data_4RBY # _entry.id 4RBY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 4RBY pdb_00004rby 10.2210/pdb4rby/pdb NDB NA3175 ? ? RCSB RCSB087155 ? ? WWPDB D_1000087155 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4RBZ . unspecified PDB 4RC0 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4RBY _pdbx_database_status.recvd_initial_deposition_date 2014-09-13 _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 'Pallan, P.S.' 1 'Egli, M.' 2 # _citation.id primary _citation.title 'Crystal Structure, Stability and siRNA Activity of Phosphorodithioate-Modified RNAs' _citation.journal_abbrev 'To be Published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pallan, P.S.' 1 ? primary 'Yang, X.' 2 ? primary 'Sierant, M.' 3 ? primary 'Abeydeera, N.D.' 4 ? primary 'Hassell, T.' 5 ? primary 'Martinez, C.' 6 ? primary 'Janicka, M.' 7 ? primary 'Nawrot, B.' 8 ? primary 'Egli, M.' 9 ? # _cell.entry_id 4RBY _cell.length_a 40.932 _cell.length_b 35.015 _cell.length_c 31.873 _cell.angle_alpha 90.00 _cell.angle_beta 128.80 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 4RBY _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _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'-R(*CP*GP*CP*(2SG)P*AP*AP*UP*UP*AP*GP*CP*G)-3'" 3885.507 1 ? ? ? 'Guanosine phosphorodithioate RNA' 2 non-polymer syn 'STRONTIUM ION' 87.620 2 ? ? ? ? 3 water nat water 18.015 100 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'CGC(2SG)AAUUAGCG' _entity_poly.pdbx_seq_one_letter_code_can CGCXAAUUAGCG _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 C n 1 2 G n 1 3 C n 1 4 2SG n 1 5 A n 1 6 A n 1 7 U n 1 8 U n 1 9 A n 1 10 G n 1 11 C n 1 12 G 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4RBY _struct_ref.pdbx_db_accession 4RBY _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code 'CGC(2SG)AAUUAGCG' _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4RBY _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 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4RBY _struct_ref_seq.db_align_beg 101 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 112 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 101 _struct_ref_seq.pdbx_auth_seq_align_end 112 # 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 2SG 'RNA linking' n 'guanosine phosphorodithioate' ? 'C10 H16 N5 O6 P S2' 397.368 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 4RBY _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.29 _exptl_crystal.density_percent_sol 46.30 _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 7.0 _exptl_crystal_grow.pdbx_details ;20 mM sodium cacodylate, 40 mM sodium chloride, 10 mM barium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 325 mm CCD' _diffrn_detector.pdbx_collection_date 2012-10-11 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'diamond(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97872 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 21-ID-F' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 21-ID-F _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97872 # _reflns.entry_id 4RBY _reflns.observed_criterion_sigma_I 5 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.19 _reflns.number_obs 11213 _reflns.number_all 11477 _reflns.percent_possible_obs 97.7 _reflns.pdbx_Rmerge_I_obs 0.044 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 16.49 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.0 _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 1.19 _reflns_shell.d_res_low 1.23 _reflns_shell.percent_possible_all 88.5 _reflns_shell.Rmerge_I_obs 0.037 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 20.71 _reflns_shell.pdbx_redundancy 5.2 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1012 _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 4RBY _refine.ls_number_reflns_obs 11213 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 50 _refine.ls_d_res_high 1.19 _refine.ls_percent_reflns_obs 97.7 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.181 _refine.ls_R_factor_R_free 0.213 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 554 _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] ? _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_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 2Q1R' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _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 ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 255 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 100 _refine_hist.number_atoms_total 357 _refine_hist.d_res_high 1.19 _refine_hist.d_res_low 50 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id s_bond_d 0.011 ? ? ? ? 'X-RAY DIFFRACTION' s_angle_d 0.028 ? ? ? ? 'X-RAY DIFFRACTION' # _pdbx_refine.entry_id 4RBY _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.R_factor_obs_no_cutoff 0.181 _pdbx_refine.free_R_factor_no_cutoff 0.213 _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? # _struct.entry_id 4RBY _struct.title 'First X-ray structure of RNA containing guanosine phosphorodithioate' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4RBY _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'phosphorodithioate RNA, guanosine phosphorodithioate, phosphorothioate, guanosine analogue, hydrophobic, backbone, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 3 ? # _struct_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 C 3 "O3'" ? ? ? 1_555 A 2SG 4 P ? ? A C 103 A 2SG 104 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale2 covale both ? A 2SG 4 "O3'" ? ? ? 1_555 A A 5 P ? ? A 2SG 104 A A 105 1_555 ? ? ? ? ? ? ? 1.598 ? ? metalc1 metalc ? ? B SR . SR ? ? ? 1_555 D HOH . O ? ? A SR 401 A HOH 515 1_555 ? ? ? ? ? ? ? 2.705 ? ? metalc2 metalc ? ? B SR . SR ? ? ? 1_555 D HOH . O ? ? A SR 401 A HOH 516 1_555 ? ? ? ? ? ? ? 2.746 ? ? metalc3 metalc ? ? C SR . SR ? ? ? 1_555 D HOH . O ? ? A SR 402 A HOH 515 1_555 ? ? ? ? ? ? ? 2.711 ? ? metalc4 metalc ? ? C SR . SR ? ? ? 1_555 D HOH . O ? ? A SR 402 A HOH 580 1_555 ? ? ? ? ? ? ? 2.794 ? ? metalc5 metalc ? ? C SR . SR ? ? ? 1_555 D HOH . O ? ? A SR 402 A HOH 585 1_555 ? ? ? ? ? ? ? 2.507 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 12 N1 ? ? A C 101 A G 112 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 12 O6 ? ? A C 101 A G 112 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 12 N2 ? ? A C 101 A G 112 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 11 N3 ? ? A G 102 A C 111 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 11 O2 ? ? A G 102 A C 111 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 11 N4 ? ? A G 102 A C 111 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 10 N1 ? ? A C 103 A G 110 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 10 O6 ? ? A C 103 A G 110 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 10 N2 ? ? A C 103 A G 110 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 8 N3 ? ? A A 105 A U 108 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 8 O4 ? ? A A 105 A U 108 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 7 N3 ? ? A A 106 A U 107 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 7 O4 ? ? A A 106 A U 107 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 6 N1 ? ? A U 107 A A 106 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 6 N6 ? ? A U 107 A A 106 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 5 N1 ? ? A U 108 A A 105 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 5 N6 ? ? A U 108 A A 105 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 3 N3 ? ? A G 110 A C 103 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 3 O2 ? ? A G 110 A C 103 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 3 N4 ? ? A G 110 A C 103 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 2 N1 ? ? A C 111 A G 102 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 2 O6 ? ? A C 111 A G 102 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 2 N2 ? ? A C 111 A G 102 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 1 N3 ? ? A G 112 A C 101 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 1 O2 ? ? A G 112 A C 101 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 1 N4 ? ? A G 112 A C 101 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SR 401 ? 6 'BINDING SITE FOR RESIDUE SR A 401' AC2 Software A SR 402 ? 7 'BINDING SITE FOR RESIDUE SR A 402' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 U A 8 ? U A 108 . ? 1_555 ? 2 AC1 6 SR C . ? SR A 402 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 515 . ? 1_555 ? 4 AC1 6 HOH D . ? HOH A 516 . ? 1_555 ? 5 AC1 6 HOH D . ? HOH A 541 . ? 2_556 ? 6 AC1 6 HOH D . ? HOH A 567 . ? 2_556 ? 7 AC2 7 SR B . ? SR A 401 . ? 1_555 ? 8 AC2 7 HOH D . ? HOH A 504 . ? 1_555 ? 9 AC2 7 HOH D . ? HOH A 515 . ? 1_555 ? 10 AC2 7 HOH D . ? HOH A 541 . ? 2_556 ? 11 AC2 7 HOH D . ? HOH A 567 . ? 2_556 ? 12 AC2 7 HOH D . ? HOH A 580 . ? 1_555 ? 13 AC2 7 HOH D . ? HOH A 585 . ? 1_555 ? # _database_PDB_matrix.entry_id 4RBY _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 4RBY _atom_sites.fract_transf_matrix[1][1] 0.024431 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.019643 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.028559 _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] 0.040258 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O P S SR # 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 1 101 101 C C A . n A 1 2 G 2 102 102 G G A . n A 1 3 C 3 103 103 C C A . n A 1 4 2SG 4 104 104 2SG GUS A . n A 1 5 A 5 105 105 A A A . n A 1 6 A 6 106 106 A A A . n A 1 7 U 7 107 107 U U A . n A 1 8 U 8 108 108 U U A . n A 1 9 A 9 109 109 A A A . n A 1 10 G 10 110 110 G G A . n A 1 11 C 11 111 111 C C A . n A 1 12 G 12 112 112 G G A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SR 1 401 401 SR SR A . C 2 SR 1 402 402 SR SR A . D 3 HOH 1 501 201 HOH HOH A . D 3 HOH 2 502 202 HOH HOH A . D 3 HOH 3 503 203 HOH HOH A . D 3 HOH 4 504 204 HOH HOH A . D 3 HOH 5 505 205 HOH HOH A . D 3 HOH 6 506 206 HOH HOH A . D 3 HOH 7 507 207 HOH HOH A . D 3 HOH 8 508 208 HOH HOH A . D 3 HOH 9 509 209 HOH HOH A . D 3 HOH 10 510 210 HOH HOH A . D 3 HOH 11 511 211 HOH HOH A . D 3 HOH 12 512 212 HOH HOH A . D 3 HOH 13 513 213 HOH HOH A . D 3 HOH 14 514 214 HOH HOH A . D 3 HOH 15 515 215 HOH HOH A . D 3 HOH 16 516 216 HOH HOH A . D 3 HOH 17 517 217 HOH HOH A . D 3 HOH 18 518 218 HOH HOH A . D 3 HOH 19 519 219 HOH HOH A . D 3 HOH 20 520 220 HOH HOH A . D 3 HOH 21 521 221 HOH HOH A . D 3 HOH 22 522 222 HOH HOH A . D 3 HOH 23 523 223 HOH HOH A . D 3 HOH 24 524 224 HOH HOH A . D 3 HOH 25 525 225 HOH HOH A . D 3 HOH 26 526 226 HOH HOH A . D 3 HOH 27 527 227 HOH HOH A . D 3 HOH 28 528 228 HOH HOH A . D 3 HOH 29 529 229 HOH HOH A . D 3 HOH 30 530 230 HOH HOH A . D 3 HOH 31 531 231 HOH HOH A . D 3 HOH 32 532 232 HOH HOH A . D 3 HOH 33 533 233 HOH HOH A . D 3 HOH 34 534 234 HOH HOH A . D 3 HOH 35 535 235 HOH HOH A . D 3 HOH 36 536 236 HOH HOH A . D 3 HOH 37 537 237 HOH HOH A . D 3 HOH 38 538 238 HOH HOH A . D 3 HOH 39 539 239 HOH HOH A . D 3 HOH 40 540 240 HOH HOH A . D 3 HOH 41 541 241 HOH HOH A . D 3 HOH 42 542 242 HOH HOH A . D 3 HOH 43 543 243 HOH HOH A . D 3 HOH 44 544 244 HOH HOH A . D 3 HOH 45 545 245 HOH HOH A . D 3 HOH 46 546 246 HOH HOH A . D 3 HOH 47 547 247 HOH HOH A . D 3 HOH 48 548 248 HOH HOH A . D 3 HOH 49 549 249 HOH HOH A . D 3 HOH 50 550 250 HOH HOH A . D 3 HOH 51 551 251 HOH HOH A . D 3 HOH 52 552 252 HOH HOH A . D 3 HOH 53 553 253 HOH HOH A . D 3 HOH 54 554 254 HOH HOH A . D 3 HOH 55 555 255 HOH HOH A . D 3 HOH 56 556 256 HOH HOH A . D 3 HOH 57 557 257 HOH HOH A . D 3 HOH 58 558 258 HOH HOH A . D 3 HOH 59 559 259 HOH HOH A . D 3 HOH 60 560 260 HOH HOH A . D 3 HOH 61 561 261 HOH HOH A . D 3 HOH 62 562 262 HOH HOH A . D 3 HOH 63 563 263 HOH HOH A . D 3 HOH 64 564 264 HOH HOH A . D 3 HOH 65 565 265 HOH HOH A . D 3 HOH 66 566 266 HOH HOH A . D 3 HOH 67 567 267 HOH HOH A . D 3 HOH 68 568 268 HOH HOH A . D 3 HOH 69 569 269 HOH HOH A . D 3 HOH 70 570 270 HOH HOH A . D 3 HOH 71 571 271 HOH HOH A . D 3 HOH 72 572 272 HOH HOH A . D 3 HOH 73 573 273 HOH HOH A . D 3 HOH 74 574 274 HOH HOH A . D 3 HOH 75 575 275 HOH HOH A . D 3 HOH 76 576 276 HOH HOH A . D 3 HOH 77 577 277 HOH HOH A . D 3 HOH 78 578 278 HOH HOH A . D 3 HOH 79 579 279 HOH HOH A . D 3 HOH 80 580 280 HOH HOH A . D 3 HOH 81 581 281 HOH HOH A . D 3 HOH 82 582 282 HOH HOH A . D 3 HOH 83 583 283 HOH HOH A . D 3 HOH 84 584 284 HOH HOH A . D 3 HOH 85 585 285 HOH HOH A . D 3 HOH 86 586 286 HOH HOH A . D 3 HOH 87 587 287 HOH HOH A . D 3 HOH 88 588 288 HOH HOH A . D 3 HOH 89 589 289 HOH HOH A . D 3 HOH 90 590 290 HOH HOH A . D 3 HOH 91 591 291 HOH HOH A . D 3 HOH 92 592 292 HOH HOH A . D 3 HOH 93 593 293 HOH HOH A . D 3 HOH 94 594 294 HOH HOH A . D 3 HOH 95 595 295 HOH HOH A . D 3 HOH 96 596 296 HOH HOH A . D 3 HOH 97 597 297 HOH HOH A . D 3 HOH 98 598 298 HOH HOH A . D 3 HOH 99 599 299 HOH HOH A . D 3 HOH 100 600 300 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id 2SG _pdbx_struct_mod_residue.label_seq_id 4 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id 2SG _pdbx_struct_mod_residue.auth_seq_id 104 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id G _pdbx_struct_mod_residue.details 'GUANOSINE PHOSPHORODITHIOATE' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2490 ? 1 MORE -173 ? 1 'SSA (A^2)' 3990 ? # 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_556 -x,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 -19.9717432796 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 24.8398389563 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 579 ? D HOH . 2 1 A HOH 586 ? D HOH . 3 1 A HOH 591 ? D HOH . 4 1 A HOH 596 ? D HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? D HOH . ? A HOH 515 ? 1_555 SR ? B SR . ? A SR 401 ? 1_555 O ? D HOH . ? A HOH 516 ? 1_555 71.7 ? 2 O ? D HOH . ? A HOH 515 ? 1_555 SR ? C SR . ? A SR 402 ? 1_555 O ? D HOH . ? A HOH 580 ? 1_555 73.3 ? 3 O ? D HOH . ? A HOH 515 ? 1_555 SR ? C SR . ? A SR 402 ? 1_555 O ? D HOH . ? A HOH 585 ? 1_555 134.2 ? 4 O ? D HOH . ? A HOH 580 ? 1_555 SR ? C SR . ? A SR 402 ? 1_555 O ? D HOH . ? A HOH 585 ? 1_555 99.6 ? # 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 2015-09-16 2 'Structure model' 1 1 2017-07-12 3 'Structure model' 1 2 2023-09-20 # _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' 'Refinement description' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 '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 2 'Structure model' pdbx_refine 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_initial_refinement_model 6 3 'Structure model' pdbx_struct_conn_angle 7 3 'Structure model' struct_conn 8 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.value' 8 3 'Structure model' '_struct_conn.pdbx_dist_value' 9 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 10 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 12 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 14 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 15 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MD2 'data collection' 'diffractometer software from EMBL (with LS-CAT developed extensions)' ? 1 MOLREP phasing '(CCP4)' ? 2 SHELXL-97 refinement . ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # 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 C2 A U 107 ? ? N3 A U 107 ? ? C4 A U 107 ? ? 123.27 127.00 -3.73 0.60 N 2 1 N1 A A 109 ? ? C6 A A 109 ? ? N6 A A 109 ? ? 122.83 118.60 4.23 0.60 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 2SG P P N N 1 2SG SP1 S N N 2 2SG SP2 S N N 3 2SG "O5'" O N N 4 2SG "C5'" C N N 5 2SG "C4'" C N R 6 2SG "C3'" C N S 7 2SG "O3'" O N N 8 2SG "C2'" C N R 9 2SG "O2'" O N N 10 2SG "C1'" C N R 11 2SG "O4'" O N N 12 2SG N9 N Y N 13 2SG C4 C Y N 14 2SG C5 C Y N 15 2SG N7 N Y N 16 2SG C8 C Y N 17 2SG N3 N N N 18 2SG C2 C N N 19 2SG N2 N N N 20 2SG N1 N N N 21 2SG C6 C N N 22 2SG O6 O N N 23 2SG H1 H N N 24 2SG H2 H N N 25 2SG H3 H N N 26 2SG H4 H N N 27 2SG H5 H N N 28 2SG H6 H N N 29 2SG H7 H N N 30 2SG H8 H N N 31 2SG H9 H N N 32 2SG H10 H N N 33 2SG H11 H N N 34 2SG H13 H N N 35 2SG H14 H N N 36 2SG OP3 O N N 37 2SG H15 H N N 38 2SG H12 H N N 39 2SG H16 H N N 40 A OP3 O N N 41 A P P N N 42 A OP1 O N N 43 A OP2 O N N 44 A "O5'" O N N 45 A "C5'" C N N 46 A "C4'" C N R 47 A "O4'" O N N 48 A "C3'" C N S 49 A "O3'" O N N 50 A "C2'" C N R 51 A "O2'" O N N 52 A "C1'" C N R 53 A N9 N Y N 54 A C8 C Y N 55 A N7 N Y N 56 A C5 C Y N 57 A C6 C Y N 58 A N6 N N N 59 A N1 N Y N 60 A C2 C Y N 61 A N3 N Y N 62 A C4 C Y N 63 A HOP3 H N N 64 A HOP2 H N N 65 A "H5'" H N N 66 A "H5''" H N N 67 A "H4'" H N N 68 A "H3'" H N N 69 A "HO3'" H N N 70 A "H2'" H N N 71 A "HO2'" H N N 72 A "H1'" H N N 73 A H8 H N N 74 A H61 H N N 75 A H62 H N N 76 A H2 H N N 77 C OP3 O N N 78 C P P N N 79 C OP1 O N N 80 C OP2 O N N 81 C "O5'" O N N 82 C "C5'" C N N 83 C "C4'" C N R 84 C "O4'" O N N 85 C "C3'" C N S 86 C "O3'" O N N 87 C "C2'" C N R 88 C "O2'" O N N 89 C "C1'" C N R 90 C N1 N N N 91 C C2 C N N 92 C O2 O N N 93 C N3 N N N 94 C C4 C N N 95 C N4 N N N 96 C C5 C N N 97 C C6 C N N 98 C HOP3 H N N 99 C HOP2 H N N 100 C "H5'" H N N 101 C "H5''" H N N 102 C "H4'" H N N 103 C "H3'" H N N 104 C "HO3'" H N N 105 C "H2'" H N N 106 C "HO2'" H N N 107 C "H1'" H N N 108 C H41 H N N 109 C H42 H N N 110 C H5 H N N 111 C H6 H N N 112 G OP3 O N N 113 G P P N N 114 G OP1 O N N 115 G OP2 O N N 116 G "O5'" O N N 117 G "C5'" C N N 118 G "C4'" C N R 119 G "O4'" O N N 120 G "C3'" C N S 121 G "O3'" O N N 122 G "C2'" C N R 123 G "O2'" O N N 124 G "C1'" C N R 125 G N9 N Y N 126 G C8 C Y N 127 G N7 N Y N 128 G C5 C Y N 129 G C6 C N N 130 G O6 O N N 131 G N1 N N N 132 G C2 C N N 133 G N2 N N N 134 G N3 N N N 135 G C4 C Y N 136 G HOP3 H N N 137 G HOP2 H N N 138 G "H5'" H N N 139 G "H5''" H N N 140 G "H4'" H N N 141 G "H3'" H N N 142 G "HO3'" H N N 143 G "H2'" H N N 144 G "HO2'" H N N 145 G "H1'" H N N 146 G H8 H N N 147 G H1 H N N 148 G H21 H N N 149 G H22 H N N 150 HOH O O N N 151 HOH H1 H N N 152 HOH H2 H N N 153 SR SR SR N N 154 U OP3 O N N 155 U P P N N 156 U OP1 O N N 157 U OP2 O N N 158 U "O5'" O N N 159 U "C5'" C N N 160 U "C4'" C N R 161 U "O4'" O N N 162 U "C3'" C N S 163 U "O3'" O N N 164 U "C2'" C N R 165 U "O2'" O N N 166 U "C1'" C N R 167 U N1 N N N 168 U C2 C N N 169 U O2 O N N 170 U N3 N N N 171 U C4 C N N 172 U O4 O N N 173 U C5 C N N 174 U C6 C N N 175 U HOP3 H N N 176 U HOP2 H N N 177 U "H5'" H N N 178 U "H5''" H N N 179 U "H4'" H N N 180 U "H3'" H N N 181 U "HO3'" H N N 182 U "H2'" H N N 183 U "HO2'" H N N 184 U "H1'" H N N 185 U H3 H N N 186 U H5 H N N 187 U H6 H N N 188 # 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 2SG "O3'" "C3'" sing N N 1 2SG "O2'" "C2'" sing N N 2 2SG "C2'" "C3'" sing N N 3 2SG "C2'" "C1'" sing N N 4 2SG "C3'" "C4'" sing N N 5 2SG "C4'" "C5'" sing N N 6 2SG "C4'" "O4'" sing N N 7 2SG "C5'" "O5'" sing N N 8 2SG "C1'" "O4'" sing N N 9 2SG "C1'" N9 sing N N 10 2SG N2 C2 sing N N 11 2SG N3 C2 doub N N 12 2SG N3 C4 sing N N 13 2SG "O5'" P sing N N 14 2SG N9 C4 sing Y N 15 2SG N9 C8 sing Y N 16 2SG C2 N1 sing N N 17 2SG C4 C5 doub Y N 18 2SG SP1 P sing N N 19 2SG C8 N7 doub Y N 20 2SG P SP2 sing N N 21 2SG N1 C6 sing N N 22 2SG C5 N7 sing Y N 23 2SG C5 C6 sing N N 24 2SG C6 O6 doub N N 25 2SG SP1 H1 sing N N 26 2SG SP2 H2 sing N N 27 2SG "C5'" H3 sing N N 28 2SG "C5'" H4 sing N N 29 2SG "C4'" H5 sing N N 30 2SG "C3'" H6 sing N N 31 2SG "O3'" H7 sing N N 32 2SG "C2'" H8 sing N N 33 2SG "O2'" H9 sing N N 34 2SG "C1'" H10 sing N N 35 2SG C8 H11 sing N N 36 2SG N2 H13 sing N N 37 2SG N2 H14 sing N N 38 2SG P OP3 sing N N 39 2SG P H15 sing N N 40 2SG N1 H12 sing N N 41 2SG OP3 H16 sing N N 42 A OP3 P sing N N 43 A OP3 HOP3 sing N N 44 A P OP1 doub N N 45 A P OP2 sing N N 46 A P "O5'" sing N N 47 A OP2 HOP2 sing N N 48 A "O5'" "C5'" sing N N 49 A "C5'" "C4'" sing N N 50 A "C5'" "H5'" sing N N 51 A "C5'" "H5''" sing N N 52 A "C4'" "O4'" sing N N 53 A "C4'" "C3'" sing N N 54 A "C4'" "H4'" sing N N 55 A "O4'" "C1'" sing N N 56 A "C3'" "O3'" sing N N 57 A "C3'" "C2'" sing N N 58 A "C3'" "H3'" sing N N 59 A "O3'" "HO3'" sing N N 60 A "C2'" "O2'" sing N N 61 A "C2'" "C1'" sing N N 62 A "C2'" "H2'" sing N N 63 A "O2'" "HO2'" sing N N 64 A "C1'" N9 sing N N 65 A "C1'" "H1'" sing N N 66 A N9 C8 sing Y N 67 A N9 C4 sing Y N 68 A C8 N7 doub Y N 69 A C8 H8 sing N N 70 A N7 C5 sing Y N 71 A C5 C6 sing Y N 72 A C5 C4 doub Y N 73 A C6 N6 sing N N 74 A C6 N1 doub Y N 75 A N6 H61 sing N N 76 A N6 H62 sing N N 77 A N1 C2 sing Y N 78 A C2 N3 doub Y N 79 A C2 H2 sing N N 80 A N3 C4 sing Y N 81 C OP3 P sing N N 82 C OP3 HOP3 sing N N 83 C P OP1 doub N N 84 C P OP2 sing N N 85 C P "O5'" sing N N 86 C OP2 HOP2 sing N N 87 C "O5'" "C5'" sing N N 88 C "C5'" "C4'" sing N N 89 C "C5'" "H5'" sing N N 90 C "C5'" "H5''" sing N N 91 C "C4'" "O4'" sing N N 92 C "C4'" "C3'" sing N N 93 C "C4'" "H4'" sing N N 94 C "O4'" "C1'" sing N N 95 C "C3'" "O3'" sing N N 96 C "C3'" "C2'" sing N N 97 C "C3'" "H3'" sing N N 98 C "O3'" "HO3'" sing N N 99 C "C2'" "O2'" sing N N 100 C "C2'" "C1'" sing N N 101 C "C2'" "H2'" sing N N 102 C "O2'" "HO2'" sing N N 103 C "C1'" N1 sing N N 104 C "C1'" "H1'" sing N N 105 C N1 C2 sing N N 106 C N1 C6 sing N N 107 C C2 O2 doub N N 108 C C2 N3 sing N N 109 C N3 C4 doub N N 110 C C4 N4 sing N N 111 C C4 C5 sing N N 112 C N4 H41 sing N N 113 C N4 H42 sing N N 114 C C5 C6 doub N N 115 C C5 H5 sing N N 116 C C6 H6 sing N N 117 G OP3 P sing N N 118 G OP3 HOP3 sing N N 119 G P OP1 doub N N 120 G P OP2 sing N N 121 G P "O5'" sing N N 122 G OP2 HOP2 sing N N 123 G "O5'" "C5'" sing N N 124 G "C5'" "C4'" sing N N 125 G "C5'" "H5'" sing N N 126 G "C5'" "H5''" sing N N 127 G "C4'" "O4'" sing N N 128 G "C4'" "C3'" sing N N 129 G "C4'" "H4'" sing N N 130 G "O4'" "C1'" sing N N 131 G "C3'" "O3'" sing N N 132 G "C3'" "C2'" sing N N 133 G "C3'" "H3'" sing N N 134 G "O3'" "HO3'" sing N N 135 G "C2'" "O2'" sing N N 136 G "C2'" "C1'" sing N N 137 G "C2'" "H2'" sing N N 138 G "O2'" "HO2'" sing N N 139 G "C1'" N9 sing N N 140 G "C1'" "H1'" sing N N 141 G N9 C8 sing Y N 142 G N9 C4 sing Y N 143 G C8 N7 doub Y N 144 G C8 H8 sing N N 145 G N7 C5 sing Y N 146 G C5 C6 sing N N 147 G C5 C4 doub Y N 148 G C6 O6 doub N N 149 G C6 N1 sing N N 150 G N1 C2 sing N N 151 G N1 H1 sing N N 152 G C2 N2 sing N N 153 G C2 N3 doub N N 154 G N2 H21 sing N N 155 G N2 H22 sing N N 156 G N3 C4 sing N N 157 HOH O H1 sing N N 158 HOH O H2 sing N N 159 U OP3 P sing N N 160 U OP3 HOP3 sing N N 161 U P OP1 doub N N 162 U P OP2 sing N N 163 U P "O5'" sing N N 164 U OP2 HOP2 sing N N 165 U "O5'" "C5'" sing N N 166 U "C5'" "C4'" sing N N 167 U "C5'" "H5'" sing N N 168 U "C5'" "H5''" sing N N 169 U "C4'" "O4'" sing N N 170 U "C4'" "C3'" sing N N 171 U "C4'" "H4'" sing N N 172 U "O4'" "C1'" sing N N 173 U "C3'" "O3'" sing N N 174 U "C3'" "C2'" sing N N 175 U "C3'" "H3'" sing N N 176 U "O3'" "HO3'" sing N N 177 U "C2'" "O2'" sing N N 178 U "C2'" "C1'" sing N N 179 U "C2'" "H2'" sing N N 180 U "O2'" "HO2'" sing N N 181 U "C1'" N1 sing N N 182 U "C1'" "H1'" sing N N 183 U N1 C2 sing N N 184 U N1 C6 sing N N 185 U C2 O2 doub N N 186 U C2 N3 sing N N 187 U N3 C4 sing N N 188 U N3 H3 sing N N 189 U C4 O4 doub N N 190 U C4 C5 sing N N 191 U C5 C6 doub N N 192 U C5 H5 sing N N 193 U C6 H6 sing N N 194 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4RBY 'double helix' 4RBY 'a-form double helix' 4RBY 'mismatched base pair' # 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 A G 12 2_556 0.157 -0.109 -0.087 7.821 -15.683 0.527 1 A_C101:G112_A A 101 ? A 112 ? 19 1 1 A G 2 1_555 A C 11 2_556 -0.267 -0.172 0.077 -5.126 -17.336 1.039 2 A_G102:C111_A A 102 ? A 111 ? 19 1 1 A C 3 1_555 A G 10 2_556 0.069 -0.168 0.275 -4.117 -14.495 -2.513 3 A_C103:G110_A A 103 ? A 110 ? 19 1 1 A A 5 1_555 A U 8 2_556 0.083 -0.045 0.329 7.713 -15.496 -3.246 4 A_A105:U108_A A 105 ? A 108 ? 20 1 1 A A 6 1_555 A U 7 2_556 0.106 -0.116 0.014 4.996 -23.454 -3.415 5 A_A106:U107_A A 106 ? A 107 ? 20 1 1 A U 7 1_555 A A 6 2_556 -0.106 -0.116 0.014 -4.996 -23.454 -3.415 6 A_U107:A106_A A 107 ? A 106 ? 20 1 1 A U 8 1_555 A A 5 2_556 -0.083 -0.045 0.329 -7.713 -15.496 -3.246 7 A_U108:A105_A A 108 ? A 105 ? 20 1 1 A G 10 1_555 A C 3 2_556 -0.069 -0.168 0.275 4.117 -14.495 -2.513 8 A_G110:C103_A A 110 ? A 103 ? 19 1 1 A C 11 1_555 A G 2 2_556 0.267 -0.172 0.077 5.126 -17.336 1.039 9 A_C111:G102_A A 111 ? A 102 ? 19 1 1 A G 12 1_555 A C 1 2_556 -0.157 -0.109 -0.087 -7.821 -15.683 0.527 10 A_G112:C101_A A 112 ? A 101 ? 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 A G 12 2_556 A G 2 1_555 A C 11 2_556 -0.456 -1.722 3.351 -3.711 13.887 31.872 -4.830 0.237 2.449 23.832 6.368 34.887 1 AA_C101G102:C111G112_AA A 101 ? A 112 ? A 102 ? A 111 ? 1 A G 2 1_555 A C 11 2_556 A C 3 1_555 A G 10 2_556 -0.553 -1.334 3.203 -1.927 4.033 35.154 -2.762 0.637 3.061 6.645 3.175 35.428 2 AA_G102C103:G110C111_AA A 102 ? A 111 ? A 103 ? A 110 ? 1 A C 3 1_555 A G 10 2_556 A A 5 1_555 A U 8 2_556 -0.122 -2.224 5.856 -0.552 16.881 58.592 -3.592 0.075 5.104 16.869 0.552 60.770 3 AA_C103A105:U108G110_AA A 103 ? A 110 ? A 105 ? A 108 ? 1 A A 5 1_555 A U 8 2_556 A A 6 1_555 A U 7 2_556 -0.395 -1.052 3.289 1.247 9.225 35.109 -2.935 0.803 2.914 14.970 -2.024 36.285 4 AA_A105A106:U107U108_AA A 105 ? A 108 ? A 106 ? A 107 ? 1 A A 6 1_555 A U 7 2_556 A U 7 1_555 A A 6 2_556 0.000 -1.283 3.462 0.000 12.357 31.951 -4.114 0.000 2.789 21.471 0.000 34.199 5 AA_A106U107:A106U107_AA A 106 ? A 107 ? A 107 ? A 106 ? 1 A U 7 1_555 A A 6 2_556 A U 8 1_555 A A 5 2_556 0.395 -1.052 3.289 -1.247 9.225 35.109 -2.935 -0.803 2.914 14.970 2.024 36.285 6 AA_U107U108:A105A106_AA A 107 ? A 106 ? A 108 ? A 105 ? 1 A U 8 1_555 A A 5 2_556 A G 10 1_555 A C 3 2_556 0.122 -2.224 5.856 0.552 16.881 58.592 -3.592 -0.075 5.104 16.870 -0.552 60.770 7 AA_U108G110:C103A105_AA A 108 ? A 105 ? A 110 ? A 103 ? 1 A G 10 1_555 A C 3 2_556 A C 11 1_555 A G 2 2_556 0.553 -1.334 3.203 1.927 4.033 35.154 -2.762 -0.637 3.061 6.645 -3.175 35.428 8 AA_G110C111:G102C103_AA A 110 ? A 103 ? A 111 ? A 102 ? 1 A C 11 1_555 A G 2 2_556 A G 12 1_555 A C 1 2_556 0.456 -1.722 3.351 3.711 13.887 31.872 -4.830 -0.237 2.449 23.832 -6.368 34.887 9 AA_C111G112:C101G102_AA A 111 ? A 102 ? A 112 ? A 101 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'STRONTIUM ION' SR 3 water 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 2Q1R _pdbx_initial_refinement_model.details 'PDB ENTRY 2Q1R' #