data_3UBI # _entry.id 3UBI # _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 3UBI pdb_00003ubi 10.2210/pdb3ubi/pdb NDB NA1401 ? ? RCSB RCSB068546 ? ? WWPDB D_1000068546 ? ? # 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 2012-05-16 2 'Structure model' 1 1 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' 'Data collection' 2 2 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3UBI _pdbx_database_status.recvd_initial_deposition_date 2011-10-24 _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nguyen, N.' 1 'Birktoft, J.J.' 2 'Sha, R.' 3 'Wang, T.' 4 'Zheng, J.' 5 'Constantinou, P.E.' 6 'Ginell, S.L.' 7 'Chen, Y.' 8 'Mao, C.' 9 'Seeman, N.C.' 10 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'The absence of tertiary interactions in a self-assembled DNA crystal structure.' J.Mol.Recognit. 25 234 237 2012 ? UK 0952-3499 ? ? 22434713 10.1002/jmr.2183 1 'From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.' Nature 461 74 77 2009 NATUAS UK 0028-0836 0006 ? 19727196 10.1038/nature08274 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nguyen, N.' 1 ? primary 'Birktoft, J.J.' 2 ? primary 'Sha, R.' 3 ? primary 'Wang, T.' 4 ? primary 'Zheng, J.' 5 ? primary 'Constantinou, P.E.' 6 ? primary 'Ginell, S.L.' 7 ? primary 'Chen, Y.' 8 ? primary 'Mao, C.' 9 ? primary 'Seeman, N.C.' 10 ? 1 'Zheng, J.' 11 ? 1 'Birktoft, J.J.' 12 ? 1 'Chen, Y.' 13 ? 1 'Wang, T.' 14 ? 1 'Sha, R.' 15 ? 1 'Constantinou, P.E.' 16 ? 1 'Ginell, S.L.' 17 ? 1 'Mao, C.' 18 ? 1 'Seeman, N.C.' 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(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*G)-3') ; 4884.168 1 ? ? 'THE 16 RESIDUES IS FROM OF THE FIRST PART OF A DNA MOLECULE USED IN EXPERIMENT, SEE REMARK 400 FOR DETAILS.' ? 2 polymer syn ;DNA (5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3') ; 5230.415 1 ? ? 'SYMMETRICALLY- AND SEQUENTIALLY REPEATING UNIT OF A CIRCULAR DNA MOLECULES, SEE REMARK 400 FOR DETAILS.' ? 3 polymer syn ;DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3') ; 4311.801 1 ? ? ? ? 4 polymer syn ;DNA (5'-D(P*GP*CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3') ; 4550.957 1 ? ? 'THE 15 RESIDUES IS FROM OF THE LAST PART OF A DNA MOLECULE USED IN EXPERIMENT, SEE REMARK 400 FOR DETAILS.' ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DG)(DA)(DG)(DC)(DA)(DG)(DC)(DC)(DC)(DG)(DT)(DA)(DC)(DT)(DC)(DG)' GAGCAGCCCGTACTCG A ? 2 polydeoxyribonucleotide no no '(DC)(DC)(DG)(DA)(DG)(DT)(DA)(DC)(DG)(DA)(DC)(DG)(DA)(DC)(DA)(DA)(DG)' CCGAGTACGACGACAAG D ? 3 polydeoxyribonucleotide no no '(DT)(DC)(DT)(DG)(DA)(DT)(DG)(DA)(DG)(DG)(DC)(DT)(DG)(DC)' TCTGATGAGGCTGC B ? 4 polydeoxyribonucleotide no no '(DG)(DC)(DT)(DT)(DG)(DT)(DC)(DG)(DT)(DT)(DC)(DA)(DT)(DC)(DA)' GCTTGTCGTTCATCA C ? # 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 DA n 1 3 DG n 1 4 DC n 1 5 DA n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DC n 1 10 DG n 1 11 DT n 1 12 DA n 1 13 DC n 1 14 DT n 1 15 DC n 1 16 DG n 2 1 DC n 2 2 DC n 2 3 DG n 2 4 DA n 2 5 DG n 2 6 DT n 2 7 DA n 2 8 DC n 2 9 DG n 2 10 DA n 2 11 DC n 2 12 DG n 2 13 DA n 2 14 DC n 2 15 DA n 2 16 DA n 2 17 DG n 3 1 DT n 3 2 DC n 3 3 DT n 3 4 DG n 3 5 DA n 3 6 DT n 3 7 DG n 3 8 DA n 3 9 DG n 3 10 DG n 3 11 DC n 3 12 DT n 3 13 DG n 3 14 DC n 4 1 DG n 4 2 DC n 4 3 DT n 4 4 DT n 4 5 DG n 4 6 DT n 4 7 DC n 4 8 DG n 4 9 DT n 4 10 DT n 4 11 DC n 4 12 DA n 4 13 DT n 4 14 DC n 4 15 DA 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 # 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 1 DG DG A . n A 1 2 DA 2 2 2 DA DA A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DT 11 11 11 DT DT A . n A 1 12 DA 12 12 12 DA DA A . n A 1 13 DC 13 13 13 DC DC A . n A 1 14 DT 14 14 14 DT DT A . n A 1 15 DC 15 15 15 DC DC A . n A 1 16 DG 16 16 16 DG DG A . n B 2 1 DC 1 1 1 DC DC D . n B 2 2 DC 2 2 2 DC DC D . n B 2 3 DG 3 3 3 DG DG D . n B 2 4 DA 4 4 4 DA DA D . n B 2 5 DG 5 5 5 DG DG D . n B 2 6 DT 6 6 6 DT DT D . n B 2 7 DA 7 7 7 DA DA D . n B 2 8 DC 8 8 8 DC DC D . n B 2 9 DG 9 9 9 DG DG D . n B 2 10 DA 10 10 10 DA DA D . n B 2 11 DC 11 11 11 DC DC D . n B 2 12 DG 12 12 12 DG DG D . n B 2 13 DA 13 13 13 DA DA D . n B 2 14 DC 14 14 14 DC DC D . n B 2 15 DA 15 15 15 DA DA D . n B 2 16 DA 16 16 16 DA DA D . n B 2 17 DG 17 17 17 DG DG D . n C 3 1 DT 1 1 1 DT DT B . n C 3 2 DC 2 2 2 DC DC B . n C 3 3 DT 3 3 3 DT DT B . n C 3 4 DG 4 4 4 DG DG B . n C 3 5 DA 5 5 5 DA DA B . n C 3 6 DT 6 6 6 DT DT B . n C 3 7 DG 7 7 7 DG DG B . n C 3 8 DA 8 8 8 DA DA B . n C 3 9 DG 9 9 9 DG DG B . n C 3 10 DG 10 10 10 DG DG B . n C 3 11 DC 11 11 11 DC DC B . n C 3 12 DT 12 12 12 DT DT B . n C 3 13 DG 13 13 13 DG DG B . n C 3 14 DC 14 14 14 DC DC B . n D 4 1 DG 1 17 17 DG DG C . n D 4 2 DC 2 18 18 DC DC C . n D 4 3 DT 3 19 19 DT DT C . n D 4 4 DT 4 20 20 DT DT C . n D 4 5 DG 5 21 21 DG DG C . n D 4 6 DT 6 22 22 DT DT C . n D 4 7 DC 7 23 23 DC DC C . n D 4 8 DG 8 24 24 DG DG C . n D 4 9 DT 9 25 25 DT DT C . n D 4 10 DT 10 26 26 DT DT C . n D 4 11 DC 11 27 27 DC DC C . n D 4 12 DA 12 28 28 DA DA C . n D 4 13 DT 13 29 29 DT DT C . n D 4 14 DC 14 30 30 DC DC C . n D 4 15 DA 15 31 31 DA DA C . n # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 PHENIX 'model building' . ? 2 PHENIX refinement '(phenix.refine: dev_873)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 3UBI _cell.length_a 169.980 _cell.length_b 169.980 _cell.length_c 88.638 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 9 _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 3UBI _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3UBI _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;CRYSTALLIZATION CONDITIONS: GROWN BY VAPOR DIFFUSION WHILE TREATED WITH A CONTROLLED TEMPERATURE GRADIENT FROM 333 DEGS TO 293 DEGS., PH 8.5, VAPOR DIFFUSION, SITTING DROP ; # _diffrn.id 1 _diffrn.ambient_temp 190 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details GRAPHITE # _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 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X25' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X25 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.1 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 3UBI _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 49.069 _reflns.d_resolution_high 6.805 _reflns.number_obs 1413 _reflns.number_all 1413 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3UBI _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 1413 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.24 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 49.069 _refine.ls_d_res_high 6.8046 _refine.ls_percent_reflns_obs 86.85 _refine.ls_R_factor_obs 0.1401 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1385 _refine.ls_R_factor_R_free 0.1520 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.98 _refine.ls_number_reflns_R_free 141 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 67.1315 _refine.aniso_B[2][2] 67.1315 _refine.aniso_B[3][3] 811.9265 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.126 _refine.solvent_model_param_bsol 0.000 _refine.pdbx_solvent_vdw_probe_radii 0.80 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.47 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values MLHL _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML -0.00 _refine.pdbx_overall_phase_error 34.47 _refine.overall_SU_B ? _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.ls_redundancy_reflns_obs ? _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_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 1265 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1265 _refine_hist.d_res_high 6.8046 _refine_hist.d_res_low 49.069 # 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 f_bond_d 0.003 ? ? 1416 'X-RAY DIFFRACTION' ? f_angle_d 0.814 ? ? 2177 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 30.989 ? ? 606 'X-RAY DIFFRACTION' ? f_chiral_restr 0.036 ? ? 246 'X-RAY DIFFRACTION' ? f_plane_restr 0.001 ? ? 62 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 6.8046 _refine_ls_shell.d_res_low ? _refine_ls_shell.number_reflns_R_work 1272 _refine_ls_shell.R_factor_R_work 0.1385 _refine_ls_shell.percent_reflns_obs 87.00 _refine_ls_shell.R_factor_R_free 0.1520 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 141 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _database_PDB_matrix.entry_id 3UBI _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 3UBI _struct.title 'The Absence of Tertiary Interactions in a Self-Assembled DNA Crystal Structure' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3UBI _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'NANOTECHNOLOGY, DNA CROSSOVER, DESIGNED CRYSTAL LATTICE, 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 ? D N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 3UBI 3UBI 1 ? GAGCAGCCCGTACTCG ? 2 PDB 3UBI 3UBI 2 ? GCTTGTCGTTCATCA ? 3 PDB 3UBI 3UBI 3 ? CCGAGTACGACGACAAG ? 4 PDB 3UBI 3UBI 4 ? TCTGATGAGGCTGC ? # 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 3UBI A 1 ? 16 ? 3UBI 1 ? 16 ? 1 16 2 2 3UBI D 1 ? 17 ? 3UBI 1 ? 17 ? 1 17 3 3 3UBI B 1 ? 14 ? 3UBI 1 ? 14 ? 1 14 4 4 3UBI C 1 ? 15 ? 3UBI 17 ? 31 ? 17 31 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 # 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)' 3520 ? 1 MORE -5 ? 1 'SSA (A^2)' 11970 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,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_555 -y,x-y,z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details ;AUTHORS STATE THAT THE CRYSTAL IS AN INFINITE NETWORK MADE FROM THREE DNA STRANDS THAT SELF-ASSOCIATE. IN THE CURRENT ENTRY THE ASYMMETRIC UNIT IS COMPRISED OF 4 CHAINS, 3 OF WHICH ARE FRAGMENTS OF LONGER DNA STRANDS. APPLYING THE SPACE GROUP H3 SYMMETRY OPERATORS (X, Y, Z,), (-Y, X-Y, Z), AND (-X+Y,-X,Z) TO THE CONTENTS OF THE ASYMMETRIC UNIT GENERATES ONE TRIMERIC UNIT OF THE SELF-ASSOCIATED DNA NETWORK. ADDITIONAL DETAILS ABOUT THE CHEMICAL COMPOSITION AND ASSOCIATION ARE INCLUDED IN REMARK 400. ; # 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 3 O6 ? ? ? 1_555 C DC 14 N4 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog2 hydrog ? ? A DA 5 N1 ? ? ? 1_555 C DT 12 N3 ? ? A DA 5 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DA 5 N6 ? ? ? 1_555 C DT 12 O4 ? ? A DA 5 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 7 N3 ? ? ? 1_555 C DG 10 N1 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 7 N4 ? ? ? 1_555 C DG 10 O6 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 7 O2 ? ? ? 1_555 C DG 10 N2 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 8 N3 ? ? ? 1_555 C DG 9 N1 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 8 N4 ? ? ? 1_555 C DG 9 O6 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 8 O2 ? ? ? 1_555 C DG 9 N2 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 9 D DG 9 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog11 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 10 D DC 8 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog12 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 12 D DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 12 D DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 13 D DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 13 D DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 13 D DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 15 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 15 D DG 3 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog18 hydrog ? ? A DG 16 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 16 D DC 2 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog19 hydrog ? ? B DG 12 N1 ? ? ? 1_555 D DC 7 N3 ? ? D DG 12 C DC 23 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog20 hydrog ? ? B DA 16 N1 ? ? ? 1_555 D DT 3 N3 ? ? D DA 16 C DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? B DA 16 N6 ? ? ? 1_555 D DT 3 O4 ? ? D DA 16 C DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? B DG 17 N2 ? ? ? 1_555 D DC 2 O2 ? ? D DG 17 C DC 18 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog23 hydrog ? ? C DT 3 N3 ? ? ? 1_555 D DA 15 N1 ? ? B DT 3 C DA 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C DT 3 O4 ? ? ? 1_555 D DA 15 N6 ? ? B DT 3 C DA 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C DG 4 N2 ? ? ? 1_555 D DC 14 N3 ? ? B DG 4 C DC 30 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog26 hydrog ? ? C DA 8 N6 ? ? ? 1_555 D DT 10 O4 ? ? B DA 8 C DT 26 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 "O3'" _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 DG _pdbx_validate_symm_contact.auth_seq_id_1 16 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 P _pdbx_validate_symm_contact.auth_asym_id_2 C _pdbx_validate_symm_contact.auth_comp_id_2 DG _pdbx_validate_symm_contact.auth_seq_id_2 17 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 2_555 _pdbx_validate_symm_contact.dist 2.11 # 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 DT 11 ? ? "C1'" A DT 11 ? ? N1 A DT 11 ? ? 110.91 108.30 2.61 0.30 N 2 1 "C3'" A DC 13 ? ? "C2'" A DC 13 ? ? "C1'" A DC 13 ? ? 97.59 102.40 -4.81 0.80 N 3 1 "O4'" A DC 13 ? ? "C1'" A DC 13 ? ? N1 A DC 13 ? ? 111.53 108.30 3.23 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 DG 16 ? ? "C1'" A DG 16 ? ? N9 A DG 16 ? ? 110.39 108.30 2.09 0.30 N 6 1 "O4'" D DG 17 ? ? "C1'" D DG 17 ? ? N9 D DG 17 ? ? 111.23 108.30 2.93 0.30 N 7 1 "O4'" C DT 20 ? ? "C1'" C DT 20 ? ? N1 C DT 20 ? ? 110.26 108.30 1.96 0.30 N 8 1 "O4'" C DC 27 ? ? "C1'" C DC 27 ? ? N1 C DC 27 ? ? 110.31 108.30 2.01 0.30 N 9 1 "O4'" C DC 30 ? ? "C1'" C DC 30 ? ? N1 C DC 30 ? ? 110.38 108.30 2.08 0.30 N # _pdbx_entry_details.entry_id 3UBI _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ;THE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH INTERNAL 3-FOLD SYMMETRY. EXTENDING OF THE STRUCTURE UNIT IN 3-D SPACE RESULTS THE CRYSTAL AT R3 SPACE GROUP (REPRESENTED AS H3). THE DNA SEQUENCES OF THE 7 STRANDS ARE: (#1) 3 STRANDS 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*CP*GP*TP*AP*CP*TP*CP*GP*GP* CP*TP*TP*GP*TP*CP*GP*TP*TP*CP*AP*TP*CP*A)-3'; (#2) 1 STRANDS 5'-D(P*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*GP*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*GP*CP*CP*GP*AP*GP*TP*AP*CP*GP*AP*CP*GP*AP*CP*AP*AP*G)-3'; (#3) 3 STRANDS 5'-D(*TP*CP*TP*GP*AP*TP*GP*AP*GP*GP*CP*TP*GP*C)-3'). THE ASYMMETRIC UNIT IS COMPRISED OF THE FIRST 16 NUCLEOTIDES OF THE FULL #1 STRAND (CHAIN A), BY THELAST 15 RESIDUES OF THE FULL #1 STRAND (CHAIN C), BY THE FIRST 17 NUCLEOTIDES OF THE #2 STRAND (CHAIN D) AND BY #3 STRAND (CHAIN B). CHAINS A (FIRST 16 RESIDUES OF STRAND #1) AND C (NEXT 15 RESIDUES OF STRAND #1) TOGETHER FORM THE FIRST DNA STRAND (#3) OF THE EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS- HENCE IT WAS DIVIDED INTO THE CURRENT CHAINS A AND C FOR CONVENIENT REPRESENTATION AND CRYSTALLOGRAPHIC COMPUTING. CHAIN A (1_555) IS COVALENTLY LINKED TO CHAIN C OF ANOTHER ASYMMETRIC UNIT (3_555); AND CHAIN C (1_555) IS COVALENTLY LINKED TO CHAIN A OF ANOTHER ASYMMETRIC UNIT (2_555). THE #2 STRAND FORM A CIRCULAR DNA MOLECULE AS A CONSEQUENCE OF INTERNAL 3-FOLD SYMMETRY OF THE TRIANGLE CHAIN D IN THE ASYMMETRIC UNIT REPRESENTS ONE OF THESE REPEATING UNITS. IT HAS 3 SYMMETRIC AND SEQUENTIAL REPEATING UNITS THAT ARE COVALENTLY LINKED TO EACH OTHER VIA THE O3' END OF RESIDUE 17D TO THE O5' END OF RESIDUE 1D) CHAIN D (1_555) IS COVALENTLY LINKED TO CHAIN D OF TWO NEIGHBOURING ASYMMETRIC UNITS (2_555) AND (3_555). THE SELECTION OF RESIDUES FROM THE DNA #2 AND #3 ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAINS A AND C. CHAIN B IN THE ASYMMETRIC UNIT REPRESENTS THE THIRD OF THESE REPEATING UNITS. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? # 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 # 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 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3UBI 'double helix' 3UBI 'b-form double helix' 3UBI 'mismatched base pair' 3UBI 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 3 1_555 C DC 14 1_555 -0.194 0.594 -0.062 2.629 -8.251 -18.996 1 A_DG3:DC14_B A 3 ? B 14 ? ? ? 1 A DA 5 1_555 C DT 12 1_555 1.041 -0.144 -0.011 -5.714 -26.416 -8.063 2 A_DA5:DT12_B A 5 ? B 12 ? 20 1 1 A DC 7 1_555 C DG 10 1_555 0.998 -0.433 0.866 -4.408 -4.013 2.016 3 A_DC7:DG10_B A 7 ? B 10 ? 19 1 1 A DC 8 1_555 C DG 9 1_555 -1.045 0.035 0.512 5.026 -12.862 -0.841 4 A_DC8:DG9_B A 8 ? B 9 ? 19 1 1 A DC 9 1_555 B DG 9 1_555 -0.655 0.229 -1.355 17.140 -16.540 -21.219 5 A_DC9:DG9_D A 9 ? D 9 ? ? ? 1 A DG 10 1_555 B DC 8 1_555 -1.371 0.146 -0.800 -13.712 -19.253 7.370 6 A_DG10:DC8_D A 10 ? D 8 ? ? 1 1 A DA 12 1_555 B DT 6 1_555 -0.019 -0.105 0.347 8.383 -20.859 -11.168 7 A_DA12:DT6_D A 12 ? D 6 ? 20 1 1 A DC 13 1_555 B DG 5 1_555 -0.042 0.218 0.481 3.760 -17.578 1.652 8 A_DC13:DG5_D A 13 ? D 5 ? 19 1 1 A DC 15 1_555 B DG 3 1_555 0.497 0.103 0.156 -3.224 2.422 -24.115 9 A_DC15:DG3_D A 15 ? D 3 ? ? 1 1 A DG 16 1_555 B DC 2 1_555 0.258 0.580 -0.093 0.770 -3.104 5.441 10 A_DG16:DC2_D A 16 ? D 2 ? ? ? 1 B DG 12 1_555 D DC 7 1_555 -0.864 0.013 -0.696 -19.477 -22.553 -11.465 11 D_DG12:DC23_C D 12 ? C 23 ? ? 1 1 B DA 16 1_555 D DT 3 1_555 0.638 -0.078 0.020 -1.476 -13.137 -3.852 12 D_DA16:DT19_C D 16 ? C 19 ? 20 1 1 B DG 17 1_555 D DC 2 1_555 2.107 0.296 -1.096 -6.600 -8.339 22.261 13 D_DG17:DC18_C D 17 ? C 18 ? ? 1 1 C DT 3 1_555 D DA 15 1_555 -1.350 -0.151 0.145 14.086 -24.298 -15.155 14 B_DT3:DA31_C B 3 ? C 31 ? 20 1 1 C DG 4 1_555 D DC 14 1_555 1.718 1.210 -0.336 -5.926 -11.946 14.407 15 B_DG4:DC30_C B 4 ? C 30 ? ? ? 1 C DA 8 1_555 D DT 10 1_555 -0.027 0.781 -0.351 -8.096 -17.681 -17.938 16 B_DA8:DT26_C B 8 ? C 26 ? ? ? # 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 3 1_555 C DC 14 1_555 A DA 5 1_555 C DT 12 1_555 -0.739 -0.845 7.345 -10.725 4.973 74.244 -1.037 -0.133 7.321 4.095 8.831 75.045 1 AA_DG3DA5:DT12DC14_BB A 3 ? B 14 ? A 5 ? B 12 ? 1 A DA 5 1_555 C DT 12 1_555 A DC 7 1_555 C DG 10 1_555 1.004 -1.142 6.586 -7.714 -13.956 65.479 0.076 -1.520 6.546 -12.707 7.024 67.182 2 AA_DA5DC7:DG10DT12_BB A 5 ? B 12 ? A 7 ? B 10 ? 1 A DC 7 1_555 C DG 10 1_555 A DC 8 1_555 C DG 9 1_555 -0.520 -0.500 3.162 -0.360 -13.396 34.498 1.018 0.772 3.141 -21.605 0.580 36.936 3 AA_DC7DC8:DG9DG10_BB A 7 ? B 10 ? A 8 ? B 9 ? 1 A DC 8 1_555 C DG 9 1_555 A DC 9 1_555 B DG 9 1_555 -2.235 -1.411 2.999 7.360 -6.996 25.063 -1.452 6.435 2.547 -15.341 -16.141 27.011 4 AA_DC8DC9:DG9DG9_DB A 8 ? B 9 ? A 9 ? D 9 ? 1 A DC 9 1_555 B DG 9 1_555 A DG 10 1_555 B DC 8 1_555 1.711 -0.903 4.609 6.621 31.698 28.070 -5.627 -1.439 2.679 49.071 -10.250 42.607 5 AA_DC9DG10:DC8DG9_DD A 9 ? D 9 ? A 10 ? D 8 ? 1 A DG 10 1_555 B DC 8 1_555 A DA 12 1_555 B DT 6 1_555 -0.401 -0.994 6.158 -16.246 -3.267 74.945 -0.620 -0.585 6.160 -2.654 13.197 76.492 6 AA_DG10DA12:DT6DC8_DD A 10 ? D 8 ? A 12 ? D 6 ? 1 A DA 12 1_555 B DT 6 1_555 A DC 13 1_555 B DG 5 1_555 1.106 -1.024 3.279 1.249 -2.157 31.224 -1.483 -1.808 3.381 -3.999 -2.317 31.321 7 AA_DA12DC13:DG5DT6_DD A 12 ? D 6 ? A 13 ? D 5 ? 1 A DC 15 1_555 B DG 3 1_555 A DG 16 1_555 B DC 2 1_555 4.139 1.014 3.090 14.464 9.691 34.072 0.034 -4.067 4.543 15.359 -22.923 38.144 8 AA_DC15DG16:DC2DG3_DD A 15 ? D 3 ? A 16 ? D 2 ? 1 B DA 16 1_555 D DT 3 1_555 B DG 17 1_555 D DC 2 1_555 1.929 -0.351 4.283 6.702 -0.963 36.921 -0.374 -1.805 4.559 -1.505 -10.475 37.515 9 DD_DA16DG17:DC18DT19_CC D 16 ? C 19 ? D 17 ? C 18 ? 1 C DT 3 1_555 D DA 15 1_555 C DG 4 1_555 D DC 14 1_555 2.147 -0.656 4.369 10.072 8.028 45.125 -1.753 -1.538 4.549 10.218 -12.819 46.834 10 BB_DT3DG4:DC30DA31_CC B 3 ? C 31 ? B 4 ? C 30 ? # _atom_sites.entry_id 3UBI _atom_sites.fract_transf_matrix[1][1] 0.005883 _atom_sites.fract_transf_matrix[1][2] 0.003397 _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] 0.006793 _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] 0.011282 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_