data_355D # _entry.id 355D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.375 _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 355D pdb_0000355d 10.2210/pdb355d/pdb RCSB BDL084 ? ? WWPDB D_1000178824 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 355D _pdbx_database_status.recvd_initial_deposition_date 1997-10-07 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Hu, L.D.' 1 ? 'Shui, X.' 2 ? 'McFail-Isom, L.' 3 ? 'Williams, G.G.' 4 ? # _citation.id primary _citation.title 'The B-DNA dodecamer at high resolution reveals a spine of water on sodium.' _citation.journal_abbrev Biochemistry _citation.journal_volume 37 _citation.page_first 8341 _citation.page_last 8355 _citation.year 1998 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9622486 _citation.pdbx_database_id_DOI 10.1021/bi973073c # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Shui, X.' 1 ? primary 'McFail-Isom, L.' 2 ? primary 'Hu, G.G.' 3 ? primary 'Williams, L.D.' 4 ? # _cell.entry_id 355D _cell.length_a 25.186 _cell.length_b 40.208 _cell.length_c 65.656 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 355D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # 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*AP*TP*TP*CP*GP*CP*G)-3') ; 3663.392 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 4 water nat water 18.015 166 ? ? ? ? # _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)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _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 DA 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 355D _struct_ref.pdbx_db_accession 355D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 355D A 1 ? 12 ? 355D 1 ? 12 ? 1 12 2 1 355D B 1 ? 12 ? 355D 13 ? 24 ? 13 24 # 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # _exptl.entry_id 355D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.27 _exptl_crystal.density_percent_sol 45.78 _exptl_crystal.description ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 298.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.50 _exptl_crystal_grow.pdbx_details 'pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.00K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'NA CACODYLATE' ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 1 SPERMINE_HCL ? ? ? 1 6 1 ;N,N'-BIS(4-AMINOBUTYL)-(2,7-ANTHROQUINONEDISULFONAMIDE DIHYDROCHLORIDE) ; ? ? ? 1 7 2 WATER ? ? ? 1 8 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 136.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type ADSC _diffrn_detector.pdbx_collection_date ? _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 GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 355D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 1.380 _reflns.number_obs 11594 _reflns.number_all 58307 _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.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? # _refine.entry_id 355D _refine.ls_number_reflns_obs 11438 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 1.400 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1970000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1970000 _refine.ls_R_factor_R_free 0.2160000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'NDB ENTRY GDL036 (PDB ENTRY 227D)' _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _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 486 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 160 _refine_hist.number_atoms_total 660 _refine_hist.d_res_high 1.400 _refine_hist.d_res_low 10.000 # 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 x_bond_d 0.007 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 1.42 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.40 _refine_ls_shell.d_res_low 1.46 _refine_ls_shell.number_reflns_R_work 784 _refine_ls_shell.R_factor_R_work 0.2410000 _refine_ls_shell.percent_reflns_obs 64.00 _refine_ls_shell.R_factor_R_free ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 355D _struct.title 'THE B-DNA DODECAMER AT HIGH RESOLUTION' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 355D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, SODIUM FORM, 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 4 ? F N N 4 ? # 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 MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 25 A HOH 188 1_555 ? ? ? ? ? ? ? 2.043 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 25 A HOH 189 1_555 ? ? ? ? ? ? ? 2.047 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 25 A HOH 191 1_555 ? ? ? ? ? ? ? 2.063 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 25 B HOH 187 1_555 ? ? ? ? ? ? ? 2.075 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 25 B HOH 190 1_555 ? ? ? ? ? ? ? 2.074 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 25 B HOH 192 1_555 ? ? ? ? ? ? ? 2.109 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B SPM 26 ? 4 'BINDING SITE FOR RESIDUE SPM B 26' AC2 Software A MG 25 ? 6 'BINDING SITE FOR RESIDUE MG A 25' # 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 4 DG A 10 ? DG A 10 . ? 1_555 ? 2 AC1 4 DC B 1 ? DC B 13 . ? 1_555 ? 3 AC1 4 DG B 2 ? DG B 14 . ? 1_555 ? 4 AC1 4 HOH F . ? HOH B 152 . ? 2_564 ? 5 AC2 6 HOH E . ? HOH A 188 . ? 1_555 ? 6 AC2 6 HOH E . ? HOH A 189 . ? 1_555 ? 7 AC2 6 HOH E . ? HOH A 191 . ? 1_555 ? 8 AC2 6 HOH F . ? HOH B 187 . ? 1_555 ? 9 AC2 6 HOH F . ? HOH B 190 . ? 1_555 ? 10 AC2 6 HOH F . ? HOH B 192 . ? 1_555 ? # _database_PDB_matrix.entry_id 355D _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 355D _atom_sites.fract_transf_matrix[1][1] 0.039705 _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] 0.024871 _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] 0.015231 _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 MG 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 C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 13 13 DC C B . n B 1 2 DG 2 14 14 DG G B . n B 1 3 DC 3 15 15 DC C B . n B 1 4 DG 4 16 16 DG G B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 DC 9 21 21 DC C B . n B 1 10 DG 10 22 22 DG G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 DG G 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 MG 1 25 25 MG MO6 A . D 3 SPM 1 26 26 SPM SPM B . E 4 HOH 1 28 28 HOH HOH A . E 4 HOH 2 29 29 HOH HOH A . E 4 HOH 3 31 31 HOH HOH A . E 4 HOH 4 32 32 HOH HOH A . E 4 HOH 5 33 33 HOH HOH A . E 4 HOH 6 35 35 HOH HOH A . E 4 HOH 7 36 36 HOH HOH A . E 4 HOH 8 39 39 HOH HOH A . E 4 HOH 9 40 40 HOH HOH A . E 4 HOH 10 41 41 HOH HOH A . E 4 HOH 11 42 42 HOH HOH A . E 4 HOH 12 47 47 HOH HOH A . E 4 HOH 13 49 49 HOH HOH A . E 4 HOH 14 51 51 HOH HOH A . E 4 HOH 15 52 52 HOH HOH A . E 4 HOH 16 53 53 HOH HOH A . E 4 HOH 17 54 54 HOH HOH A . E 4 HOH 18 55 55 HOH HOH A . E 4 HOH 19 57 57 HOH HOH A . E 4 HOH 20 58 58 HOH HOH A . E 4 HOH 21 59 59 HOH HOH A . E 4 HOH 22 60 60 HOH HOH A . E 4 HOH 23 62 62 HOH HOH A . E 4 HOH 24 64 64 HOH HOH A . E 4 HOH 25 65 65 HOH HOH A . E 4 HOH 26 66 66 HOH HOH A . E 4 HOH 27 67 67 HOH HOH A . E 4 HOH 28 68 68 HOH HOH A . E 4 HOH 29 69 69 HOH HOH A . E 4 HOH 30 71 71 HOH HOH A . E 4 HOH 31 72 72 HOH HOH A . E 4 HOH 32 76 76 HOH HOH A . E 4 HOH 33 78 78 HOH HOH A . E 4 HOH 34 80 80 HOH HOH A . E 4 HOH 35 84 84 HOH HOH A . E 4 HOH 36 86 86 HOH HOH A . E 4 HOH 37 87 87 HOH HOH A . E 4 HOH 38 91 91 HOH HOH A . E 4 HOH 39 92 92 HOH HOH A . E 4 HOH 40 95 95 HOH HOH A . E 4 HOH 41 96 96 HOH HOH A . E 4 HOH 42 97 97 HOH HOH A . E 4 HOH 43 98 98 HOH HOH A . E 4 HOH 44 99 99 HOH HOH A . E 4 HOH 45 100 100 HOH HOH A . E 4 HOH 46 101 101 HOH HOH A . E 4 HOH 47 102 102 HOH HOH A . E 4 HOH 48 104 104 HOH HOH A . E 4 HOH 49 106 106 HOH HOH A . E 4 HOH 50 110 110 HOH HOH A . E 4 HOH 51 111 111 HOH HOH A . E 4 HOH 52 113 113 HOH HOH A . E 4 HOH 53 115 115 HOH HOH A . E 4 HOH 54 118 118 HOH HOH A . E 4 HOH 55 119 119 HOH HOH A . E 4 HOH 56 120 120 HOH HOH A . E 4 HOH 57 122 122 HOH HOH A . E 4 HOH 58 123 123 HOH HOH A . E 4 HOH 59 124 124 HOH HOH A . E 4 HOH 60 125 125 HOH HOH A . E 4 HOH 61 126 126 HOH HOH A . E 4 HOH 62 127 127 HOH HOH A . E 4 HOH 63 130 130 HOH HOH A . E 4 HOH 64 131 131 HOH HOH A . E 4 HOH 65 135 135 HOH HOH A . E 4 HOH 66 137 137 HOH HOH A . E 4 HOH 67 142 142 HOH HOH A . E 4 HOH 68 150 150 HOH HOH A . E 4 HOH 69 155 155 HOH HOH A . E 4 HOH 70 158 158 HOH HOH A . E 4 HOH 71 159 159 HOH HOH A . E 4 HOH 72 160 160 HOH HOH A . E 4 HOH 73 161 161 HOH HOH A . E 4 HOH 74 162 162 HOH HOH A . E 4 HOH 75 166 166 HOH HOH A . E 4 HOH 76 168 168 HOH HOH A . E 4 HOH 77 170 170 HOH HOH A . E 4 HOH 78 172 172 HOH HOH A . E 4 HOH 79 173 173 HOH HOH A . E 4 HOH 80 174 174 HOH HOH A . E 4 HOH 81 175 175 HOH HOH A . E 4 HOH 82 182 182 HOH HOH A . E 4 HOH 83 183 183 HOH HOH A . E 4 HOH 84 185 185 HOH HOH A . E 4 HOH 85 186 186 HOH HOH A . E 4 HOH 86 188 25 HOH MO6 A . E 4 HOH 87 189 25 HOH MO6 A . E 4 HOH 88 191 25 HOH MO6 A . F 4 HOH 1 27 27 HOH HOH B . F 4 HOH 2 30 30 HOH HOH B . F 4 HOH 3 34 34 HOH HOH B . F 4 HOH 4 37 37 HOH HOH B . F 4 HOH 5 38 38 HOH HOH B . F 4 HOH 6 43 43 HOH HOH B . F 4 HOH 7 44 44 HOH HOH B . F 4 HOH 8 45 45 HOH HOH B . F 4 HOH 9 46 46 HOH HOH B . F 4 HOH 10 48 48 HOH HOH B . F 4 HOH 11 50 50 HOH HOH B . F 4 HOH 12 56 56 HOH HOH B . F 4 HOH 13 61 61 HOH HOH B . F 4 HOH 14 63 63 HOH HOH B . F 4 HOH 15 70 70 HOH HOH B . F 4 HOH 16 73 73 HOH HOH B . F 4 HOH 17 74 74 HOH HOH B . F 4 HOH 18 75 75 HOH HOH B . F 4 HOH 19 77 77 HOH HOH B . F 4 HOH 20 79 79 HOH HOH B . F 4 HOH 21 81 81 HOH HOH B . F 4 HOH 22 82 82 HOH HOH B . F 4 HOH 23 83 83 HOH HOH B . F 4 HOH 24 85 85 HOH HOH B . F 4 HOH 25 88 88 HOH HOH B . F 4 HOH 26 89 89 HOH HOH B . F 4 HOH 27 90 90 HOH HOH B . F 4 HOH 28 93 93 HOH HOH B . F 4 HOH 29 94 94 HOH HOH B . F 4 HOH 30 103 103 HOH HOH B . F 4 HOH 31 105 105 HOH HOH B . F 4 HOH 32 107 107 HOH HOH B . F 4 HOH 33 108 108 HOH HOH B . F 4 HOH 34 109 109 HOH HOH B . F 4 HOH 35 112 112 HOH HOH B . F 4 HOH 36 114 114 HOH HOH B . F 4 HOH 37 116 116 HOH HOH B . F 4 HOH 38 117 117 HOH HOH B . F 4 HOH 39 121 121 HOH HOH B . F 4 HOH 40 128 128 HOH HOH B . F 4 HOH 41 129 129 HOH HOH B . F 4 HOH 42 132 132 HOH HOH B . F 4 HOH 43 133 133 HOH HOH B . F 4 HOH 44 134 134 HOH HOH B . F 4 HOH 45 136 136 HOH HOH B . F 4 HOH 46 138 138 HOH HOH B . F 4 HOH 47 139 139 HOH HOH B . F 4 HOH 48 140 140 HOH HOH B . F 4 HOH 49 141 141 HOH HOH B . F 4 HOH 50 143 143 HOH HOH B . F 4 HOH 51 144 144 HOH HOH B . F 4 HOH 52 145 145 HOH HOH B . F 4 HOH 53 146 146 HOH HOH B . F 4 HOH 54 147 147 HOH HOH B . F 4 HOH 55 148 148 HOH HOH B . F 4 HOH 56 149 149 HOH HOH B . F 4 HOH 57 151 151 HOH HOH B . F 4 HOH 58 152 152 HOH HOH B . F 4 HOH 59 153 153 HOH HOH B . F 4 HOH 60 154 154 HOH HOH B . F 4 HOH 61 156 156 HOH HOH B . F 4 HOH 62 157 157 HOH HOH B . F 4 HOH 63 163 163 HOH HOH B . F 4 HOH 64 164 164 HOH HOH B . F 4 HOH 65 165 165 HOH HOH B . F 4 HOH 66 167 167 HOH HOH B . F 4 HOH 67 169 169 HOH HOH B . F 4 HOH 68 171 171 HOH HOH B . F 4 HOH 69 176 176 HOH HOH B . F 4 HOH 70 177 177 HOH HOH B . F 4 HOH 71 178 178 HOH HOH B . F 4 HOH 72 179 179 HOH HOH B . F 4 HOH 73 180 180 HOH HOH B . F 4 HOH 74 181 181 HOH HOH B . F 4 HOH 75 184 184 HOH HOH B . F 4 HOH 76 187 25 HOH MO6 B . F 4 HOH 77 190 25 HOH MO6 B . F 4 HOH 78 192 25 HOH MO6 B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _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_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? A HOH 188 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 189 ? 1_555 92.2 ? 2 O ? E HOH . ? A HOH 188 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 191 ? 1_555 92.6 ? 3 O ? E HOH . ? A HOH 189 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? A HOH 191 ? 1_555 85.1 ? 4 O ? E HOH . ? A HOH 188 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 187 ? 1_555 86.0 ? 5 O ? E HOH . ? A HOH 189 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 187 ? 1_555 177.9 ? 6 O ? E HOH . ? A HOH 191 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 187 ? 1_555 96.3 ? 7 O ? E HOH . ? A HOH 188 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 190 ? 1_555 173.2 ? 8 O ? E HOH . ? A HOH 189 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 190 ? 1_555 93.9 ? 9 O ? E HOH . ? A HOH 191 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 190 ? 1_555 91.0 ? 10 O ? F HOH . ? B HOH 187 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 190 ? 1_555 87.8 ? 11 O ? E HOH . ? A HOH 188 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 192 ? 1_555 90.2 ? 12 O ? E HOH . ? A HOH 189 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 192 ? 1_555 89.7 ? 13 O ? E HOH . ? A HOH 191 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 192 ? 1_555 174.1 ? 14 O ? F HOH . ? B HOH 187 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 192 ? 1_555 89.1 ? 15 O ? F HOH . ? B HOH 190 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? F HOH . ? B HOH 192 ? 1_555 86.7 ? # 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 1997-10-13 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-02 # _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' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 '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 4 'Structure model' database_2 2 4 'Structure model' pdbx_initial_refinement_model 3 4 'Structure model' pdbx_struct_conn_angle 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.value' 10 4 'Structure model' '_struct_conn.pdbx_dist_value' 11 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 14 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 15 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 16 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language X-PLOR refinement . ? 1 ? ? ? ? ADSC 'data collection' . ? 2 ? ? ? ? # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 N 1 B SPM 26 ? C8 ? D SPM 1 C8 2 1 N 1 B SPM 26 ? C9 ? D SPM 1 C9 3 1 N 1 B SPM 26 ? N10 ? D SPM 1 N10 4 1 N 1 B SPM 26 ? C11 ? D SPM 1 C11 5 1 N 1 B SPM 26 ? C12 ? D SPM 1 C12 6 1 N 1 B SPM 26 ? C13 ? D SPM 1 C13 7 1 N 1 B SPM 26 ? N14 ? D SPM 1 N14 # _ndb_struct_conf_na.entry_id 355D _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 DC 1 1_555 B DG 12 1_555 0.276 -0.140 0.073 6.930 -17.308 -0.606 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.236 -0.182 0.491 9.341 -14.302 -2.077 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.244 -0.171 0.159 -4.433 -5.405 0.434 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.255 -0.115 0.008 10.806 -9.449 1.012 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 -0.037 -0.107 0.011 4.724 -15.314 1.601 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.051 -0.050 0.065 0.442 -15.001 6.233 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.037 -0.117 0.173 -0.264 -16.744 3.928 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.108 -0.120 -0.004 -1.561 -16.364 5.120 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.209 -0.127 0.003 -12.410 -10.274 -1.223 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.106 -0.053 0.239 4.205 -9.603 3.206 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.156 -0.130 0.208 0.283 -17.417 -1.755 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.244 -0.069 0.254 4.671 -4.954 -1.620 12 A_DG12:DC13_B A 12 ? B 13 ? 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 0.087 0.039 3.200 -3.216 8.520 32.731 -1.273 -0.654 3.090 14.766 5.573 33.940 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.496 0.668 3.691 2.847 -9.055 43.879 1.792 -0.363 3.517 -11.952 -3.757 44.844 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.138 0.593 3.000 0.967 11.300 25.114 -1.405 0.518 2.977 24.457 -2.092 27.519 3 AA_DC3DG4:DC21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 -0.453 -0.139 3.388 -1.585 1.373 37.500 -0.402 0.489 3.396 2.133 2.463 37.556 4 AA_DG4DA5:DT20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.171 -0.325 3.298 -0.330 0.459 37.520 -0.566 -0.310 3.293 0.713 0.514 37.524 5 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 -0.011 -0.601 3.219 -0.311 -2.675 32.403 -0.610 -0.034 3.256 -4.783 0.556 32.512 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.082 -0.397 3.216 1.681 -0.974 33.744 -0.529 0.408 3.218 -1.676 -2.893 33.798 7 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 -0.267 -0.226 3.465 0.684 -1.686 42.136 -0.130 0.446 3.467 -2.344 -0.951 42.174 8 AA_DT8DC9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.700 0.776 3.068 -3.656 4.180 26.581 0.660 -2.360 3.031 8.967 7.844 27.145 9 AA_DC9DG10:DC15DG16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.311 0.360 3.371 -2.853 -9.368 41.601 1.467 1.504 3.297 -12.975 3.951 42.688 10 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 -0.309 0.211 3.174 -0.679 6.692 33.310 -0.686 0.423 3.161 11.528 1.169 33.964 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 SPERMINE SPM 4 water 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 227D _pdbx_initial_refinement_model.details 'NDB ENTRY GDL036 (PDB ENTRY 227D)' #