data_3OT0 # _entry.id 3OT0 # _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 3OT0 pdb_00003ot0 10.2210/pdb3ot0/pdb NDB NA0821 ? ? RCSB RCSB061535 ? ? WWPDB D_1000061535 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1DPL ;Same sequence containing a C at position 2 and a 2'-O-methoxymethyl T at position 6 ; unspecified PDB 1KGK ;Same sequence containing a phenoxazine-derived G-clamp modified C at position 2 and a 2'-O-methoxymethyl T at position 6 ; unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3OT0 _pdbx_database_status.recvd_initial_deposition_date 2010-09-10 _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 _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _audit_author.name 'Edwards, T.E.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 10 _citation.page_first 4419 _citation.page_last 4426 _citation.year 2011 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21252294 _citation.pdbx_database_id_DOI 10.1093/nar/gkr015 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Edwards, T.E.' 1 ? primary 'Cekan, P.' 2 ? primary 'Reginsson, G.W.' 3 ? primary 'Shelke, S.A.' 4 ? primary ;Ferre-D'Amare, A.R. ; 5 ? primary 'Schiemann, O.' 6 ? primary 'Sigurdsson, S.T.' 7 ? # _cell.entry_id 3OT0 _cell.length_a 24.710 _cell.length_b 44.550 _cell.length_c 45.940 _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 3OT0 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 'Spin-labeled DNA' 3263.234 2 ? ? ? ? 2 water nat water 18.015 83 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(EXC)(DG)(DT)(DA)(OMU)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GXGTAUACGC _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 DG n 1 2 EXC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 OMU n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC 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 'Chemical synthesis' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3OT0 _struct_ref.pdbx_db_accession 3OT0 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GXGTAUACGC _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 3OT0 A 1 ? 10 ? 3OT0 1 ? 10 ? 1 10 2 1 3OT0 B 1 ? 10 ? 3OT0 1 ? 10 ? 1 10 # 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 EXC 'DNA linking' n ;3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-7,7,9,9-tetramethyl-7,8,9,11-tetrahydropyrimido[4',5' :5,6][1,4]oxazino[2,3-f]isoindol-2(3H)-one radical ; 'nitroxide spin-labeled nucleotide C-spin' 'C21 H26 N4 O9 P' 509.426 HOH non-polymer . WATER ? 'H2 O' 18.015 OMU 'RNA linking' n ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; ? 'C10 H15 N2 O9 P' 338.208 # _exptl.entry_id 3OT0 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.94 _exptl_crystal.density_percent_sol 36.51 _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 289 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;1.2 mM DNA in 10% 2-methane-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 12 mM spermine-HCl, 80 mM NaCl, 12 mM KCl, 12 mM MgCl2 against a reserviore of 35% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 289K ; _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 'RIGAKU SATURN 944+' _diffrn_detector.pdbx_collection_date 2010-04-17 _diffrn_detector.details VariMax # _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU FR-E+ SUPERBRIGHT' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 3OT0 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.7 _reflns.number_obs 5613 _reflns.number_all 5955 _reflns.percent_possible_obs 94.3 _reflns.pdbx_Rmerge_I_obs 0.022 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 53.95 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.4 _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 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_redundancy _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 _reflns_shell.pdbx_diffrn_id 1.70 1.74 82.9 0.070 ? 20.03 6.4 ? 427 ? ? ? ? 1 1 1.74 1.79 83.9 0.066 ? 22.09 ? ? 415 ? ? ? ? 2 1 1.79 1.84 86.8 0.062 ? 24.02 ? ? 408 ? ? ? ? 3 1 1.84 1.90 89.4 0.059 ? 24.38 ? ? 397 ? ? ? ? 4 1 1.90 1.96 92.7 0.051 ? 29.14 ? ? 383 ? ? ? ? 5 1 1.96 2.03 93.6 0.044 ? 34.12 ? ? 374 ? ? ? ? 6 1 2.03 2.11 95.6 0.041 ? 36.44 ? ? 363 ? ? ? ? 7 1 2.11 2.19 96.9 0.042 ? 37.82 ? ? 351 ? ? ? ? 8 1 2.19 2.29 98.2 0.034 ? 46.96 ? ? 332 ? ? ? ? 9 1 2.29 2.40 98.1 0.030 ? 52.62 ? ? 315 ? ? ? ? 10 1 2.40 2.53 99.0 0.031 ? 58.44 ? ? 311 ? ? ? ? 11 1 2.53 2.69 98.3 0.030 ? 64.15 ? ? 294 ? ? ? ? 12 1 2.69 2.87 98.6 0.026 ? 71.03 ? ? 277 ? ? ? ? 13 1 2.87 3.10 99.6 0.021 ? 83.74 ? ? 263 ? ? ? ? 14 1 3.10 3.40 98.7 0.018 ? 102.89 ? ? 238 ? ? ? ? 15 1 3.40 3.80 100.0 0.018 ? 111.58 ? ? 214 ? ? ? ? 16 1 3.80 4.39 100.0 0.017 ? 115.45 ? ? 198 ? ? ? ? 17 1 4.39 5.38 100.0 0.019 ? 111.51 ? ? 170 ? ? ? ? 18 1 5.38 7.60 100.0 0.020 ? 108.16 ? ? 139 ? ? ? ? 19 1 7.60 50 100.0 0.020 ? 100.41 ? ? 86 ? ? ? ? 20 1 # _refine.entry_id 3OT0 _refine.ls_number_reflns_obs 5586 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.37 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 16.824 _refine.ls_d_res_high 1.7004 _refine.ls_percent_reflns_obs 93.99 _refine.ls_R_factor_obs 0.1632 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1594 _refine.ls_R_factor_R_free 0.1975 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.54 _refine.ls_number_reflns_R_free 533 _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] -0.0439 _refine.aniso_B[2][2] -0.3863 _refine.aniso_B[3][3] 0.4302 _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 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.406 _refine.solvent_model_param_bsol 45.023 _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 1KGK' _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 ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.17 _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_overall_phase_error 19.50 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _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 436 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 83 _refine_hist.number_atoms_total 519 _refine_hist.d_res_high 1.7004 _refine_hist.d_res_low 16.824 # 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 f_bond_d 0.007 ? ? 490 'X-RAY DIFFRACTION' ? f_angle_d 1.738 ? ? 762 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 25.722 ? ? 208 'X-RAY DIFFRACTION' ? f_chiral_restr 0.067 ? ? 80 'X-RAY DIFFRACTION' ? f_plane_restr 0.007 ? ? 22 '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 . 1.7004 1.8713 1105 0.1380 85.00 0.2182 . . 116 . . . . 'X-RAY DIFFRACTION' . 1.8713 2.1416 1253 0.1584 94.00 0.2342 . . 117 . . . . 'X-RAY DIFFRACTION' . 2.1416 2.6964 1290 0.1770 98.00 0.2186 . . 152 . . . . 'X-RAY DIFFRACTION' . 2.6964 16.8246 1405 0.1557 99.00 0.1728 . . 148 . . . . 'X-RAY DIFFRACTION' # _struct.entry_id 3OT0 _struct.title 'Crystal structure of a DNA containing the rigid nitroxide spin-labeled nucleotide C-spin' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3OT0 _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;nitroxide, spin-label, EPR spectroscopy, fluorescence spectroscopy, modified nucleic acid, C-spin, deoxycytosine analog, phenoxazine, spectroscopic probe, PELDOR, 2'-O-methyl U, 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 covale1 covale both ? A DG 1 "O3'" ? ? ? 1_555 A EXC 2 P ? ? A DG 1 A EXC 2 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale2 covale both ? A DA 5 "O3'" ? ? ? 1_555 A OMU 6 P ? ? A DA 5 A OMU 6 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale3 covale both ? A OMU 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A OMU 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale4 covale both ? B DG 1 "O3'" ? ? ? 1_555 B EXC 2 P ? ? B DG 1 B EXC 2 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale5 covale both ? B DA 5 "O3'" ? ? ? 1_555 B OMU 6 P ? ? B DA 5 B OMU 6 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale6 covale both ? B OMU 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B OMU 6 B DA 7 1_555 ? ? ? ? ? ? ? 1.608 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B OMU 6 N3 ? ? A DA 5 B OMU 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B OMU 6 O4 ? ? A DA 5 B OMU 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A OMU 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A OMU 6 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A OMU 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A OMU 6 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 3OT0 _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 3OT0 _atom_sites.fract_transf_matrix[1][1] 0.040469 _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] 0.022447 _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] 0.021768 _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 DG 1 1 1 DG DG A . n A 1 2 EXC 2 2 2 EXC EXC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DT 4 4 4 DT DT A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 OMU 6 6 6 OMU OMU A . n A 1 7 DA 7 7 7 DA DA A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DC 10 10 10 DC DC A . n B 1 1 DG 1 1 1 DG DG B . n B 1 2 EXC 2 2 2 EXC EXC B . n B 1 3 DG 3 3 3 DG DG B . n B 1 4 DT 4 4 4 DT DT B . n B 1 5 DA 5 5 5 DA DA B . n B 1 6 OMU 6 6 6 OMU OMU B . n B 1 7 DA 7 7 7 DA DA B . n B 1 8 DC 8 8 8 DC DC B . n B 1 9 DG 9 9 9 DG DG B . n B 1 10 DC 10 10 10 DC DC 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 11 11 HOH HOH A . C 2 HOH 2 12 2 HOH HOH A . C 2 HOH 3 13 13 HOH HOH A . C 2 HOH 4 14 14 HOH HOH A . C 2 HOH 5 15 15 HOH HOH A . C 2 HOH 6 16 5 HOH HOH A . C 2 HOH 7 17 7 HOH HOH A . C 2 HOH 8 18 18 HOH HOH A . C 2 HOH 9 19 19 HOH HOH A . C 2 HOH 10 20 20 HOH HOH A . C 2 HOH 11 21 21 HOH HOH A . C 2 HOH 12 22 22 HOH HOH A . C 2 HOH 13 23 23 HOH HOH A . C 2 HOH 14 24 24 HOH HOH A . C 2 HOH 15 25 25 HOH HOH A . C 2 HOH 16 26 26 HOH HOH A . C 2 HOH 17 27 27 HOH HOH A . C 2 HOH 18 28 8 HOH HOH A . C 2 HOH 19 29 9 HOH HOH A . C 2 HOH 20 37 37 HOH HOH A . C 2 HOH 21 38 38 HOH HOH A . C 2 HOH 22 39 39 HOH HOH A . C 2 HOH 23 40 40 HOH HOH A . C 2 HOH 24 41 41 HOH HOH A . C 2 HOH 25 44 44 HOH HOH A . C 2 HOH 26 45 45 HOH HOH A . C 2 HOH 27 46 46 HOH HOH A . C 2 HOH 28 47 47 HOH HOH A . C 2 HOH 29 48 48 HOH HOH A . C 2 HOH 30 49 49 HOH HOH A . C 2 HOH 31 50 50 HOH HOH A . C 2 HOH 32 51 51 HOH HOH A . C 2 HOH 33 53 53 HOH HOH A . C 2 HOH 34 54 54 HOH HOH A . C 2 HOH 35 55 55 HOH HOH A . C 2 HOH 36 56 56 HOH HOH A . C 2 HOH 37 57 57 HOH HOH A . C 2 HOH 38 58 58 HOH HOH A . C 2 HOH 39 59 59 HOH HOH A . C 2 HOH 40 60 60 HOH HOH A . C 2 HOH 41 66 66 HOH HOH A . C 2 HOH 42 67 67 HOH HOH A . C 2 HOH 43 68 68 HOH HOH A . C 2 HOH 44 71 71 HOH HOH A . C 2 HOH 45 72 72 HOH HOH A . C 2 HOH 46 77 77 HOH HOH A . C 2 HOH 47 78 78 HOH HOH A . C 2 HOH 48 80 80 HOH HOH A . C 2 HOH 49 81 81 HOH HOH A . C 2 HOH 50 82 82 HOH HOH A . D 2 HOH 1 11 1 HOH HOH B . D 2 HOH 2 12 12 HOH HOH B . D 2 HOH 3 13 3 HOH HOH B . D 2 HOH 4 14 4 HOH HOH B . D 2 HOH 5 15 6 HOH HOH B . D 2 HOH 6 16 16 HOH HOH B . D 2 HOH 7 17 17 HOH HOH B . D 2 HOH 8 18 10 HOH HOH B . D 2 HOH 9 28 28 HOH HOH B . D 2 HOH 10 29 29 HOH HOH B . D 2 HOH 11 30 30 HOH HOH B . D 2 HOH 12 31 31 HOH HOH B . D 2 HOH 13 32 32 HOH HOH B . D 2 HOH 14 33 33 HOH HOH B . D 2 HOH 15 34 34 HOH HOH B . D 2 HOH 16 35 35 HOH HOH B . D 2 HOH 17 36 36 HOH HOH B . D 2 HOH 18 42 42 HOH HOH B . D 2 HOH 19 43 43 HOH HOH B . D 2 HOH 20 52 52 HOH HOH B . D 2 HOH 21 61 61 HOH HOH B . D 2 HOH 22 62 62 HOH HOH B . D 2 HOH 23 63 63 HOH HOH B . D 2 HOH 24 64 64 HOH HOH B . D 2 HOH 25 65 65 HOH HOH B . D 2 HOH 26 69 69 HOH HOH B . D 2 HOH 27 70 70 HOH HOH B . D 2 HOH 28 73 73 HOH HOH B . D 2 HOH 29 74 74 HOH HOH B . D 2 HOH 30 75 75 HOH HOH B . D 2 HOH 31 76 76 HOH HOH B . D 2 HOH 32 79 79 HOH HOH B . D 2 HOH 33 83 83 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A EXC 2 A EXC 2 ? DC ? 2 A OMU 6 A OMU 6 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 3 B EXC 2 B EXC 2 ? DC ? 4 B OMU 6 B OMU 6 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _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 2011-01-19 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2020-07-22 4 'Structure model' 1 3 2023-09-06 # _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' 'Version format compliance' 2 3 'Structure model' 'Derived calculations' 3 3 'Structure model' 'Structure summary' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp 2 3 'Structure model' pdbx_struct_assembly 3 3 'Structure model' pdbx_struct_assembly_gen 4 3 'Structure model' struct_conn 5 4 'Structure model' chem_comp_atom 6 4 'Structure model' chem_comp_bond 7 4 'Structure model' database_2 8 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' '_chem_comp.name' 2 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal StructureStudio 'data collection' . ? 1 PHASER phasing . ? 2 PHENIX refinement '(phenix.refine: 1.6.1_357)' ? 3 XDS 'data reduction' . ? 4 XSCALE '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 "C3'" A DG 9 ? ? "C2'" A DG 9 ? ? "C1'" A DG 9 ? ? 97.32 102.40 -5.08 0.80 N 2 1 "O4'" B DG 3 ? ? "C4'" B DG 3 ? ? "C3'" B DG 3 ? ? 101.34 104.50 -3.16 0.40 N 3 1 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 110.11 108.30 1.81 0.30 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 EXC P P N N 144 EXC C1 C N N 145 EXC N2 N N N 146 EXC C3 C N N 147 EXC N4 N N N 148 EXC C5 C N N 149 EXC C6 C N N 150 EXC N7 N N N 151 EXC C8 C Y N 152 EXC C9 C Y N 153 EXC "C1'" C N R 154 EXC O10 O N N 155 EXC C11 C Y N 156 EXC C12 C Y N 157 EXC C13 C Y N 158 EXC C14 C Y N 159 EXC C15 C N N 160 EXC N16 N N N 161 EXC C17 C N N 162 EXC O18 O N N 163 EXC C19 C N N 164 EXC "C2'" C N N 165 EXC C20 C N N 166 EXC O21 O N N 167 EXC C22 C N N 168 EXC C23 C N N 169 EXC "C3'" C N S 170 EXC "O3'" O N N 171 EXC "C4'" C N R 172 EXC "O4'" O N N 173 EXC "C5'" C N N 174 EXC "O5'" O N N 175 EXC OP1 O N N 176 EXC OP2 O N N 177 EXC OP3 O N N 178 EXC H5 H N N 179 EXC "H1'" H N N 180 EXC H11 H N N 181 EXC H14 H N N 182 EXC H19 H N N 183 EXC H19A H N N 184 EXC H19B H N N 185 EXC "H2'" H N N 186 EXC "H2'A" H N N 187 EXC H20 H N N 188 EXC H20A H N N 189 EXC H20B H N N 190 EXC H22 H N N 191 EXC H22A H N N 192 EXC H22B H N N 193 EXC H23 H N N 194 EXC H23A H N N 195 EXC H23B H N N 196 EXC "H3'" H N N 197 EXC "HO3'" H N N 198 EXC "H4'" H N N 199 EXC "H5'" H N N 200 EXC "H5'A" H N N 201 EXC HOP1 H N N 202 EXC HOP3 H N N 203 EXC H26 H N N 204 HOH O O N N 205 HOH H1 H N N 206 HOH H2 H N N 207 OMU N1 N N N 208 OMU C2 C N N 209 OMU N3 N N N 210 OMU C4 C N N 211 OMU C5 C N N 212 OMU C6 C N N 213 OMU O2 O N N 214 OMU O4 O N N 215 OMU "C1'" C N R 216 OMU "C2'" C N R 217 OMU "O2'" O N N 218 OMU CM2 C N N 219 OMU "C3'" C N R 220 OMU "C4'" C N R 221 OMU "O3'" O N N 222 OMU "O4'" O N N 223 OMU "C5'" C N N 224 OMU "O5'" O N N 225 OMU P P N N 226 OMU OP1 O N N 227 OMU OP2 O N N 228 OMU OP3 O N N 229 OMU HN3 H N N 230 OMU H5 H N N 231 OMU H6 H N N 232 OMU "H1'" H N N 233 OMU "H2'" H N N 234 OMU HM21 H N N 235 OMU HM22 H N N 236 OMU HM23 H N N 237 OMU "H3'" H N N 238 OMU "H4'" H N N 239 OMU "HO3'" H N N 240 OMU "H5'" H N N 241 OMU "H5''" H N N 242 OMU HOP2 H N N 243 OMU HOP3 H N N 244 # 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 EXC P OP3 sing N N 150 EXC P OP1 sing N N 151 EXC C1 C6 sing N N 152 EXC N2 C1 doub N N 153 EXC N2 C3 sing N N 154 EXC C3 N4 sing N N 155 EXC N4 "C1'" sing N N 156 EXC N4 C5 sing N N 157 EXC C5 H5 sing N N 158 EXC C6 C5 doub N N 159 EXC C6 O10 sing N N 160 EXC N7 C1 sing N N 161 EXC N7 C8 sing N N 162 EXC C8 C9 sing Y N 163 EXC C9 O10 sing N N 164 EXC C9 C11 doub Y N 165 EXC "C1'" "C2'" sing N N 166 EXC "C1'" "O4'" sing N N 167 EXC "C1'" "H1'" sing N N 168 EXC C11 H11 sing N N 169 EXC C12 C11 sing Y N 170 EXC C12 C17 sing N N 171 EXC C13 C12 doub Y N 172 EXC C14 C8 doub Y N 173 EXC C14 C13 sing Y N 174 EXC C14 H14 sing N N 175 EXC C15 C13 sing N N 176 EXC C15 N16 sing N N 177 EXC N16 O21 sing N N 178 EXC N16 C17 sing N N 179 EXC C17 C23 sing N N 180 EXC C17 C22 sing N N 181 EXC O18 C3 doub N N 182 EXC C19 C15 sing N N 183 EXC C19 H19 sing N N 184 EXC C19 H19A sing N N 185 EXC C19 H19B sing N N 186 EXC "C2'" "C3'" sing N N 187 EXC "C2'" "H2'" sing N N 188 EXC "C2'" "H2'A" sing N N 189 EXC C20 C15 sing N N 190 EXC C20 H20 sing N N 191 EXC C20 H20A sing N N 192 EXC C20 H20B sing N N 193 EXC C22 H22 sing N N 194 EXC C22 H22A sing N N 195 EXC C22 H22B sing N N 196 EXC C23 H23 sing N N 197 EXC C23 H23A sing N N 198 EXC C23 H23B sing N N 199 EXC "C3'" "O3'" sing N N 200 EXC "C3'" "C4'" sing N N 201 EXC "C3'" "H3'" sing N N 202 EXC "O3'" "HO3'" sing N N 203 EXC "C4'" "C5'" sing N N 204 EXC "C4'" "H4'" sing N N 205 EXC "O4'" "C4'" sing N N 206 EXC "C5'" "O5'" sing N N 207 EXC "C5'" "H5'" sing N N 208 EXC "C5'" "H5'A" sing N N 209 EXC "O5'" P sing N N 210 EXC OP1 HOP1 sing N N 211 EXC OP2 P doub N N 212 EXC OP3 HOP3 sing N N 213 EXC N7 H26 sing N N 214 HOH O H1 sing N N 215 HOH O H2 sing N N 216 OMU N1 C2 sing N N 217 OMU N1 C6 sing N N 218 OMU N1 "C1'" sing N N 219 OMU C2 N3 sing N N 220 OMU C2 O2 doub N N 221 OMU N3 C4 sing N N 222 OMU N3 HN3 sing N N 223 OMU C4 C5 sing N N 224 OMU C4 O4 doub N N 225 OMU C5 C6 doub N N 226 OMU C5 H5 sing N N 227 OMU C6 H6 sing N N 228 OMU "C1'" "C2'" sing N N 229 OMU "C1'" "O4'" sing N N 230 OMU "C1'" "H1'" sing N N 231 OMU "C2'" "O2'" sing N N 232 OMU "C2'" "C3'" sing N N 233 OMU "C2'" "H2'" sing N N 234 OMU "O2'" CM2 sing N N 235 OMU CM2 HM21 sing N N 236 OMU CM2 HM22 sing N N 237 OMU CM2 HM23 sing N N 238 OMU "C3'" "C4'" sing N N 239 OMU "C3'" "O3'" sing N N 240 OMU "C3'" "H3'" sing N N 241 OMU "C4'" "O4'" sing N N 242 OMU "C4'" "C5'" sing N N 243 OMU "C4'" "H4'" sing N N 244 OMU "O3'" "HO3'" sing N N 245 OMU "C5'" "O5'" sing N N 246 OMU "C5'" "H5'" sing N N 247 OMU "C5'" "H5''" sing N N 248 OMU "O5'" P sing N N 249 OMU P OP1 doub N N 250 OMU P OP2 sing N N 251 OMU P OP3 sing N N 252 OMU OP2 HOP2 sing N N 253 OMU OP3 HOP3 sing N N 254 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3OT0 'double helix' 3OT0 '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 DG 1 1_555 B DC 10 1_555 -0.306 -0.099 0.117 1.881 -1.359 0.303 1 A_DG1:DC10_B A 1 ? B 10 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.348 -0.173 0.174 -7.970 -14.815 -0.010 2 A_DG3:DC8_B A 3 ? B 8 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.177 -0.125 0.111 -5.594 -18.043 -0.641 3 A_DT4:DA7_B A 4 ? B 7 ? 20 1 1 A DA 5 1_555 B OMU 6 1_555 0.160 -0.100 0.189 -1.604 -16.106 -2.892 4 A_DA5:OMU6_B A 5 ? B 6 ? 20 1 1 A OMU 6 1_555 B DA 5 1_555 0.043 -0.027 0.436 4.057 -13.973 8.548 5 A_OMU6:DA5_B A 6 ? B 5 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 -0.027 -0.127 0.016 6.640 -9.709 2.927 6 A_DA7:DT4_B A 7 ? B 4 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.220 -0.148 -0.229 8.754 -11.018 1.952 7 A_DC8:DG3_B A 8 ? B 3 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.216 -0.146 0.269 -4.483 4.730 -0.113 8 A_DC10:DG1_B A 10 ? 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 DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.124 -1.578 3.138 -1.886 4.140 36.802 -3.004 1.529 3.001 6.527 2.974 37.073 1 AA_DG3DT4:DA7DC8_BB A 3 ? B 8 ? A 4 ? B 7 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B OMU 6 1_555 0.543 -1.604 3.118 1.640 15.920 26.149 -5.651 -0.760 1.883 31.691 -3.264 30.584 2 AA_DT4DA5:OMU6DA7_BB A 4 ? B 7 ? A 5 ? B 6 ? 1 A DA 5 1_555 B OMU 6 1_555 A OMU 6 1_555 B DA 5 1_555 0.918 -1.302 3.057 -0.096 8.231 32.959 -3.401 -1.586 2.662 14.234 0.165 33.943 3 AA_DA5OMU6:DA5OMU6_BB A 5 ? B 6 ? A 6 ? B 5 ? 1 A OMU 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.344 -1.433 3.019 1.813 13.051 28.469 -4.699 0.922 2.146 24.920 -3.462 31.313 4 AA_OMU6DA7:DT4DA5_BB A 6 ? B 5 ? A 7 ? B 4 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 0.144 -1.780 3.358 1.208 3.478 31.031 -3.962 -0.039 3.148 6.473 -2.248 31.244 5 AA_DA7DC8:DG3DT4_BB A 7 ? B 4 ? A 8 ? B 3 ? # _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 1KGK _pdbx_initial_refinement_model.details 'PDB ENTRY 1KGK' #