data_3HR3 # _entry.id 3HR3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.378 _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 3HR3 pdb_00003hr3 10.2210/pdb3hr3/pdb NDB NA0041 ? ? RCSB RCSB053479 ? ? WWPDB D_1000053479 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3HR3 _pdbx_database_status.recvd_initial_deposition_date 2009-06-08 _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 'Egli, M.' 1 'Pallan, P.S.' 2 # _citation.id primary _citation.title ;Interplay of structure, hydration and thermal stability in formacetal modified oligonucleotides: RNA may tolerate nonionic modifications better than DNA. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 131 _citation.page_first 14932 _citation.page_last 14937 _citation.year 2009 _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 19824732 _citation.pdbx_database_id_DOI 10.1021/ja904926e # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kolarovic, A.' 1 ? primary 'Schweizer, E.' 2 ? primary 'Greene, E.' 3 ? primary 'Gironda, M.' 4 ? primary 'Pallan, P.S.' 5 ? primary 'Egli, M.' 6 ? primary 'Rozners, E.' 7 ? # _cell.entry_id 3HR3 _cell.length_a 33.199 _cell.length_b 33.199 _cell.length_c 68.508 _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 3HR3 _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'" 3011.051 1 ? ? ? ? 2 water nat water 18.015 23 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DG)(US4)(OMU)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGXUACGC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DG n 1 4 US4 n 1 5 OMU n 1 6 DA n 1 7 DC n 1 8 DG n 1 9 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ;Chemically synthesize deoxyribonucleotide, US4 = Formacetal linked thymidine and 2'-deoxyadenosine (TfA) ; # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3HR3 _struct_ref.pdbx_db_accession 3HR3 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GCGNUACGC _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3HR3 _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 9 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3HR3 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 OMU 'RNA linking' n ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; ? 'C10 H15 N2 O9 P' 338.208 US4 'DNA linking' . ;[(2R,3S,5R)-3-({[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxytetrahydrofuran-2-yl]methoxy}methoxy)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate ; ? 'C21 H28 N7 O11 P' 585.461 # _exptl.entry_id 3HR3 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.13 _exptl_crystal.density_percent_sol 60.76 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;Sodium cacodylate (20 mM, pH 6.0), potassium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2-methyl-2,4-pentanediol (MPD 5% v/v) , VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 110 _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 2009-01-20 _diffrn_detector.details 'Monochromator Si(111)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _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 0.9795 # _reflns.entry_id 3HR3 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.75 _reflns.number_obs 4006 _reflns.number_all 4208 _reflns.percent_possible_obs 95.2 _reflns.pdbx_Rmerge_I_obs 0.058 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 18.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 17 _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 # _reflns_shell.d_res_high 1.75 _reflns_shell.d_res_low 1.78 _reflns_shell.percent_possible_all 72.4 _reflns_shell.Rmerge_I_obs 0.187 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 5.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 139 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3HR3 _refine.ls_number_reflns_obs 3714 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.88 _refine.ls_d_res_high 1.75 _refine.ls_percent_reflns_obs 95.00 _refine.ls_R_factor_obs 0.23147 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.22786 _refine.ls_R_factor_R_free 0.28185 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.3 _refine.ls_number_reflns_R_free 291 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.960 _refine.correlation_coeff_Fo_to_Fc_free 0.940 _refine.B_iso_mean 35.242 _refine.aniso_B[1][1] 1.35 _refine.aniso_B[2][2] 1.35 _refine.aniso_B[3][3] -2.71 _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 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 ? _refine.pdbx_starting_model 'Single strand from the duplex of PDB ID 411D.' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.156 _refine.pdbx_overall_ESU_R_Free 0.128 _refine.overall_SU_ML 0.099 _refine.overall_SU_B 7.139 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _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 201 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 23 _refine_hist.number_atoms_total 224 _refine_hist.d_res_high 1.75 _refine_hist.d_res_low 29.88 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.022 0.021 ? 225 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.037 2.974 ? 344 'X-RAY DIFFRACTION' ? r_chiral_restr 0.120 0.200 ? 39 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.015 0.020 ? 104 'X-RAY DIFFRACTION' ? r_scbond_it 3.515 3.000 ? 225 'X-RAY DIFFRACTION' ? r_scangle_it 4.519 4.500 ? 343 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 3.280 3.000 ? 225 'X-RAY DIFFRACTION' ? r_sphericity_free 7.990 3.000 ? 29 'X-RAY DIFFRACTION' ? r_sphericity_bonded 6.083 3.000 ? 201 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.753 _refine_ls_shell.d_res_low 1.799 _refine_ls_shell.number_reflns_R_work 199 _refine_ls_shell.R_factor_R_work 0.376 _refine_ls_shell.percent_reflns_obs 73.65 _refine_ls_shell.R_factor_R_free 0.373 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 19 _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' # _struct.entry_id 3HR3 _struct.title ;Interplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Hydrophobic Modifications Better than DNA ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3HR3 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, RNA, formacetal-DNA, RNA hydration' # 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 ? # _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 covale1 covale both ? A DG 3 "O3'" ? ? ? 1_555 A US4 4 P ? ? A DG 3 A US4 4 1_555 ? ? ? ? ? ? ? 1.553 ? ? covale2 covale both ? A US4 4 "OZ'" ? ? ? 1_555 A OMU 5 P ? ? A US4 4 A OMU 6 1_555 ? ? ? ? ? ? ? 1.557 ? ? covale3 covale both ? A OMU 5 "O3'" ? ? ? 1_555 A DA 6 P ? ? A OMU 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.597 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 9 N3 ? ? A DG 1 A DC 10 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 9 O2 ? ? A DG 1 A DC 10 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 9 N4 ? ? A DG 1 A DC 10 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 8 N1 ? ? A DC 2 A DG 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 8 O6 ? ? A DC 2 A DG 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 8 N2 ? ? A DC 2 A DG 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 7 N3 ? ? A DG 3 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 7 O2 ? ? A DG 3 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 7 N4 ? ? A DG 3 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 8 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 8 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 8 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 8 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 9 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 10 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 9 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 10 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 10 A DG 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 3HR3 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3HR3 _atom_sites.fract_transf_matrix[1][1] 0.030121 _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] 0.030121 _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] 0.014597 _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_ _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 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 US4 4 4 4 US4 US4 A . n A 1 5 OMU 5 6 6 OMU OMU A . n A 1 6 DA 6 7 7 DA DA A . n A 1 7 DC 7 8 8 DC DC A . n A 1 8 DG 8 9 9 DG DG A . n A 1 9 DC 9 10 10 DC DC 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 HOH 1 5 5 HOH HOH A . B 2 HOH 2 11 11 HOH HOH A . B 2 HOH 3 12 12 HOH HOH A . B 2 HOH 4 13 13 HOH HOH A . B 2 HOH 5 15 15 HOH HOH A . B 2 HOH 6 16 16 HOH HOH A . B 2 HOH 7 17 17 HOH HOH A . B 2 HOH 8 18 18 HOH HOH A . B 2 HOH 9 20 20 HOH HOH A . B 2 HOH 10 21 21 HOH HOH A . B 2 HOH 11 22 22 HOH HOH A . B 2 HOH 12 23 23 HOH HOH A . B 2 HOH 13 24 24 HOH HOH A . B 2 HOH 14 25 25 HOH HOH A . B 2 HOH 15 26 26 HOH HOH A . B 2 HOH 16 27 27 HOH HOH A . B 2 HOH 17 28 28 HOH HOH A . B 2 HOH 18 29 29 HOH HOH A . B 2 HOH 19 30 30 HOH HOH A . B 2 HOH 20 31 31 HOH HOH A . B 2 HOH 21 32 32 HOH HOH A . B 2 HOH 22 33 33 HOH HOH A . B 2 HOH 23 34 34 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id OMU _pdbx_struct_mod_residue.label_seq_id 5 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id OMU _pdbx_struct_mod_residue.auth_seq_id 6 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id U _pdbx_struct_mod_residue.details ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B # 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)' 2100 ? 1 MORE 4 ? 1 'SSA (A^2)' 3470 ? # 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' 7_555 y,x,-z 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # 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 2009-10-27 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2015-03-25 4 'Structure model' 1 3 2023-09-06 # _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' Other 3 4 'Structure model' Advisory 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' pdbx_validate_polymer_linkage 6 4 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_dist_value' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 6 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 12 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 MOLREP phasing . ? 2 REFMAC refinement 5.5.0088 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DG 1 ? ? "C3'" A DG 1 ? ? 1.382 1.419 -0.037 0.006 N 2 1 "O3'" A DG 3 ? ? "C3'" A DG 3 ? ? 1.374 1.419 -0.045 0.006 N 3 1 C5 A DG 3 ? ? N7 A DG 3 ? ? 1.428 1.388 0.040 0.006 N 4 1 "O3'" A DG 9 ? ? "C3'" A DG 9 ? ? 1.352 1.419 -0.067 0.006 N 5 1 N1 A DC 10 ? ? C6 A DC 10 ? ? 1.325 1.367 -0.042 0.006 N # 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 N1 A DG 1 ? ? C6 A DG 1 ? ? O6 A DG 1 ? ? 124.65 119.90 4.75 0.60 N 2 1 N3 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 126.22 121.90 4.32 0.70 N 3 1 C5 A DC 2 ? ? C4 A DC 2 ? ? N4 A DC 2 ? ? 115.70 120.20 -4.50 0.70 N 4 1 C5 A DG 3 ? ? C6 A DG 3 ? ? N1 A DG 3 ? ? 115.13 111.50 3.63 0.50 N 5 1 "O3'" A OMU 6 ? ? P A DA 7 ? ? OP2 A DA 7 ? ? 117.21 110.50 6.71 1.10 Y 6 1 "O4'" A DG 9 ? ? "C4'" A DG 9 ? ? "C3'" A DG 9 ? ? 99.22 104.50 -5.28 0.40 N 7 1 "C3'" A DG 9 ? ? "C2'" A DG 9 ? ? "C1'" A DG 9 ? ? 95.52 102.40 -6.88 0.80 N 8 1 C8 A DG 9 ? ? N9 A DG 9 ? ? C4 A DG 9 ? ? 108.89 106.40 2.49 0.40 N 9 1 "O4'" A DC 10 ? ? "C4'" A DC 10 ? ? "C3'" A DC 10 ? ? 100.90 104.50 -3.60 0.40 N 10 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? N1 A DC 10 ? ? 114.34 108.30 6.04 0.30 N 11 1 N3 A DC 10 ? ? C4 A DC 10 ? ? N4 A DC 10 ? ? 123.71 118.00 5.71 0.70 N 12 1 C5 A DC 10 ? ? C4 A DC 10 ? ? N4 A DC 10 ? ? 112.10 120.20 -8.10 0.70 N # 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 HOH O O N N 108 HOH H1 H N N 109 HOH H2 H N N 110 OMU N1 N N N 111 OMU C2 C N N 112 OMU N3 N N N 113 OMU C4 C N N 114 OMU C5 C N N 115 OMU C6 C N N 116 OMU O2 O N N 117 OMU O4 O N N 118 OMU "C1'" C N R 119 OMU "C2'" C N R 120 OMU "O2'" O N N 121 OMU CM2 C N N 122 OMU "C3'" C N R 123 OMU "C4'" C N R 124 OMU "O3'" O N N 125 OMU "O4'" O N N 126 OMU "C5'" C N N 127 OMU "O5'" O N N 128 OMU P P N N 129 OMU OP1 O N N 130 OMU OP2 O N N 131 OMU OP3 O N N 132 OMU HN3 H N N 133 OMU H5 H N N 134 OMU H6 H N N 135 OMU "H1'" H N N 136 OMU "H2'" H N N 137 OMU HM21 H N N 138 OMU HM22 H N N 139 OMU HM23 H N N 140 OMU "H3'" H N N 141 OMU "H4'" H N N 142 OMU "HO3'" H N N 143 OMU "H5'" H N N 144 OMU "H5''" H N N 145 OMU HOP2 H N N 146 OMU HOP3 H N N 147 US4 P P N N 148 US4 O1P O N N 149 US4 O2P O N N 150 US4 "O5'" O N N 151 US4 "C5'" C N N 152 US4 "C4'" C N R 153 US4 "C3'" C N S 154 US4 "C2'" C N N 155 US4 "C1'" C N R 156 US4 "O4'" O N N 157 US4 N1 N N N 158 US4 C2 C N N 159 US4 N3 N N N 160 US4 C4 C N N 161 US4 O4 O N N 162 US4 C5 C N N 163 US4 C5M C N N 164 US4 C6 C N N 165 US4 O2 O N N 166 US4 "O3'" O N N 167 US4 "C7'" C N N 168 US4 "O8'" O N N 169 US4 "C9'" C N N 170 US4 "CU'" C N R 171 US4 "CY'" C N S 172 US4 "OZ'" O N N 173 US4 "CX'" C N N 174 US4 "CW'" C N R 175 US4 "OV'" O N N 176 US4 N19 N Y N 177 US4 C14 C Y N 178 US4 N13 N Y N 179 US4 C12 C Y N 180 US4 N11 N Y N 181 US4 C16 C Y N 182 US4 N16 N N N 183 US4 C15 C Y N 184 US4 N17 N Y N 185 US4 C18 C Y N 186 US4 "H15'" H N N 187 US4 "H25'" H N N 188 US4 "H4'" H N N 189 US4 "H3'" H N N 190 US4 "H12'" H N N 191 US4 "H22'" H N N 192 US4 "H1'" H N N 193 US4 HN3 H N N 194 US4 H15M H N N 195 US4 H25M H N N 196 US4 H35M H N N 197 US4 H6 H N N 198 US4 "H17'" H N N 199 US4 "H27'" H N N 200 US4 "H19'" H N N 201 US4 "H29'" H N N 202 US4 "HU'" H N N 203 US4 "HY'" H N N 204 US4 "HOZ'" H N N 205 US4 "H1X'" H N N 206 US4 "H2X'" H N N 207 US4 "HW'" H N N 208 US4 H12 H N N 209 US4 H116 H N N 210 US4 H216 H N N 211 US4 H18 H N N 212 US4 O3P O N N 213 US4 H27 H N N 214 US4 HO3P H N N 215 # 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 HOH O H1 sing N N 113 HOH O H2 sing N N 114 OMU N1 C2 sing N N 115 OMU N1 C6 sing N N 116 OMU N1 "C1'" sing N N 117 OMU C2 N3 sing N N 118 OMU C2 O2 doub N N 119 OMU N3 C4 sing N N 120 OMU N3 HN3 sing N N 121 OMU C4 C5 sing N N 122 OMU C4 O4 doub N N 123 OMU C5 C6 doub N N 124 OMU C5 H5 sing N N 125 OMU C6 H6 sing N N 126 OMU "C1'" "C2'" sing N N 127 OMU "C1'" "O4'" sing N N 128 OMU "C1'" "H1'" sing N N 129 OMU "C2'" "O2'" sing N N 130 OMU "C2'" "C3'" sing N N 131 OMU "C2'" "H2'" sing N N 132 OMU "O2'" CM2 sing N N 133 OMU CM2 HM21 sing N N 134 OMU CM2 HM22 sing N N 135 OMU CM2 HM23 sing N N 136 OMU "C3'" "C4'" sing N N 137 OMU "C3'" "O3'" sing N N 138 OMU "C3'" "H3'" sing N N 139 OMU "C4'" "O4'" sing N N 140 OMU "C4'" "C5'" sing N N 141 OMU "C4'" "H4'" sing N N 142 OMU "O3'" "HO3'" sing N N 143 OMU "C5'" "O5'" sing N N 144 OMU "C5'" "H5'" sing N N 145 OMU "C5'" "H5''" sing N N 146 OMU "O5'" P sing N N 147 OMU P OP1 doub N N 148 OMU P OP2 sing N N 149 OMU P OP3 sing N N 150 OMU OP2 HOP2 sing N N 151 OMU OP3 HOP3 sing N N 152 US4 P O2P doub N N 153 US4 P O1P sing N N 154 US4 "O5'" P sing N N 155 US4 "C5'" "O5'" sing N N 156 US4 "C5'" "H15'" sing N N 157 US4 "C5'" "H25'" sing N N 158 US4 "C4'" "C5'" sing N N 159 US4 "C4'" "C3'" sing N N 160 US4 "C4'" "H4'" sing N N 161 US4 "C3'" "O3'" sing N N 162 US4 "C3'" "H3'" sing N N 163 US4 "C2'" "C3'" sing N N 164 US4 "C2'" "H12'" sing N N 165 US4 "C2'" "H22'" sing N N 166 US4 "C1'" N1 sing N N 167 US4 "C1'" "C2'" sing N N 168 US4 "C1'" "H1'" sing N N 169 US4 "O4'" "C1'" sing N N 170 US4 "O4'" "C4'" sing N N 171 US4 N1 C6 sing N N 172 US4 C2 N1 sing N N 173 US4 C2 N3 sing N N 174 US4 N3 C4 sing N N 175 US4 N3 HN3 sing N N 176 US4 C4 C5 sing N N 177 US4 C4 O4 doub N N 178 US4 C5 C5M sing N N 179 US4 C5M H15M sing N N 180 US4 C5M H25M sing N N 181 US4 C5M H35M sing N N 182 US4 C6 C5 doub N N 183 US4 C6 H6 sing N N 184 US4 O2 C2 doub N N 185 US4 "O3'" "C7'" sing N N 186 US4 "C7'" "O8'" sing N N 187 US4 "C7'" "H17'" sing N N 188 US4 "C7'" "H27'" sing N N 189 US4 "C9'" "CU'" sing N N 190 US4 "C9'" "O8'" sing N N 191 US4 "C9'" "H19'" sing N N 192 US4 "C9'" "H29'" sing N N 193 US4 "CU'" "CY'" sing N N 194 US4 "CU'" "HU'" sing N N 195 US4 "CY'" "OZ'" sing N N 196 US4 "CY'" "HY'" sing N N 197 US4 "OZ'" "HOZ'" sing N N 198 US4 "CX'" "CY'" sing N N 199 US4 "CX'" "H1X'" sing N N 200 US4 "CX'" "H2X'" sing N N 201 US4 "CW'" N19 sing N N 202 US4 "CW'" "CX'" sing N N 203 US4 "CW'" "HW'" sing N N 204 US4 "OV'" "CW'" sing N N 205 US4 "OV'" "CU'" sing N N 206 US4 N19 C14 sing Y N 207 US4 N19 C18 sing Y N 208 US4 C14 C15 sing Y N 209 US4 N13 C14 doub Y N 210 US4 N13 C12 sing Y N 211 US4 C12 N11 doub Y N 212 US4 C12 H12 sing N N 213 US4 N11 C16 sing Y N 214 US4 C16 N16 sing N N 215 US4 N16 H116 sing N N 216 US4 N16 H216 sing N N 217 US4 C15 N17 sing Y N 218 US4 C15 C16 doub Y N 219 US4 C18 N17 doub Y N 220 US4 C18 H18 sing N N 221 US4 P O3P sing N N 222 US4 O1P H27 sing N N 223 US4 O3P HO3P sing N N 224 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3HR3 'a-form double helix' 3HR3 '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 1 1_555 A DC 9 7_555 -0.242 -0.214 0.003 -4.933 -4.812 -1.909 1 A_DG1:DC10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 8 7_555 0.192 -0.137 -0.018 -2.305 -6.333 2.154 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DG 3 1_555 A DC 7 7_555 -0.154 -0.116 0.029 -6.356 -13.798 3.633 3 A_DG3:DC8_A A 3 ? A 8 ? 19 1 1 A DG 1 1_555 A DC 9 1_555 -0.242 -0.214 0.003 -4.933 -4.812 -1.909 4 A_DG1:DC10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 8 1_555 0.192 -0.137 -0.018 -2.305 -6.333 2.154 5 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DG 3 1_555 A DC 7 1_555 -0.154 -0.116 0.029 -6.355 -13.798 3.633 6 A_DG3:DC8_A A 3 ? A 8 ? 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 1 1_555 A DC 9 7_555 A DC 2 1_555 A DG 8 7_555 -0.324 -1.558 3.339 -0.726 -2.385 36.285 -2.152 0.415 3.437 -3.823 1.164 36.368 1 AA_DG1DC2:DG9DC10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 8 7_555 A DG 3 1_555 A DC 7 7_555 0.094 -1.612 3.317 0.385 11.853 27.622 -5.351 -0.109 2.435 23.500 -0.764 30.015 2 AA_DC2DG3:DC8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DG 1 1_555 A DC 9 1_555 A DC 2 1_555 A DG 8 1_555 -0.324 -1.558 3.339 -0.726 -2.385 36.285 -2.152 0.415 3.437 -3.823 1.164 36.368 3 AA_DG1DC2:DG9DC10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 8 1_555 A DG 3 1_555 A DC 7 1_555 0.094 -1.612 3.317 0.385 11.853 27.622 -5.351 -0.109 2.435 23.500 -0.764 30.015 4 AA_DC2DG3:DC8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 411D _pdbx_initial_refinement_model.details 'Single strand from the duplex of PDB ID 411D.' #