data_1JB8 # _entry.id 1JB8 # _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 1JB8 pdb_00001jb8 10.2210/pdb1jb8/pdb NDB AH0019 ? ? RCSB RCSB013579 ? ? WWPDB D_1000013579 ? ? # 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 2003-07-01 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-04 5 'Structure model' 1 4 2024-02-07 6 'Structure model' 1 5 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' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 6 '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' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 6 '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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1JB8 _pdbx_database_status.recvd_initial_deposition_date 2001-06-02 _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name NDB _pdbx_database_related.db_id AH0012 _pdbx_database_related.details 'Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 Angstrom resolution' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Han, G.W.' 1 'Kopka, M.L.' 2 'Langs, D.' 3 'Dickerson, R.E.' 4 # _citation.id primary _citation.title ;Crystal structure of an RNADNA hybrid reveals intermolecular intercalation: Dimer formation by base-pair swapping ; _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 100 _citation.page_first 9214 _citation.page_last 9219 _citation.year 2003 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12872000 _citation.pdbx_database_id_DOI 10.1073/pnas.1533326100 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Han, G.W.' 1 ? primary 'Kopka, M.L.' 2 ? primary 'Langs, D.' 3 ? primary 'Sawaya, M.R.' 4 ? primary 'Dickerson, R.E.' 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'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'" 3255.076 1 ? ? ? 'RNA/DNA hybrid of PPT sequence of HIV' 2 polymer syn "5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'" 2991.961 1 ? ? ? 'RNA/DNA hybrid of PPT sequence of HIV' 3 water nat water 18.015 66 ? ? ? ? # 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 polyribonucleotide no no CAAAGAAAAG CAAAGAAAAG A ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DT)(DT)(DT)(DC)(DT)(DT)(DT)(DG)' CTTTTCTTTG B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 A n 1 3 A n 1 4 A n 1 5 G n 1 6 A n 1 7 A n 1 8 A n 1 9 A n 1 10 G n 2 1 DC n 2 2 DT n 2 3 DT n 2 4 DT n 2 5 DT n 2 6 DC n 2 7 DT n 2 8 DT n 2 9 DT n 2 10 DG n # _pdbx_entity_src_syn.entity_id 2 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Synthesized by the solid-phase phosphoramidate method on an Eppendorf ECOSYN D300 Synthesizer.' # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 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 C 1 1 1 C CYT A . n A 1 2 A 2 2 2 A ADE A . n A 1 3 A 3 3 3 A ADE A . n A 1 4 A 4 4 4 A ADE A . n A 1 5 G 5 5 5 G GUA A . n A 1 6 A 6 6 6 A ADE A . n A 1 7 A 7 7 7 A ADE A . n A 1 8 A 8 8 8 A ADE A . n A 1 9 A 9 9 9 A ADE A . n A 1 10 G 10 10 10 G GUA A . n B 2 1 DC 1 11 11 DC CYT B . n B 2 2 DT 2 12 12 DT THY B . n B 2 3 DT 3 13 13 DT THY B . n B 2 4 DT 4 14 14 DT THY B . n B 2 5 DT 5 15 15 DT THY B . n B 2 6 DC 6 16 16 DC CYT B . n B 2 7 DT 7 17 17 DT THY B . n B 2 8 DT 8 18 18 DT THY B . n B 2 9 DT 9 19 19 DT THY B . n B 2 10 DG 10 20 20 DG GUA B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 HOH 1 120 120 HOH HOH A . C 3 HOH 2 122 122 HOH HOH A . C 3 HOH 3 124 124 HOH HOH A . C 3 HOH 4 126 126 HOH HOH A . C 3 HOH 5 128 128 HOH HOH A . C 3 HOH 6 129 129 HOH HOH A . C 3 HOH 7 130 130 HOH HOH A . C 3 HOH 8 131 131 HOH HOH A . C 3 HOH 9 132 132 HOH HOH A . C 3 HOH 10 134 134 HOH HOH A . C 3 HOH 11 135 135 HOH HOH A . C 3 HOH 12 137 137 HOH HOH A . C 3 HOH 13 138 138 HOH HOH A . C 3 HOH 14 139 139 HOH HOH A . C 3 HOH 15 140 140 HOH HOH A . C 3 HOH 16 142 142 HOH HOH A . C 3 HOH 17 143 143 HOH HOH A . C 3 HOH 18 145 145 HOH HOH A . C 3 HOH 19 146 146 HOH HOH A . C 3 HOH 20 147 147 HOH HOH A . C 3 HOH 21 148 148 HOH HOH A . C 3 HOH 22 149 149 HOH HOH A . C 3 HOH 23 150 150 HOH HOH A . C 3 HOH 24 152 152 HOH HOH A . C 3 HOH 25 157 157 HOH HOH A . C 3 HOH 26 158 158 HOH HOH A . C 3 HOH 27 160 160 HOH HOH A . C 3 HOH 28 162 162 HOH HOH A . C 3 HOH 29 165 165 HOH HOH A . C 3 HOH 30 166 166 HOH HOH A . C 3 HOH 31 171 171 HOH HOH A . C 3 HOH 32 173 173 HOH HOH A . C 3 HOH 33 175 175 HOH HOH A . C 3 HOH 34 176 176 HOH HOH A . C 3 HOH 35 180 180 HOH HOH A . C 3 HOH 36 181 181 HOH HOH A . C 3 HOH 37 182 182 HOH HOH A . D 3 HOH 1 121 121 HOH HOH B . D 3 HOH 2 123 123 HOH HOH B . D 3 HOH 3 125 125 HOH HOH B . D 3 HOH 4 127 127 HOH HOH B . D 3 HOH 5 133 133 HOH HOH B . D 3 HOH 6 136 136 HOH HOH B . D 3 HOH 7 141 141 HOH HOH B . D 3 HOH 8 144 144 HOH HOH B . D 3 HOH 9 151 151 HOH HOH B . D 3 HOH 10 153 153 HOH HOH B . D 3 HOH 11 154 154 HOH HOH B . D 3 HOH 12 155 155 HOH HOH B . D 3 HOH 13 156 156 HOH HOH B . D 3 HOH 14 159 159 HOH HOH B . D 3 HOH 15 161 161 HOH HOH B . D 3 HOH 16 163 163 HOH HOH B . D 3 HOH 17 164 164 HOH HOH B . D 3 HOH 18 167 167 HOH HOH B . D 3 HOH 19 168 168 HOH HOH B . D 3 HOH 20 170 170 HOH HOH B . D 3 HOH 21 172 172 HOH HOH B . D 3 HOH 22 174 174 HOH HOH B . D 3 HOH 23 178 178 HOH HOH B . D 3 HOH 24 179 179 HOH HOH B . D 3 HOH 25 183 183 HOH HOH B . D 3 HOH 26 184 184 HOH HOH B . D 3 HOH 27 185 185 HOH HOH B . D 3 HOH 28 186 186 HOH HOH B . D 3 HOH 29 188 188 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 EPMR phasing . ? 2 CNS refinement . ? 3 # _cell.entry_id 1JB8 _cell.length_a 45.234 _cell.length_b 46.780 _cell.length_c 56.560 _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 1JB8 _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 # _exptl.entry_id 1JB8 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.38 _exptl_crystal.density_percent_sol 48.24 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'MPD, magnesium acetate, spermidine, Na cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 277K' _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 'magnesium acetate' ? ? ? 1 3 1 spermidine ? ? ? 1 4 1 'sodium cacodylate' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 93 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2000-08-15 _diffrn_detector.details mirrors # _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type ENRAF-NONIUS _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 1JB8 _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 10 _reflns.d_resolution_high 2.38 _reflns.number_obs 2814 _reflns.number_all 18386 _reflns.percent_possible_obs 98.9 _reflns.pdbx_Rmerge_I_obs 0.053 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.5 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.30 _reflns_shell.d_res_low 2.38 _reflns_shell.percent_possible_all 96.9 _reflns_shell.Rmerge_I_obs 0.78 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1JB8 _refine.ls_number_reflns_obs 2171 _refine.ls_number_reflns_all 2369 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_d_res_low 10 _refine.ls_d_res_high 2.38 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all 0.238 _refine.ls_R_factor_R_work 0.223 _refine.ls_R_factor_R_free 0.251 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5 _refine.ls_number_reflns_R_free 109 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'P2(1)2(1)2(1) structure of the same sequence of RNA/DNA hybrid' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_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 414 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 66 _refine_hist.number_atoms_total 480 _refine_hist.d_res_high 2.38 _refine_hist.d_res_low 10 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function x_bond_d 0.004 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 0.82 ? ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_low _refine_ls_shell.d_res_high _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 4 2.62 2.38 . 0.451 . 0.483 . . 22 . 'X-RAY DIFFRACTION' . . 4 2.99 2.62 . 0.305 . 0.36 . . 27 . 'X-RAY DIFFRACTION' . . 4 3.73 2.99 . 0.221 . 0.244 . . 41 . 'X-RAY DIFFRACTION' . . 4 10.0 3.73 . 0.158 . 0.162 . . 19 . 'X-RAY DIFFRACTION' . . # _database_PDB_matrix.entry_id 1JB8 _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 1JB8 _struct.title 'The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1JB8 _struct_keywords.pdbx_keywords DNA/RNA _struct_keywords.text 'DNA/DNA intercalation, RNA/DNA hybrid, RNA/DNA polypurine tract, DNA-RNA COMPLEX' # 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 3 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1JB8 1JB8 ? ? ? 2 2 PDB 1JB8 1JB8 ? ? ? # 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 1JB8 A 1 ? 10 ? 1JB8 1 ? 10 ? 1 10 2 2 1JB8 B 1 ? 10 ? 1JB8 11 ? 20 ? 11 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _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 hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A C 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A C 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A C 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N1 ? ? ? 1_555 B DT 9 N3 ? ? A A 2 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 2 N6 ? ? ? 1_555 B DT 9 O4 ? ? A A 2 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A A 3 N1 ? ? ? 1_555 B DT 8 N3 ? ? A A 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N6 ? ? ? 1_555 B DT 8 O4 ? ? A A 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 4 N1 ? ? ? 1_555 B DT 7 N3 ? ? A A 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A A 4 N6 ? ? ? 1_555 B DT 7 O4 ? ? A A 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 N1 ? ? ? 1_555 B DC 6 N3 ? ? A G 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 N2 ? ? ? 1_555 B DC 6 O2 ? ? A G 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 O6 ? ? ? 1_555 B DC 6 N4 ? ? A G 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A A 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A A 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A A 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A A 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 8 N1 ? ? ? 1_555 B DT 3 N3 ? ? A A 8 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N6 ? ? ? 1_555 B DT 3 O4 ? ? A A 8 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 9 N1 ? ? ? 1_555 B DT 2 N3 ? ? A A 9 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 9 N6 ? ? ? 1_555 B DT 2 O4 ? ? A A 9 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? A G 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 10 N2 ? ? ? 1_555 B DC 1 O2 ? ? A G 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 10 O6 ? ? ? 1_555 B DC 1 N4 ? ? A G 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 160 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id C _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 DG OP3 O N N 107 DG P P N N 108 DG OP1 O N N 109 DG OP2 O N N 110 DG "O5'" O N N 111 DG "C5'" C N N 112 DG "C4'" C N R 113 DG "O4'" O N N 114 DG "C3'" C N S 115 DG "O3'" O N N 116 DG "C2'" C N N 117 DG "C1'" C N R 118 DG N9 N Y N 119 DG C8 C Y N 120 DG N7 N Y N 121 DG C5 C Y N 122 DG C6 C N N 123 DG O6 O N N 124 DG N1 N N N 125 DG C2 C N N 126 DG N2 N N N 127 DG N3 N N N 128 DG C4 C Y N 129 DG HOP3 H N N 130 DG HOP2 H N N 131 DG "H5'" H N N 132 DG "H5''" H N N 133 DG "H4'" H N N 134 DG "H3'" H N N 135 DG "HO3'" H N N 136 DG "H2'" H N N 137 DG "H2''" H N N 138 DG "H1'" H N N 139 DG H8 H N N 140 DG H1 H N N 141 DG H21 H N N 142 DG H22 H N N 143 DT OP3 O N N 144 DT P P N N 145 DT OP1 O N N 146 DT OP2 O N N 147 DT "O5'" O N N 148 DT "C5'" C N N 149 DT "C4'" C N R 150 DT "O4'" O N N 151 DT "C3'" C N S 152 DT "O3'" O N N 153 DT "C2'" C N N 154 DT "C1'" C N R 155 DT N1 N N N 156 DT C2 C N N 157 DT O2 O N N 158 DT N3 N N N 159 DT C4 C N N 160 DT O4 O N N 161 DT C5 C N N 162 DT C7 C N N 163 DT C6 C N N 164 DT HOP3 H N N 165 DT HOP2 H N N 166 DT "H5'" H N N 167 DT "H5''" H N N 168 DT "H4'" H N N 169 DT "H3'" H N N 170 DT "HO3'" H N N 171 DT "H2'" H N N 172 DT "H2''" H N N 173 DT "H1'" H N N 174 DT H3 H N N 175 DT H71 H N N 176 DT H72 H N N 177 DT H73 H N N 178 DT H6 H N N 179 G OP3 O N N 180 G P P N N 181 G OP1 O N N 182 G OP2 O N N 183 G "O5'" O N N 184 G "C5'" C N N 185 G "C4'" C N R 186 G "O4'" O N N 187 G "C3'" C N S 188 G "O3'" O N N 189 G "C2'" C N R 190 G "O2'" O N N 191 G "C1'" C N R 192 G N9 N Y N 193 G C8 C Y N 194 G N7 N Y N 195 G C5 C Y N 196 G C6 C N N 197 G O6 O N N 198 G N1 N N N 199 G C2 C N N 200 G N2 N N N 201 G N3 N N N 202 G C4 C Y N 203 G HOP3 H N N 204 G HOP2 H N N 205 G "H5'" H N N 206 G "H5''" H N N 207 G "H4'" H N N 208 G "H3'" H N N 209 G "HO3'" H N N 210 G "H2'" H N N 211 G "HO2'" H N N 212 G "H1'" H N N 213 G H8 H N N 214 G H1 H N N 215 G H21 H N N 216 G H22 H N N 217 HOH O O N N 218 HOH H1 H N N 219 HOH H2 H N N 220 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 DG OP3 P sing N N 111 DG OP3 HOP3 sing N N 112 DG P OP1 doub N N 113 DG P OP2 sing N N 114 DG P "O5'" sing N N 115 DG OP2 HOP2 sing N N 116 DG "O5'" "C5'" sing N N 117 DG "C5'" "C4'" sing N N 118 DG "C5'" "H5'" sing N N 119 DG "C5'" "H5''" sing N N 120 DG "C4'" "O4'" sing N N 121 DG "C4'" "C3'" sing N N 122 DG "C4'" "H4'" sing N N 123 DG "O4'" "C1'" sing N N 124 DG "C3'" "O3'" sing N N 125 DG "C3'" "C2'" sing N N 126 DG "C3'" "H3'" sing N N 127 DG "O3'" "HO3'" sing N N 128 DG "C2'" "C1'" sing N N 129 DG "C2'" "H2'" sing N N 130 DG "C2'" "H2''" sing N N 131 DG "C1'" N9 sing N N 132 DG "C1'" "H1'" sing N N 133 DG N9 C8 sing Y N 134 DG N9 C4 sing Y N 135 DG C8 N7 doub Y N 136 DG C8 H8 sing N N 137 DG N7 C5 sing Y N 138 DG C5 C6 sing N N 139 DG C5 C4 doub Y N 140 DG C6 O6 doub N N 141 DG C6 N1 sing N N 142 DG N1 C2 sing N N 143 DG N1 H1 sing N N 144 DG C2 N2 sing N N 145 DG C2 N3 doub N N 146 DG N2 H21 sing N N 147 DG N2 H22 sing N N 148 DG N3 C4 sing N N 149 DT OP3 P sing N N 150 DT OP3 HOP3 sing N N 151 DT P OP1 doub N N 152 DT P OP2 sing N N 153 DT P "O5'" sing N N 154 DT OP2 HOP2 sing N N 155 DT "O5'" "C5'" sing N N 156 DT "C5'" "C4'" sing N N 157 DT "C5'" "H5'" sing N N 158 DT "C5'" "H5''" sing N N 159 DT "C4'" "O4'" sing N N 160 DT "C4'" "C3'" sing N N 161 DT "C4'" "H4'" sing N N 162 DT "O4'" "C1'" sing N N 163 DT "C3'" "O3'" sing N N 164 DT "C3'" "C2'" sing N N 165 DT "C3'" "H3'" sing N N 166 DT "O3'" "HO3'" sing N N 167 DT "C2'" "C1'" sing N N 168 DT "C2'" "H2'" sing N N 169 DT "C2'" "H2''" sing N N 170 DT "C1'" N1 sing N N 171 DT "C1'" "H1'" sing N N 172 DT N1 C2 sing N N 173 DT N1 C6 sing N N 174 DT C2 O2 doub N N 175 DT C2 N3 sing N N 176 DT N3 C4 sing N N 177 DT N3 H3 sing N N 178 DT C4 O4 doub N N 179 DT C4 C5 sing N N 180 DT C5 C7 sing N N 181 DT C5 C6 doub N N 182 DT C7 H71 sing N N 183 DT C7 H72 sing N N 184 DT C7 H73 sing N N 185 DT C6 H6 sing N N 186 G OP3 P sing N N 187 G OP3 HOP3 sing N N 188 G P OP1 doub N N 189 G P OP2 sing N N 190 G P "O5'" sing N N 191 G OP2 HOP2 sing N N 192 G "O5'" "C5'" sing N N 193 G "C5'" "C4'" sing N N 194 G "C5'" "H5'" sing N N 195 G "C5'" "H5''" sing N N 196 G "C4'" "O4'" sing N N 197 G "C4'" "C3'" sing N N 198 G "C4'" "H4'" sing N N 199 G "O4'" "C1'" sing N N 200 G "C3'" "O3'" sing N N 201 G "C3'" "C2'" sing N N 202 G "C3'" "H3'" sing N N 203 G "O3'" "HO3'" sing N N 204 G "C2'" "O2'" sing N N 205 G "C2'" "C1'" sing N N 206 G "C2'" "H2'" sing N N 207 G "O2'" "HO2'" sing N N 208 G "C1'" N9 sing N N 209 G "C1'" "H1'" sing N N 210 G N9 C8 sing Y N 211 G N9 C4 sing Y N 212 G C8 N7 doub Y N 213 G C8 H8 sing N N 214 G N7 C5 sing Y N 215 G C5 C6 sing N N 216 G C5 C4 doub Y N 217 G C6 O6 doub N N 218 G C6 N1 sing N N 219 G N1 C2 sing N N 220 G N1 H1 sing N N 221 G C2 N2 sing N N 222 G C2 N3 doub N N 223 G N2 H21 sing N N 224 G N2 H22 sing N N 225 G N3 C4 sing N N 226 HOH O H1 sing N N 227 HOH O H2 sing N N 228 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1JB8 'double helix' 1JB8 '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 C 1 1_555 B DG 10 1_555 -0.268 -0.035 -0.025 -4.355 -6.104 2.948 1 A_C1:DG20_B A 1 ? B 20 ? 19 1 1 A A 2 1_555 B DT 9 1_555 0.005 -0.198 0.193 7.935 -11.307 5.142 2 A_A2:DT19_B A 2 ? B 19 ? 20 1 1 A A 3 1_555 B DT 8 1_555 0.042 -0.036 0.254 11.878 -18.420 2.096 3 A_A3:DT18_B A 3 ? B 18 ? 20 1 1 A A 4 1_555 B DT 7 1_555 -0.260 -0.189 -0.112 2.380 -16.977 14.072 4 A_A4:DT17_B A 4 ? B 17 ? 20 1 1 A G 5 1_555 B DC 6 1_555 -0.363 -0.294 -0.204 -10.198 -2.594 -0.465 5 A_G5:DC16_B A 5 ? B 16 ? 19 1 1 A A 6 1_555 B DT 5 1_555 0.708 -0.234 -0.226 -9.277 -4.959 5.663 6 A_A6:DT15_B A 6 ? B 15 ? 20 1 1 A A 7 1_555 B DT 4 1_555 0.189 -0.261 -0.535 -14.170 -6.783 4.615 7 A_A7:DT14_B A 7 ? B 14 ? 20 1 1 A A 8 1_555 B DT 3 1_555 0.119 -0.394 -0.286 -3.829 -4.525 -0.439 8 A_A8:DT13_B A 8 ? B 13 ? 20 1 1 A A 9 1_555 B DT 2 1_555 0.169 -0.293 0.162 5.574 -1.230 0.446 9 A_A9:DT12_B A 9 ? B 12 ? 20 1 1 A G 10 1_555 B DC 1 1_555 -0.344 -0.174 -0.010 11.470 1.386 2.814 10 A_G10:DC11_B A 10 ? B 11 ? 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 C 1 1_555 B DG 10 1_555 A A 2 1_555 B DT 9 1_555 0.723 -0.011 6.406 -2.022 2.787 13.668 -5.139 -6.642 6.108 11.473 8.323 14.093 1 AA_C1A2:DT19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A A 2 1_555 B DT 9 1_555 A A 3 1_555 B DT 8 1_555 0.285 -0.642 3.130 -1.074 -3.478 32.811 -0.559 -0.678 3.169 -6.134 1.893 33.007 2 AA_A2A3:DT18DT19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A A 3 1_555 B DT 8 1_555 A A 4 1_555 B DT 7 1_555 0.758 -1.206 3.520 0.210 7.883 31.394 -3.606 -1.322 3.137 14.287 -0.380 32.345 3 AA_A3A4:DT17DT18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A A 4 1_555 B DT 7 1_555 A G 5 1_555 B DC 6 1_555 -1.832 -1.316 3.388 -7.519 14.654 35.440 -3.781 1.818 2.955 22.627 11.610 38.968 4 AA_A4G5:DC16DT17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A G 5 1_555 B DC 6 1_555 A A 6 1_555 B DT 5 1_555 0.683 -1.618 3.332 3.882 9.375 36.186 -3.704 -0.570 2.894 14.741 -6.103 37.536 5 AA_G5A6:DT15DC16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A A 6 1_555 B DT 5 1_555 A A 7 1_555 B DT 4 1_555 0.729 -1.985 3.509 7.204 7.585 26.656 -5.776 0.195 2.938 15.703 -14.915 28.600 6 AA_A6A7:DT14DT15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A A 7 1_555 B DT 4 1_555 A A 8 1_555 B DT 3 1_555 0.020 -1.920 3.195 -1.509 1.991 28.862 -4.260 -0.359 3.054 3.984 3.020 28.968 7 AA_A7A8:DT13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A A 8 1_555 B DT 3 1_555 A A 9 1_555 B DT 2 1_555 -0.339 -1.827 3.096 -2.559 0.287 28.174 -3.801 0.132 3.095 0.588 5.242 28.289 8 AA_A8A9:DT12DT13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A A 9 1_555 B DT 2 1_555 A G 10 1_555 B DC 1 1_555 0.686 -1.919 3.205 2.493 -1.201 26.024 -3.912 -0.837 3.339 -2.659 -5.516 26.168 9 AA_A9G10:DC11DT12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _pdbx_initial_refinement_model.accession_code 1G4Q _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 'P2(1)2(1)2(1) structure of the same sequence of RNA/DNA hybrid' # _atom_sites.entry_id 1JB8 _atom_sites.fract_transf_matrix[1][1] 0.022107 _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] 0.021377 _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] 0.017680 _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_