data_3V9D # _entry.id 3V9D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 3V9D pdb_00003v9d 10.2210/pdb3v9d/pdb NDB NA1531 ? ? RCSB RCSB069759 ? ? WWPDB D_1000069759 ? ? # 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 2012-04-18 2 'Structure model' 1 1 2014-03-12 3 'Structure model' 1 2 2024-03-20 4 'Structure model' 1 3 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_site 5 4 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3V9D _pdbx_database_status.recvd_initial_deposition_date 2011-12-26 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3QK4 _pdbx_database_related.details 'The sequence crystallizes as an A-DNA duplex and represents more than one full turn of the A-helix.' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mandal, P.K.' 1 'Venkadesh, S.' 2 'Gautham, N.' 3 # _citation.id primary _citation.title 'Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex' _citation.journal_abbrev 'Acta Crystallogr.,Sect.F' _citation.journal_volume 68 _citation.page_first 393 _citation.page_last 399 _citation.year 2012 _citation.journal_id_ASTM ? _citation.country DK _citation.journal_id_ISSN 1744-3091 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22505405 _citation.pdbx_database_id_DOI 10.1107/S174430911200869X # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mandal, P.K.' 1 ? primary 'Venkadesh, S.' 2 ? primary 'Gautham, N.' 3 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*GP*G)-3') ; 4282.768 2 ? ? ? ? 2 non-polymer syn 'MANGANESE (II) ION' 54.938 1 ? ? ? ? 3 water nat water 18.015 15 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DC)(DC)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DG)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCCCGGTACCGGGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MANGANESE (II) ION' MN 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DC n 1 4 DC n 1 5 DG n 1 6 DG n 1 7 DT n 1 8 DA n 1 9 DC n 1 10 DC n 1 11 DG n 1 12 DG n 1 13 DG n 1 14 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DC 10 10 10 DC DC A . n A 1 11 DG 11 11 11 DG DG A . n A 1 12 DG 12 12 12 DG DG A . n A 1 13 DG 13 13 13 DG DG A . n A 1 14 DG 14 14 14 DG DG A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DC 2 2 2 DC DC B . n B 1 3 DC 3 3 3 DC DC B . n B 1 4 DC 4 4 4 DC DC B . n B 1 5 DG 5 5 5 DG DG B . n B 1 6 DG 6 6 6 DG DG B . n B 1 7 DT 7 7 7 DT DT B . n B 1 8 DA 8 8 8 DA DA B . n B 1 9 DC 9 9 9 DC DC B . n B 1 10 DC 10 10 10 DC DC B . n B 1 11 DG 11 11 11 DG DG B . n B 1 12 DG 12 12 12 DG DG B . n B 1 13 DG 13 13 13 DG DG B . n B 1 14 DG 14 14 14 DG DG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 MN 1 101 2 MN MN B . D 3 HOH 1 101 2 HOH HOH A . D 3 HOH 2 102 5 HOH HOH A . D 3 HOH 3 103 6 HOH HOH A . D 3 HOH 4 104 8 HOH HOH A . D 3 HOH 5 105 11 HOH HOH A . D 3 HOH 6 106 12 HOH HOH A . D 3 HOH 7 107 14 HOH HOH A . E 3 HOH 1 201 1 HOH HOH B . E 3 HOH 2 202 3 HOH HOH B . E 3 HOH 3 203 4 HOH HOH B . E 3 HOH 4 204 7 HOH HOH B . E 3 HOH 5 205 9 HOH HOH B . E 3 HOH 6 206 10 HOH HOH B . E 3 HOH 7 207 13 HOH HOH B . E 3 HOH 8 208 15 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 AMoRE phasing . ? 2 REFMAC refinement 5.5.0109 ? 3 AUTOMAR 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # _cell.entry_id 3V9D _cell.length_a 29.340 _cell.length_b 29.340 _cell.length_c 87.687 _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 3V9D _symmetry.space_group_name_H-M 'P 41' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3V9D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.20 _exptl_crystal.density_percent_sol 44.17 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details ;1mM DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 12mM MnCl2, 10mM spermine, equilibrated against 50 % methyl pentane diol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'MAR scanner 345 mm plate' _diffrn_detector.pdbx_collection_date 2011-06-28 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator graphite _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 'BRUKER AXS MICROSTAR' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 3V9D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 29.34 _reflns.d_resolution_high 2.5 _reflns.number_obs 2599 _reflns.number_all 2606 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.045 _reflns.pdbx_Rsym_value 0.042 _reflns.pdbx_netI_over_sigmaI 6.6 _reflns.B_iso_Wilson_estimate 57.3 _reflns.pdbx_redundancy 4.64 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.50 _reflns_shell.d_res_low 2.59 _reflns_shell.percent_possible_all 99.6 _reflns_shell.Rmerge_I_obs 0.282 _reflns_shell.pdbx_Rsym_value 0.272 _reflns_shell.meanI_over_sigI_obs 1.5 _reflns_shell.pdbx_redundancy 4.69 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 253 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3V9D _refine.ls_number_reflns_obs 2449 _refine.ls_number_reflns_all 2467 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.34 _refine.ls_d_res_high 2.50 _refine.ls_percent_reflns_obs 99.30 _refine.ls_R_factor_obs 0.21783 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21651 _refine.ls_R_factor_R_free 0.24435 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.4 _refine.ls_number_reflns_R_free 113 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.960 _refine.correlation_coeff_Fo_to_Fc_free 0.946 _refine.B_iso_mean 33.3799 _refine.aniso_B[1][1] -0.0600 _refine.aniso_B[2][2] -0.0600 _refine.aniso_B[3][3] 0.1200 _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 MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;Molecular replacement was carried out using AMoRe [Navaza, 1994] of the CCP4 suite. The A-DNA duplex gave the best correlation coefficient (83%) ; _refine.pdbx_starting_model 'A-DNA duplex Fiber model (tetra-decanucleotide) built using Insight-II' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 1.252 _refine.pdbx_overall_ESU_R_Free 0.304 _refine.overall_SU_ML 0.252 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 568 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 15 _refine_hist.number_atoms_total 584 _refine_hist.d_res_high 2.50 _refine_hist.d_res_low 29.34 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' r_bond_refined_d 636 0.023 0.021 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 978 3.216 3.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 110 0.122 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 294 0.012 0.020 ? ? 'X-RAY DIFFRACTION' r_scbond_it 636 2.281 3.000 ? ? 'X-RAY DIFFRACTION' r_scangle_it 978 3.427 4.500 ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.501 _refine_ls_shell.d_res_low 2.565 _refine_ls_shell.number_reflns_R_work 173 _refine_ls_shell.R_factor_R_work 0.468 _refine_ls_shell.percent_reflns_obs 98.90 _refine_ls_shell.R_factor_R_free 0.486 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 7 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # _database_PDB_matrix.entry_id 3V9D _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 # _struct.entry_id 3V9D _struct.title 'Crystal structure of the tetra-decanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3V9D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Tetra-decanucleotide, A-DNA duplex, Crystal packing, A-type double helix, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3V9D _struct_ref.pdbx_db_accession 3V9D _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _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 3V9D A 1 ? 14 ? 3V9D 1 ? 14 ? 1 14 2 1 3V9D B 1 ? 14 ? 3V9D 1 ? 14 ? 1 14 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1580 ? 1 MORE -8 ? 1 'SSA (A^2)' 5160 ? # _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,E # _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 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? C MN . MN ? ? ? 1_555 E HOH . O ? ? B MN 101 B HOH 208 1_555 ? ? ? ? ? ? ? 2.428 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 14 N1 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 14 O6 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 14 N2 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 13 N1 ? ? A DC 2 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 13 O6 ? ? A DC 2 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 13 N2 ? ? A DC 2 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 3 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 3 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 3 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 4 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 4 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 4 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 5 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 5 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 5 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 6 B DC 9 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 8 N1 ? ? A DT 7 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 8 N6 ? ? A DT 7 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 8 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 8 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 9 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 9 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 9 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 10 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 12 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DG 13 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 13 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DG 13 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 13 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DG 13 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 13 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DG 14 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DG 14 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A DG 14 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id MN _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 2 _struct_site.details 'BINDING SITE FOR RESIDUE MN B 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 2 DG B 13 ? DG B 13 . ? 1_555 ? 2 AC1 2 HOH E . ? HOH B 208 . ? 1_555 ? # 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 "O3'" A DC 2 ? ? "C3'" A DC 2 ? ? 1.375 1.419 -0.044 0.006 N 2 1 "O3'" A DC 4 ? ? "C3'" A DC 4 ? ? 1.364 1.419 -0.055 0.006 N 3 1 "O3'" A DG 5 ? ? "C3'" A DG 5 ? ? 1.360 1.419 -0.059 0.006 N 4 1 "O3'" A DG 6 ? ? "C3'" A DG 6 ? ? 1.363 1.419 -0.056 0.006 N 5 1 "O3'" A DT 7 ? ? "C3'" A DT 7 ? ? 1.378 1.419 -0.041 0.006 N 6 1 "O3'" B DC 3 ? ? "C3'" B DC 3 ? ? 1.378 1.419 -0.041 0.006 N 7 1 "O3'" B DC 4 ? ? "C3'" B DC 4 ? ? 1.381 1.419 -0.038 0.006 N 8 1 "O3'" B DG 6 ? ? "C3'" B DG 6 ? ? 1.366 1.419 -0.053 0.006 N 9 1 "O3'" B DG 11 ? ? "C3'" B DG 11 ? ? 1.382 1.419 -0.037 0.006 N 10 1 C5 B DG 11 ? ? N7 B DG 11 ? ? 1.349 1.388 -0.039 0.006 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 "O5'" A DC 1 ? ? "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 101.05 109.40 -8.35 0.80 N 2 1 "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? 97.98 102.20 -4.22 0.70 N 3 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 113.34 108.30 5.04 0.30 N 4 1 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 98.20 104.50 -6.30 0.40 N 5 1 "O4'" A DC 4 ? ? "C4'" A DC 4 ? ? "C3'" A DC 4 ? ? 101.68 104.50 -2.82 0.40 N 6 1 "C4'" A DG 5 ? ? "C3'" A DG 5 ? ? "C2'" A DG 5 ? ? 94.89 102.20 -7.31 0.70 N 7 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? "C2'" A DG 5 ? ? 99.39 105.90 -6.51 0.80 N 8 1 "O4'" A DG 6 ? ? "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? 98.97 104.50 -5.53 0.40 N 9 1 "O4'" A DT 7 ? ? "C4'" A DT 7 ? ? "C3'" A DT 7 ? ? 99.97 104.50 -4.53 0.40 N 10 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 111.11 108.30 2.81 0.30 N 11 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 111.35 108.30 3.05 0.30 N 12 1 N1 A DC 9 ? ? C2 A DC 9 ? ? O2 A DC 9 ? ? 115.29 118.90 -3.61 0.60 N 13 1 "C4'" A DC 10 ? ? "C3'" A DC 10 ? ? "C2'" A DC 10 ? ? 96.38 102.20 -5.82 0.70 N 14 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? N1 A DC 10 ? ? 113.66 108.30 5.36 0.30 N 15 1 C6 A DC 10 ? ? N1 A DC 10 ? ? C2 A DC 10 ? ? 117.23 120.30 -3.07 0.40 N 16 1 C5 A DC 10 ? ? C6 A DC 10 ? ? N1 A DC 10 ? ? 124.36 121.00 3.36 0.50 N 17 1 "O4'" A DG 11 ? ? "C4'" A DG 11 ? ? "C3'" A DG 11 ? ? 100.52 104.50 -3.98 0.40 N 18 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 114.38 108.30 6.08 0.30 N 19 1 N3 A DG 11 ? ? C2 A DG 11 ? ? N2 A DG 11 ? ? 125.24 119.90 5.34 0.70 N 20 1 "O4'" A DG 12 ? ? "C4'" A DG 12 ? ? "C3'" A DG 12 ? ? 97.34 104.50 -7.16 0.40 N 21 1 "C4'" A DG 12 ? ? "C3'" A DG 12 ? ? "C2'" A DG 12 ? ? 97.61 102.20 -4.59 0.70 N 22 1 C4 A DG 12 ? ? C5 A DG 12 ? ? N7 A DG 12 ? ? 113.83 110.80 3.03 0.40 N 23 1 C5 A DG 12 ? ? N7 A DG 12 ? ? C8 A DG 12 ? ? 101.30 104.30 -3.00 0.50 N 24 1 C6 A DG 12 ? ? C5 A DG 12 ? ? N7 A DG 12 ? ? 126.50 130.40 -3.90 0.60 N 25 1 "C3'" A DG 13 ? ? "C2'" A DG 13 ? ? "C1'" A DG 13 ? ? 96.35 102.40 -6.05 0.80 N 26 1 C4 A DG 13 ? ? C5 A DG 13 ? ? N7 A DG 13 ? ? 113.79 110.80 2.99 0.40 N 27 1 C5 A DG 13 ? ? N7 A DG 13 ? ? C8 A DG 13 ? ? 101.27 104.30 -3.03 0.50 N 28 1 N3 A DG 13 ? ? C2 A DG 13 ? ? N2 A DG 13 ? ? 124.85 119.90 4.95 0.70 N 29 1 "O4'" A DG 14 ? ? "C4'" A DG 14 ? ? "C3'" A DG 14 ? ? 98.81 104.50 -5.69 0.40 N 30 1 "C4'" A DG 14 ? ? "C3'" A DG 14 ? ? "C2'" A DG 14 ? ? 95.29 102.20 -6.91 0.70 N 31 1 C5 A DG 14 ? ? N7 A DG 14 ? ? C8 A DG 14 ? ? 101.15 104.30 -3.15 0.50 N 32 1 N7 A DG 14 ? ? C8 A DG 14 ? ? N9 A DG 14 ? ? 116.26 113.10 3.16 0.50 N 33 1 "O4'" B DC 1 ? ? "C4'" B DC 1 ? ? "C3'" B DC 1 ? ? 101.10 104.50 -3.40 0.40 N 34 1 "C4'" B DC 1 ? ? "C3'" B DC 1 ? ? "C2'" B DC 1 ? ? 96.75 102.20 -5.45 0.70 N 35 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? N1 B DC 1 ? ? 113.00 108.30 4.70 0.30 N 36 1 "O4'" B DC 2 ? ? "C4'" B DC 2 ? ? "C3'" B DC 2 ? ? 100.24 104.50 -4.26 0.40 N 37 1 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? N1 B DC 2 ? ? 103.75 108.00 -4.25 0.70 N 38 1 "O4'" B DC 3 ? ? "C4'" B DC 3 ? ? "C3'" B DC 3 ? ? 101.69 104.50 -2.81 0.40 N 39 1 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 111.45 108.30 3.15 0.30 N 40 1 "O5'" B DC 4 ? ? P B DC 4 ? ? OP1 B DC 4 ? ? 99.93 105.70 -5.77 0.90 N 41 1 P B DC 4 ? ? "O5'" B DC 4 ? ? "C5'" B DC 4 ? ? 109.82 120.90 -11.08 1.60 N 42 1 "O4'" B DC 4 ? ? "C4'" B DC 4 ? ? "C3'" B DC 4 ? ? 100.06 104.50 -4.44 0.40 N 43 1 "C4'" B DC 4 ? ? "C3'" B DC 4 ? ? "C2'" B DC 4 ? ? 96.41 102.20 -5.79 0.70 N 44 1 "C4'" B DG 5 ? ? "C3'" B DG 5 ? ? "C2'" B DG 5 ? ? 97.34 102.20 -4.86 0.70 N 45 1 "O4'" B DG 5 ? ? "C1'" B DG 5 ? ? "C2'" B DG 5 ? ? 99.22 105.90 -6.68 0.80 N 46 1 "O4'" B DG 5 ? ? "C1'" B DG 5 ? ? N9 B DG 5 ? ? 114.42 108.30 6.12 0.30 N 47 1 N7 B DG 5 ? ? C8 B DG 5 ? ? N9 B DG 5 ? ? 116.14 113.10 3.04 0.50 N 48 1 C8 B DG 5 ? ? N9 B DG 5 ? ? C4 B DG 5 ? ? 103.86 106.40 -2.54 0.40 N 49 1 "O4'" B DG 6 ? ? "C4'" B DG 6 ? ? "C3'" B DG 6 ? ? 99.41 104.50 -5.09 0.40 N 50 1 "O4'" B DT 7 ? ? "C4'" B DT 7 ? ? "C3'" B DT 7 ? ? 99.29 104.50 -5.21 0.40 N 51 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 111.09 108.30 2.79 0.30 N 52 1 N3 B DT 7 ? ? C4 B DT 7 ? ? O4 B DT 7 ? ? 124.31 119.90 4.41 0.60 N 53 1 "C5'" B DA 8 ? ? "C4'" B DA 8 ? ? "C3'" B DA 8 ? ? 102.72 114.10 -11.38 1.80 N 54 1 "O4'" B DA 8 ? ? "C1'" B DA 8 ? ? N9 B DA 8 ? ? 112.10 108.30 3.80 0.30 N 55 1 N1 B DA 8 ? ? C6 B DA 8 ? ? N6 B DA 8 ? ? 114.92 118.60 -3.68 0.60 N 56 1 N1 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 114.03 118.90 -4.87 0.60 N 57 1 N3 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 126.58 121.90 4.68 0.70 N 58 1 "C4'" B DC 10 ? ? "C3'" B DC 10 ? ? "C2'" B DC 10 ? ? 96.76 102.20 -5.44 0.70 N 59 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? N1 B DC 10 ? ? 116.12 108.30 7.82 0.30 N 60 1 C6 B DC 10 ? ? N1 B DC 10 ? ? C2 B DC 10 ? ? 116.37 120.30 -3.93 0.40 N 61 1 C2 B DC 10 ? ? N3 B DC 10 ? ? C4 B DC 10 ? ? 123.36 119.90 3.46 0.50 N 62 1 N3 B DC 10 ? ? C4 B DC 10 ? ? C5 B DC 10 ? ? 119.08 121.90 -2.82 0.40 N 63 1 C5 B DC 10 ? ? C6 B DC 10 ? ? N1 B DC 10 ? ? 125.50 121.00 4.50 0.50 N 64 1 "O5'" B DG 11 ? ? P B DG 11 ? ? OP2 B DG 11 ? ? 97.07 105.70 -8.63 0.90 N 65 1 "O4'" B DG 11 ? ? "C4'" B DG 11 ? ? "C3'" B DG 11 ? ? 102.01 104.50 -2.49 0.40 N 66 1 "O4'" B DG 11 ? ? "C1'" B DG 11 ? ? N9 B DG 11 ? ? 113.53 108.30 5.23 0.30 N 67 1 "O4'" B DG 12 ? ? "C4'" B DG 12 ? ? "C3'" B DG 12 ? ? 98.44 104.50 -6.06 0.40 N 68 1 "C4'" B DG 12 ? ? "C3'" B DG 12 ? ? "C2'" B DG 12 ? ? 97.90 102.20 -4.30 0.70 N 69 1 "O5'" B DG 13 ? ? "C5'" B DG 13 ? ? "C4'" B DG 13 ? ? 104.33 109.40 -5.07 0.80 N 70 1 "O4'" B DG 13 ? ? "C4'" B DG 13 ? ? "C3'" B DG 13 ? ? 96.06 104.50 -8.44 0.40 N 71 1 "C4'" B DG 13 ? ? "C3'" B DG 13 ? ? "C2'" B DG 13 ? ? 96.61 102.20 -5.59 0.70 N 72 1 "O4'" B DG 14 ? ? "C4'" B DG 14 ? ? "C3'" B DG 14 ? ? 97.80 104.50 -6.70 0.40 N 73 1 "C1'" B DG 14 ? ? "O4'" B DG 14 ? ? "C4'" B DG 14 ? ? 103.91 110.10 -6.19 1.00 N 74 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? "C2'" B DG 14 ? ? 100.45 105.90 -5.45 0.80 N 75 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 103.42 108.00 -4.58 0.70 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 MN MN MN N N 147 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3V9D 'double helix' 3V9D 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 14 1_555 0.758 -0.529 -0.254 3.474 2.861 -5.280 1 A_DC1:DG14_B A 1 ? B 14 ? 19 1 1 A DC 2 1_555 B DG 13 1_555 0.441 -0.455 0.111 -0.307 -2.859 -7.744 2 A_DC2:DG13_B A 2 ? B 13 ? 19 1 1 A DC 3 1_555 B DG 12 1_555 0.100 -0.263 -0.286 5.959 -1.616 0.412 3 A_DC3:DG12_B A 3 ? B 12 ? 19 1 1 A DC 4 1_555 B DG 11 1_555 -0.134 -0.188 0.219 4.100 -5.433 -6.710 4 A_DC4:DG11_B A 4 ? B 11 ? 19 1 1 A DG 5 1_555 B DC 10 1_555 -0.088 -0.057 -0.026 2.777 -15.473 -1.406 5 A_DG5:DC10_B A 5 ? B 10 ? 19 1 1 A DG 6 1_555 B DC 9 1_555 -0.696 0.024 -0.450 -8.757 -13.285 13.163 6 A_DG6:DC9_B A 6 ? B 9 ? ? 1 1 A DT 7 1_555 B DA 8 1_555 -0.174 -0.258 -0.106 1.697 -13.895 5.171 7 A_DT7:DA8_B A 7 ? B 8 ? 20 1 1 A DA 8 1_555 B DT 7 1_555 0.582 -0.191 0.252 3.344 -7.656 1.908 8 A_DA8:DT7_B A 8 ? B 7 ? 20 1 1 A DC 9 1_555 B DG 6 1_555 0.378 0.059 -0.670 16.286 -16.330 12.134 9 A_DC9:DG6_B A 9 ? B 6 ? 19 1 1 A DC 10 1_555 B DG 5 1_555 -0.065 -0.169 0.201 -9.651 -11.290 -2.158 10 A_DC10:DG5_B A 10 ? B 5 ? 19 1 1 A DG 11 1_555 B DC 4 1_555 0.054 -0.489 -0.173 -8.098 -5.299 -6.117 11 A_DG11:DC4_B A 11 ? B 4 ? 19 1 1 A DG 12 1_555 B DC 3 1_555 0.144 -0.313 -0.226 -8.851 -4.962 -1.677 12 A_DG12:DC3_B A 12 ? B 3 ? 19 1 1 A DG 13 1_555 B DC 2 1_555 -0.207 -0.316 -0.183 -6.889 -7.474 -2.693 13 A_DG13:DC2_B A 13 ? B 2 ? 19 1 1 A DG 14 1_555 B DC 1 1_555 0.071 -0.087 -0.096 -1.106 -2.050 2.602 14 A_DG14:DC1_B A 14 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 14 1_555 A DC 2 1_555 B DG 13 1_555 -0.818 -2.427 3.482 -2.582 3.115 25.430 -6.349 1.088 3.232 7.020 5.818 25.744 1 AA_DC1DC2:DG13DG14_BB A 1 ? B 14 ? A 2 ? B 13 ? 1 A DC 2 1_555 B DG 13 1_555 A DC 3 1_555 B DG 12 1_555 0.252 -2.338 3.242 0.222 -3.458 25.457 -4.247 -0.501 3.525 -7.801 -0.501 25.688 2 AA_DC2DC3:DG12DG13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A DC 3 1_555 B DG 12 1_555 A DC 4 1_555 B DG 11 1_555 -0.765 -1.993 3.435 -4.978 0.015 30.272 -3.770 0.400 3.512 0.028 9.451 30.669 3 AA_DC3DC4:DG11DG12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A DC 4 1_555 B DG 11 1_555 A DG 5 1_555 B DC 10 1_555 -1.022 -2.013 3.201 -0.998 7.689 28.498 -5.432 1.813 2.613 15.265 1.982 29.513 4 AA_DC4DG5:DC10DG11_BB A 4 ? B 11 ? A 5 ? B 10 ? 1 A DG 5 1_555 B DC 10 1_555 A DG 6 1_555 B DC 9 1_555 1.381 -1.356 3.494 3.995 14.523 28.422 -5.070 -1.777 2.671 27.290 -7.506 32.094 5 AA_DG5DG6:DC9DC10_BB A 5 ? B 10 ? A 6 ? B 9 ? 1 A DG 6 1_555 B DC 9 1_555 A DT 7 1_555 B DA 8 1_555 -0.674 -0.983 3.129 -3.873 5.704 31.926 -2.682 0.564 2.973 10.221 6.940 32.643 6 AA_DG6DT7:DA8DC9_BB A 6 ? B 9 ? A 7 ? B 8 ? 1 A DT 7 1_555 B DA 8 1_555 A DA 8 1_555 B DT 7 1_555 0.009 -1.121 3.193 -1.638 2.393 37.898 -2.015 -0.215 3.116 3.678 2.518 38.004 7 AA_DT7DA8:DT7DA8_BB A 7 ? B 8 ? A 8 ? B 7 ? 1 A DA 8 1_555 B DT 7 1_555 A DC 9 1_555 B DG 6 1_555 0.736 -0.904 3.055 8.695 3.369 29.147 -2.350 0.245 3.023 6.487 -16.745 30.572 8 AA_DA8DC9:DG6DT7_BB A 8 ? B 7 ? A 9 ? B 6 ? 1 A DC 9 1_555 B DG 6 1_555 A DC 10 1_555 B DG 5 1_555 -1.360 -1.432 3.846 -9.353 19.232 29.845 -5.253 0.723 2.760 32.600 15.855 36.574 9 AA_DC9DC10:DG5DG6_BB A 9 ? B 6 ? A 10 ? B 5 ? 1 A DC 10 1_555 B DG 5 1_555 A DG 11 1_555 B DC 4 1_555 1.100 -1.917 3.316 6.055 5.266 28.623 -4.843 -0.878 3.085 10.397 -11.954 29.704 10 AA_DC10DG11:DC4DG5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A DG 11 1_555 B DC 4 1_555 A DG 12 1_555 B DC 3 1_555 0.655 -2.062 3.502 3.318 0.470 32.516 -3.752 -0.546 3.520 0.836 -5.906 32.683 11 AA_DG11DG12:DC3DC4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A DG 12 1_555 B DC 3 1_555 A DG 13 1_555 B DC 2 1_555 -0.027 -2.021 3.316 0.699 0.254 26.228 -4.521 0.249 3.294 0.560 -1.540 26.239 12 AA_DG12DG13:DC2DC3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 A DG 13 1_555 B DC 2 1_555 A DG 14 1_555 B DC 1 1_555 0.517 -2.303 3.270 0.422 1.905 28.927 -5.012 -0.942 3.122 3.808 -0.844 28.991 13 AA_DG13DG14:DC1DC2_BB A 13 ? B 2 ? A 14 ? B 1 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'A-DNA duplex Fiber model (tetra-decanucleotide) built using Insight-II' # _atom_sites.entry_id 3V9D _atom_sites.fract_transf_matrix[1][1] 0.034083 _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] 0.034083 _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] 0.011404 _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 MN N O P # loop_