data_4B8D # _entry.id 4B8D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 4B8D pdb_00004b8d 10.2210/pdb4b8d/pdb PDBE EBI-53887 ? ? WWPDB D_1290053887 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4B8D _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2012-08-26 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ducani, C.' 1 'Kaul, C.D.' 2 'Moche, M.' 3 'Shih, W.M.' 4 'Hogberg, B.' 5 # _citation.id primary _citation.title ;Enzymatic Production of 'Monoclonal Stoichiometric' Single-Stranded DNA Oligonucleotides ; _citation.journal_abbrev Nat.Methods _citation.journal_volume 10 _citation.page_first 647 _citation.page_last ? _citation.year 2013 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1548-7091 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23727986 _citation.pdbx_database_id_DOI 10.1038/NMETH.2503 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ducani, C.' 1 ? primary 'Kaul, C.D.' 2 ? primary 'Moche, M.' 3 ? primary 'Shih, W.M.' 4 ? primary 'Hogberg, B.' 5 ? # _cell.entry_id 4B8D _cell.length_a 106.437 _cell.length_b 106.437 _cell.length_c 95.154 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4B8D _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 # 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 man ;5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3' ; 6457.188 1 ? ? ? ? 2 polymer man "5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'" 2082.400 1 ? ? ? ? 3 polymer man "5'-D(*GP*GP*CP*TP*GP*CP)-3'" 1825.216 1 ? ? ? ? 4 polymer man "5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'" 2432.614 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no ;(DG)(DA)(DG)(DC)(DA)(DG)(DC)(DC)(DT)(DG)(DT)(DA)(DC)(DG)(DG)(DA)(DC)(DA)(DT)(DC) (DA) ; GAGCAGCCTGTACGGACATCA A ? 2 polydeoxyribonucleotide no no '(DC)(DC)(DG)(DT)(DA)(DC)(DA)' CCGTACA B ? 3 polydeoxyribonucleotide no no '(DG)(DG)(DC)(DT)(DG)(DC)' GGCTGC C ? 4 polydeoxyribonucleotide no no '(DT)(DC)(DT)(DG)(DA)(DT)(DG)(DT)' TCTGATGT D ? # 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 DA n 1 3 DG n 1 4 DC n 1 5 DA n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DT n 1 10 DG n 1 11 DT n 1 12 DA n 1 13 DC n 1 14 DG n 1 15 DG n 1 16 DA n 1 17 DC n 1 18 DA n 1 19 DT n 1 20 DC n 1 21 DA n 2 1 DC n 2 2 DC n 2 3 DG n 2 4 DT n 2 5 DA n 2 6 DC n 2 7 DA n 3 1 DG n 3 2 DG n 3 3 DC n 3 4 DT n 3 5 DG n 3 6 DC n 4 1 DT n 4 2 DC n 4 3 DT n 4 4 DG n 4 5 DA n 4 6 DT n 4 7 DG n 4 8 DT n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample ? ? ? ? ? ? ? ? ? ? ? ? 'SYNTHETIC CONSTRUCT' 32630 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 'SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED' 2 1 sample ? ? ? ? ? ? ? ? ? ? ? ? 'SYNTHETIC CONSTRUCT' 32630 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 'SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED' 3 1 sample ? ? ? ? ? ? ? ? ? ? ? ? 'SYNTHETIC CONSTRUCT' 32630 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 'SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED' 4 1 sample ? ? ? ? ? ? ? ? ? ? ? ? 'SYNTHETIC CONSTRUCT' 32630 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 'SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 4B8D 1 ? ? 4B8D ? 2 PDB 4B8D 2 ? ? 4B8D ? 3 PDB 4B8D 3 ? ? 4B8D ? 4 PDB 4B8D 4 ? ? 4B8D ? # 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 4B8D A 1 ? 21 ? 4B8D 101 ? 121 ? 101 121 2 2 4B8D B 1 ? 7 ? 4B8D 119 ? 125 ? 119 125 3 3 4B8D C 1 ? 6 ? 4B8D 209 ? 214 ? 209 214 4 4 4B8D D 1 ? 8 ? 4B8D 101 ? 108 ? 101 108 # 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 # _exptl.entry_id 4B8D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 8.59 _exptl_crystal.density_percent_sol 85.56 _exptl_crystal.description NONE # _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 2012-04-25 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.91841 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'BESSY BEAMLINE 14.1' _diffrn_source.pdbx_synchrotron_site BESSY _diffrn_source.pdbx_synchrotron_beamline 14.1 _diffrn_source.pdbx_wavelength 0.91841 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4B8D _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 42.30 _reflns.d_resolution_high 4.79 _reflns.number_obs 1980 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 16.30 _reflns.B_iso_Wilson_estimate 273.09 _reflns.pdbx_redundancy 5.8 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 4.79 _reflns_shell.d_res_low 5.05 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.80 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.30 _reflns_shell.pdbx_redundancy 5.8 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4B8D _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 1980 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 42.28 _refine.ls_d_res_high 4.79 _refine.ls_percent_reflns_obs 99.60 _refine.ls_R_factor_obs 0.1872 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1848 _refine.ls_R_factor_R_free 0.2046 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.34 _refine.ls_number_reflns_R_free 185 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.8711 _refine.correlation_coeff_Fo_to_Fc_free 0.8744 _refine.B_iso_mean 20.00 _refine.aniso_B[1][1] 65.6198 _refine.aniso_B[2][2] 65.6198 _refine.aniso_B[3][3] -131.2396 _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.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=0. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=861. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2. ; _refine.pdbx_starting_model 'PDB ENTRY 3GBI' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _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.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI 0.644 # _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.entry_id 4B8D _refine_analyze.Luzzati_coordinate_error_obs 0.672 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? # _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 863 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 863 _refine_hist.d_res_high 4.79 _refine_hist.d_res_low 42.28 # 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 t_bond_d 0.010 ? 2.00 988 'X-RAY DIFFRACTION' HARMONIC t_angle_deg 2.46 ? 2.00 1517 'X-RAY DIFFRACTION' HARMONIC t_dihedral_angle_d ? ? 2.00 514 'X-RAY DIFFRACTION' SINUSOIDAL t_incorr_chiral_ct ? ? ? ? 'X-RAY DIFFRACTION' ? t_pseud_angle ? ? ? ? 'X-RAY DIFFRACTION' ? t_trig_c_planes ? ? ? ? 'X-RAY DIFFRACTION' ? t_gen_planes ? ? 5.00 42 'X-RAY DIFFRACTION' HARMONIC t_it ? ? 20.00 988 'X-RAY DIFFRACTION' HARMONIC t_nbd ? ? 5.00 0 'X-RAY DIFFRACTION' SEMIHARMONIC t_omega_torsion ? ? ? ? 'X-RAY DIFFRACTION' ? t_other_torsion 29.75 ? ? ? 'X-RAY DIFFRACTION' ? t_improper_torsion ? ? ? ? 'X-RAY DIFFRACTION' ? t_chiral_improper_torsion ? ? 5.00 130 'X-RAY DIFFRACTION' SEMIHARMONIC t_sum_occupancies ? ? ? ? 'X-RAY DIFFRACTION' ? t_utility_distance ? ? ? ? 'X-RAY DIFFRACTION' ? t_utility_angle ? ? ? ? 'X-RAY DIFFRACTION' ? t_utility_torsion ? ? ? ? 'X-RAY DIFFRACTION' ? t_ideal_dist_contact ? ? 4.00 1014 'X-RAY DIFFRACTION' SEMIHARMONIC # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 5 _refine_ls_shell.d_res_high 4.79 _refine_ls_shell.d_res_low 5.36 _refine_ls_shell.number_reflns_R_work 509 _refine_ls_shell.R_factor_R_work 0.2433 _refine_ls_shell.percent_reflns_obs 99.60 _refine_ls_shell.R_factor_R_free 0.2933 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free 8.78 _refine_ls_shell.number_reflns_R_free 49 _refine_ls_shell.number_reflns_all 558 _refine_ls_shell.R_factor_all 0.2475 # _struct.entry_id 4B8D _struct.title 'TENSEGRITY TRIANGLE FROM ENZYMATICALLY MANUFACTURED DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4B8D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, ROLLING CIRCLE AMPLIFICATION, DNA ORIGAMI' # 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 3 ? D N N 4 ? # _struct_biol.id 1 # 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 DG 3 N1 ? ? ? 1_555 C DC 6 N3 ? ? A DG 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 3 N2 ? ? ? 1_555 C DC 6 O2 ? ? A DG 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 3 O6 ? ? ? 1_555 C DC 6 N4 ? ? A DG 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DG 5 O6 ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog5 hydrog ? ? A DG 6 O6 ? ? ? 1_555 C DC 3 N4 ? ? A DG 106 C DC 211 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog6 hydrog ? ? A DC 7 N3 ? ? ? 1_555 C DG 2 N1 ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 7 N4 ? ? ? 1_555 C DG 2 O6 ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 7 O2 ? ? ? 1_555 C DG 2 N2 ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 8 N4 ? ? ? 1_555 C DG 1 O6 ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog10 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 109 B DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 109 B DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DA 5 N1 ? ? A DG 110 B DA 123 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog13 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DA 5 N6 ? ? A DG 110 B DA 123 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog14 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog20 hydrog ? ? A DG 14 N2 ? ? ? 1_555 B DC 2 N3 ? ? A DG 114 B DC 120 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog21 hydrog ? ? A DG 15 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog22 hydrog ? ? A DG 15 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 115 B DC 120 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog23 hydrog ? ? A DA 16 N1 ? ? ? 1_555 D DT 8 N3 ? ? A DA 116 D DT 108 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog24 hydrog ? ? A DC 17 N3 ? ? ? 1_555 D DG 7 N1 ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 17 N4 ? ? ? 1_555 D DG 7 O6 ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 17 O2 ? ? ? 1_555 D DG 7 N2 ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DA 18 N1 ? ? ? 1_555 D DT 6 N3 ? ? A DA 118 D DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DA 18 N6 ? ? ? 1_555 D DT 6 O4 ? ? A DA 118 D DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DT 19 N3 ? ? ? 1_555 D DA 5 N1 ? ? A DT 119 D DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DT 19 O4 ? ? ? 1_555 D DA 5 N6 ? ? A DT 119 D DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DA 21 N1 ? ? ? 1_555 D DC 2 N4 ? ? A DA 121 D DC 102 1_555 ? ? ? ? ? ? 'DA-DC MISPAIR' ? ? ? hydrog32 hydrog ? ? A DA 21 N3 ? ? ? 1_555 D DG 4 N2 ? ? A DA 121 D DG 104 1_555 ? ? ? ? ? ? 'DA-DG MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 4B8D _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 4B8D _atom_sites.fract_transf_matrix[1][1] 0.009395 _atom_sites.fract_transf_matrix[1][2] 0.005424 _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] 0.010849 _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] 0.010509 _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 1 101 101 DG DG A . n A 1 2 DA 2 102 102 DA DA A . n A 1 3 DG 3 103 103 DG DG A . n A 1 4 DC 4 104 104 DC DC A . n A 1 5 DA 5 105 105 DA DA A . n A 1 6 DG 6 106 106 DG DG A . n A 1 7 DC 7 107 107 DC DC A . n A 1 8 DC 8 108 108 DC DC A . n A 1 9 DT 9 109 109 DT DT A . n A 1 10 DG 10 110 110 DG DG A . n A 1 11 DT 11 111 111 DT DT A . n A 1 12 DA 12 112 112 DA DA A . n A 1 13 DC 13 113 113 DC DC A . n A 1 14 DG 14 114 114 DG DG A . n A 1 15 DG 15 115 115 DG DG A . n A 1 16 DA 16 116 116 DA DA A . n A 1 17 DC 17 117 117 DC DC A . n A 1 18 DA 18 118 118 DA DA A . n A 1 19 DT 19 119 119 DT DT A . n A 1 20 DC 20 120 120 DC DC A . n A 1 21 DA 21 121 121 DA DA A . n B 2 1 DC 1 119 119 DC DC B . n B 2 2 DC 2 120 120 DC DC B . n B 2 3 DG 3 121 121 DG DG B . n B 2 4 DT 4 122 122 DT DT B . n B 2 5 DA 5 123 123 DA DA B . n B 2 6 DC 6 124 124 DC DC B . n B 2 7 DA 7 125 125 DA DA B . n C 3 1 DG 1 209 209 DG DG C . n C 3 2 DG 2 210 210 DG DG C . n C 3 3 DC 3 211 211 DC DC C . n C 3 4 DT 4 212 212 DT DT C . n C 3 5 DG 5 213 213 DG DG C . n C 3 6 DC 6 214 214 DC DC C . n D 4 1 DT 1 101 101 DT DT D . n D 4 2 DC 2 102 102 DC DC D . n D 4 3 DT 3 103 103 DT DT D . n D 4 4 DG 4 104 104 DG DG D . n D 4 5 DA 5 105 105 DA DA D . n D 4 6 DT 6 106 106 DT DT D . n D 4 7 DG 7 107 107 DG DG D . n D 4 8 DT 8 108 108 DT DT D . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 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 2013-06-05 2 'Structure model' 1 1 2013-06-12 3 'Structure model' 1 2 2013-07-10 4 'Structure model' 1 3 2019-10-30 5 'Structure model' 1 4 2023-12-20 # _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' 'Database references' 3 4 'Structure model' Advisory 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' Other 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Database references' 9 5 '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 4 'Structure model' pdbx_database_status 2 4 'Structure model' pdbx_validate_symm_contact 3 4 'Structure model' struct_conn 4 4 'Structure model' struct_conn_type 5 5 'Structure model' chem_comp_atom 6 5 'Structure model' chem_comp_bond 7 5 'Structure model' database_2 8 5 '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 4 'Structure model' '_pdbx_database_status.status_code_sf' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal BUSTER refinement 2.11.2 ? 1 XDS 'data reduction' . ? 2 SCALA 'data scaling' . ? 3 MOLREP phasing . ? 4 # _pdbx_entry_details.entry_id 4B8D _pdbx_entry_details.compound_details ;THE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH INTERNAL 3-FOLD SYMMETRY. EXTENDING OF THE STRUCTURE UNIT IN 3-D SPACE RESULTS THE CRYSTAL AT R3 SPACE GROUP (REPRESENTED AS H3). THE DNA SEQUENCES OF THE 7 STRANDS ARE: (#1) 3 STRANDS 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP *CP*A)-3' (#2) 1 STRAND 5'-D(*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP* CP*G)-3' (#3) 3 STRANDS 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3' THE ASYMMETRIC UNIT IS COMPRISED OF ONE FULL #1 STRAND (CHAIN A), 7-RESIDUE REPEATING UNIT OF #2 STRAND (CHAIN B) AND TWO FRAGMENTS OF #3 STRAND (CHAINS C AND D). THE #2 STRAND SELF-ASSOICATES TO FORM A CIRCULAR DNA MOLECULE WITH INTERNAL 3-FOLD SYMMETRY. IT HAS 3 SYMMETRIC AND SEQUENTIAL REPEATING UNITS. CHAIN B IN THE ASYMMETRIC UNIT REPRESENTS ONE OF THESE REPEATING UNITS. CHAINS D (FIRST 8 RESIDUES OF STRAND #3) AND C (NEXT 6 RESIDUES OF STRAND #3) TOGETHER FORM THE THIRD DNA STRAND (#3) OF THE EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS - HENCE IT WAS DIVIDED INTO THE CURRENT CHAINS C AND D FOR CONVENIENT REPRESENTATION. CHAIN C (1_555) IS COVALENTLY LINKED TO CHAIN D OF ANOTHER ASYMMETRIC UNIT (3_555); AND CHAIN D (1_555) IS COVALENTLY LINKED TO CHAIN C OF ANOTHER ASYMMETRIC UNIT (2_555). THE SELECTION OF RESIDUES FROM THE DNA #2 AND #3 ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAIN A. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 P B DC 119 ? ? 1_555 "O3'" B DA 125 ? ? 2_555 1.59 2 1 P C DG 209 ? ? 1_555 "O3'" D DT 108 ? ? 3_555 1.60 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 P A DG 101 ? ? OP3 A DG 101 ? ? 1.483 1.607 -0.124 0.012 N 2 1 P D DT 101 ? ? OP3 D DT 101 ? ? 1.490 1.607 -0.117 0.012 N # 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 OP1 A DG 101 ? ? P A DG 101 ? ? OP2 A DG 101 ? ? 109.04 119.60 -10.56 1.50 N 2 1 "O4'" A DG 101 ? ? "C4'" A DG 101 ? ? "C3'" A DG 101 ? ? 99.28 104.50 -5.22 0.40 N 3 1 "C4'" A DG 101 ? ? "C3'" A DG 101 ? ? "C2'" A DG 101 ? ? 97.32 102.20 -4.88 0.70 N 4 1 "O4'" A DG 101 ? ? "C1'" A DG 101 ? ? N9 A DG 101 ? ? 112.14 108.30 3.84 0.30 N 5 1 "O4'" A DA 102 ? ? "C1'" A DA 102 ? ? N9 A DA 102 ? ? 117.67 108.30 9.37 0.30 N 6 1 "O4'" A DG 103 ? ? "C1'" A DG 103 ? ? N9 A DG 103 ? ? 116.30 108.30 8.00 0.30 N 7 1 "C3'" A DG 103 ? ? "O3'" A DG 103 ? ? P A DC 104 ? ? 129.95 119.70 10.25 1.20 Y 8 1 "O4'" A DC 104 ? ? "C1'" A DC 104 ? ? N1 A DC 104 ? ? 113.37 108.30 5.07 0.30 N 9 1 "C3'" A DC 104 ? ? "O3'" A DC 104 ? ? P A DA 105 ? ? 128.15 119.70 8.45 1.20 Y 10 1 "O4'" A DA 105 ? ? "C1'" A DA 105 ? ? N9 A DA 105 ? ? 110.64 108.30 2.34 0.30 N 11 1 "O4'" A DG 106 ? ? "C1'" A DG 106 ? ? N9 A DG 106 ? ? 112.74 108.30 4.44 0.30 N 12 1 "C3'" A DG 106 ? ? "O3'" A DG 106 ? ? P A DC 107 ? ? 133.80 119.70 14.10 1.20 Y 13 1 "O4'" A DC 107 ? ? "C1'" A DC 107 ? ? N1 A DC 107 ? ? 115.40 108.30 7.10 0.30 N 14 1 "O4'" A DC 108 ? ? "C4'" A DC 108 ? ? "C3'" A DC 108 ? ? 101.63 104.50 -2.87 0.40 N 15 1 "O4'" A DC 108 ? ? "C1'" A DC 108 ? ? N1 A DC 108 ? ? 113.39 108.30 5.09 0.30 N 16 1 N1 A DC 108 ? ? C2 A DC 108 ? ? O2 A DC 108 ? ? 122.88 118.90 3.98 0.60 N 17 1 "O4'" A DT 109 ? ? "C1'" A DT 109 ? ? N1 A DT 109 ? ? 112.56 108.30 4.26 0.30 N 18 1 N3 A DT 109 ? ? C2 A DT 109 ? ? O2 A DT 109 ? ? 118.55 122.30 -3.75 0.60 N 19 1 "C3'" A DG 110 ? ? "O3'" A DG 110 ? ? P A DT 111 ? ? 128.15 119.70 8.45 1.20 Y 20 1 "O4'" A DT 111 ? ? "C1'" A DT 111 ? ? N1 A DT 111 ? ? 120.07 108.30 11.77 0.30 N 21 1 "C5'" A DA 112 ? ? "C4'" A DA 112 ? ? "C3'" A DA 112 ? ? 122.92 115.70 7.22 1.20 N 22 1 "C3'" A DA 112 ? ? "O3'" A DA 112 ? ? P A DC 113 ? ? 132.92 119.70 13.22 1.20 Y 23 1 "C3'" A DG 115 ? ? "O3'" A DG 115 ? ? P A DA 116 ? ? 131.60 119.70 11.90 1.20 Y 24 1 "C3'" A DC 117 ? ? "C2'" A DC 117 ? ? "C1'" A DC 117 ? ? 97.49 102.40 -4.91 0.80 N 25 1 "O4'" A DC 117 ? ? "C1'" A DC 117 ? ? N1 A DC 117 ? ? 115.87 108.30 7.57 0.30 N 26 1 "C3'" A DA 118 ? ? "O3'" A DA 118 ? ? P A DT 119 ? ? 129.16 119.70 9.46 1.20 Y 27 1 "O4'" A DT 119 ? ? "C1'" A DT 119 ? ? "C2'" A DT 119 ? ? 110.33 106.80 3.53 0.50 N 28 1 "C3'" A DT 119 ? ? "O3'" A DT 119 ? ? P A DC 120 ? ? 130.53 119.70 10.83 1.20 Y 29 1 "O4'" A DC 120 ? ? "C1'" A DC 120 ? ? N1 A DC 120 ? ? 111.12 108.30 2.82 0.30 N 30 1 "C3'" B DC 119 ? ? "O3'" B DC 119 ? ? P B DC 120 ? ? 130.40 119.70 10.70 1.20 Y 31 1 "O4'" B DC 120 ? ? "C1'" B DC 120 ? ? N1 B DC 120 ? ? 110.14 108.30 1.84 0.30 N 32 1 "C3'" B DG 121 ? ? "O3'" B DG 121 ? ? P B DT 122 ? ? 133.54 119.70 13.84 1.20 Y 33 1 "O4'" B DC 124 ? ? "C1'" B DC 124 ? ? N1 B DC 124 ? ? 111.14 108.30 2.84 0.30 N 34 1 "C3'" B DC 124 ? ? "O3'" B DC 124 ? ? P B DA 125 ? ? 127.24 119.70 7.54 1.20 Y 35 1 "O4'" C DG 210 ? ? "C1'" C DG 210 ? ? N9 C DG 210 ? ? 114.51 108.30 6.21 0.30 N 36 1 "C5'" C DC 211 ? ? "C4'" C DC 211 ? ? "O4'" C DC 211 ? ? 117.47 109.80 7.67 1.10 N 37 1 "O4'" C DC 211 ? ? "C1'" C DC 211 ? ? N1 C DC 211 ? ? 115.10 108.30 6.80 0.30 N 38 1 "C3'" C DC 211 ? ? "O3'" C DC 211 ? ? P C DT 212 ? ? 131.06 119.70 11.36 1.20 Y 39 1 "O4'" C DT 212 ? ? "C1'" C DT 212 ? ? N1 C DT 212 ? ? 111.01 108.30 2.71 0.30 N 40 1 "C3'" C DT 212 ? ? "O3'" C DT 212 ? ? P C DG 213 ? ? 130.54 119.70 10.84 1.20 Y 41 1 "C3'" C DG 213 ? ? "C2'" C DG 213 ? ? "C1'" C DG 213 ? ? 96.66 102.40 -5.74 0.80 N 42 1 "O4'" C DG 213 ? ? "C1'" C DG 213 ? ? N9 C DG 213 ? ? 119.33 108.30 11.03 0.30 N 43 1 "C3'" C DG 213 ? ? "O3'" C DG 213 ? ? P C DC 214 ? ? 129.38 119.70 9.68 1.20 Y 44 1 "O4'" C DC 214 ? ? "C1'" C DC 214 ? ? N1 C DC 214 ? ? 111.38 108.30 3.08 0.30 N 45 1 OP1 D DT 101 ? ? P D DT 101 ? ? OP2 D DT 101 ? ? 109.08 119.60 -10.52 1.50 N 46 1 "O4'" D DT 101 ? ? "C1'" D DT 101 ? ? N1 D DT 101 ? ? 112.06 108.30 3.76 0.30 N 47 1 "C3'" D DT 101 ? ? "O3'" D DT 101 ? ? P D DC 102 ? ? 128.14 119.70 8.44 1.20 Y 48 1 "O4'" D DC 102 ? ? "C1'" D DC 102 ? ? N1 D DC 102 ? ? 121.87 108.30 13.57 0.30 N 49 1 "C3'" D DC 102 ? ? "O3'" D DC 102 ? ? P D DT 103 ? ? 128.33 119.70 8.63 1.20 Y 50 1 "O4'" D DT 103 ? ? "C1'" D DT 103 ? ? N1 D DT 103 ? ? 112.65 108.30 4.35 0.30 N 51 1 "C3'" D DT 103 ? ? "O3'" D DT 103 ? ? P D DG 104 ? ? 130.40 119.70 10.70 1.20 Y 52 1 "C3'" D DG 104 ? ? "C2'" D DG 104 ? ? "C1'" D DG 104 ? ? 96.72 102.40 -5.68 0.80 N 53 1 "O4'" D DG 104 ? ? "C1'" D DG 104 ? ? N9 D DG 104 ? ? 114.49 108.30 6.19 0.30 N 54 1 "C3'" D DG 104 ? ? "O3'" D DG 104 ? ? P D DA 105 ? ? 133.39 119.70 13.69 1.20 Y 55 1 "O4'" D DA 105 ? ? "C1'" D DA 105 ? ? N9 D DA 105 ? ? 110.36 108.30 2.06 0.30 N 56 1 "C1'" D DT 106 ? ? "O4'" D DT 106 ? ? "C4'" D DT 106 ? ? 103.63 110.10 -6.47 1.00 N 57 1 "C3'" D DT 106 ? ? "C2'" D DT 106 ? ? "C1'" D DT 106 ? ? 97.10 102.40 -5.30 0.80 N 58 1 "O4'" D DT 106 ? ? "C1'" D DT 106 ? ? N1 D DT 106 ? ? 116.70 108.30 8.40 0.30 N 59 1 "O4'" D DT 108 ? ? "C1'" D DT 108 ? ? N1 D DT 108 ? ? 112.04 108.30 3.74 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 # 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 # _ndb_struct_conf_na.entry_id 4B8D _ndb_struct_conf_na.feature '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 3 1_555 C DC 6 1_555 -0.999 -0.241 0.680 5.704 -4.961 -14.855 1 A_DG103:DC214_C A 103 ? C 214 ? 19 1 1 A DC 4 1_555 C DG 5 1_555 0.670 0.764 -1.209 5.705 -33.300 -26.675 2 A_DC104:DG213_C A 104 ? C 213 ? ? ? 1 A DG 6 1_555 C DC 3 1_555 -0.939 -0.378 -1.062 15.623 -16.249 -24.155 3 A_DG106:DC211_C A 106 ? C 211 ? ? 1 1 A DC 7 1_555 C DG 2 1_555 0.062 -0.422 -1.902 21.949 -2.897 -10.864 4 A_DC107:DG210_C A 107 ? C 210 ? 19 1 1 A DC 8 1_555 C DG 1 1_555 -0.603 0.237 -0.114 -5.614 -3.608 -25.249 5 A_DC108:DG209_C A 108 ? C 209 ? ? 1 1 A DT 9 1_555 B DA 7 1_555 0.131 -0.427 0.842 -17.239 -2.129 4.023 6 A_DT109:DA125_B A 109 ? B 125 ? 20 1 1 A DG 10 1_555 B DC 6 1_555 1.451 -0.388 1.748 -2.278 -4.386 -6.692 7 A_DG110:DC124_B A 110 ? B 124 ? 19 1 1 A DA 12 1_555 B DT 4 1_555 -0.231 -0.592 -1.720 -6.605 -15.778 -7.262 8 A_DA112:DT122_B A 112 ? B 122 ? 20 1 1 A DC 13 1_555 B DG 3 1_555 0.363 -0.281 -1.745 13.982 -36.694 -6.019 9 A_DC113:DG121_B A 113 ? B 121 ? ? 1 1 A DG 14 1_555 B DC 2 1_555 0.149 0.586 -1.211 -23.495 -46.866 31.868 10 A_DG114:DC120_B A 114 ? B 120 ? ? 1 1 A DG 15 1_555 B DC 1 1_555 1.147 0.138 -1.225 -0.551 -31.607 -5.962 11 A_DG115:DC119_B A 115 ? B 119 ? ? 1 1 A DA 16 1_555 D DT 8 1_555 1.322 0.326 0.305 14.861 -37.162 16.888 12 A_DA116:DT108_D A 116 ? D 108 ? ? ? 1 A DC 17 1_555 D DG 7 1_555 -0.778 0.228 -0.520 34.018 -36.315 -3.832 13 A_DC117:DG107_D A 117 ? D 107 ? 19 1 1 A DA 18 1_555 D DT 6 1_555 -0.268 -0.504 0.744 -16.133 -20.379 -16.193 14 A_DA118:DT106_D A 118 ? D 106 ? 20 1 1 A DT 19 1_555 D DA 5 1_555 0.066 -0.437 -0.593 -30.803 -10.744 8.146 15 A_DT119:DA105_D A 119 ? D 105 ? 20 1 1 A DA 21 1_555 D DC 2 1_555 2.289 0.485 -1.369 -24.457 -32.962 -27.699 16 A_DA121:DC102_D A 121 ? D 102 ? ? ? # 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 C DC 6 1_555 A DC 4 1_555 C DG 5 1_555 -0.733 -1.233 3.210 10.050 16.069 49.109 -2.358 1.432 2.534 18.554 -11.605 52.427 1 AA_DG103DC104:DG213DC214_CC A 103 ? C 214 ? A 104 ? C 213 ? 1 A DC 4 1_555 C DG 5 1_555 A DG 6 1_555 C DC 3 1_555 -0.170 -1.184 6.798 -5.669 15.008 48.739 -3.489 -0.603 6.188 17.641 6.663 51.158 2 AA_DC104DG106:DC211DG213_CC A 104 ? C 213 ? A 106 ? C 211 ? 1 A DG 6 1_555 C DC 3 1_555 A DC 7 1_555 C DG 2 1_555 2.224 -1.037 3.247 5.546 0.776 38.472 -1.657 -2.643 3.501 1.170 -8.363 38.862 3 AA_DG106DC107:DG210DC211_CC A 106 ? C 211 ? A 107 ? C 210 ? 1 A DC 7 1_555 C DG 2 1_555 A DC 8 1_555 C DG 1 1_555 -0.148 -0.974 4.220 -10.861 7.862 36.513 -2.686 -1.461 3.828 12.061 16.660 38.818 4 AA_DC107DC108:DG209DG210_CC A 107 ? C 210 ? A 108 ? C 209 ? 1 A DC 8 1_555 C DG 1 1_555 A DT 9 1_555 B DA 7 1_555 -0.049 -2.081 3.742 -4.590 0.200 22.196 -5.379 -1.777 3.658 0.511 11.762 22.660 5 AA_DC108DT109:DA125DG209_BC A 108 ? C 209 ? A 109 ? B 125 ? 1 A DT 9 1_555 B DA 7 1_555 A DG 10 1_555 B DC 6 1_555 -0.144 -0.572 3.194 0.259 -9.540 37.006 0.329 0.253 3.236 -14.732 -0.400 38.175 6 AA_DT109DG110:DC124DA125_BB A 109 ? B 125 ? A 110 ? B 124 ? 1 A DG 10 1_555 B DC 6 1_555 A DA 12 1_555 B DT 4 1_555 -0.761 -0.038 7.226 28.696 17.658 67.866 -1.240 2.590 6.372 14.924 -24.254 74.863 7 AA_DG110DA112:DT122DC124_BB A 110 ? B 124 ? A 112 ? B 122 ? 1 A DA 12 1_555 B DT 4 1_555 A DC 13 1_555 B DG 3 1_555 -0.346 0.209 2.860 5.446 1.502 30.957 0.143 1.521 2.768 2.784 -10.097 31.455 8 AA_DA112DC113:DG121DT122_BB A 112 ? B 122 ? A 113 ? B 121 ? 1 A DC 13 1_555 B DG 3 1_555 A DG 14 1_555 B DC 2 1_555 2.138 3.894 3.512 10.458 5.967 49.468 4.033 -1.607 4.265 7.011 -12.288 50.822 9 AA_DC113DG114:DC120DG121_BB A 113 ? B 121 ? A 114 ? B 120 ? 1 A DG 14 1_555 B DC 2 1_555 A DG 15 1_555 B DC 1 1_555 -0.469 2.718 2.401 -9.069 5.629 42.221 3.232 -0.070 2.763 7.668 12.354 43.490 10 AA_DG114DG115:DC119DC120_BB A 114 ? B 120 ? A 115 ? B 119 ? 1 A DG 15 1_555 B DC 1 1_555 A DA 16 1_555 D DT 8 1_555 1.210 0.057 2.770 -2.268 4.910 30.366 -0.691 -2.645 2.651 9.281 4.287 30.833 11 AA_DG115DA116:DT108DC119_DB A 115 ? B 119 ? A 116 ? D 108 ? 1 A DA 16 1_555 D DT 8 1_555 A DC 17 1_555 D DG 7 1_555 -0.723 -0.562 2.812 5.240 13.157 11.756 -7.210 4.433 1.196 46.914 -18.684 18.387 12 AA_DA116DC117:DG107DT108_DD A 116 ? D 108 ? A 117 ? D 107 ? 1 A DC 17 1_555 D DG 7 1_555 A DA 18 1_555 D DT 6 1_555 -0.488 -0.162 4.361 -12.858 7.221 49.567 -0.851 -0.623 4.295 8.401 14.959 51.581 13 AA_DC117DA118:DT106DG107_DD A 117 ? D 107 ? A 118 ? D 106 ? 1 A DA 18 1_555 D DT 6 1_555 A DT 19 1_555 D DA 5 1_555 -0.018 -0.395 3.770 11.820 -3.431 37.630 -0.116 1.640 3.624 -5.153 -17.753 39.522 14 AA_DA118DT119:DA105DT106_DD A 118 ? D 106 ? A 119 ? D 105 ? # _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 3GBI _pdbx_initial_refinement_model.details 'PDB ENTRY 3GBI' #