data_4OKL # _entry.id 4OKL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4OKL pdb_00004okl 10.2210/pdb4okl/pdb NDB NA2897 ? ? RCSB RCSB084610 ? ? WWPDB D_1000084610 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3V9D . unspecified PDB 3QK4 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4OKL _pdbx_database_status.recvd_initial_deposition_date 2014-01-22 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Anna, V.' 1 'Monica, P.' 2 'Mandal, P.K.' 3 'Gautham, N.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _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 _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Structure of d(CCCCGGTACCGGGG)2 at 1.65 angstrom resolution.' 'Acta Crystallogr F Struct Biol Commun' 70 860 865 2014 ? DK 1744-3091 ? ? 25005078 10.1107/S2053230X1401084X 1 'The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)2.' Biochem.Biophys.Res.Commun. 407 307 312 2011 BBRCA9 US 0006-291X 0146 ? 21397589 10.1016/j.bbrc.2011.03.007 2 'Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex.' 'Acta Crystallogr.,Sect.F' 68 393 399 2012 ? DK 1744-3091 ? ? 22505405 10.1107/S174430911200869X # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Purushothaman, M.' 1 ? primary 'Varghese, A.' 2 ? primary 'Mandal, P.K.' 3 ? primary 'Gautham, N.' 4 ? 1 'Venkadesh, S.' 5 ? 1 'Mandal, P.K.' 6 ? 1 'Gautham, N.' 7 ? 2 'Mandal, P.K.' 8 ? 2 'Venkadesh, S.' 9 ? 2 'Gautham, N.' 10 ? # _cell.entry_id 4OKL _cell.length_a 41.270 _cell.length_b 41.270 _cell.length_c 87.670 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _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 4OKL _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _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 '14 mer A-DNA' 4282.768 2 ? ? ? ? 2 water nat water 18.015 44 ? ? ? ? # _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 '(DC)(DC)(DC)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DG)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCCCGGTACCGGGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DC n 1 4 DC n 1 5 DG n 1 6 DG n 1 7 DT n 1 8 DA n 1 9 DC n 1 10 DC n 1 11 DG n 1 12 DG n 1 13 DG n 1 14 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _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 'Chemically synthesized oligo nucleotide fragment.' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4OKL _struct_ref.pdbx_db_accession 4OKL _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CCCCGGTACCGGGG _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 4OKL A 1 ? 14 ? 4OKL 1 ? 14 ? 1 14 2 1 4OKL B 1 ? 14 ? 4OKL 1 ? 14 ? 1 14 # 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 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 4OKL _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_percent_sol 43.55 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;1mM DNA, 50mM Sodium Cacodylate buffer, 10mM ZnCl2, 10mM Spermine, 33% MPD (v/v), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _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 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2012-07-19 _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 'SI (111) Monochromator' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.95372 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.95372 # _reflns.entry_id 4OKL _reflns.observed_criterion_sigma_I 1.65 _reflns.observed_criterion_sigma_F 1.65 _reflns.d_resolution_low 30.05 _reflns.d_resolution_high 1.65 _reflns.number_obs 9714 _reflns.number_all 9714 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs 0.063 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 23.8 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 13.8 _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.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _reflns_shell.d_res_high 1.65 _reflns_shell.d_res_low 1.74 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.409 _reflns_shell.pdbx_Rsym_value 0.141 _reflns_shell.meanI_over_sigI_obs 6.7 _reflns_shell.pdbx_redundancy 1357 _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_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_Rrim_I_all ? # _refine.entry_id 4OKL _refine.ls_number_reflns_obs 9654 _refine.ls_number_reflns_all 9654 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.35 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30.048 _refine.ls_d_res_high 1.650 _refine.ls_percent_reflns_obs 99.79 _refine.ls_R_factor_obs 0.2284 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2267 _refine.ls_R_factor_R_free 0.2425 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.99 _refine.ls_number_reflns_R_free 964 _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 ? _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 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 3V9D' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _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 0.16 _refine.pdbx_overall_phase_error 26.57 _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 568 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 44 _refine_hist.number_atoms_total 612 _refine_hist.d_res_high 1.650 _refine_hist.d_res_low 30.048 # 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 f_bond_d 0.003 ? ? 636 ? 'X-RAY DIFFRACTION' f_angle_d 0.846 ? ? 978 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 16.582 ? ? 272 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.033 ? ? 110 ? 'X-RAY DIFFRACTION' f_plane_restr 0.002 ? ? 28 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _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 _refine_ls_shell.R_factor_obs . 1.6501 1.7371 1188 0.2228 100.00 0.2647 . . 131 . . . . 'X-RAY DIFFRACTION' . . 1.7371 1.8459 1211 0.2587 100.00 0.3033 . . 135 . . . . 'X-RAY DIFFRACTION' . . 1.8459 1.9884 1223 0.2658 100.00 0.3323 . . 137 . . . . 'X-RAY DIFFRACTION' . . 1.9884 2.1884 1227 0.2753 100.00 0.2940 . . 136 . . . . 'X-RAY DIFFRACTION' . . 2.1884 2.5050 1237 0.2644 100.00 0.2707 . . 137 . . . . 'X-RAY DIFFRACTION' . . 2.5050 3.1554 1256 0.2539 100.00 0.2839 . . 138 . . . . 'X-RAY DIFFRACTION' . . 3.1554 30.0531 1348 0.1831 99.00 0.1759 . . 150 . . . . 'X-RAY DIFFRACTION' . # _struct.entry_id 4OKL _struct.title 'Crystal Structure of d(CCCCGGTACCGGGG)2 at 1.65 Angstrom' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4OKL _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'A-DNA, Tetra-decanucleotide, Crystal packing, Right handed, double helix, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # 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 hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 14 N1 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 14 O6 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 14 N2 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 13 N1 ? ? A DC 2 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 13 O6 ? ? A DC 2 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 13 N2 ? ? A DC 2 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 3 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 3 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 3 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 4 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 4 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 4 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 5 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 5 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 5 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 6 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 6 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 6 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 8 N1 ? ? A DT 7 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 8 N6 ? ? A DT 7 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 8 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 8 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 9 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 9 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 9 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DG 13 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 13 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DG 13 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 13 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DG 13 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 13 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A DG 14 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A DG 14 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A DG 14 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 4OKL _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 4OKL _atom_sites.fract_transf_matrix[1][1] 0.024231 _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] 0.024231 _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] 0.011406 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DC 10 10 10 DC DC A . n A 1 11 DG 11 11 11 DG DG A . n A 1 12 DG 12 12 12 DG DG A . n A 1 13 DG 13 13 13 DG DG A . n A 1 14 DG 14 14 14 DG DG A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DC 2 2 2 DC DC B . n B 1 3 DC 3 3 3 DC DC B . n B 1 4 DC 4 4 4 DC DC B . n B 1 5 DG 5 5 5 DG DG B . n B 1 6 DG 6 6 6 DG DG B . n B 1 7 DT 7 7 7 DT DT B . n B 1 8 DA 8 8 8 DA DA B . n B 1 9 DC 9 9 9 DC DC B . n B 1 10 DC 10 10 10 DC DC B . n B 1 11 DG 11 11 11 DG DG B . n B 1 12 DG 12 12 12 DG DG B . n B 1 13 DG 13 13 13 DG DG B . n B 1 14 DG 14 14 14 DG DG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 101 1 HOH HOH A . C 2 HOH 2 102 2 HOH HOH A . C 2 HOH 3 103 3 HOH HOH A . C 2 HOH 4 104 4 HOH HOH A . C 2 HOH 5 105 5 HOH HOH A . C 2 HOH 6 106 6 HOH HOH A . C 2 HOH 7 107 12 HOH HOH A . C 2 HOH 8 108 13 HOH HOH A . C 2 HOH 9 109 17 HOH HOH A . C 2 HOH 10 110 19 HOH HOH A . C 2 HOH 11 111 21 HOH HOH A . C 2 HOH 12 112 22 HOH HOH A . C 2 HOH 13 113 23 HOH HOH A . C 2 HOH 14 114 30 HOH HOH A . C 2 HOH 15 115 31 HOH HOH A . C 2 HOH 16 116 32 HOH HOH A . C 2 HOH 17 117 33 HOH HOH A . C 2 HOH 18 118 36 HOH HOH A . C 2 HOH 19 119 37 HOH HOH A . C 2 HOH 20 120 39 HOH HOH A . C 2 HOH 21 121 40 HOH HOH A . C 2 HOH 22 122 41 HOH HOH A . C 2 HOH 23 123 44 HOH HOH A . D 2 HOH 1 101 7 HOH HOH B . D 2 HOH 2 102 8 HOH HOH B . D 2 HOH 3 103 9 HOH HOH B . D 2 HOH 4 104 10 HOH HOH B . D 2 HOH 5 105 11 HOH HOH B . D 2 HOH 6 106 14 HOH HOH B . D 2 HOH 7 107 15 HOH HOH B . D 2 HOH 8 108 16 HOH HOH B . D 2 HOH 9 109 18 HOH HOH B . D 2 HOH 10 110 20 HOH HOH B . D 2 HOH 11 111 25 HOH HOH B . D 2 HOH 12 112 26 HOH HOH B . D 2 HOH 13 113 27 HOH HOH B . D 2 HOH 14 114 28 HOH HOH B . D 2 HOH 15 115 29 HOH HOH B . D 2 HOH 16 116 34 HOH HOH B . D 2 HOH 17 117 35 HOH HOH B . D 2 HOH 18 118 38 HOH HOH B . D 2 HOH 19 119 42 HOH HOH B . D 2 HOH 20 120 43 HOH HOH B . D 2 HOH 21 121 45 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # 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)' 1460 ? 1 MORE -5 ? 1 'SSA (A^2)' 5170 ? # _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 # 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 2014-02-19 2 'Structure model' 1 1 2014-12-10 3 'Structure model' 1 2 2020-10-21 4 'Structure model' 1 3 2023-09-20 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 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' reflns_shell 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 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' '_reflns_shell.Rmerge_I_obs' 2 3 'Structure model' '_reflns_shell.pdbx_Rsym_value' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' # 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[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 9.5823 12.0202 23.3993 0.1935 0.3024 0.2661 0.0370 0.0098 -0.0221 1.2664 2.3356 5.9608 0.9078 -0.2788 -3.4059 0.0234 0.2323 0.0572 0.0196 0.1263 0.1409 -0.0380 -0.2980 -0.1513 'X-RAY DIFFRACTION' 2 ? refined 9.2229 11.7887 20.5773 0.2590 0.3357 0.2803 0.0276 -0.0091 0.0449 5.2683 1.8366 2.4457 1.4676 -1.2619 0.4985 0.0298 0.8860 0.2783 -0.1578 0.1950 0.0600 -0.0663 -0.1599 -0.2360 # 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.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 1 through 14 ) ; 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? ;chain 'B' and (resid 1 through 14 ) ; # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MxCuBE 'data collection' . ? 1 AMoRE phasing . ? 2 PHENIX refinement '(phenix.refine: 1.8_1069)' ? 3 MOSFLM 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # 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 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.67 108.30 2.37 0.30 N 2 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 110.93 108.30 2.63 0.30 N 3 1 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? N9 B DG 6 ? ? 110.11 108.30 1.81 0.30 N 4 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 112.03 108.30 3.73 0.30 N 5 1 "O4'" B DG 13 ? ? "C4'" B DG 13 ? ? "C3'" B DG 13 ? ? 101.84 104.50 -2.66 0.40 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 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 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 # 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 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4OKL 'double helix' 4OKL 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 14 1_555 0.185 -0.178 -0.390 7.811 -3.235 -1.831 1 A_DC1:DG14_B A 1 ? B 14 ? 19 1 1 A DC 2 1_555 B DG 13 1_555 0.244 -0.331 -0.046 3.955 -2.512 -0.470 2 A_DC2:DG13_B A 2 ? B 13 ? 19 1 1 A DC 3 1_555 B DG 12 1_555 0.063 -0.195 -0.318 5.401 -0.603 -0.375 3 A_DC3:DG12_B A 3 ? B 12 ? 19 1 1 A DC 4 1_555 B DG 11 1_555 0.176 -0.138 -0.199 4.185 0.670 -1.688 4 A_DC4:DG11_B A 4 ? B 11 ? 19 1 1 A DG 5 1_555 B DC 10 1_555 -0.325 -0.290 0.129 8.857 -8.167 -3.479 5 A_DG5:DC10_B A 5 ? B 10 ? 19 1 1 A DG 6 1_555 B DC 9 1_555 -0.489 -0.147 -0.319 -12.481 -13.577 4.808 6 A_DG6:DC9_B A 6 ? B 9 ? 19 1 1 A DT 7 1_555 B DA 8 1_555 -0.084 -0.140 0.039 -6.027 -5.276 0.811 7 A_DT7:DA8_B A 7 ? B 8 ? 20 1 1 A DA 8 1_555 B DT 7 1_555 -0.025 -0.225 0.274 1.503 -7.715 2.168 8 A_DA8:DT7_B A 8 ? B 7 ? 20 1 1 A DC 9 1_555 B DG 6 1_555 0.358 -0.121 -0.071 6.947 -15.770 5.759 9 A_DC9:DG6_B A 9 ? B 6 ? 19 1 1 A DC 10 1_555 B DG 5 1_555 0.241 -0.222 0.011 -4.300 -7.915 -0.791 10 A_DC10:DG5_B A 10 ? B 5 ? 19 1 1 A DG 11 1_555 B DC 4 1_555 -0.262 -0.184 -0.180 -6.099 -1.630 0.032 11 A_DG11:DC4_B A 11 ? B 4 ? 19 1 1 A DG 12 1_555 B DC 3 1_555 -0.201 -0.194 -0.245 -11.647 -4.795 -0.257 12 A_DG12:DC3_B A 12 ? B 3 ? 19 1 1 A DG 13 1_555 B DC 2 1_555 -0.201 -0.154 0.003 -4.957 1.463 -0.027 13 A_DG13:DC2_B A 13 ? B 2 ? 19 1 1 A DG 14 1_555 B DC 1 1_555 -0.283 -0.115 0.089 5.817 1.252 -0.952 14 A_DG14:DC1_B A 14 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 14 1_555 A DC 2 1_555 B DG 13 1_555 -0.543 -2.305 3.448 -4.115 2.433 28.389 -5.202 0.138 3.287 4.917 8.316 28.780 1 AA_DC1DC2:DG13DG14_BB A 1 ? B 14 ? A 2 ? B 13 ? 1 A DC 2 1_555 B DG 13 1_555 A DC 3 1_555 B DG 12 1_555 -0.211 -2.162 3.292 0.647 -0.640 26.888 -4.480 0.622 3.336 -1.377 -1.391 26.903 2 AA_DC2DC3:DG12DG13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A DC 3 1_555 B DG 12 1_555 A DC 4 1_555 B DG 11 1_555 -0.557 -2.060 3.442 -3.575 -0.348 30.859 -3.776 0.309 3.505 -0.652 6.690 31.063 3 AA_DC3DC4:DG11DG12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A DC 4 1_555 B DG 11 1_555 A DG 5 1_555 B DC 10 1_555 -1.151 -1.786 3.210 -4.229 4.320 24.745 -5.248 1.441 3.011 9.894 9.685 25.461 4 AA_DC4DG5:DC10DG11_BB A 4 ? B 11 ? A 5 ? B 10 ? 1 A DG 5 1_555 B DC 10 1_555 A DG 6 1_555 B DC 9 1_555 1.359 -1.027 3.773 7.305 12.813 37.428 -3.171 -1.026 3.450 19.084 -10.881 40.132 5 AA_DG5DG6:DC9DC10_BB A 5 ? B 10 ? A 6 ? B 9 ? 1 A DG 6 1_555 B DC 9 1_555 A DT 7 1_555 B DA 8 1_555 -0.516 -1.244 3.202 -0.668 3.234 29.351 -3.100 0.877 3.061 6.357 1.314 29.532 6 AA_DG6DT7:DA8DC9_BB A 6 ? B 9 ? A 7 ? B 8 ? 1 A DT 7 1_555 B DA 8 1_555 A DA 8 1_555 B DT 7 1_555 0.279 -1.075 3.031 -0.881 7.265 31.765 -3.043 -0.634 2.716 13.058 1.583 32.576 7 AA_DT7DA8:DT7DA8_BB A 7 ? B 8 ? A 8 ? B 7 ? 1 A DA 8 1_555 B DT 7 1_555 A DC 9 1_555 B DG 6 1_555 0.532 -1.336 3.185 2.375 6.298 32.696 -3.312 -0.556 2.914 11.041 -4.164 33.363 8 AA_DA8DC9:DG6DT7_BB A 8 ? B 7 ? A 9 ? B 6 ? 1 A DC 9 1_555 B DG 6 1_555 A DC 10 1_555 B DG 5 1_555 -1.176 -1.631 3.427 -2.699 15.102 32.421 -4.742 1.541 2.531 25.354 4.532 35.779 9 AA_DC9DC10:DG5DG6_BB A 9 ? B 6 ? A 10 ? B 5 ? 1 A DC 10 1_555 B DG 5 1_555 A DG 11 1_555 B DC 4 1_555 1.209 -1.961 3.345 4.465 5.483 25.535 -5.724 -1.465 3.028 12.112 -9.864 26.480 10 AA_DC10DG11:DC4DG5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A DG 11 1_555 B DC 4 1_555 A DG 12 1_555 B DC 3 1_555 0.392 -2.101 3.541 3.839 1.420 31.912 -4.064 0.030 3.469 2.569 -6.946 32.167 11 AA_DG11DG12:DC3DC4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A DG 12 1_555 B DC 3 1_555 A DG 13 1_555 B DC 2 1_555 0.107 -2.076 3.185 -0.705 -1.986 28.127 -3.799 -0.384 3.317 -4.079 1.449 28.204 12 AA_DG12DG13:DC2DC3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 A DG 13 1_555 B DC 2 1_555 A DG 14 1_555 B DC 1 1_555 0.613 -2.344 3.070 1.124 -2.234 25.217 -4.713 -1.080 3.286 -5.102 -2.566 25.339 13 AA_DG13DG14:DC1DC2_BB A 13 ? B 2 ? A 14 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3V9D _pdbx_initial_refinement_model.details 'PDB ENTRY 3V9D' #