data_4QNO # _entry.id 4QNO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.309 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4QNO NDB NA3052 RCSB RCSB086283 WWPDB D_1000086283 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2019-05-15 _pdbx_database_PDB_obs_spr.pdb_id 5ZT2 _pdbx_database_PDB_obs_spr.replace_pdb_id 4QNO _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 4QNO _pdbx_database_status.recvd_initial_deposition_date 2014-06-18 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf OBS _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 'Chen, Y.W.' 1 'Jhan, C.R.' 2 'Hou, M.H.' 3 # _citation.id primary _citation.title 'A 1.66 angstrom resulotion of Crystal structure of CCG DNA repeats' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chen, Y.W.' 1 ? primary 'Jhan, C.R.' 2 ? primary 'Hou, M.H.' 3 ? # _cell.entry_id 4QNO _cell.length_a 38.299 _cell.length_b 38.299 _cell.length_c 54.328 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 4QNO _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _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 ;DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3') ; 3295.150 1 ? ? ? ? 2 non-polymer syn 'COBALT (II) ION' 58.933 2 ? ? ? ? 3 water nat water 18.015 88 ? ? ? ? # _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 '(DT)(DC)(DC)(DG)(DC)(DC)(DG)(DC)(DC)(DG)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TCCGCCGCCGA _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 DT n 1 2 DC n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 DC n 1 7 DG n 1 8 DC n 1 9 DC n 1 10 DG n 1 11 DA 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 4QNO _struct_ref.pdbx_db_accession 4QNO _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4QNO _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 11 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4QNO _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 11 _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 11 # 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 CO non-polymer . 'COBALT (II) ION' ? 'Co 2' 58.933 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # _exptl.entry_id 4QNO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.02 _exptl_crystal.density_percent_sol 59.31 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;50mM Sodium cacodylate, 1mM Magnesium chloride, 5% MPD, 2mM Cobalt(II) chloride, 1mM Chromomycin A3, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 _diffrn.pdbx_serial_crystal_experiment ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'RAYONIX MX-300' _diffrn_detector.pdbx_collection_date 2013-10-18 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'LN2-Cooled, Fixed-Exit Double Crystal Monochromator' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.60572 1.0 2 1.56518 1.0 3 1.60490 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSRRC BEAMLINE BL15A1' _diffrn_source.pdbx_synchrotron_site NSRRC _diffrn_source.pdbx_synchrotron_beamline BL15A1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '1.60572, 1.56518, 1.60490' # _reflns.entry_id 4QNO _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.66 _reflns.number_obs 8712 _reflns.number_all ? _reflns.percent_possible_obs 95.2 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.1 _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.66 _reflns_shell.d_res_low 1.72 _reflns_shell.percent_possible_all 68.4 _reflns_shell.Rmerge_I_obs 0.241 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.765 _reflns_shell.pdbx_redundancy 2.6 _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_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4QNO _refine.ls_number_reflns_obs 7104 _refine.ls_number_reflns_all 9126 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 3 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30 _refine.ls_d_res_high 1.66 _refine.ls_percent_reflns_obs 77.8000 _refine.ls_R_factor_obs 0.2465 _refine.ls_R_factor_all 0.247255 _refine.ls_R_factor_R_work 0.2465 _refine.ls_R_factor_R_free 0.2616 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.1000 _refine.ls_number_reflns_R_free 373 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 42.7153 _refine.solvent_model_param_bsol 61.1559 _refine.solvent_model_param_ksol ? _refine.aniso_B[1][1] -4.3420 _refine.aniso_B[2][2] -4.3420 _refine.aniso_B[3][3] 8.6830 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 218 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 88 _refine_hist.number_atoms_total 308 _refine_hist.d_res_high 1.66 _refine_hist.d_res_low 30 # 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_restraint_function _refine_ls_restr.pdbx_refine_id c_bond_d 0.019902 ? ? ? ? 'X-RAY DIFFRACTION' c_angle_deg 1.82421 ? ? ? ? 'X-RAY DIFFRACTION' # _struct.entry_id 4QNO _struct.title 'Crystal structure of CCG DNA repeats at 1.66 angstrom resolution' _struct.pdbx_descriptor ;DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3') ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4QNO _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'i-motif, hemiprotonated CC+ pairs, CCG triplet repeat, high resolution structure, 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 2 ? C N N 2 ? D 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 metalc1 metalc ? ? B CO . CO ? ? ? 1_555 D HOH . O ? ? A CO 101 A HOH 240 1_555 ? ? ? ? ? ? ? 2.165 ? metalc2 metalc ? ? A DG 4 N7 ? ? ? 1_555 B CO . CO ? ? A DG 4 A CO 101 1_555 ? ? ? ? ? ? ? 2.346 ? metalc3 metalc ? ? B CO . CO ? ? ? 1_555 D HOH . O ? ? A CO 101 A HOH 243 1_555 ? ? ? ? ? ? ? 2.361 ? metalc4 metalc ? ? B CO . CO ? ? ? 1_555 D HOH . O ? ? A CO 101 A HOH 201 1_555 ? ? ? ? ? ? ? 2.362 ? hydrog1 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DC 2 O2 ? ? A DC 2 A DC 2 8_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? hydrog2 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DC 2 N4 ? ? A DC 2 A DC 2 8_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? hydrog3 hydrog ? ? A DC 3 N4 ? ? ? 1_555 A DC 3 O2 ? ? A DC 3 A DC 3 8_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? hydrog4 hydrog ? ? A DC 3 O2 ? ? ? 1_555 A DC 3 N4 ? ? A DC 3 A DC 3 8_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? hydrog5 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DG 4 N3 ? ? A DG 4 A DG 4 8_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? hydrog6 hydrog ? ? A DG 4 N3 ? ? ? 1_555 A DG 4 N2 ? ? A DG 4 A DG 4 8_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? hydrog7 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DC 8 O2 ? ? A DC 8 A DC 8 8_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? hydrog8 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DC 8 N4 ? ? A DC 8 A DC 8 8_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? hydrog9 hydrog ? ? A DC 9 N4 ? ? ? 1_555 A DC 9 O2 ? ? A DC 9 A DC 9 8_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? hydrog10 hydrog ? ? A DC 9 O2 ? ? ? 1_555 A DC 9 N4 ? ? A DC 9 A DC 9 8_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? hydrog11 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DG 10 N3 ? ? A DG 10 A DG 10 8_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? hydrog12 hydrog ? ? A DG 10 N3 ? ? ? 1_555 A DG 10 N2 ? ? A DG 10 A DG 10 8_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? hydrog13 hydrog ? ? A DA 11 N6 ? ? ? 1_555 A DA 11 N7 ? ? A DA 11 A DA 11 8_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? hydrog14 hydrog ? ? A DA 11 N7 ? ? ? 1_555 A DA 11 N6 ? ? A DA 11 A DA 11 8_555 ? ? ? ? ? ? TYPE_2_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 ? ? ? ? 6 'BINDING SITE FOR RESIDUE CO A 101' AC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE CO A 102' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 DG A 4 ? DG A 4 . ? 1_555 ? 2 AC1 6 HOH D . ? HOH A 201 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 219 . ? 1_555 ? 4 AC1 6 HOH D . ? HOH A 240 . ? 1_555 ? 5 AC1 6 HOH D . ? HOH A 242 . ? 1_555 ? 6 AC1 6 HOH D . ? HOH A 243 . ? 1_555 ? 7 AC2 3 DC A 6 ? DC A 6 . ? 8_555 ? 8 AC2 3 DG A 7 ? DG A 7 . ? 8_555 ? 9 AC2 3 HOH D . ? HOH A 287 . ? 8_555 ? # _database_PDB_matrix.entry_id 4QNO _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 4QNO _atom_sites.fract_transf_matrix[1][1] 0.026110 _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] 0.026110 _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] 0.018407 _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 CO 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 DT 1 1 1 DT T A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DA 11 11 11 DA A A . 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 B 2 CO 1 101 31 CO CO A . C 2 CO 1 102 32 CO CO A . D 3 HOH 1 201 33 HOH HOH A . D 3 HOH 2 202 34 HOH HOH A . D 3 HOH 3 203 35 HOH HOH A . D 3 HOH 4 204 36 HOH HOH A . D 3 HOH 5 205 37 HOH HOH A . D 3 HOH 6 206 38 HOH HOH A . D 3 HOH 7 207 39 HOH HOH A . D 3 HOH 8 208 40 HOH HOH A . D 3 HOH 9 209 41 HOH HOH A . D 3 HOH 10 210 42 HOH HOH A . D 3 HOH 11 211 43 HOH HOH A . D 3 HOH 12 212 44 HOH HOH A . D 3 HOH 13 213 45 HOH HOH A . D 3 HOH 14 214 46 HOH HOH A . D 3 HOH 15 215 47 HOH HOH A . D 3 HOH 16 216 48 HOH HOH A . D 3 HOH 17 217 49 HOH HOH A . D 3 HOH 18 218 50 HOH HOH A . D 3 HOH 19 219 51 HOH HOH A . D 3 HOH 20 220 52 HOH HOH A . D 3 HOH 21 221 53 HOH HOH A . D 3 HOH 22 222 54 HOH HOH A . D 3 HOH 23 223 55 HOH HOH A . D 3 HOH 24 224 56 HOH HOH A . D 3 HOH 25 225 57 HOH HOH A . D 3 HOH 26 226 58 HOH HOH A . D 3 HOH 27 227 59 HOH HOH A . D 3 HOH 28 228 60 HOH HOH A . D 3 HOH 29 229 61 HOH HOH A . D 3 HOH 30 230 62 HOH HOH A . D 3 HOH 31 231 63 HOH HOH A . D 3 HOH 32 232 64 HOH HOH A . D 3 HOH 33 233 65 HOH HOH A . D 3 HOH 34 234 66 HOH HOH A . D 3 HOH 35 235 67 HOH HOH A . D 3 HOH 36 236 68 HOH HOH A . D 3 HOH 37 237 69 HOH HOH A . D 3 HOH 38 238 70 HOH HOH A . D 3 HOH 39 239 71 HOH HOH A . D 3 HOH 40 240 72 HOH HOH A . D 3 HOH 41 241 73 HOH HOH A . D 3 HOH 42 242 74 HOH HOH A . D 3 HOH 43 243 75 HOH HOH A . D 3 HOH 44 244 76 HOH HOH A . D 3 HOH 45 245 77 HOH HOH A . D 3 HOH 46 246 78 HOH HOH A . D 3 HOH 47 247 79 HOH HOH A . D 3 HOH 48 248 80 HOH HOH A . D 3 HOH 49 249 81 HOH HOH A . D 3 HOH 50 250 82 HOH HOH A . D 3 HOH 51 251 83 HOH HOH A . D 3 HOH 52 252 84 HOH HOH A . D 3 HOH 53 253 85 HOH HOH A . D 3 HOH 54 254 86 HOH HOH A . D 3 HOH 55 255 87 HOH HOH A . D 3 HOH 56 256 88 HOH HOH A . D 3 HOH 57 257 89 HOH HOH A . D 3 HOH 58 258 90 HOH HOH A . D 3 HOH 59 259 91 HOH HOH A . D 3 HOH 60 260 92 HOH HOH A . D 3 HOH 61 261 93 HOH HOH A . D 3 HOH 62 262 94 HOH HOH A . D 3 HOH 63 263 95 HOH HOH A . D 3 HOH 64 264 96 HOH HOH A . D 3 HOH 65 265 97 HOH HOH A . D 3 HOH 66 266 98 HOH HOH A . D 3 HOH 67 267 99 HOH HOH A . D 3 HOH 68 268 100 HOH HOH A . D 3 HOH 69 269 101 HOH HOH A . D 3 HOH 70 270 102 HOH HOH A . D 3 HOH 71 271 103 HOH HOH A . D 3 HOH 72 272 104 HOH HOH A . D 3 HOH 73 273 105 HOH HOH A . D 3 HOH 74 274 106 HOH HOH A . D 3 HOH 75 275 107 HOH HOH A . D 3 HOH 76 276 108 HOH HOH A . D 3 HOH 77 277 109 HOH HOH A . D 3 HOH 78 278 110 HOH HOH A . D 3 HOH 79 279 111 HOH HOH A . D 3 HOH 80 280 112 HOH HOH A . D 3 HOH 81 281 113 HOH HOH A . D 3 HOH 82 282 114 HOH HOH A . D 3 HOH 83 283 115 HOH HOH A . D 3 HOH 84 284 116 HOH HOH A . D 3 HOH 85 285 117 HOH HOH A . D 3 HOH 86 286 118 HOH HOH A . D 3 HOH 87 287 119 HOH HOH A . D 3 HOH 88 288 120 HOH HOH A . # _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _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 # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 222 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 ? D HOH . ? A HOH 240 ? 1_555 CO ? B CO . ? A CO 101 ? 1_555 N7 ? A DG 4 ? A DG 4 ? 1_555 82.4 ? 2 O ? D HOH . ? A HOH 240 ? 1_555 CO ? B CO . ? A CO 101 ? 1_555 O ? D HOH . ? A HOH 243 ? 1_555 113.4 ? 3 N7 ? A DG 4 ? A DG 4 ? 1_555 CO ? B CO . ? A CO 101 ? 1_555 O ? D HOH . ? A HOH 243 ? 1_555 111.1 ? 4 O ? D HOH . ? A HOH 240 ? 1_555 CO ? B CO . ? A CO 101 ? 1_555 O ? D HOH . ? A HOH 201 ? 1_555 162.3 ? 5 N7 ? A DG 4 ? A DG 4 ? 1_555 CO ? B CO . ? A CO 101 ? 1_555 O ? D HOH . ? A HOH 201 ? 1_555 86.3 ? 6 O ? D HOH . ? A HOH 243 ? 1_555 CO ? B CO . ? A CO 101 ? 1_555 O ? D HOH . ? A HOH 201 ? 1_555 83.4 ? # 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 2015-07-01 2 'Structure model' 1 1 2019-05-15 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 2 'Structure model' repository Obsolete ? # 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' 'Data collection' 3 2 'Structure model' Other # 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 2 'Structure model' diffrn_source 2 2 'Structure model' pdbx_database_PDB_obs_spr 3 2 'Structure model' pdbx_database_status # 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 2 'Structure model' '_diffrn_source.pdbx_synchrotron_beamline' 2 2 'Structure model' '_diffrn_source.type' 3 2 'Structure model' '_pdbx_database_status.status_code' 4 2 'Structure model' '_pdbx_database_status.status_code_sf' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language HKL-2000 'data collection' . ? 1 ? ? ? ? SHELXS phasing . ? 2 ? ? ? ? CNS refinement 1.1 ? 3 ? ? ? ? HKL-2000 'data reduction' . ? 4 ? ? ? ? HKL-2000 'data scaling' . ? 5 ? ? ? ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 N1 _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 8 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 C2 _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 8 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.461 _pdbx_validate_rmsd_bond.bond_target_value 1.397 _pdbx_validate_rmsd_bond.bond_deviation 0.064 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.010 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4QNO 'double helix' 4QNO 'parallel strands' 4QNO 'mismatched base pair' 4QNO 'internal loop' # 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 DG 4 1_555 A DG 4 8_555 -3.486 -8.027 0.000 20.092 -41.553 -180.000 1 A_DG4:DG4_A A 4 ? A 4 ? 4 12 1 A DC 3 1_555 A DC 3 8_555 1.898 1.218 0.000 -10.695 -2.706 180.000 2 A_DC3:DC3_A A 3 ? A 3 ? 15 2 1 A DC 8 1_555 A DC 8 1_555 -1.946 -1.267 0.000 0.335 -11.487 -180.000 3 A_DC8:DC8_A A 8 ? A 8 ? 15 2 1 A DC 2 1_555 A DC 2 1_555 -2.042 -1.300 0.000 7.786 -13.277 -180.000 4 A_DC2:DC2_A A 2 ? A 2 ? 15 2 1 A DC 9 1_555 A DC 9 1_555 -2.004 -1.375 0.000 -3.156 5.902 -180.000 5 A_DC9:DC9_A A 9 ? A 9 ? 15 2 1 A DG 10 1_555 A DG 10 1_555 -3.274 -8.067 0.000 18.718 -22.800 -180.000 6 A_DG10:DG10_A A 10 ? A 10 ? 4 12 1 A DA 11 1_555 A DA 11 1_555 6.129 -5.382 0.000 22.701 -22.131 180.000 7 A_DA11:DA11_A A 11 ? A 11 ? 2 7 # 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 DG 4 1_555 A DG 4 8_555 A DC 3 1_555 A DC 3 8_555 0.000 0.000 -2.553 0.000 0.000 123.908 0.000 0.000 -2.553 0.000 0.000 123.908 1 AA_DG4DC3:DC3DG4_AA A 4 ? A 4 ? A 3 ? A 3 ? 1 A DC 3 1_555 A DC 3 8_555 A DC 8 1_555 A DC 8 1_555 0.000 0.000 2.871 -149.094 -100.851 111.430 -2.135 -1.455 0.000 89.996 0.831 -67.512 2 AA_DC3DC8:DC8DC3_AA A 3 ? A 3 ? A 8 ? A 8 ? 1 A DC 8 1_555 A DC 8 1_555 A DC 2 1_555 A DC 2 1_555 2.971 -2.498 0.000 -115.817 -137.791 -75.327 1.249 1.486 0.000 68.895 -57.909 -180.000 3 AA_DC8DC2:DC2DC8_AA A 8 ? A 8 ? A 2 ? A 2 ? 1 A DC 2 1_555 A DC 2 1_555 A DC 9 1_555 A DC 9 1_555 1.697 -2.457 0.000 148.114 102.284 118.087 -1.229 -0.848 0.000 51.142 -74.057 180.000 4 AA_DC2DC9:DC9DC2_AA A 2 ? A 2 ? A 9 ? A 9 ? 1 A DC 9 1_555 A DC 9 1_555 A DG 10 1_555 A DG 10 1_555 0.000 0.000 2.816 0.000 0.000 51.388 0.000 0.000 2.816 0.000 0.000 51.388 5 AA_DC9DG10:DG10DC9_AA A 9 ? A 9 ? A 10 ? A 10 ? 1 A DG 10 1_555 A DG 10 1_555 A DA 11 1_555 A DA 11 1_555 0.000 0.000 4.625 0.000 0.000 170.250 0.000 0.000 4.625 0.000 0.000 170.250 6 AA_DG10DA11:DA11DG10_AA A 10 ? A 10 ? A 11 ? A 11 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT (II) ION' CO 3 water HOH #