data_3HCL # _entry.id 3HCL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 3HCL pdb_00003hcl 10.2210/pdb3hcl/pdb NDB UD0082 ? ? RCSB RCSB052968 ? ? WWPDB D_1000052968 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3HCL _pdbx_database_status.recvd_initial_deposition_date 2009-05-06 _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.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'De Luchi, D.' 1 'Martinez de Ilarduya, I.' 2 'Subirana, J.A.' 3 'Uson, I.' 4 'Campos, J.L.' 5 # _citation.id primary _citation.title 'A geometric approach to the crystallographic solution of nonconventional DNA structures: helical superstructures of d(CGATAT)' _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 49 _citation.page_first 7920 _citation.page_last 7922 _citation.year 2010 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1433-7851 _citation.journal_id_CSD 9999 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20848628 _citation.pdbx_database_id_DOI 10.1002/anie.201003647 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Martinez de Ilarduya, I.' 1 ? primary 'De Luchi, D.' 2 ? primary 'Subirana, J.A.' 3 ? primary 'Campos, J.L.' 4 ? primary 'Uson, I.' 5 ? # _cell.entry_id 3HCL _cell.length_a 38.326 _cell.length_b 38.326 _cell.length_c 56.821 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 3HCL _symmetry.space_group_name_H-M 'P 62 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*AP*TP*AP*T)-3') ; 1808.229 1 ? ? ? ? 2 water nat water 18.015 2 ? ? ? ? # _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)(DG)(DA)(DT)(DA)(DT)' _entity_poly.pdbx_seq_one_letter_code_can CGATAT _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DA n 1 4 DT n 1 5 DA n 1 6 DT n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3HCL _struct_ref.pdbx_db_accession 3HCL _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3HCL _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3HCL _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 6 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # _exptl.entry_id 3HCL _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.33 _exptl_crystal.density_percent_sol 63.08 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2007-12-08 _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 0.9783 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM16' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM16 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9783 # _reflns.entry_id 3HCL _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 35 _reflns.d_resolution_high 2.59 _reflns.number_obs 924 _reflns.number_all 924 _reflns.percent_possible_obs 98.8 _reflns.pdbx_Rmerge_I_obs 0.046 _reflns.pdbx_Rsym_value 0.017 _reflns.pdbx_netI_over_sigmaI 43.8 _reflns.B_iso_Wilson_estimate 80 _reflns.pdbx_redundancy 0.99 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.59 _reflns_shell.d_res_low 2.63 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.071 _reflns_shell.meanI_over_sigI_obs 12.5 _reflns_shell.pdbx_redundancy 1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 56 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3HCL _refine.ls_number_reflns_obs 869 _refine.ls_number_reflns_all ? _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 33.19 _refine.ls_d_res_high 2.59 _refine.ls_percent_reflns_obs 99.35 _refine.ls_R_factor_obs 0.23862 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23653 _refine.ls_R_factor_R_free 0.27509 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.6 _refine.ls_number_reflns_R_free 52 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.950 _refine.correlation_coeff_Fo_to_Fc_free 0.942 _refine.B_iso_mean 40.871 _refine.aniso_B[1][1] 1.26 _refine.aniso_B[2][2] 1.26 _refine.aniso_B[3][3] -1.88 _refine.aniso_B[1][2] 0.63 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 231D _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _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 0.354 _refine.pdbx_overall_ESU_R_Free 0.272 _refine.overall_SU_ML 0.222 _refine.overall_SU_B 11.662 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 120 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 122 _refine_hist.d_res_high 2.59 _refine_hist.d_res_low 33.19 # 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 r_bond_refined_d 0.013 0.021 ? 134 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.661 3.000 ? 205 'X-RAY DIFFRACTION' ? r_chiral_restr 0.099 0.200 ? 23 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 0.020 ? 63 'X-RAY DIFFRACTION' ? r_scbond_it 1.949 3.000 ? 134 'X-RAY DIFFRACTION' ? r_scangle_it 2.971 4.500 ? 205 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.586 _refine_ls_shell.d_res_low 2.653 _refine_ls_shell.number_reflns_R_work 60 _refine_ls_shell.R_factor_R_work 0.586 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.720 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 2 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3HCL _struct.title 'Helical superstructures in a DNA oligonucleotide crystal' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3HCL _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, oligonucleotide, superhelices, supramolecular chemistry' # 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 ? # _struct_biol.id 1 _struct_biol.details ;The ATAT part of the structure forms a B-DNA structure by the symmetry operation: x-y,-y+1,-z. The CG part of the sequence forms a Z-DNA step by the symmetry operation: x,x-y,-z+1/3. The cgatat sequence pairs itself with various symmetry equivalents leading to a complex interconnected superstructure. ; # 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 DA 3 N1 ? ? ? 1_555 A DT 6 N3 ? ? A DA 3 A DT 6 8_676 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DT 6 O4 ? ? A DA 3 A DT 6 8_676 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DT 4 N3 ? ? ? 1_555 A DA 5 N1 ? ? A DT 4 A DA 5 8_676 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 4 O4 ? ? ? 1_555 A DA 5 N6 ? ? A DT 4 A DA 5 8_676 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A DT 4 N3 ? ? A DA 5 A DT 4 8_676 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A DT 4 O4 ? ? A DA 5 A DT 4 8_676 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 6 N3 ? ? ? 1_555 A DA 3 N1 ? ? A DT 6 A DA 3 8_676 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 6 O4 ? ? ? 1_555 A DA 3 N6 ? ? A DT 6 A DA 3 8_676 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 3HCL _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 3HCL _atom_sites.fract_transf_matrix[1][1] 0.026092 _atom_sites.fract_transf_matrix[1][2] 0.015064 _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] 0.030128 _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] 0.017599 _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_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 O "O5'" . DC A 1 1 ? 6.463 31.951 41.054 1.00 38.42 ? 1 DC A "O5'" 1 ATOM 2 C "C5'" . DC A 1 1 ? 5.132 32.047 40.647 1.00 38.19 ? 1 DC A "C5'" 1 ATOM 3 C "C4'" . DC A 1 1 ? 4.744 30.730 40.024 1.00 36.84 ? 1 DC A "C4'" 1 ATOM 4 O "O4'" . DC A 1 1 ? 5.893 30.135 39.348 1.00 37.08 ? 1 DC A "O4'" 1 ATOM 5 C "C3'" . DC A 1 1 ? 4.309 29.724 41.057 1.00 36.07 ? 1 DC A "C3'" 1 ATOM 6 O "O3'" . DC A 1 1 ? 3.358 28.929 40.451 1.00 35.43 ? 1 DC A "O3'" 1 ATOM 7 C "C2'" . DC A 1 1 ? 5.588 28.923 41.277 1.00 36.21 ? 1 DC A "C2'" 1 ATOM 8 C "C1'" . DC A 1 1 ? 6.079 28.820 39.841 1.00 36.39 ? 1 DC A "C1'" 1 ATOM 9 N N1 . DC A 1 1 ? 7.504 28.443 39.723 1.00 35.93 ? 1 DC A N1 1 ATOM 10 C C2 . DC A 1 1 ? 7.924 27.114 39.715 1.00 36.64 ? 1 DC A C2 1 ATOM 11 O O2 . DC A 1 1 ? 7.087 26.201 39.811 1.00 37.32 ? 1 DC A O2 1 ATOM 12 N N3 . DC A 1 1 ? 9.244 26.861 39.603 1.00 36.40 ? 1 DC A N3 1 ATOM 13 C C4 . DC A 1 1 ? 10.101 27.871 39.504 1.00 38.13 ? 1 DC A C4 1 ATOM 14 N N4 . DC A 1 1 ? 11.406 27.635 39.385 1.00 40.71 ? 1 DC A N4 1 ATOM 15 C C5 . DC A 1 1 ? 9.695 29.213 39.502 1.00 37.31 ? 1 DC A C5 1 ATOM 16 C C6 . DC A 1 1 ? 8.399 29.441 39.613 1.00 36.65 ? 1 DC A C6 1 ATOM 17 P P . DG A 1 2 ? 1.835 29.289 40.713 1.00 40.40 ? 2 DG A P 1 ATOM 18 O OP1 . DG A 1 2 ? 1.693 29.784 42.102 1.00 35.78 ? 2 DG A OP1 1 ATOM 19 O OP2 . DG A 1 2 ? 0.962 28.186 40.190 1.00 38.36 ? 2 DG A OP2 1 ATOM 20 O "O5'" . DG A 1 2 ? 1.759 30.522 39.690 1.00 37.63 ? 2 DG A "O5'" 1 ATOM 21 C "C5'" . DG A 1 2 ? 1.027 30.364 38.494 1.00 34.47 ? 2 DG A "C5'" 1 ATOM 22 C "C4'" . DG A 1 2 ? 1.175 31.556 37.588 1.00 32.26 ? 2 DG A "C4'" 1 ATOM 23 O "O4'" . DG A 1 2 ? 2.358 32.292 37.914 1.00 31.65 ? 2 DG A "O4'" 1 ATOM 24 C "C3'" . DG A 1 2 ? 1.372 31.128 36.162 1.00 32.68 ? 2 DG A "C3'" 1 ATOM 25 O "O3'" . DG A 1 2 ? 0.110 31.024 35.700 1.00 34.74 ? 2 DG A "O3'" 1 ATOM 26 C "C2'" . DG A 1 2 ? 2.123 32.273 35.532 1.00 31.40 ? 2 DG A "C2'" 1 ATOM 27 C "C1'" . DG A 1 2 ? 2.758 32.954 36.748 1.00 31.38 ? 2 DG A "C1'" 1 ATOM 28 N N9 . DG A 1 2 ? 4.187 32.907 36.787 1.00 32.25 ? 2 DG A N9 1 ATOM 29 C C8 . DG A 1 2 ? 5.055 33.940 37.056 1.00 34.59 ? 2 DG A C8 1 ATOM 30 N N7 . DG A 1 2 ? 6.317 33.572 37.024 1.00 35.09 ? 2 DG A N7 1 ATOM 31 C C5 . DG A 1 2 ? 6.254 32.200 36.729 1.00 33.81 ? 2 DG A C5 1 ATOM 32 C C6 . DG A 1 2 ? 7.283 31.244 36.576 1.00 32.36 ? 2 DG A C6 1 ATOM 33 O O6 . DG A 1 2 ? 8.497 31.477 36.658 1.00 32.87 ? 2 DG A O6 1 ATOM 34 N N1 . DG A 1 2 ? 6.802 29.959 36.300 1.00 30.41 ? 2 DG A N1 1 ATOM 35 C C2 . DG A 1 2 ? 5.454 29.649 36.193 1.00 32.40 ? 2 DG A C2 1 ATOM 36 N N2 . DG A 1 2 ? 5.086 28.388 35.928 1.00 30.64 ? 2 DG A N2 1 ATOM 37 N N3 . DG A 1 2 ? 4.479 30.531 36.330 1.00 33.16 ? 2 DG A N3 1 ATOM 38 C C4 . DG A 1 2 ? 4.948 31.782 36.591 1.00 33.94 ? 2 DG A C4 1 ATOM 39 P P . DA A 1 3 ? -0.221 29.936 34.600 1.00 42.78 ? 3 DA A P 1 ATOM 40 O OP1 . DA A 1 3 ? 0.345 28.563 34.769 1.00 43.23 ? 3 DA A OP1 1 ATOM 41 O OP2 . DA A 1 3 ? 0.070 30.716 33.386 1.00 41.53 ? 3 DA A OP2 1 ATOM 42 O "O5'" . DA A 1 3 ? -1.768 29.624 34.844 1.00 42.13 ? 3 DA A "O5'" 1 ATOM 43 C "C5'" . DA A 1 3 ? -2.079 28.768 35.908 1.00 42.44 ? 3 DA A "C5'" 1 ATOM 44 C "C4'" . DA A 1 3 ? -3.495 28.264 35.752 1.00 44.66 ? 3 DA A "C4'" 1 ATOM 45 O "O4'" . DA A 1 3 ? -4.502 29.312 35.692 1.00 42.78 ? 3 DA A "O4'" 1 ATOM 46 C "C3'" . DA A 1 3 ? -3.738 27.402 34.525 1.00 46.72 ? 3 DA A "C3'" 1 ATOM 47 O "O3'" . DA A 1 3 ? -4.755 26.490 34.952 1.00 51.32 ? 3 DA A "O3'" 1 ATOM 48 C "C2'" . DA A 1 3 ? -4.266 28.419 33.526 1.00 44.91 ? 3 DA A "C2'" 1 ATOM 49 C "C1'" . DA A 1 3 ? -5.084 29.360 34.407 1.00 42.28 ? 3 DA A "C1'" 1 ATOM 50 N N9 . DA A 1 3 ? -4.995 30.753 34.005 1.00 41.63 ? 3 DA A N9 1 ATOM 51 C C8 . DA A 1 3 ? -3.825 31.450 33.757 1.00 42.20 ? 3 DA A C8 1 ATOM 52 N N7 . DA A 1 3 ? -3.993 32.713 33.419 1.00 40.72 ? 3 DA A N7 1 ATOM 53 C C5 . DA A 1 3 ? -5.375 32.848 33.451 1.00 38.73 ? 3 DA A C5 1 ATOM 54 C C6 . DA A 1 3 ? -6.172 33.957 33.190 1.00 36.94 ? 3 DA A C6 1 ATOM 55 N N6 . DA A 1 3 ? -5.612 35.113 32.847 1.00 35.23 ? 3 DA A N6 1 ATOM 56 N N1 . DA A 1 3 ? -7.513 33.820 33.308 1.00 36.71 ? 3 DA A N1 1 ATOM 57 C C2 . DA A 1 3 ? -8.020 32.617 33.652 1.00 37.71 ? 3 DA A C2 1 ATOM 58 N N3 . DA A 1 3 ? -7.359 31.479 33.930 1.00 39.01 ? 3 DA A N3 1 ATOM 59 C C4 . DA A 1 3 ? -6.022 31.664 33.806 1.00 40.17 ? 3 DA A C4 1 ATOM 60 P P . DT A 1 4 ? -5.351 25.298 34.064 1.00 53.58 ? 4 DT A P 1 ATOM 61 O OP1 . DT A 1 4 ? -5.887 24.322 35.065 1.00 50.66 ? 4 DT A OP1 1 ATOM 62 O OP2 . DT A 1 4 ? -4.365 25.047 32.962 1.00 49.66 ? 4 DT A OP2 1 ATOM 63 O "O5'" . DT A 1 4 ? -6.618 25.973 33.366 1.00 51.59 ? 4 DT A "O5'" 1 ATOM 64 C "C5'" . DT A 1 4 ? -7.780 26.369 34.087 1.00 50.92 ? 4 DT A "C5'" 1 ATOM 65 C "C4'" . DT A 1 4 ? -8.705 26.928 33.019 1.00 50.36 ? 4 DT A "C4'" 1 ATOM 66 O "O4'" . DT A 1 4 ? -8.401 28.314 32.688 1.00 48.94 ? 4 DT A "O4'" 1 ATOM 67 C "C3'" . DT A 1 4 ? -8.546 26.244 31.664 1.00 50.93 ? 4 DT A "C3'" 1 ATOM 68 O "O3'" . DT A 1 4 ? -9.824 26.265 31.060 1.00 52.44 ? 4 DT A "O3'" 1 ATOM 69 C "C2'" . DT A 1 4 ? -7.566 27.139 30.892 1.00 47.58 ? 4 DT A "C2'" 1 ATOM 70 C "C1'" . DT A 1 4 ? -8.257 28.435 31.279 1.00 45.20 ? 4 DT A "C1'" 1 ATOM 71 N N1 . DT A 1 4 ? -7.510 29.648 30.899 1.00 41.89 ? 4 DT A N1 1 ATOM 72 C C2 . DT A 1 4 ? -8.160 30.858 30.706 1.00 40.85 ? 4 DT A C2 1 ATOM 73 O O2 . DT A 1 4 ? -9.359 31.028 30.835 1.00 42.27 ? 4 DT A O2 1 ATOM 74 N N3 . DT A 1 4 ? -7.366 31.897 30.351 1.00 38.11 ? 4 DT A N3 1 ATOM 75 C C4 . DT A 1 4 ? -6.013 31.834 30.161 1.00 39.31 ? 4 DT A C4 1 ATOM 76 O O4 . DT A 1 4 ? -5.362 32.831 29.839 1.00 40.51 ? 4 DT A O4 1 ATOM 77 C C5 . DT A 1 4 ? -5.406 30.541 30.381 1.00 39.17 ? 4 DT A C5 1 ATOM 78 C C7 . DT A 1 4 ? -3.926 30.338 30.228 1.00 40.63 ? 4 DT A C7 1 ATOM 79 C C6 . DT A 1 4 ? -6.166 29.514 30.728 1.00 39.35 ? 4 DT A C6 1 ATOM 80 P P . DA A 1 5 ? -10.529 24.878 30.744 1.00 50.99 ? 5 DA A P 1 ATOM 81 O OP1 . DA A 1 5 ? -10.811 24.378 32.124 1.00 49.85 ? 5 DA A OP1 1 ATOM 82 O OP2 . DA A 1 5 ? -9.661 24.180 29.728 1.00 48.94 ? 5 DA A OP2 1 ATOM 83 O "O5'" . DA A 1 5 ? -11.913 25.311 30.059 1.00 47.19 ? 5 DA A "O5'" 1 ATOM 84 C "C5'" . DA A 1 5 ? -12.665 26.312 30.719 1.00 44.82 ? 5 DA A "C5'" 1 ATOM 85 C "C4'" . DA A 1 5 ? -13.347 27.218 29.717 1.00 43.35 ? 5 DA A "C4'" 1 ATOM 86 O "O4'" . DA A 1 5 ? -12.509 28.329 29.297 1.00 41.33 ? 5 DA A "O4'" 1 ATOM 87 C "C3'" . DA A 1 5 ? -13.739 26.513 28.439 1.00 43.99 ? 5 DA A "C3'" 1 ATOM 88 O "O3'" . DA A 1 5 ? -14.943 27.110 28.017 1.00 47.33 ? 5 DA A "O3'" 1 ATOM 89 C "C2'" . DA A 1 5 ? -12.567 26.839 27.511 1.00 41.43 ? 5 DA A "C2'" 1 ATOM 90 C "C1'" . DA A 1 5 ? -12.238 28.277 27.906 1.00 39.04 ? 5 DA A "C1'" 1 ATOM 91 N N9 . DA A 1 5 ? -10.834 28.667 27.726 1.00 35.89 ? 5 DA A N9 1 ATOM 92 C C8 . DA A 1 5 ? -9.738 27.853 27.834 1.00 35.19 ? 5 DA A C8 1 ATOM 93 N N7 . DA A 1 5 ? -8.579 28.443 27.639 1.00 32.92 ? 5 DA A N7 1 ATOM 94 C C5 . DA A 1 5 ? -8.932 29.743 27.393 1.00 31.78 ? 5 DA A C5 1 ATOM 95 C C6 . DA A 1 5 ? -8.157 30.865 27.137 1.00 31.10 ? 5 DA A C6 1 ATOM 96 N N6 . DA A 1 5 ? -6.841 30.805 27.070 1.00 31.13 ? 5 DA A N6 1 ATOM 97 N N1 . DA A 1 5 ? -8.760 32.048 26.932 1.00 32.55 ? 5 DA A N1 1 ATOM 98 C C2 . DA A 1 5 ? -10.098 32.086 26.984 1.00 34.78 ? 5 DA A C2 1 ATOM 99 N N3 . DA A 1 5 ? -10.947 31.065 27.232 1.00 36.60 ? 5 DA A N3 1 ATOM 100 C C4 . DA A 1 5 ? -10.298 29.906 27.441 1.00 34.27 ? 5 DA A C4 1 ATOM 101 P P . DT A 1 6 ? -15.518 26.783 26.558 1.00 50.94 ? 6 DT A P 1 ATOM 102 O OP1 . DT A 1 6 ? -16.945 27.185 26.657 1.00 50.49 ? 6 DT A OP1 1 ATOM 103 O OP2 . DT A 1 6 ? -15.058 25.422 26.155 1.00 48.73 ? 6 DT A OP2 1 ATOM 104 O "O5'" . DT A 1 6 ? -14.887 27.866 25.577 1.00 49.87 ? 6 DT A "O5'" 1 ATOM 105 C "C5'" . DT A 1 6 ? -15.418 29.160 25.794 1.00 50.87 ? 6 DT A "C5'" 1 ATOM 106 C "C4'" . DT A 1 6 ? -14.953 30.091 24.710 1.00 50.56 ? 6 DT A "C4'" 1 ATOM 107 O "O4'" . DT A 1 6 ? -13.521 30.203 24.827 1.00 49.12 ? 6 DT A "O4'" 1 ATOM 108 C "C3'" . DT A 1 6 ? -15.234 29.578 23.304 1.00 50.73 ? 6 DT A "C3'" 1 ATOM 109 O "O3'" . DT A 1 6 ? -15.766 30.659 22.550 1.00 52.17 ? 6 DT A "O3'" 1 ATOM 110 C "C2'" . DT A 1 6 ? -13.859 29.164 22.792 1.00 49.56 ? 6 DT A "C2'" 1 ATOM 111 C "C1'" . DT A 1 6 ? -12.988 30.170 23.529 1.00 47.70 ? 6 DT A "C1'" 1 ATOM 112 N N1 . DT A 1 6 ? -11.558 29.826 23.696 1.00 45.69 ? 6 DT A N1 1 ATOM 113 C C2 . DT A 1 6 ? -10.665 30.862 23.667 1.00 44.11 ? 6 DT A C2 1 ATOM 114 O O2 . DT A 1 6 ? -11.012 32.020 23.501 1.00 44.63 ? 6 DT A O2 1 ATOM 115 N N3 . DT A 1 6 ? -9.361 30.487 23.829 1.00 42.39 ? 6 DT A N3 1 ATOM 116 C C4 . DT A 1 6 ? -8.898 29.208 24.019 1.00 42.83 ? 6 DT A C4 1 ATOM 117 O O4 . DT A 1 6 ? -7.707 28.976 24.152 1.00 42.94 ? 6 DT A O4 1 ATOM 118 C C5 . DT A 1 6 ? -9.892 28.166 24.033 1.00 42.20 ? 6 DT A C5 1 ATOM 119 C C7 . DT A 1 6 ? -9.506 26.742 24.230 1.00 41.34 ? 6 DT A C7 1 ATOM 120 C C6 . DT A 1 6 ? -11.161 28.517 23.884 1.00 43.56 ? 6 DT A C6 1 HETATM 121 O O . HOH B 2 . ? -13.684 31.445 27.438 1.00 40.78 ? 7 HOH A O 1 HETATM 122 O O . HOH B 2 . ? -8.643 29.731 35.642 1.00 46.80 ? 8 HOH A O 1 # 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 C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DT 6 6 6 DT T A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 7 1 HOH HOH A . B 2 HOH 2 8 2 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details 'representative helical assembly' _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details helical _pdbx_struct_assembly.oligomeric_count 2 # _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 # 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' 8_676 x-y+1,-y+2,-z+1 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 66.3825792509 0.0000000000 0.0000000000 -1.0000000000 56.8210000000 3 'crystal symmetry operation' 12_566 x,x-y+1,-z+4/3 0.5000000000 0.8660254038 0.0000000000 -19.1630000000 0.8660254038 -0.5000000000 0.0000000000 33.1912896254 0.0000000000 0.0000000000 -1.0000000000 75.7613333333 # 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 2010-05-19 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-11-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 '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' 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' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOLREP phasing 'VERSION 10.2.6' ? 1 REFMAC refinement 5.5.0046 ? 2 # 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 1 ? ? "C3'" A DC 1 ? ? 1.380 1.419 -0.039 0.006 N 2 1 "O3'" A DG 2 ? ? "C3'" A DG 2 ? ? 1.348 1.419 -0.071 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 "O3'" A DG 2 ? ? P A DA 3 ? ? OP1 A DA 3 ? ? 118.28 110.50 7.78 1.10 Y 2 1 "O5'" A DA 3 ? ? P A DA 3 ? ? OP1 A DA 3 ? ? 99.79 105.70 -5.91 0.90 N 3 1 "O5'" A DT 4 ? ? "C5'" A DT 4 ? ? "C4'" A DT 4 ? ? 104.08 109.40 -5.32 0.80 N 4 1 "O4'" A DT 4 ? ? "C4'" A DT 4 ? ? "C3'" A DT 4 ? ? 101.71 104.50 -2.79 0.40 N 5 1 "C3'" A DT 4 ? ? "C2'" A DT 4 ? ? "C1'" A DT 4 ? ? 94.52 102.40 -7.88 0.80 N 6 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 112.14 108.30 3.84 0.30 N 7 1 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 119.18 122.90 -3.72 0.60 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # _ndb_struct_conf_na.entry_id 3HCL _ndb_struct_conf_na.feature 'b-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 DA 3 1_555 A DT 6 8_676 -0.020 -0.146 -0.132 -7.728 -4.999 1.543 1 A_DA3:DT6_A A 3 ? A 6 ? 20 1 1 A DT 4 1_555 A DA 5 8_676 0.068 -0.096 0.070 2.426 -10.952 0.951 2 A_DT4:DA5_A A 4 ? A 5 ? 20 1 1 A DA 5 1_555 A DT 4 8_676 -0.068 -0.096 0.070 -2.426 -10.952 0.951 3 A_DA5:DT4_A A 5 ? A 4 ? 20 1 1 A DT 6 1_555 A DA 3 8_676 0.020 -0.146 -0.132 7.728 -4.999 1.543 4 A_DT6:DA3_A A 6 ? A 3 ? 20 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 DA 3 1_555 A DT 6 8_676 A DT 4 1_555 A DA 5 8_676 -0.172 -0.357 3.126 -2.143 0.351 27.200 -0.841 -0.147 3.126 0.744 4.547 27.284 1 AA_DA3DT4:DA5DT6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A DT 4 1_555 A DA 5 8_676 A DA 5 1_555 A DT 4 8_676 0.000 1.215 3.396 0.000 5.197 42.526 1.114 0.000 3.514 7.134 0.000 42.827 2 AA_DT4DA5:DT4DA5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A DA 5 1_555 A DT 4 8_676 A DT 6 1_555 A DA 3 8_676 0.172 -0.357 3.126 2.143 0.351 27.200 -0.841 0.147 3.126 0.744 -4.547 27.284 3 AA_DA5DT6:DA3DT4_AA A 5 ? A 4 ? A 6 ? A 3 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 231D _pdbx_initial_refinement_model.details ? #