data_3MIJ # _entry.id 3MIJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3MIJ NDB NA0512 RCSB RCSB058588 WWPDB D_1000058588 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3MIJ _pdbx_database_status.recvd_initial_deposition_date 2010-04-10 _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.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Collie, G.W.' 1 'Neidle, S.' 2 'Parkinson, G.N.' 3 # _citation.id primary _citation.title 'Structural basis of telomeric RNA quadruplex-acridine ligand recognition.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 133 _citation.page_first 2721 _citation.page_last 2728 _citation.year 2011 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21291211 _citation.pdbx_database_id_DOI 10.1021/ja109767y # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Collie, G.W.' 1 primary 'Sparapani, S.' 2 primary 'Parkinson, G.N.' 3 primary 'Neidle, S.' 4 # _cell.entry_id 3MIJ _cell.length_a 56.606 _cell.length_b 56.606 _cell.length_c 56.606 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 12 _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 3MIJ _symmetry.space_group_name_H-M 'P 2 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 195 _symmetry.space_group_name_Hall ? # 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 ;RNA (5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') ; 3909.352 1 ? ? ? 'Human telomeric RNA sequence' 2 non-polymer syn 'POTASSIUM ION' 39.098 2 ? ? ? ? 3 non-polymer syn "N,N'-[acridine-3,6-diylbis(1H-1,2,3-triazole-1,4-diylbenzene-3,1-diyl)]bis[3-(diethylamino)propanamide]" 749.906 1 ? ? ? ? 4 water nat water 18.015 16 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code UAGGGUUAGGGU _entity_poly.pdbx_seq_one_letter_code_can UAGGGUUAGGGU _entity_poly.pdbx_strand_id A _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 U n 1 2 A n 1 3 G n 1 4 G n 1 5 G n 1 6 U n 1 7 U n 1 8 A n 1 9 G n 1 10 G n 1 11 G n 1 12 U 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 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details 'This sequence occurs naturally in humans.' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3MIJ _struct_ref.pdbx_db_accession 3MIJ _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code UAGGGUUAGGGU _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3MIJ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3MIJ _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 12 # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 R14 non-polymer . "N,N'-[acridine-3,6-diylbis(1H-1,2,3-triazole-1,4-diylbenzene-3,1-diyl)]bis[3-(diethylamino)propanamide]" 'triazole-acridine conjugate' 'C43 H47 N11 O2' 749.906 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 3MIJ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.87 _exptl_crystal.density_percent_sol 68.19 _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 285 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details ;MPD, sodium chloride, potassium chloride, sodium cacodylate, potassium cacodylate, spermine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2010-02-01 _diffrn_detector.details Monochromator # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97630 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I04' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I04 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97630 # _reflns.entry_id 3MIJ _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 17.90 _reflns.d_resolution_high 2.40 _reflns.number_obs 2511 _reflns.number_all 2511 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs 0.055 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 16.1 _reflns.B_iso_Wilson_estimate 26.462 _reflns.pdbx_redundancy 6.6 _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.40 _reflns_shell.d_res_low 2.49 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.368 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.3 _reflns_shell.pdbx_redundancy 6.78 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3MIJ _refine.ls_number_reflns_obs 1901 _refine.ls_number_reflns_all ? _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 16.34 _refine.ls_d_res_high 2.60 _refine.ls_percent_reflns_obs 99.95 _refine.ls_R_factor_obs 0.23603 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23543 _refine.ls_R_factor_R_free 0.24752 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 91 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.942 _refine.correlation_coeff_Fo_to_Fc_free 0.956 _refine.B_iso_mean 26.462 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _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 'PDB ID 3IBK' _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 0.476 _refine.pdbx_overall_ESU_R_Free 0.274 _refine.overall_SU_ML 0.227 _refine.overall_SU_B 21.757 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 259 _refine_hist.pdbx_number_atoms_ligand 58 _refine_hist.number_atoms_solvent 16 _refine_hist.number_atoms_total 333 _refine_hist.d_res_high 2.60 _refine_hist.d_res_low 16.34 # 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 0.010 0.021 ? 352 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.018 2.994 ? 538 'X-RAY DIFFRACTION' ? r_chiral_restr 0.052 0.200 ? 59 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.021 ? 186 'X-RAY DIFFRACTION' ? r_scbond_it 1.244 3.000 ? 352 'X-RAY DIFFRACTION' ? r_scangle_it 2.138 4.500 ? 538 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.600 _refine_ls_shell.d_res_low 2.666 _refine_ls_shell.number_reflns_R_work 142 _refine_ls_shell.R_factor_R_work 0.497 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.456 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 2 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 142 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3MIJ _struct.title 'Crystal structure of a telomeric RNA G-quadruplex complexed with an acridine-based ligand.' _struct.pdbx_descriptor "5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3MIJ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Quadruplex, RNA-ligand complex, RNA, telomeric' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 3 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc1 metalc ? ? A G 3 O6 ? ? ? 1_555 C K . K ? ? A G 3 A K 22 1_555 ? ? ? ? ? ? ? 2.623 ? metalc2 metalc ? ? A G 9 O6 ? ? ? 1_555 C K . K ? ? A G 9 A K 22 1_555 ? ? ? ? ? ? ? 2.635 ? metalc3 metalc ? ? A G 5 O6 ? ? ? 1_555 B K . K ? ? A G 5 A K 21 1_555 ? ? ? ? ? ? ? 2.701 ? metalc4 metalc ? ? A G 10 O6 ? ? ? 1_555 B K . K ? ? A G 10 A K 21 1_555 ? ? ? ? ? ? ? 2.727 ? metalc5 metalc ? ? A G 4 O6 ? ? ? 1_555 B K . K ? ? A G 4 A K 21 1_555 ? ? ? ? ? ? ? 2.775 ? metalc6 metalc ? ? A G 11 O6 ? ? ? 1_555 B K . K ? ? A G 11 A K 21 1_555 ? ? ? ? ? ? ? 2.813 ? metalc7 metalc ? ? A G 10 O6 ? ? ? 1_555 C K . K ? ? A G 10 A K 22 1_555 ? ? ? ? ? ? ? 2.982 ? metalc8 metalc ? ? A G 4 O6 ? ? ? 1_555 C K . K ? ? A G 4 A K 22 1_555 ? ? ? ? ? ? ? 3.334 ? hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 A G 9 O6 ? ? A G 3 A G 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 A G 9 N7 ? ? A G 3 A G 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? hydrog3 hydrog ? ? A G 4 N1 ? ? ? 1_555 A G 10 O6 ? ? A G 4 A G 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? hydrog4 hydrog ? ? A G 4 N2 ? ? ? 1_555 A G 10 N7 ? ? A G 4 A G 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? hydrog5 hydrog ? ? A G 5 N1 ? ? ? 1_555 A G 11 O6 ? ? A G 5 A G 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? hydrog6 hydrog ? ? A G 5 N2 ? ? ? 1_555 A G 11 N7 ? ? A G 5 A G 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference 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 ? ? ? ? 10 'BINDING SITE FOR RESIDUE K A 21' AC2 Software ? ? ? ? 10 'BINDING SITE FOR RESIDUE K A 22' AC3 Software ? ? ? ? 12 'BINDING SITE FOR RESIDUE R14 A 30' # 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 10 G A 4 ? G A 4 . ? 4_545 ? 2 AC1 10 G A 4 ? G A 4 . ? 1_555 ? 3 AC1 10 G A 5 ? G A 5 . ? 4_545 ? 4 AC1 10 G A 5 ? G A 5 . ? 1_555 ? 5 AC1 10 G A 10 ? G A 10 . ? 1_555 ? 6 AC1 10 G A 10 ? G A 10 . ? 4_545 ? 7 AC1 10 G A 11 ? G A 11 . ? 4_545 ? 8 AC1 10 G A 11 ? G A 11 . ? 1_555 ? 9 AC1 10 K C . ? K A 22 . ? 4_545 ? 10 AC1 10 K C . ? K A 22 . ? 1_555 ? 11 AC2 10 G A 3 ? G A 3 . ? 4_545 ? 12 AC2 10 G A 3 ? G A 3 . ? 1_555 ? 13 AC2 10 G A 4 ? G A 4 . ? 1_555 ? 14 AC2 10 G A 4 ? G A 4 . ? 4_545 ? 15 AC2 10 G A 9 ? G A 9 . ? 4_545 ? 16 AC2 10 G A 9 ? G A 9 . ? 1_555 ? 17 AC2 10 G A 10 ? G A 10 . ? 1_555 ? 18 AC2 10 G A 10 ? G A 10 . ? 4_545 ? 19 AC2 10 K B . ? K A 21 . ? 4_545 ? 20 AC2 10 K B . ? K A 21 . ? 1_555 ? 21 AC3 12 U A 1 ? U A 1 . ? 1_555 ? 22 AC3 12 U A 1 ? U A 1 . ? 3_655 ? 23 AC3 12 A A 2 ? A A 2 . ? 1_555 ? 24 AC3 12 G A 3 ? G A 3 . ? 1_555 ? 25 AC3 12 U A 6 ? U A 6 . ? 10_555 ? 26 AC3 12 A A 8 ? A A 8 . ? 1_555 ? 27 AC3 12 G A 9 ? G A 9 . ? 4_545 ? 28 AC3 12 G A 10 ? G A 10 . ? 10_555 ? 29 AC3 12 HOH E . ? HOH A 45 . ? 1_555 ? 30 AC3 12 HOH E . ? HOH A 48 . ? 1_555 ? 31 AC3 12 HOH E . ? HOH A 54 . ? 1_555 ? 32 AC3 12 HOH E . ? HOH A 56 . ? 3_655 ? # _database_PDB_matrix.entry_id 3MIJ _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 # _atom_sites.entry_id 3MIJ _atom_sites.fract_transf_matrix[1][1] 0.017666 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.017666 _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] 0.017666 _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 K 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 U 1 1 1 U U A . n A 1 2 A 2 2 2 A A A . n A 1 3 G 3 3 3 G G A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 U 7 7 7 U U A . n A 1 8 A 8 8 8 A A A . n A 1 9 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n A 1 11 G 11 11 11 G G A . n A 1 12 U 12 12 12 U U A . n # _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 # _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 # 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)' 2230 ? 1 MORE -17 ? 1 'SSA (A^2)' 4880 ? # 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' 4_545 x,-y-1,-z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 -56.6060000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A K 21 ? B K . 2 1 A K 22 ? C K . # 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 O6 ? A G 3 ? A G 3 ? 1_555 K ? C K . ? A K 22 ? 1_555 O6 ? A G 9 ? A G 9 ? 1_555 81.0 ? 2 O6 ? A G 3 ? A G 3 ? 1_555 K ? C K . ? A K 22 ? 1_555 O6 ? A G 10 ? A G 10 ? 1_555 135.5 ? 3 O6 ? A G 9 ? A G 9 ? 1_555 K ? C K . ? A K 22 ? 1_555 O6 ? A G 10 ? A G 10 ? 1_555 77.3 ? 4 O6 ? A G 3 ? A G 3 ? 1_555 K ? C K . ? A K 22 ? 1_555 O6 ? A G 4 ? A G 4 ? 1_555 73.8 ? 5 O6 ? A G 9 ? A G 9 ? 1_555 K ? C K . ? A K 22 ? 1_555 O6 ? A G 4 ? A G 4 ? 1_555 87.3 ? 6 O6 ? A G 10 ? A G 10 ? 1_555 K ? C K . ? A K 22 ? 1_555 O6 ? A G 4 ? A G 4 ? 1_555 66.9 ? 7 O6 ? A G 5 ? A G 5 ? 1_555 K ? B K . ? A K 21 ? 1_555 O6 ? A G 10 ? A G 10 ? 1_555 97.9 ? 8 O6 ? A G 5 ? A G 5 ? 1_555 K ? B K . ? A K 21 ? 1_555 O6 ? A G 4 ? A G 4 ? 1_555 63.3 ? 9 O6 ? A G 10 ? A G 10 ? 1_555 K ? B K . ? A K 21 ? 1_555 O6 ? A G 4 ? A G 4 ? 1_555 78.8 ? 10 O6 ? A G 5 ? A G 5 ? 1_555 K ? B K . ? A K 21 ? 1_555 O6 ? A G 11 ? A G 11 ? 1_555 74.6 ? 11 O6 ? A G 10 ? A G 10 ? 1_555 K ? B K . ? A K 21 ? 1_555 O6 ? A G 11 ? A G 11 ? 1_555 66.4 ? 12 O6 ? A G 4 ? A G 4 ? 1_555 K ? B K . ? A K 21 ? 1_555 O6 ? A G 11 ? A G 11 ? 1_555 120.0 ? # 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 2011-02-16 2 'Structure model' 1 1 2011-07-13 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Version format compliance' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 19.9659 -21.4686 -2.7363 0.1264 0.1472 0.2204 0.0291 0.0452 0.0420 6.8194 5.0378 2.5129 -1.0818 -0.7852 -3.3089 -0.1504 -0.1088 0.2592 -0.0514 0.3473 0.1893 -0.0798 -0.4133 0.0868 'X-RAY DIFFRACTION' 2 ? refined 19.1291 -29.4003 -6.8385 0.1336 0.1870 0.1853 0.0498 -0.0186 -0.0234 7.8860 5.3643 5.8467 1.0090 0.5586 4.0655 0.0286 0.4676 -0.4961 0.4748 0.4414 0.6362 -0.0921 -0.1051 -0.5266 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _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 'X-RAY DIFFRACTION' 1 1 A 1 A 6 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 A 7 A 12 ? . . . . ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DNA 'data collection' . ? 1 PHASER phasing . ? 2 REFMAC refinement 5.5.0072 ? 3 CrystalClear 'data reduction' . ? 4 CrystalClear 'data scaling' . ? 5 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3MIJ 'double helix' 3MIJ 'parallel strands' 3MIJ 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 3 1_555 A G 9 1_555 1.799 3.439 0.266 -7.931 2.474 -88.368 1 A_G3:G9_A A 3 ? A 9 ? 6 3 1 A G 4 1_555 A G 10 1_555 1.653 3.863 0.510 -8.953 -0.269 -87.937 2 A_G4:G10_A A 4 ? A 10 ? 6 3 1 A G 5 1_555 A G 11 1_555 1.793 3.246 -0.011 6.900 -9.546 -92.780 3 A_G5:G11_A A 5 ? A 11 ? 6 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 G 3 1_555 A G 9 1_555 A G 4 1_555 A G 10 1_555 -0.427 -1.320 3.171 2.164 -0.788 30.571 -2.346 1.220 3.166 -1.492 -4.097 30.656 1 AA_G3G4:G10G9_AA A 3 ? A 9 ? A 4 ? A 10 ? 1 A G 4 1_555 A G 10 1_555 A G 5 1_555 A G 11 1_555 -0.321 -0.862 2.901 8.836 4.613 26.731 -2.648 2.372 2.490 9.565 -18.321 28.497 2 AA_G4G5:G11G10_AA A 4 ? A 10 ? A 5 ? A 11 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'POTASSIUM ION' K 3 "N,N'-[acridine-3,6-diylbis(1H-1,2,3-triazole-1,4-diylbenzene-3,1-diyl)]bis[3-(diethylamino)propanamide]" R14 4 water HOH # 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 B 2 K 1 21 21 K K A . C 2 K 1 22 22 K K A . D 3 R14 1 30 30 R14 R14 A . E 4 HOH 1 41 41 HOH HOH A . E 4 HOH 2 42 42 HOH HOH A . E 4 HOH 3 43 43 HOH HOH A . E 4 HOH 4 44 44 HOH HOH A . E 4 HOH 5 45 45 HOH HOH A . E 4 HOH 6 46 46 HOH HOH A . E 4 HOH 7 47 47 HOH HOH A . E 4 HOH 8 48 48 HOH HOH A . E 4 HOH 9 49 49 HOH HOH A . E 4 HOH 10 50 50 HOH HOH A . E 4 HOH 11 51 51 HOH HOH A . E 4 HOH 12 52 52 HOH HOH A . E 4 HOH 13 53 53 HOH HOH A . E 4 HOH 14 54 54 HOH HOH A . E 4 HOH 15 55 55 HOH HOH A . E 4 HOH 16 56 56 HOH HOH A . #