data_4F8G # _entry.id 4F8G # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 4F8G pdb_00004f8g 10.2210/pdb4f8g/pdb NDB NA1789 ? ? RCSB RCSB072586 ? ? WWPDB D_1000072586 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2012-07-25 2 'Structure model' 1 1 2012-08-15 3 'Structure model' 1 2 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4F8G _pdbx_database_status.recvd_initial_deposition_date 2012-05-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 4F8I _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Paukstelis, P.J.' 1 'Muser, S.E.' 2 # _citation.id primary _citation.title 'Three-Dimensional DNA Crystals with pH-Responsive Noncanonical Junctions.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 134 _citation.page_first 12557 _citation.page_last 12564 _citation.year 2012 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22768973 _citation.pdbx_database_id_DOI 10.1021/ja3025033 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Muser, S.E.' 1 ? primary 'Paukstelis, P.J.' 2 ? # 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(*G*CP*GP*AP*AP*AP*GP*GP*GP*CP*AP*CP*GP*TP*GP*CP*CP*CP*T)-3') ; 5855.787 1 ? ? ? ? 2 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 3 water nat water 18.015 75 ? ? ? ? # _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 '(DG)(DC)(DG)(DA)(DA)(DA)(DG)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DC)(DT)' _entity_poly.pdbx_seq_one_letter_code_can GCGAAAGGGCACGTGCCCT _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 HEXAMMINE(III)' NCO 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DG n 1 4 DA n 1 5 DA n 1 6 DA n 1 7 DG n 1 8 DG n 1 9 DG n 1 10 DC n 1 11 DA n 1 12 DC n 1 13 DG n 1 14 DT n 1 15 DG n 1 16 DC n 1 17 DC n 1 18 DC n 1 19 DT n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 # 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 DG 1 1 ? ? ? A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G 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 DA 6 6 6 DA A A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DC 10 10 10 DC C A . n A 1 11 DA 11 11 11 DA A A . n A 1 12 DC 12 12 12 DC C A . n A 1 13 DG 13 13 13 DG G A . n A 1 14 DT 14 14 14 DT T A . n A 1 15 DG 15 15 15 DG G A . n A 1 16 DC 16 16 16 DC C A . n A 1 17 DC 17 17 17 DC C A . n A 1 18 DC 18 18 18 DC C A . n A 1 19 DT 19 19 19 DT T A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NCO 1 101 1 NCO NCO A . C 2 NCO 1 102 2 NCO NCO A . D 3 HOH 1 201 1 HOH HOH A . D 3 HOH 2 202 2 HOH HOH A . D 3 HOH 3 203 3 HOH HOH A . D 3 HOH 4 204 4 HOH HOH A . D 3 HOH 5 205 5 HOH HOH A . D 3 HOH 6 206 6 HOH HOH A . D 3 HOH 7 207 7 HOH HOH A . D 3 HOH 8 208 8 HOH HOH A . D 3 HOH 9 209 9 HOH HOH A . D 3 HOH 10 210 10 HOH HOH A . D 3 HOH 11 211 11 HOH HOH A . D 3 HOH 12 212 12 HOH HOH A . D 3 HOH 13 213 13 HOH HOH A . D 3 HOH 14 214 14 HOH HOH A . D 3 HOH 15 215 15 HOH HOH A . D 3 HOH 16 216 16 HOH HOH A . D 3 HOH 17 217 17 HOH HOH A . D 3 HOH 18 218 18 HOH HOH A . D 3 HOH 19 219 19 HOH HOH A . D 3 HOH 20 220 20 HOH HOH A . D 3 HOH 21 221 21 HOH HOH A . D 3 HOH 22 222 22 HOH HOH A . D 3 HOH 23 223 23 HOH HOH A . D 3 HOH 24 224 24 HOH HOH A . D 3 HOH 25 225 25 HOH HOH A . D 3 HOH 26 226 26 HOH HOH A . D 3 HOH 27 227 27 HOH HOH A . D 3 HOH 28 228 28 HOH HOH A . D 3 HOH 29 229 29 HOH HOH A . D 3 HOH 30 230 30 HOH HOH A . D 3 HOH 31 231 31 HOH HOH A . D 3 HOH 32 232 32 HOH HOH A . D 3 HOH 33 233 33 HOH HOH A . D 3 HOH 34 234 34 HOH HOH A . D 3 HOH 35 235 35 HOH HOH A . D 3 HOH 36 236 36 HOH HOH A . D 3 HOH 37 237 37 HOH HOH A . D 3 HOH 38 238 38 HOH HOH A . D 3 HOH 39 239 39 HOH HOH A . D 3 HOH 40 240 40 HOH HOH A . D 3 HOH 41 241 41 HOH HOH A . D 3 HOH 42 242 42 HOH HOH A . D 3 HOH 43 243 43 HOH HOH A . D 3 HOH 44 244 44 HOH HOH A . D 3 HOH 45 245 45 HOH HOH A . D 3 HOH 46 246 46 HOH HOH A . D 3 HOH 47 247 47 HOH HOH A . D 3 HOH 48 248 48 HOH HOH A . D 3 HOH 49 249 49 HOH HOH A . D 3 HOH 50 250 50 HOH HOH A . D 3 HOH 51 251 51 HOH HOH A . D 3 HOH 52 252 52 HOH HOH A . D 3 HOH 53 253 53 HOH HOH A . D 3 HOH 54 254 54 HOH HOH A . D 3 HOH 55 255 55 HOH HOH A . D 3 HOH 56 256 56 HOH HOH A . D 3 HOH 57 257 57 HOH HOH A . D 3 HOH 58 258 58 HOH HOH A . D 3 HOH 59 259 59 HOH HOH A . D 3 HOH 60 260 60 HOH HOH A . D 3 HOH 61 261 61 HOH HOH A . D 3 HOH 62 262 62 HOH HOH A . D 3 HOH 63 263 63 HOH HOH A . D 3 HOH 64 264 64 HOH HOH A . D 3 HOH 65 265 65 HOH HOH A . D 3 HOH 66 266 66 HOH HOH A . D 3 HOH 67 267 67 HOH HOH A . D 3 HOH 68 268 68 HOH HOH A . D 3 HOH 69 269 69 HOH HOH A . D 3 HOH 70 270 71 HOH HOH A . D 3 HOH 71 271 72 HOH HOH A . D 3 HOH 72 272 73 HOH HOH A . D 3 HOH 73 273 75 HOH HOH A . D 3 HOH 74 274 76 HOH HOH A . D 3 HOH 75 275 77 HOH HOH A . # 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 Y 1 A DC 2 ? P ? A DC 2 P 2 1 Y 1 A DC 2 ? OP1 ? A DC 2 OP1 3 1 Y 1 A DC 2 ? OP2 ? A DC 2 OP2 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal 'PROTEUM PLUS' 'data collection' PLUS ? 1 PHENIX 'model building' . ? 2 REFMAC refinement 5.5.0102 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 4F8G _cell.length_a 31.655 _cell.length_b 44.820 _cell.length_c 73.157 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4F8G _symmetry.space_group_name_H-M 'I 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4F8G _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.22 _exptl_crystal.density_percent_sol 44.48 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'pH 7.0' _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 CCD _diffrn_detector.type 'Bruker Platinum 135' _diffrn_detector.pdbx_collection_date 2012-02-13 _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 Mirrors _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'BRUKER AXS MICROSTAR' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 4F8G _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 1.93 _reflns.number_obs 3985 _reflns.number_all 4059 _reflns.percent_possible_obs 98.2 _reflns.pdbx_Rmerge_I_obs 0.11 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 79.1 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11 _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 4F8G _refine.ls_number_reflns_obs 3875 _refine.ls_number_reflns_all 3875 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.11 _refine.ls_d_res_high 1.93 _refine.ls_percent_reflns_obs 97.83 _refine.ls_R_factor_obs 0.17698 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.17433 _refine.ls_R_factor_R_free 0.24136 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.5 _refine.ls_number_reflns_R_free 182 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.958 _refine.correlation_coeff_Fo_to_Fc_free 0.922 _refine.B_iso_mean 21.402 _refine.aniso_B[1][1] 0.03 _refine.aniso_B[2][2] 0.06 _refine.aniso_B[3][3] -0.09 _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 ? _refine.pdbx_method_to_determine_struct SAD _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 0.170 _refine.pdbx_overall_ESU_R_Free 0.167 _refine.overall_SU_ML 0.094 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 6.029 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 367 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 75 _refine_hist.number_atoms_total 456 _refine_hist.d_res_high 1.93 _refine_hist.d_res_low 19.11 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.004 0.021 ? 449 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.002 0.020 ? 172 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 0.989 3.000 ? 705 ? 'X-RAY DIFFRACTION' r_angle_other_deg 1.107 3.000 ? 438 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.042 0.200 ? 75 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.004 0.020 ? 201 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.001 0.020 ? 38 ? 'X-RAY DIFFRACTION' r_scbond_it 0.611 3.000 ? 449 ? 'X-RAY DIFFRACTION' r_scangle_it 0.943 4.500 ? 705 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.93 _refine_ls_shell.d_res_low 1.982 _refine_ls_shell.number_reflns_R_work 238 _refine_ls_shell.R_factor_R_work 0.198 _refine_ls_shell.percent_reflns_obs 80.13 _refine_ls_shell.R_factor_R_free 0.512 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 8 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 4F8G _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 4F8G _struct.title 'Three-dimensional DNA lattices with non-canonical base pairs' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4F8G _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Non-canonical DNA, DNA nanotechnology, crystal design, parallel DNA, 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 2 ? D N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4F8G _struct_ref.pdbx_db_accession 4F8G _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4F8G _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 19 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4F8G _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 19 _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 19 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2390 ? 1 MORE -17 ? 1 'SSA (A^2)' 7480 ? # _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,D # 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' 2_765 -x+2,-y+1,z -1.0000000000 0.0000000000 0.0000000000 63.3100000000 0.0000000000 -1.0000000000 0.0000000000 44.8200000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DG 7 N1 ? ? ? 1_555 A DC 18 N3 ? ? A DG 7 A DC 18 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 7 N2 ? ? ? 1_555 A DC 18 O2 ? ? A DG 7 A DC 18 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 7 O6 ? ? ? 1_555 A DC 18 N4 ? ? A DG 7 A DC 18 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DC 17 N3 ? ? A DG 8 A DC 17 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DC 17 O2 ? ? A DG 8 A DC 17 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 8 O6 ? ? ? 1_555 A DC 17 N4 ? ? A DG 8 A DC 17 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 16 N3 ? ? A DG 9 A DC 16 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 16 O2 ? ? A DG 9 A DC 16 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 16 N4 ? ? A DG 9 A DC 16 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 10 N3 ? ? ? 1_555 A DG 15 N1 ? ? A DC 10 A DG 15 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 10 N4 ? ? ? 1_555 A DG 15 O6 ? ? A DC 10 A DG 15 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 10 O2 ? ? ? 1_555 A DG 15 N2 ? ? A DC 10 A DG 15 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 11 N1 ? ? ? 1_555 A DT 14 N3 ? ? A DA 11 A DT 14 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 11 N6 ? ? ? 1_555 A DT 14 O4 ? ? A DA 11 A DT 14 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 12 N3 ? ? ? 1_555 A DG 13 N1 ? ? A DC 12 A DG 13 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 12 N4 ? ? ? 1_555 A DG 13 O6 ? ? A DC 12 A DG 13 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 12 O2 ? ? ? 1_555 A DG 13 N2 ? ? A DC 12 A DG 13 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 13 N1 ? ? ? 1_555 A DC 12 N3 ? ? A DG 13 A DC 12 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 13 N2 ? ? ? 1_555 A DC 12 O2 ? ? A DG 13 A DC 12 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 13 O6 ? ? ? 1_555 A DC 12 N4 ? ? A DG 13 A DC 12 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 14 N3 ? ? ? 1_555 A DA 11 N1 ? ? A DT 14 A DA 11 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 14 O4 ? ? ? 1_555 A DA 11 N6 ? ? A DT 14 A DA 11 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 15 N1 ? ? ? 1_555 A DC 10 N3 ? ? A DG 15 A DC 10 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 15 N2 ? ? ? 1_555 A DC 10 O2 ? ? A DG 15 A DC 10 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 15 O6 ? ? ? 1_555 A DC 10 N4 ? ? A DG 15 A DC 10 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 16 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 16 A DG 9 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 16 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 16 A DG 9 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 16 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 16 A DG 9 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 17 N3 ? ? ? 1_555 A DG 8 N1 ? ? A DC 17 A DG 8 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 17 N4 ? ? ? 1_555 A DG 8 O6 ? ? A DC 17 A DG 8 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DC 17 O2 ? ? ? 1_555 A DG 8 N2 ? ? A DC 17 A DG 8 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DC 18 N3 ? ? ? 1_555 A DG 7 N1 ? ? A DC 18 A DG 7 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DC 18 N4 ? ? ? 1_555 A DG 7 O6 ? ? A DC 18 A DG 7 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DC 18 O2 ? ? ? 1_555 A DG 7 N2 ? ? A DC 18 A DG 7 2_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 A NCO 101 ? 10 'BINDING SITE FOR RESIDUE NCO A 101' AC2 Software A NCO 102 ? 8 'BINDING SITE FOR RESIDUE NCO A 102' # 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 10 DG A 7 ? DG A 7 . ? 1_555 ? 2 AC1 10 DG A 8 ? DG A 8 . ? 1_555 ? 3 AC1 10 DC A 12 ? DC A 12 . ? 2_765 ? 4 AC1 10 DC A 17 ? DC A 17 . ? 7_745 ? 5 AC1 10 DC A 18 ? DC A 18 . ? 7_745 ? 6 AC1 10 NCO C . ? NCO A 102 . ? 1_555 ? 7 AC1 10 HOH D . ? HOH A 201 . ? 1_555 ? 8 AC1 10 HOH D . ? HOH A 217 . ? 1_555 ? 9 AC1 10 HOH D . ? HOH A 223 . ? 8_565 ? 10 AC1 10 HOH D . ? HOH A 253 . ? 7_745 ? 11 AC2 8 DA A 6 ? DA A 6 . ? 1_555 ? 12 AC2 8 DG A 7 ? DG A 7 . ? 1_555 ? 13 AC2 8 DG A 8 ? DG A 8 . ? 1_555 ? 14 AC2 8 DG A 9 ? DG A 9 . ? 1_555 ? 15 AC2 8 NCO B . ? NCO A 101 . ? 1_555 ? 16 AC2 8 HOH D . ? HOH A 209 . ? 1_555 ? 17 AC2 8 HOH D . ? HOH A 215 . ? 1_555 ? 18 AC2 8 HOH D . ? HOH A 260 . ? 2_765 ? # 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 "C3'" A DA 4 ? ? "O3'" A DA 4 ? ? P A DA 5 ? A 128.20 119.70 8.50 1.20 Y 2 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? N1 A DC 10 ? ? 110.40 108.30 2.10 0.30 N 3 1 "O4'" A DC 12 ? ? "C1'" A DC 12 ? ? N1 A DC 12 ? ? 110.76 108.30 2.46 0.30 N 4 1 "O4'" A DT 14 ? ? "C1'" A DT 14 ? ? N1 A DT 14 ? ? 110.80 108.30 2.50 0.30 N 5 1 "O4'" A DC 17 ? ? "C1'" A DC 17 ? ? N1 A DC 17 ? ? 111.23 108.30 2.93 0.30 N # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 41.1815 -4.3267 37.2482 0.4779 0.6164 0.5778 -0.1327 -0.1923 0.5386 -14.2778 29.1922 93.5025 13.6772 6.2854 32.7532 -1.8700 0.3311 1.0158 -2.4872 1.3876 4.5010 0.0149 -4.5336 0.4825 'X-RAY DIFFRACTION' 2 ? refined 44.1841 1.1704 32.4858 0.1538 0.2534 0.1443 0.0058 -0.0006 0.1496 6.1815 10.1561 18.8859 -9.5754 -8.2966 -0.1092 -0.1369 -0.1523 -0.3831 0.2714 0.6848 1.5525 0.0678 -0.2642 -0.5479 'X-RAY DIFFRACTION' 3 ? refined 33.6017 22.1451 21.9653 0.0695 0.0700 0.0802 -0.0023 -0.0022 0.0003 0.1216 0.3446 0.1519 -0.1728 -0.0795 0.0121 -0.0161 -0.0170 0.0013 0.0595 0.0031 0.0092 -0.0032 0.0209 0.0131 'X-RAY DIFFRACTION' 4 ? refined 28.7501 37.3263 9.5978 0.1371 0.0883 0.0486 0.0087 -0.0113 0.0125 13.9107 7.6730 9.9279 4.4075 7.5722 8.6980 -0.0257 0.4383 0.0613 -0.5488 0.1757 -0.0960 -0.4433 0.3513 -0.1500 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 A 2 ? ? A 2 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 3 ? ? A 4 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 5 ? ? A 18 ? ? ? ? 'X-RAY DIFFRACTION' 4 4 A 19 ? ? A 19 ? ? ? ? # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id DG _pdbx_unobs_or_zero_occ_residues.auth_seq_id 1 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id DG _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 # 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 NCO CO CO N N 147 NCO N1 N N N 148 NCO N2 N N N 149 NCO N3 N N N 150 NCO N4 N N N 151 NCO N5 N N N 152 NCO N6 N N N 153 NCO HN11 H N N 154 NCO HN12 H N N 155 NCO HN13 H N N 156 NCO HN21 H N N 157 NCO HN22 H N N 158 NCO HN23 H N N 159 NCO HN31 H N N 160 NCO HN32 H N N 161 NCO HN33 H N N 162 NCO HN41 H N N 163 NCO HN42 H N N 164 NCO HN43 H N N 165 NCO HN51 H N N 166 NCO HN52 H N N 167 NCO HN53 H N N 168 NCO HN61 H N N 169 NCO HN62 H N N 170 NCO HN63 H N N 171 # 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 NCO CO N1 sing N N 152 NCO CO N2 sing N N 153 NCO CO N3 sing N N 154 NCO CO N4 sing N N 155 NCO CO N5 sing N N 156 NCO CO N6 sing N N 157 NCO N1 HN11 sing N N 158 NCO N1 HN12 sing N N 159 NCO N1 HN13 sing N N 160 NCO N2 HN21 sing N N 161 NCO N2 HN22 sing N N 162 NCO N2 HN23 sing N N 163 NCO N3 HN31 sing N N 164 NCO N3 HN32 sing N N 165 NCO N3 HN33 sing N N 166 NCO N4 HN41 sing N N 167 NCO N4 HN42 sing N N 168 NCO N4 HN43 sing N N 169 NCO N5 HN51 sing N N 170 NCO N5 HN52 sing N N 171 NCO N5 HN53 sing N N 172 NCO N6 HN61 sing N N 173 NCO N6 HN62 sing N N 174 NCO N6 HN63 sing N N 175 # _ndb_struct_conf_na.entry_id 4F8G _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 7 1_555 A DC 18 2_765 -0.245 -0.167 0.119 -1.184 -5.373 -2.348 1 A_DG7:DC18_A A 7 ? A 18 ? 19 1 1 A DG 8 1_555 A DC 17 2_765 -0.235 -0.169 -0.507 -22.172 -10.131 -2.941 2 A_DG8:DC17_A A 8 ? A 17 ? 19 1 1 A DG 9 1_555 A DC 16 2_765 -0.219 -0.134 -0.031 -7.497 -14.954 3.515 3 A_DG9:DC16_A A 9 ? A 16 ? 19 1 1 A DC 10 1_555 A DG 15 2_765 0.164 -0.152 0.149 5.205 -10.658 -0.200 4 A_DC10:DG15_A A 10 ? A 15 ? 19 1 1 A DA 11 1_555 A DT 14 2_765 0.103 -0.199 0.101 7.069 -16.462 -4.687 5 A_DA11:DT14_A A 11 ? A 14 ? 20 1 1 A DC 12 1_555 A DG 13 2_765 0.314 -0.236 0.018 8.395 -17.993 -0.588 6 A_DC12:DG13_A A 12 ? A 13 ? 19 1 1 A DG 13 1_555 A DC 12 2_765 -0.314 -0.236 0.018 -8.395 -17.993 -0.588 7 A_DG13:DC12_A A 13 ? A 12 ? 19 1 1 A DT 14 1_555 A DA 11 2_765 -0.103 -0.199 0.101 -7.069 -16.462 -4.687 8 A_DT14:DA11_A A 14 ? A 11 ? 20 1 1 A DG 15 1_555 A DC 10 2_765 -0.164 -0.152 0.149 -5.205 -10.658 -0.200 9 A_DG15:DC10_A A 15 ? A 10 ? 19 1 1 A DC 16 1_555 A DG 9 2_765 0.219 -0.134 -0.031 7.497 -14.954 3.515 10 A_DC16:DG9_A A 16 ? A 9 ? 19 1 1 A DC 17 1_555 A DG 8 2_765 0.235 -0.169 -0.507 22.172 -10.131 -2.941 11 A_DC17:DG8_A A 17 ? A 8 ? 19 1 1 A DC 18 1_555 A DG 7 2_765 0.245 -0.167 0.119 1.184 -5.373 -2.348 12 A_DC18:DG7_A A 18 ? A 7 ? 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 7 1_555 A DC 18 2_765 A DG 8 1_555 A DC 17 2_765 0.517 -1.570 3.852 11.087 3.877 38.945 -2.771 0.709 3.692 5.660 -16.186 40.612 1 AA_DG7DG8:DC17DC18_AA A 7 ? A 18 ? A 8 ? A 17 ? 1 A DG 8 1_555 A DC 17 2_765 A DG 9 1_555 A DC 16 2_765 0.276 -0.553 3.038 -3.878 8.999 30.003 -2.527 -1.160 2.707 16.828 7.252 31.528 2 AA_DG8DG9:DC16DC17_AA A 8 ? A 17 ? A 9 ? A 16 ? 1 A DG 9 1_555 A DC 16 2_765 A DC 10 1_555 A DG 15 2_765 -0.474 -0.961 2.988 -1.957 7.501 33.193 -2.699 0.533 2.735 12.913 3.368 34.062 3 AA_DG9DC10:DG15DC16_AA A 9 ? A 16 ? A 10 ? A 15 ? 1 A DC 10 1_555 A DG 15 2_765 A DA 11 1_555 A DT 14 2_765 -0.429 -1.124 3.126 0.162 11.010 31.616 -3.594 0.770 2.598 19.482 -0.286 33.432 4 AA_DC10DA11:DT14DG15_AA A 10 ? A 15 ? A 11 ? A 14 ? 1 A DA 11 1_555 A DT 14 2_765 A DC 12 1_555 A DG 13 2_765 0.594 -1.238 3.217 1.001 3.757 34.906 -2.595 -0.840 3.086 6.238 -1.662 35.116 5 AA_DA11DC12:DG13DT14_AA A 11 ? A 14 ? A 12 ? A 13 ? 1 A DC 12 1_555 A DG 13 2_765 A DG 13 1_555 A DC 12 2_765 0.000 -1.701 3.382 0.000 15.746 31.632 -4.960 0.000 2.304 26.901 0.000 35.244 6 AA_DC12DG13:DC12DG13_AA A 12 ? A 13 ? A 13 ? A 12 ? 1 A DG 13 1_555 A DC 12 2_765 A DT 14 1_555 A DA 11 2_765 -0.594 -1.238 3.217 -1.001 3.757 34.906 -2.595 0.840 3.086 6.238 1.662 35.116 7 AA_DG13DT14:DA11DC12_AA A 13 ? A 12 ? A 14 ? A 11 ? 1 A DT 14 1_555 A DA 11 2_765 A DG 15 1_555 A DC 10 2_765 0.429 -1.124 3.126 -0.162 11.010 31.616 -3.594 -0.770 2.598 19.482 0.286 33.432 8 AA_DT14DG15:DC10DA11_AA A 14 ? A 11 ? A 15 ? A 10 ? 1 A DG 15 1_555 A DC 10 2_765 A DC 16 1_555 A DG 9 2_765 0.474 -0.961 2.988 1.957 7.501 33.193 -2.699 -0.533 2.735 12.913 -3.368 34.062 9 AA_DG15DC16:DG9DC10_AA A 15 ? A 10 ? A 16 ? A 9 ? 1 A DC 16 1_555 A DG 9 2_765 A DC 17 1_555 A DG 8 2_765 -0.276 -0.553 3.038 3.878 8.999 30.003 -2.527 1.160 2.707 16.828 -7.252 31.528 10 AA_DC16DC17:DG8DG9_AA A 16 ? A 9 ? A 17 ? A 8 ? 1 A DC 17 1_555 A DG 8 2_765 A DC 18 1_555 A DG 7 2_765 -0.517 -1.570 3.852 -11.087 3.877 38.945 -2.771 -0.709 3.692 5.660 16.186 40.612 11 AA_DC17DC18:DG7DG8_AA A 17 ? A 8 ? A 18 ? A 7 ? # _atom_sites.entry_id 4F8G _atom_sites.fract_transf_matrix[1][1] 0.031591 _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] 0.022311 _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] 0.013669 _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_