data_4L25 # _entry.id 4L25 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _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 4L25 pdb_00004l25 10.2210/pdb4l25/pdb NDB NA2492 ? ? RCSB RCSB080085 ? ? WWPDB D_1000080085 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4L24 . unspecified PDB 4L26 . unspecified # _pdbx_database_status.entry_id 4L25 _pdbx_database_status.methods_development_category ? _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2013-06-04 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Yamada, T.' 2 'Hirose, C.' 3 'Tanaka, Y.' 4 'Ono, A.' 5 # _citation.id primary _citation.title 'Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs' _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 53 _citation.page_first 2385 _citation.page_last 2388 _citation.year 2014 _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 24478025 _citation.pdbx_database_id_DOI 10.1002/anie.201309066 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Yamada, T.' 2 ? primary 'Hirose, C.' 3 ? primary 'Okamoto, I.' 4 ? primary 'Tanaka, Y.' 5 ? primary 'Ono, A.' 6 ? # _cell.length_a 27.340 _cell.length_b 39.330 _cell.length_c 30.680 _cell.angle_alpha 90.000 _cell.angle_beta 98.280 _cell.angle_gamma 90.000 _cell.entry_id 4L25 _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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.space_group_name_H-M 'P 1 21 1' _symmetry.entry_id 4L25 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 4 _symmetry.cell_setting ? _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*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3') ; 3654.378 2 ? ? ? ? 2 water nat water 18.015 170 ? ? ? ? # _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)(DC)(DG)(DA)(DT)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGATTTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 DT n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Chemically synthesized' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4L25 _struct_ref.pdbx_db_accession 4L25 _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 4L25 A 1 ? 12 ? 4L25 1 ? 12 ? 1 12 2 1 4L25 B 1 ? 12 ? 4L25 1 ? 12 ? 1 12 # 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.crystals_number 1 _exptl.entry_id 4L25 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 2.23 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 44.92 _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _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.pH 7.0 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;Sodium Cacodylate, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, ammonium chloride , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _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 ? _diffrn_detector.type ? _diffrn_detector.pdbx_collection_date 2011-10-16 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-1A' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-1A # _reflns.entry_id 4L25 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 1.1 _reflns.d_resolution_low 19.1 _reflns.number_all ? _reflns.number_obs 24441 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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 # _refine.entry_id 4L25 _refine.ls_d_res_high 1.1000 _refine.ls_d_res_low 19.08 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 93.1000 _refine.ls_number_reflns_obs 24438 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.2305 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2405 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 9.2000 _refine.ls_number_reflns_R_free 2409 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 15.1144 _refine.solvent_model_param_bsol 50.0215 _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.0690 _refine.aniso_B[2][2] -2.2110 _refine.aniso_B[3][3] 2.2800 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 3.4160 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.solvent_model_details ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 4L26 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 51.240 _refine.B_iso_min 6.300 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.500 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_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 484 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 170 _refine_hist.number_atoms_total 654 _refine_hist.d_res_high 1.1000 _refine_hist.d_res_low 19.08 # loop_ _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 _refine_ls_restr.pdbx_refine_id c_bond_d ? 0.003 ? ? ? 'X-RAY DIFFRACTION' c_angle_deg ? 0.895 ? ? ? 'X-RAY DIFFRACTION' c_mcbond_it ? 1.013 1.500 ? ? 'X-RAY DIFFRACTION' c_mcangle_it ? 1.462 2.000 ? ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.redundancy_reflns_obs 1.1000 1.1400 10 91.6000 2173 . 0.3527 0.3521 . 251 . 2424 . 'X-RAY DIFFRACTION' . 1.1400 1.1800 10 91.8000 2141 . 0.3190 0.3317 . 233 . 2374 . 'X-RAY DIFFRACTION' . 1.1800 1.2400 10 92.9000 2186 . 0.2756 0.2816 . 219 . 2405 . 'X-RAY DIFFRACTION' . 1.2400 1.3000 10 93.5000 2217 . 0.2775 0.2840 . 238 . 2455 . 'X-RAY DIFFRACTION' . 1.3000 1.3900 10 94.3000 2214 . 0.2690 0.2625 . 248 . 2462 . 'X-RAY DIFFRACTION' . 1.3900 1.4900 10 95.4000 2233 . 0.2432 0.2482 . 245 . 2478 . 'X-RAY DIFFRACTION' . 1.4900 1.6400 10 95.9000 2288 . 0.2262 0.2440 . 241 . 2529 . 'X-RAY DIFFRACTION' . 1.6400 1.8800 10 97.1000 2268 . 0.2039 0.2232 . 268 . 2536 . 'X-RAY DIFFRACTION' . 1.8800 2.3700 10 97.8000 2333 . 0.2044 0.2184 . 261 . 2594 . 'X-RAY DIFFRACTION' . 2.3700 100.0000 10 81.5000 1976 . 0.2173 0.2237 . 205 . 2181 . 'X-RAY DIFFRACTION' . # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 dna-rna_free.param ? 'X-RAY DIFFRACTION' 2 water_rep.param ? 'X-RAY DIFFRACTION' 3 ion.param ? # _struct.entry_id 4L25 _struct.title 'Crystal structure of DNA duplex containing consecutive T-T mispairs' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4L25 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'T-T mispair, A-T-T triplet, non-helical DNA duplex, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _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 hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 7 O2 ? ? A DA 5 B DT 7 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog14 hydrog ? ? A DA 5 N7 ? ? ? 1_555 B DT 7 N3 ? ? A DA 5 B DT 7 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog15 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog16 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 5 N7 ? ? A DT 7 B DA 5 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog17 hydrog ? ? A DT 7 O2 ? ? ? 1_555 B DA 5 N6 ? ? A DT 7 B DA 5 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog18 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 5 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog19 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 4L25 _atom_sites.fract_transf_matrix[1][1] 0.036576 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005323 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.025426 _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] 0.032938 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DG 2 2 2 DG DG B . n B 1 3 DC 3 3 3 DC DC B . n B 1 4 DG 4 4 4 DG DG B . n B 1 5 DA 5 5 5 DA DA B . n B 1 6 DT 6 6 6 DT DT B . n B 1 7 DT 7 7 7 DT DT B . n B 1 8 DT 8 8 8 DT DT B . n B 1 9 DC 9 9 9 DC DC B . n B 1 10 DG 10 10 10 DG DG B . n B 1 11 DC 11 11 11 DC DC B . n B 1 12 DG 12 12 12 DG DG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 101 102 HOH HOH A . C 2 HOH 2 102 103 HOH HOH A . C 2 HOH 3 103 104 HOH HOH A . C 2 HOH 4 104 106 HOH HOH A . C 2 HOH 5 105 107 HOH HOH A . C 2 HOH 6 106 109 HOH HOH A . C 2 HOH 7 107 115 HOH HOH A . C 2 HOH 8 108 117 HOH HOH A . C 2 HOH 9 109 118 HOH HOH A . C 2 HOH 10 110 121 HOH HOH A . C 2 HOH 11 111 122 HOH HOH A . C 2 HOH 12 112 123 HOH HOH A . C 2 HOH 13 113 124 HOH HOH A . C 2 HOH 14 114 125 HOH HOH A . C 2 HOH 15 115 128 HOH HOH A . C 2 HOH 16 116 130 HOH HOH A . C 2 HOH 17 117 134 HOH HOH A . C 2 HOH 18 118 137 HOH HOH A . C 2 HOH 19 119 139 HOH HOH A . C 2 HOH 20 120 141 HOH HOH A . C 2 HOH 21 121 142 HOH HOH A . C 2 HOH 22 122 147 HOH HOH A . C 2 HOH 23 123 149 HOH HOH A . C 2 HOH 24 124 151 HOH HOH A . C 2 HOH 25 125 152 HOH HOH A . C 2 HOH 26 126 155 HOH HOH A . C 2 HOH 27 127 156 HOH HOH A . C 2 HOH 28 128 158 HOH HOH A . C 2 HOH 29 129 159 HOH HOH A . C 2 HOH 30 130 162 HOH HOH A . C 2 HOH 31 131 164 HOH HOH A . C 2 HOH 32 132 165 HOH HOH A . C 2 HOH 33 133 166 HOH HOH A . C 2 HOH 34 134 167 HOH HOH A . C 2 HOH 35 135 170 HOH HOH A . C 2 HOH 36 136 171 HOH HOH A . C 2 HOH 37 137 172 HOH HOH A . C 2 HOH 38 138 173 HOH HOH A . C 2 HOH 39 139 174 HOH HOH A . C 2 HOH 40 140 175 HOH HOH A . C 2 HOH 41 141 177 HOH HOH A . C 2 HOH 42 142 179 HOH HOH A . C 2 HOH 43 143 181 HOH HOH A . C 2 HOH 44 144 184 HOH HOH A . C 2 HOH 45 145 188 HOH HOH A . C 2 HOH 46 146 190 HOH HOH A . C 2 HOH 47 147 192 HOH HOH A . C 2 HOH 48 148 194 HOH HOH A . C 2 HOH 49 149 195 HOH HOH A . C 2 HOH 50 150 196 HOH HOH A . C 2 HOH 51 151 199 HOH HOH A . C 2 HOH 52 152 200 HOH HOH A . C 2 HOH 53 153 202 HOH HOH A . C 2 HOH 54 154 206 HOH HOH A . C 2 HOH 55 155 207 HOH HOH A . C 2 HOH 56 156 211 HOH HOH A . C 2 HOH 57 157 213 HOH HOH A . C 2 HOH 58 158 215 HOH HOH A . C 2 HOH 59 159 216 HOH HOH A . C 2 HOH 60 160 217 HOH HOH A . C 2 HOH 61 161 220 HOH HOH A . C 2 HOH 62 162 222 HOH HOH A . C 2 HOH 63 163 224 HOH HOH A . C 2 HOH 64 164 234 HOH HOH A . C 2 HOH 65 165 235 HOH HOH A . C 2 HOH 66 166 238 HOH HOH A . C 2 HOH 67 167 239 HOH HOH A . C 2 HOH 68 168 240 HOH HOH A . C 2 HOH 69 169 245 HOH HOH A . C 2 HOH 70 170 246 HOH HOH A . C 2 HOH 71 171 251 HOH HOH A . C 2 HOH 72 172 254 HOH HOH A . C 2 HOH 73 173 255 HOH HOH A . C 2 HOH 74 174 263 HOH HOH A . C 2 HOH 75 175 272 HOH HOH A . C 2 HOH 76 176 276 HOH HOH A . C 2 HOH 77 177 277 HOH HOH A . C 2 HOH 78 178 278 HOH HOH A . D 2 HOH 1 101 101 HOH HOH B . D 2 HOH 2 102 105 HOH HOH B . D 2 HOH 3 103 108 HOH HOH B . D 2 HOH 4 104 110 HOH HOH B . D 2 HOH 5 105 111 HOH HOH B . D 2 HOH 6 106 112 HOH HOH B . D 2 HOH 7 107 113 HOH HOH B . D 2 HOH 8 108 114 HOH HOH B . D 2 HOH 9 109 116 HOH HOH B . D 2 HOH 10 110 119 HOH HOH B . D 2 HOH 11 111 120 HOH HOH B . D 2 HOH 12 112 126 HOH HOH B . D 2 HOH 13 113 127 HOH HOH B . D 2 HOH 14 114 129 HOH HOH B . D 2 HOH 15 115 131 HOH HOH B . D 2 HOH 16 116 132 HOH HOH B . D 2 HOH 17 117 133 HOH HOH B . D 2 HOH 18 118 135 HOH HOH B . D 2 HOH 19 119 136 HOH HOH B . D 2 HOH 20 120 138 HOH HOH B . D 2 HOH 21 121 140 HOH HOH B . D 2 HOH 22 122 143 HOH HOH B . D 2 HOH 23 123 144 HOH HOH B . D 2 HOH 24 124 145 HOH HOH B . D 2 HOH 25 125 146 HOH HOH B . D 2 HOH 26 126 148 HOH HOH B . D 2 HOH 27 127 150 HOH HOH B . D 2 HOH 28 128 153 HOH HOH B . D 2 HOH 29 129 154 HOH HOH B . D 2 HOH 30 130 157 HOH HOH B . D 2 HOH 31 131 160 HOH HOH B . D 2 HOH 32 132 161 HOH HOH B . D 2 HOH 33 133 163 HOH HOH B . D 2 HOH 34 134 168 HOH HOH B . D 2 HOH 35 135 176 HOH HOH B . D 2 HOH 36 136 178 HOH HOH B . D 2 HOH 37 137 180 HOH HOH B . D 2 HOH 38 138 182 HOH HOH B . D 2 HOH 39 139 185 HOH HOH B . D 2 HOH 40 140 186 HOH HOH B . D 2 HOH 41 141 187 HOH HOH B . D 2 HOH 42 142 189 HOH HOH B . D 2 HOH 43 143 193 HOH HOH B . D 2 HOH 44 144 197 HOH HOH B . D 2 HOH 45 145 198 HOH HOH B . D 2 HOH 46 146 201 HOH HOH B . D 2 HOH 47 147 203 HOH HOH B . D 2 HOH 48 148 204 HOH HOH B . D 2 HOH 49 149 205 HOH HOH B . D 2 HOH 50 150 208 HOH HOH B . D 2 HOH 51 151 209 HOH HOH B . D 2 HOH 52 152 210 HOH HOH B . D 2 HOH 53 153 212 HOH HOH B . D 2 HOH 54 154 214 HOH HOH B . D 2 HOH 55 155 218 HOH HOH B . D 2 HOH 56 156 219 HOH HOH B . D 2 HOH 57 157 221 HOH HOH B . D 2 HOH 58 158 223 HOH HOH B . D 2 HOH 59 159 225 HOH HOH B . D 2 HOH 60 160 226 HOH HOH B . D 2 HOH 61 161 228 HOH HOH B . D 2 HOH 62 162 229 HOH HOH B . D 2 HOH 63 163 230 HOH HOH B . D 2 HOH 64 164 231 HOH HOH B . D 2 HOH 65 165 232 HOH HOH B . D 2 HOH 66 166 233 HOH HOH B . D 2 HOH 67 167 237 HOH HOH B . D 2 HOH 68 168 241 HOH HOH B . D 2 HOH 69 169 242 HOH HOH B . D 2 HOH 70 170 243 HOH HOH B . D 2 HOH 71 171 244 HOH HOH B . D 2 HOH 72 172 247 HOH HOH B . D 2 HOH 73 173 248 HOH HOH B . D 2 HOH 74 174 249 HOH HOH B . D 2 HOH 75 175 250 HOH HOH B . D 2 HOH 76 176 252 HOH HOH B . D 2 HOH 77 177 253 HOH HOH B . D 2 HOH 78 178 256 HOH HOH B . D 2 HOH 79 179 257 HOH HOH B . D 2 HOH 80 180 258 HOH HOH B . D 2 HOH 81 181 259 HOH HOH B . D 2 HOH 82 182 260 HOH HOH B . D 2 HOH 83 183 262 HOH HOH B . D 2 HOH 84 184 265 HOH HOH B . D 2 HOH 85 185 266 HOH HOH B . D 2 HOH 86 186 269 HOH HOH B . D 2 HOH 87 187 270 HOH HOH B . D 2 HOH 88 188 273 HOH HOH B . D 2 HOH 89 189 274 HOH HOH B . D 2 HOH 90 190 275 HOH HOH B . D 2 HOH 91 191 279 HOH HOH B . D 2 HOH 92 192 280 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1380 ? 1 MORE -11 ? 1 'SSA (A^2)' 3970 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2014-03-05 2 'Structure model' 1 1 2023-11-08 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns-online.org/ Fortran_77 ? 2 PDB_EXTRACT 3.11 'April 22, 2011' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 CrystalClear . ? ? ? ? 'data reduction' ? ? ? 4 CrystalClear . ? ? ? ? 'data scaling' ? ? ? 5 PHENIX . ? ? ? ? phasing ? ? ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4L25 'double helix' 4L25 'internal loop' # 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 12 1_555 0.330 -0.147 -0.318 5.853 -2.725 -0.282 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.234 -0.140 -0.138 3.381 4.912 -2.544 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.469 -0.176 -0.214 -5.930 0.349 0.135 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.285 -0.062 -0.102 13.793 -5.944 -2.771 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 3.190 3.036 -0.215 1.290 -10.484 -103.728 5 A_DA5:DT8_B A 5 ? B 8 ? ? ? 1 B DA 5 1_555 A DT 8 1_555 3.210 3.055 -0.190 4.150 -8.325 -103.740 6 B_DA5:DT8_A B 5 ? A 8 ? ? ? 1 B DG 4 1_555 A DC 9 1_555 -0.289 -0.099 -0.055 12.770 -4.729 -3.475 7 B_DG4:DC9_A B 4 ? A 9 ? 19 1 1 B DC 3 1_555 A DG 10 1_555 0.522 -0.255 -0.290 -3.706 1.660 -1.278 8 B_DC3:DG10_A B 3 ? A 10 ? 19 1 1 B DG 2 1_555 A DC 11 1_555 -0.317 -0.158 -0.095 1.465 5.534 -1.703 9 B_DG2:DC11_A B 2 ? A 11 ? 19 1 1 B DC 1 1_555 A DG 12 1_555 0.421 -0.203 -0.457 8.448 -2.989 -1.892 10 B_DC1:DG12_A B 1 ? A 12 ? 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 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.291 5.299 -3.527 -2.203 -1.153 9.257 28.973 6.980 -3.976 -6.980 13.338 9.585 1 AA_DC1DG2:DC11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.409 -1.069 -3.154 -0.075 -7.391 51.867 -1.671 -0.459 -2.987 -8.402 0.085 52.355 2 AA_DG2DC3:DG10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.045 5.661 -4.181 6.030 -0.263 5.728 38.083 -21.190 -3.092 -2.030 -46.497 8.319 3 AA_DC3DG4:DC9DG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 3.023 -2.188 2.916 2.658 168.870 84.076 -1.828 -1.504 0.371 86.263 -1.358 171.755 4 AA_DG4DA5:DT8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DA 5 1_555 B DT 8 1_555 B DA 5 1_555 A DT 8 1_555 -1.010 -6.477 -2.646 -110.473 -139.649 131.392 -3.467 0.686 -0.063 -69.892 55.290 179.202 5 AB_DA5DA5:DT8DT8_AB A 5 ? B 8 ? B 5 ? A 8 ? 1 B DA 5 1_555 A DT 8 1_555 B DG 4 1_555 A DC 9 1_555 -2.964 2.160 -2.953 -2.768 -169.096 -82.008 -1.836 -1.474 -0.352 86.413 -1.415 -171.794 6 BB_DA5DG4:DC9DT8_AA B 5 ? A 8 ? B 4 ? A 9 ? 1 B DG 4 1_555 A DC 9 1_555 B DC 3 1_555 A DG 10 1_555 0.039 -5.504 4.087 -5.301 -0.009 -4.726 44.485 -24.388 2.743 0.080 -48.311 -7.100 7 BB_DG4DC3:DG10DC9_AA B 4 ? A 9 ? B 3 ? A 10 ? 1 B DC 3 1_555 A DG 10 1_555 B DG 2 1_555 A DC 11 1_555 -0.143 0.988 3.249 -1.419 6.814 -53.154 -1.514 -0.246 3.106 -7.578 -1.578 -53.575 8 BB_DC3DG2:DC11DG10_AA B 3 ? A 10 ? B 2 ? A 11 ? 1 B DG 2 1_555 A DC 11 1_555 B DC 1 1_555 A DG 12 1_555 0.361 -5.209 3.479 4.300 -0.603 -9.874 28.680 8.805 2.752 3.302 23.542 -10.785 9 BB_DG2DC1:DG12DC11_AA B 2 ? A 11 ? B 1 ? A 12 ? # _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 4L26 _pdbx_initial_refinement_model.details ? #