data_1S23 # _entry.id 1S23 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1S23 pdb_00001s23 10.2210/pdb1s23/pdb NDB BD0066 ? ? RCSB RCSB021269 ? ? WWPDB D_1000021269 ? ? # 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 2004-04-06 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 5 'Structure model' 1 4 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site 7 5 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_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.ptnr1_label_atom_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 4 'Structure model' '_struct_conn.ptnr1_symmetry' 26 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 32 4 'Structure model' '_struct_conn.ptnr2_symmetry' 33 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 34 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 35 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1S23 _pdbx_database_status.recvd_initial_deposition_date 2004-01-08 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _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 'Valls, N.' 1 'Wright, G.' 2 'Steiner, R.A.' 3 'Murshudov, G.N.' 4 'Subirana, J.A.' 5 # _citation.id primary _citation.title 'DNA variability in five crystal structures of d(CGCAATTGCG).' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 60 _citation.page_first 680 _citation.page_last 685 _citation.year 2004 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15039556 _citation.pdbx_database_id_DOI 10.1107/S0907444904002896 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Valls, N.' 1 ? primary 'Wright, G.' 2 ? primary 'Steiner, R.A.' 3 ? primary 'Murshudov, G.N.' 4 ? primary 'Subirana, J.A.' 5 ? # 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 "5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3'" 3045.005 1 ? ? ? ? 2 non-polymer syn 'COBALT (II) ION' 58.933 1 ? ? ? ? 3 water nat water 18.015 46 ? ? ? ? # _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)(DA)(DA)(DT)(DT)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCAATTGCG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT (II) ION' CO 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DA n 1 5 DA n 1 6 DT n 1 7 DT n 1 8 DG n 1 9 DC n 1 10 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight CO non-polymer . 'COBALT (II) ION' ? 'Co 2' 58.933 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 # 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 DA 4 4 4 DA A A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DT 6 6 6 DT T A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG G 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 CO 1 300 300 CO CO A . C 3 HOH 1 301 1 HOH HOH A . C 3 HOH 2 302 2 HOH HOH A . C 3 HOH 3 303 3 HOH HOH A . C 3 HOH 4 304 4 HOH HOH A . C 3 HOH 5 305 5 HOH HOH A . C 3 HOH 6 306 6 HOH HOH A . C 3 HOH 7 307 7 HOH HOH A . C 3 HOH 8 308 8 HOH HOH A . C 3 HOH 9 309 9 HOH HOH A . C 3 HOH 10 310 10 HOH HOH A . C 3 HOH 11 311 11 HOH HOH A . C 3 HOH 12 312 12 HOH HOH A . C 3 HOH 13 313 13 HOH HOH A . C 3 HOH 14 314 14 HOH HOH A . C 3 HOH 15 315 15 HOH HOH A . C 3 HOH 16 316 16 HOH HOH A . C 3 HOH 17 317 17 HOH HOH A . C 3 HOH 18 318 18 HOH HOH A . C 3 HOH 19 319 19 HOH HOH A . C 3 HOH 20 320 20 HOH HOH A . C 3 HOH 21 321 21 HOH HOH A . C 3 HOH 22 322 22 HOH HOH A . C 3 HOH 23 323 23 HOH HOH A . C 3 HOH 24 324 24 HOH HOH A . C 3 HOH 25 325 25 HOH HOH A . C 3 HOH 26 326 26 HOH HOH A . C 3 HOH 27 327 27 HOH HOH A . C 3 HOH 28 328 28 HOH HOH A . C 3 HOH 29 329 29 HOH HOH A . C 3 HOH 30 330 30 HOH HOH A . C 3 HOH 31 331 31 HOH HOH A . C 3 HOH 32 332 32 HOH HOH A . C 3 HOH 33 333 33 HOH HOH A . C 3 HOH 34 334 34 HOH HOH A . C 3 HOH 35 335 35 HOH HOH A . C 3 HOH 36 336 36 HOH HOH A . C 3 HOH 37 337 37 HOH HOH A . C 3 HOH 38 338 38 HOH HOH A . C 3 HOH 39 339 39 HOH HOH A . C 3 HOH 40 340 40 HOH HOH A . C 3 HOH 41 341 41 HOH HOH A . C 3 HOH 42 342 42 HOH HOH A . C 3 HOH 43 343 43 HOH HOH A . C 3 HOH 44 344 44 HOH HOH A . C 3 HOH 45 345 45 HOH HOH A . C 3 HOH 46 346 46 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.19 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 EPMR phasing . ? 4 # _cell.entry_id 1S23 _cell.length_a 26.220 _cell.length_b 44.359 _cell.length_c 52.336 _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 1S23 _symmetry.space_group_name_H-M 'I 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 # _exptl.entry_id 1S23 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 51.65 _exptl_crystal.description ? _exptl_crystal.density_Matthews 2.56 # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details ;MPD, acridine(RGR), cacodylate, calcium chloride, cobalt chloride, spermine , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _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 MPD ? ? ? 1 2 1 'acridine(RGR)' ? ? ? 1 3 1 cacodylate ? ? ? 1 4 1 'calcium chloride' ? ? ? 1 5 1 'cobalt chloride' ? ? ? 1 6 1 spermine ? ? ? 1 7 2 MPD ? ? ? 1 8 2 'calcium chloride' ? ? ? 1 9 2 'cobalt chloride' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 120 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.917 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.917 # _reflns.entry_id 1S23 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 1.6 _reflns.d_resolution_low 25 _reflns.number_all ? _reflns.number_obs 4174 _reflns.percent_possible_obs 98.4 _reflns.pdbx_Rmerge_I_obs 0.061 _reflns.pdbx_Rsym_value 0.077 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 17.7 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.60 _reflns_shell.d_res_low 1.66 _reflns_shell.percent_possible_all 89.1 _reflns_shell.Rmerge_I_obs 0.23 _reflns_shell.pdbx_Rsym_value 0.6 _reflns_shell.meanI_over_sigI_obs 2.93 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 376 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1S23 _refine.ls_number_reflns_obs 3746 _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 22.59 _refine.ls_d_res_high 1.60 _refine.ls_percent_reflns_obs 97.86 _refine.ls_R_factor_obs 0.21601 _refine.ls_R_factor_all 0.214 _refine.ls_R_factor_R_work 0.20969 _refine.ls_R_factor_R_free 0.28152 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 414 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.961 _refine.correlation_coeff_Fo_to_Fc_free 0.911 _refine.B_iso_mean 24.833 _refine.aniso_B[1][1] -0.02 _refine.aniso_B[2][2] 2.26 _refine.aniso_B[3][3] -2.24 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'NDB ENTRY UDJ031' _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 0.108 _refine.pdbx_overall_ESU_R_Free 0.124 _refine.overall_SU_ML 0.088 _refine.overall_SU_B 2.747 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 211 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 47 _refine_hist.number_atoms_total 259 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 22.59 # 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 0.015 0.021 ? 238 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 101 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.595 3.000 ? 369 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.431 3.000 ? 258 'X-RAY DIFFRACTION' ? r_chiral_restr 0.082 0.200 ? 33 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.013 0.020 ? 117 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 2 'X-RAY DIFFRACTION' ? r_nbd_refined 0.130 0.200 ? 20 'X-RAY DIFFRACTION' ? r_nbd_other 0.190 0.200 ? 102 'X-RAY DIFFRACTION' ? r_nbtor_other 0.098 0.200 ? 51 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.182 0.200 ? 18 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.279 0.200 ? 5 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.354 0.200 ? 16 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.158 0.200 ? 16 'X-RAY DIFFRACTION' ? r_scbond_it 2.305 3.000 ? 238 'X-RAY DIFFRACTION' ? r_scangle_it 3.387 4.500 ? 369 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.60 _refine_ls_shell.d_res_low 1.644 _refine_ls_shell.number_reflns_R_work 221 _refine_ls_shell.R_factor_R_work 0.459 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.416 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 26 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 1S23 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1S23 _struct.title 'Crystal Structure Analysis of the B-DNA Decamer CGCAATTGCG' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1S23 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'deoxyoligonucleotide, cobalt, variability, 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 2 ? C N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1S23 _struct_ref.pdbx_db_accession 1S23 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1S23 _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 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1S23 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _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 10 # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # 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_575 x,-y+2,-z+1/2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 88.7180000000 0.0000000000 0.0000000000 -1.0000000000 26.1680000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A DG 10 N7 ? ? ? 1_555 B CO . CO ? ? A DG 10 A CO 300 1_555 ? ? ? ? ? ? ? 2.176 ? ? metalc2 metalc ? ? A DG 10 N7 ? ? ? 6_675 B CO . CO ? ? A DG 10 A CO 300 1_555 ? ? ? ? ? ? ? 2.184 ? ? metalc3 metalc ? ? B CO . CO ? ? ? 1_555 C HOH . O ? ? A CO 300 A HOH 324 1_555 ? ? ? ? ? ? ? 1.979 ? ? metalc4 metalc ? ? B CO . CO ? ? ? 1_555 C HOH . O ? ? A CO 300 A HOH 324 6_675 ? ? ? ? ? ? ? 1.981 ? ? metalc5 metalc ? ? B CO . CO ? ? ? 1_555 C HOH . O ? ? A CO 300 A HOH 325 1_555 ? ? ? ? ? ? ? 1.942 ? ? metalc6 metalc ? ? B CO . CO ? ? ? 1_555 C HOH . O ? ? A CO 300 A HOH 325 6_675 ? ? ? ? ? ? ? 1.938 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DC 9 N3 ? ? A DG 2 A DC 9 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DC 9 O2 ? ? A DG 2 A DC 9 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 9 N4 ? ? A DG 2 A DC 9 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 3 N3 ? ? ? 1_555 A DG 8 N1 ? ? A DC 3 A DG 8 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 N4 ? ? ? 1_555 A DG 8 O6 ? ? A DC 3 A DG 8 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 O2 ? ? ? 1_555 A DG 8 N2 ? ? A DC 3 A DG 8 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 4 N1 ? ? ? 1_555 A DT 7 N3 ? ? A DA 4 A DT 7 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 4 N6 ? ? ? 1_555 A DT 7 O4 ? ? A DA 4 A DT 7 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A DT 6 N3 ? ? A DA 5 A DT 6 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A DT 6 O4 ? ? A DA 5 A DT 6 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 6 N3 ? ? ? 1_555 A DA 5 N1 ? ? A DT 6 A DA 5 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 6 O4 ? ? ? 1_555 A DA 5 N6 ? ? A DT 6 A DA 5 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 7 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 7 A DA 4 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 7 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 7 A DA 4 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DC 3 N3 ? ? A DG 8 A DC 3 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DC 3 O2 ? ? A DG 8 A DC 3 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 8 O6 ? ? ? 1_555 A DC 3 N4 ? ? A DG 8 A DC 3 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N3 ? ? ? 1_555 A DG 2 N1 ? ? A DC 9 A DG 2 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 N4 ? ? ? 1_555 A DG 2 O6 ? ? A DC 9 A DG 2 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 O2 ? ? ? 1_555 A DG 2 N2 ? ? A DC 9 A DG 2 8_575 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 N7 ? A DG 10 ? A DG 10 ? 1_555 CO ? B CO . ? A CO 300 ? 1_555 N7 ? A DG 10 ? A DG 10 ? 6_675 176.9 ? 2 N7 ? A DG 10 ? A DG 10 ? 1_555 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 324 ? 1_555 95.7 ? 3 N7 ? A DG 10 ? A DG 10 ? 6_675 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 324 ? 1_555 82.3 ? 4 N7 ? A DG 10 ? A DG 10 ? 1_555 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 324 ? 6_675 82.5 ? 5 N7 ? A DG 10 ? A DG 10 ? 6_675 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 324 ? 6_675 95.4 ? 6 O ? C HOH . ? A HOH 324 ? 1_555 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 324 ? 6_675 96.8 ? 7 N7 ? A DG 10 ? A DG 10 ? 1_555 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 325 ? 1_555 95.1 ? 8 N7 ? A DG 10 ? A DG 10 ? 6_675 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 325 ? 1_555 87.2 ? 9 O ? C HOH . ? A HOH 324 ? 1_555 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 325 ? 1_555 166.6 ? 10 O ? C HOH . ? A HOH 324 ? 6_675 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 325 ? 1_555 92.5 ? 11 N7 ? A DG 10 ? A DG 10 ? 1_555 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 325 ? 6_675 87.6 ? 12 N7 ? A DG 10 ? A DG 10 ? 6_675 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 325 ? 6_675 94.9 ? 13 O ? C HOH . ? A HOH 324 ? 1_555 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 325 ? 6_675 92.7 ? 14 O ? C HOH . ? A HOH 324 ? 6_675 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 325 ? 6_675 166.8 ? 15 O ? C HOH . ? A HOH 325 ? 1_555 CO ? B CO . ? A CO 300 ? 1_555 O ? C HOH . ? A HOH 325 ? 6_675 79.8 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id CO _struct_site.pdbx_auth_seq_id 300 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE CO A 300' # 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 6 DG A 10 ? DG A 10 . ? 1_555 ? 2 AC1 6 DG A 10 ? DG A 10 . ? 6_675 ? 3 AC1 6 HOH C . ? HOH A 324 . ? 1_555 ? 4 AC1 6 HOH C . ? HOH A 324 . ? 6_675 ? 5 AC1 6 HOH C . ? HOH A 325 . ? 1_555 ? 6 AC1 6 HOH C . ? HOH A 325 . ? 6_675 ? # 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 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.61 108.30 2.31 0.30 N 2 1 C2 A DC 3 ? ? N3 A DC 3 ? ? C4 A DC 3 ? ? 123.53 119.90 3.63 0.50 N 3 1 N3 A DC 3 ? ? C4 A DC 3 ? ? C5 A DC 3 ? ? 118.34 121.90 -3.56 0.40 N 4 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 103.02 108.00 -4.98 0.70 N 5 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 102.61 108.00 -5.39 0.70 N 6 1 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? N1 A DT 6 ? ? 102.78 108.00 -5.22 0.70 N 7 1 C2 A DT 6 ? ? N3 A DT 6 ? ? C4 A DT 6 ? ? 131.01 127.20 3.81 0.60 N 8 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.01 122.90 -3.89 0.60 N 9 1 "O4'" A DG 8 ? A "C1'" A DG 8 ? A N9 A DG 8 ? ? 103.04 108.00 -4.96 0.70 N 10 1 P A DC 9 ? A "O5'" A DC 9 ? ? "C5'" A DC 9 ? ? 102.67 120.90 -18.23 1.60 N 11 1 P A DC 9 ? B "O5'" A DC 9 ? ? "C5'" A DC 9 ? ? 136.31 120.90 15.41 1.60 N # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A CO 300 ? B CO . 2 1 A HOH 322 ? C HOH . 3 1 A HOH 323 ? C HOH . 4 1 A HOH 334 ? C HOH . # 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 CO CO CO N N 1 DA OP3 O N N 2 DA P P N N 3 DA OP1 O N N 4 DA OP2 O N N 5 DA "O5'" O N N 6 DA "C5'" C N N 7 DA "C4'" C N R 8 DA "O4'" O N N 9 DA "C3'" C N S 10 DA "O3'" O N N 11 DA "C2'" C N N 12 DA "C1'" C N R 13 DA N9 N Y N 14 DA C8 C Y N 15 DA N7 N Y N 16 DA C5 C Y N 17 DA C6 C Y N 18 DA N6 N N N 19 DA N1 N Y N 20 DA C2 C Y N 21 DA N3 N Y N 22 DA C4 C Y N 23 DA HOP3 H N N 24 DA HOP2 H N N 25 DA "H5'" H N N 26 DA "H5''" H N N 27 DA "H4'" H N N 28 DA "H3'" H N N 29 DA "HO3'" H N N 30 DA "H2'" H N N 31 DA "H2''" H N N 32 DA "H1'" H N N 33 DA H8 H N N 34 DA H61 H N N 35 DA H62 H N N 36 DA H2 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DG OP3 O N N 72 DG P P N N 73 DG OP1 O N N 74 DG OP2 O N N 75 DG "O5'" O N N 76 DG "C5'" C N N 77 DG "C4'" C N R 78 DG "O4'" O N N 79 DG "C3'" C N S 80 DG "O3'" O N N 81 DG "C2'" C N N 82 DG "C1'" C N R 83 DG N9 N Y N 84 DG C8 C Y N 85 DG N7 N Y N 86 DG C5 C Y N 87 DG C6 C N N 88 DG O6 O N N 89 DG N1 N N N 90 DG C2 C N N 91 DG N2 N N N 92 DG N3 N N N 93 DG C4 C Y N 94 DG HOP3 H N N 95 DG HOP2 H N N 96 DG "H5'" H N N 97 DG "H5''" H N N 98 DG "H4'" H N N 99 DG "H3'" H N N 100 DG "HO3'" H N N 101 DG "H2'" H N N 102 DG "H2''" H N N 103 DG "H1'" H N N 104 DG H8 H N N 105 DG H1 H N N 106 DG H21 H N N 107 DG H22 H N N 108 DT OP3 O N N 109 DT P P N N 110 DT OP1 O N N 111 DT OP2 O N N 112 DT "O5'" O N N 113 DT "C5'" C N N 114 DT "C4'" C N R 115 DT "O4'" O N N 116 DT "C3'" C N S 117 DT "O3'" O N N 118 DT "C2'" C N N 119 DT "C1'" C N R 120 DT N1 N N N 121 DT C2 C N N 122 DT O2 O N N 123 DT N3 N N N 124 DT C4 C N N 125 DT O4 O N N 126 DT C5 C N N 127 DT C7 C N N 128 DT C6 C N N 129 DT HOP3 H N N 130 DT HOP2 H N N 131 DT "H5'" H N N 132 DT "H5''" H N N 133 DT "H4'" H N N 134 DT "H3'" H N N 135 DT "HO3'" H N N 136 DT "H2'" H N N 137 DT "H2''" H N N 138 DT "H1'" H N N 139 DT H3 H N N 140 DT H71 H N N 141 DT H72 H N N 142 DT H73 H N N 143 DT H6 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # _ndb_struct_conf_na.entry_id 1S23 _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 DG 2 1_555 A DC 9 8_575 -0.371 -0.151 0.079 -3.138 -2.233 -0.170 1 A_DG2:DC9_A A 2 ? A 9 ? 19 1 1 A DC 3 1_555 A DG 8 8_575 0.253 -0.166 0.044 5.746 -5.679 1.238 2 A_DC3:DG8_A A 3 ? A 8 ? 19 1 1 A DA 4 1_555 A DT 7 8_575 -0.186 -0.131 -0.132 3.972 -16.309 2.111 3 A_DA4:DT7_A A 4 ? A 7 ? 20 1 1 A DA 5 1_555 A DT 6 8_575 -0.030 -0.033 0.137 1.733 -16.885 4.931 4 A_DA5:DT6_A A 5 ? A 6 ? 20 1 1 A DT 6 1_555 A DA 5 8_575 0.030 -0.033 0.137 -1.733 -16.885 4.931 5 A_DT6:DA5_A A 6 ? A 5 ? 20 1 1 A DT 7 1_555 A DA 4 8_575 0.186 -0.131 -0.132 -3.972 -16.309 2.111 6 A_DT7:DA4_A A 7 ? A 4 ? 20 1 1 A DG 8 1_555 A DC 3 8_575 -0.253 -0.166 0.044 -5.746 -5.679 1.238 7 A_DG8:DC3_A A 8 ? A 3 ? 19 1 1 A DC 9 1_555 A DG 2 8_575 0.371 -0.151 0.079 3.138 -2.233 -0.170 8 A_DC9:DG2_A A 9 ? A 2 ? 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 DG 2 1_555 A DC 9 8_575 A DC 3 1_555 A DG 8 8_575 0.133 -0.162 3.137 0.129 -0.124 31.876 -0.273 -0.220 3.138 -0.226 -0.234 31.877 1 AA_DG2DC3:DG8DC9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DC 3 1_555 A DG 8 8_575 A DA 4 1_555 A DT 7 8_575 -0.404 0.009 3.294 2.197 6.153 32.964 -0.995 1.060 3.210 10.713 -3.825 33.588 2 AA_DC3DA4:DT7DG8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DA 4 1_555 A DT 7 8_575 A DA 5 1_555 A DT 6 8_575 0.147 -0.262 3.265 -2.963 -0.099 36.459 -0.404 -0.641 3.244 -0.158 4.727 36.575 3 AA_DA4DA5:DT6DT7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DA 5 1_555 A DT 6 8_575 A DT 6 1_555 A DA 5 8_575 0.000 -0.448 3.330 0.000 -4.869 34.964 0.002 0.000 3.360 -8.056 0.000 35.291 4 AA_DA5DT6:DA5DT6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DT 6 1_555 A DA 5 8_575 A DT 7 1_555 A DA 4 8_575 -0.147 -0.262 3.265 2.963 -0.099 36.459 -0.404 0.641 3.244 -0.158 -4.727 36.575 5 AA_DT6DT7:DA4DA5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DT 7 1_555 A DA 4 8_575 A DG 8 1_555 A DC 3 8_575 0.404 0.009 3.294 -2.197 6.153 32.964 -0.995 -1.060 3.210 10.713 3.825 33.588 6 AA_DT7DG8:DC3DA4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DG 8 1_555 A DC 3 8_575 A DC 9 1_555 A DG 2 8_575 -0.133 -0.162 3.137 -0.129 -0.124 31.876 -0.273 0.220 3.138 -0.226 0.234 31.877 7 AA_DG8DC9:DG2DC3_AA A 8 ? A 3 ? A 9 ? A 2 ? # _pdbx_initial_refinement_model.accession_code 237D _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.details 'NDB ENTRY UDJ031' # _atom_sites.entry_id 1S23 _atom_sites.fract_transf_matrix[1][1] 0.038139 _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] 0.022543 _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] 0.019107 _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 CO N O P # loop_