 sing N N 95 PNT C8 H82 sing N N 96 PNT C9 N1 doub N N 97 PNT C9 N2 sing N N 98 PNT C10 "C8'" sing N N 99 PNT C10 H101 sing N N 100 PNT C10 H102 sing N N 101 PNT "C1'" "C2'" doub Y N 102 PNT "C1'" "C6'" sing Y N 103 PNT "C1'" "O1'" sing N N 104 PNT "C2'" "C3'" sing Y N 105 PNT "C2'" "H2'" sing N N 106 PNT "C3'" "C4'" doub Y N 107 PNT "C3'" "H3'" sing N N 108 PNT "C4'" "C5'" sing Y N 109 PNT "C4'" "C9'" sing N N 110 PNT "C5'" "C6'" doub Y N 111 PNT "C5'" "H5'" sing N N 112 PNT "C6'" "H6'" sing N N 113 PNT "C7'" "C8'" sing N N 114 PNT "C7'" "O1'" sing N N 115 PNT "C7'" "H7'1" sing N N 116 PNT "C7'" "H7'2" sing N N 117 PNT "C8'" "H8'1" sing N N 118 PNT "C8'" "H8'2" sing N N 119 PNT "C9'" "N1'" doub N N 120 PNT "C9'" "N2'" sing N N 121 PNT N1 HN1 sing N N 122 PNT N2 HN2 sing N N 123 PNT N2 HN3 sing N N 124 PNT "N1'" "HN'1" sing N N 125 PNT "N2'" "HN'2" sing N N 126 PNT "N2'" "HN'3" sing N N 127 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3EY0 'double helix' 3EY0 '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 DA 1 1_555 B DT 10 1_555 -0.377 -0.038 0.063 -10.466 -15.217 3.292 1 A_DA1:DT10_B A 1 ? B 10 ? 20 1 1 A DT 2 1_555 B DA 9 1_555 -0.016 -0.217 -0.189 3.364 -6.020 -0.908 2 A_DT2:DA9_B A 2 ? B 9 ? 20 1 1 A DA 3 1_555 B DT 8 1_555 -0.092 -0.148 -0.142 -3.973 -11.059 4.672 3 A_DA3:DT8_B A 3 ? B 8 ? 20 1 1 A DT 4 1_555 B DA 7 1_555 -0.066 -0.126 0.035 3.771 -9.902 -5.234 4 A_DT4:DA7_B A 4 ? B 7 ? 20 1 1 A DA 5 1_555 B DT 6 1_555 -0.130 -0.044 0.152 -2.000 -5.414 3.488 5 A_DA5:DT6_B A 5 ? B 6 ? 20 1 1 A DT 6 1_555 B DA 5 1_555 0.345 -0.095 -0.230 9.106 -7.511 5.843 6 A_DT6:DA5_B A 6 ? B 5 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.036 0.014 0.069 -1.216 -15.791 4.267 7 A_DA7:DT4_B A 7 ? B 4 ? 20 1 1 A DT 8 1_555 B DA 3 1_555 -0.206 0.021 -0.063 6.140 -13.421 3.781 8 A_DT8:DA3_B A 8 ? B 3 ? 20 1 1 A DA 9 1_555 B DT 2 1_555 -0.150 -0.167 -0.043 0.764 -8.394 13.135 9 A_DA9:DT2_B A 9 ? B 2 ? 20 1 1 A DT 10 1_555 B DA 1 1_555 -0.090 3.254 0.258 -2.629 -18.658 -69.635 10 A_DT10:DA1_B A 10 ? B 1 ? 23 3 # 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 DA 1 1_555 B DT 10 1_555 A DT 2 1_555 B DA 9 1_555 -0.706 -1.016 3.031 3.720 5.504 32.743 -2.581 1.778 2.734 9.639 -6.515 33.392 1 AA_DA1DT2:DA9DT10_BB A 1 ? B 10 ? A 2 ? B 9 ? 1 A DT 2 1_555 B DA 9 1_555 A DA 3 1_555 B DT 8 1_555 0.115 -0.403 3.452 0.035 7.660 35.115 -1.796 -0.181 3.295 12.512 -0.057 35.915 2 AA_DT2DA3:DT8DA9_BB A 2 ? B 9 ? A 3 ? B 8 ? 1 A DA 3 1_555 B DT 8 1_555 A DT 4 1_555 B DA 7 1_555 -0.693 -0.456 3.086 -0.823 2.346 31.499 -1.248 1.130 3.061 4.313 1.513 31.595 3 AA_DA3DT4:DA7DT8_BB A 3 ? B 8 ? A 4 ? B 7 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B DT 6 1_555 0.462 0.675 3.477 -1.219 -6.351 45.399 1.444 -0.704 3.345 -8.179 1.571 45.833 4 AA_DT4DA5:DT6DA7_BB A 4 ? B 7 ? A 5 ? B 6 ? 1 A DA 5 1_555 B DT 6 1_555 A DT 6 1_555 B DA 5 1_555 0.139 -0.158 3.072 3.221 -2.033 30.419 0.079 0.335 3.074 -3.856 -6.108 30.651 5 AA_DA5DT6:DA5DT6_BB A 5 ? B 6 ? A 6 ? B 5 ? 1 A DT 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.423 0.942 3.487 -2.812 0.482 43.671 1.215 0.280 3.516 0.648 3.775 43.760 6 AA_DT6DA7:DT4DA5_BB A 6 ? B 5 ? A 7 ? B 4 ? 1 A DA 7 1_555 B DT 4 1_555 A DT 8 1_555 B DA 3 1_555 0.318 -0.444 3.148 0.955 -5.303 33.496 0.068 -0.395 3.187 -9.128 -1.643 33.915 7 AA_DA7DT8:DA3DT4_BB A 7 ? B 4 ? A 8 ? B 3 ? 1 A DT 8 1_555 B DA 3 1_555 A DA 9 1_555 B DT 2 1_555 0.935 0.461 3.432 2.576 1.882 39.800 0.446 -1.055 3.501 2.759 -3.777 39.923 8 AA_DT8DA9:DT2DA3_BB A 8 ? B 3 ? A 9 ? B 2 ? 1 A DA 9 1_555 B DT 2 1_555 A DT 10 1_555 B DA 1 1_555 0.776 -2.110 3.165 -4.020 -1.268 73.501 -1.722 -0.772 3.156 -1.059 3.356 73.605 9 AA_DA9DT10:DA1DT2_BB A 9 ? B 2 ? A 10 ? B 1 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'standard watson-crick DNA' # _atom_sites.entry_id 3EY0 _atom_sites.fract_transf_matrix[1][1] 0.035985 _atom_sites.fract_transf_matrix[1][2] 0.020776 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.041552 _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] 0.003206 _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 MG N O P # loop_