data_353D # _entry.id 353D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.375 _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 353D pdb_0000353d 10.2210/pdb353d/pdb RCSB URX063 ? ? WWPDB D_1000178822 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 353D _pdbx_database_status.recvd_initial_deposition_date 1997-09-29 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Betzel, C.' 1 'Lorenz, S.' 2 'Furste, J.P.' 3 'Bald, R.' 4 'Zhang, M.' 5 'Schneider, T.R.' 6 'Wilson, K.S.' 7 'Erdmann, V.A.' 8 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Crystal structure of domain A of Thermus flavus 5S rRNA and the contribution of water molecules to its structure.' 'FEBS Lett.' 351 159 164 1994 FEBLAL NE 0014-5793 0165 ? 8082756 '10.1016/0014-5793(94)00834-5' 1 ;Structure of Domain A of Thermus flavus 5S rRNA at 2.3 A Resolution. Comparison of Nearest Neighbor Parameters for Mismatches and the Influence of Solvent ; 'To be Published' ? ? ? ? ? ? ? 0353 ? ? ? 2 ;Crystallization and Preliminary Diffraction Studies of the Chemically Synthesized Domain A of Thermus flavus 5S rRNA: An Dodecamer Double Helix ; 'Acta Crystallogr.,Sect.D' 49 418 420 1993 ABCRE6 DK 0907-4449 0766 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Betzel, C.' 1 ? primary 'Lorenz, S.' 2 ? primary 'Furste, J.P.' 3 ? primary 'Bald, R.' 4 ? primary 'Zhang, M.' 5 ? primary 'Schneider, T.R.' 6 ? primary 'Wilson, K.S.' 7 ? primary 'Erdmann, V.A.' 8 ? 1 'Perbandt, M.' 9 ? 1 'Lorenz, S.' 10 ? 1 'Betzel, C.' 11 ? 1 'Erdmann, V.A.' 12 ? 2 'Lorenz, S.' 13 ? 2 'Furste, J.' 14 ? 2 'Bald, R.' 15 ? 2 'Zhang, M.' 16 ? 2 'Raderschall, E.' 17 ? 2 'Betzel, C.' 18 ? 2 'Dauter, Z.' 19 ? 2 'Wilson, K.' 20 ? # _cell.entry_id 353D _cell.length_a 30.100 _cell.length_b 30.100 _cell.length_c 86.800 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _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 353D _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _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 ;RNA (5'-R(*AP*UP*CP*CP*CP*CP*CP*GP*UP*GP*CP*C)-3') ; 3723.264 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3') ; 3963.408 1 ? ? ? ? 3 water nat water 18.015 158 ? ? ? ? # 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 AUCCCCCGUGCC AUCCCCCGUGCC A ? 2 polyribonucleotide no no GGUGCGGGGGAU GGUGCGGGGGAU B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 A n 1 2 U n 1 3 C n 1 4 C n 1 5 C n 1 6 C n 1 7 C n 1 8 G n 1 9 U n 1 10 G n 1 11 C n 1 12 C n 2 1 G n 2 2 G n 2 3 U n 2 4 G n 2 5 C n 2 6 G n 2 7 G n 2 8 G n 2 9 G n 2 10 G n 2 11 A n 2 12 U n # 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 353D 353D ? ? ? 2 2 PDB 353D 353D ? ? ? # 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 353D A 1 ? 12 ? 353D 1 ? 12 ? 1 12 2 2 353D B 1 ? 12 ? 353D 13 ? 24 ? 13 24 # 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 353D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.60 _exptl_crystal.density_percent_sol 51.91 _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 6.50 _exptl_crystal_grow.pdbx_details 'pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K' _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 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 MGCL2 ? ? ? 1 4 1 'NA CACODYLATE' ? ? ? 1 5 2 WATER ? ? ? 1 6 2 MPD ? ? ? 1 7 2 MGCL2 ? ? ? 1 8 2 'NA CACODYLATE' ? ? ? # loop_ _diffrn.id _diffrn.crystal_id _diffrn.ambient_temp _diffrn.ambient_temp_details 1 1 153 ? 2 1 153 ? # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 'IMAGE PLATE' MARRESEARCH ? ? 2 'IMAGE PLATE' MARRESEARCH ? ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M GRAPHITE ? x-ray 2 2 M ? ? x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.7107 1.0 2 0.9200 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 'SEALED TUBE' 'CONVENTIONAL Mo' ? ? 0.7107 0.7107 2 SYNCHROTRON 'EMBL/DESY, HAMBURG BEAMLINE X11' 'EMBL/DESY, HAMBURG' X11 0.9200 0.9200 # _reflns.entry_id 353D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 2.400 _reflns.number_obs 2477 _reflns.number_all ? _reflns.percent_possible_obs 83.500 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1,2 _reflns.pdbx_ordinal 1 # _refine.entry_id 353D _refine.ls_number_reflns_obs 2477 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 2.400 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1800000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _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 ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 23.90 _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 'X-PLOR (BRUNGER) ALSO WAS USED.' _refine.pdbx_starting_model 'NDB ENTRY ARN035 (PDB ENTRY 1RNA)' _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _refine.correlation_coeff_Fo_to_Fc ? _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.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_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 508 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 158 _refine_hist.number_atoms_total 666 _refine_hist.d_res_high 2.400 _refine_hist.d_res_low 8.000 # 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 n_bond_d 0.025 ? ? ? 'X-RAY DIFFRACTION' ? n_angle_d 0.068 ? ? ? 'X-RAY DIFFRACTION' ? n_planar_d 0.014 ? ? ? 'X-RAY DIFFRACTION' ? n_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_angle_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_angle_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_bond_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_dihedral_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_impr_tor ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_plane_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_chiral_restr 0.036 ? ? ? 'X-RAY DIFFRACTION' ? n_singtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_multtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.30 _refine_ls_shell.d_res_low 2.40 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work ? _refine_ls_shell.percent_reflns_obs 50.00 _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.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 353D _struct.title 'CRYSTAL STRUCTURE OF DOMAIN A OF THERMUS FLAVUS 5S RRNA AND THE CONTRIBUTION OF WATER MOLECULES TO ITS STRUCTURE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 353D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'A-RNA, DOUBLE STRAND, 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 3 ? D N N 3 ? # 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 A 1 N1 ? ? ? 1_555 B U 12 N3 ? ? A A 1 B U 24 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog2 hydrog ? ? A U 2 N3 ? ? ? 1_555 B A 11 N1 ? ? A U 2 B A 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A U 2 O4 ? ? ? 1_555 B A 11 N6 ? ? A U 2 B A 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 3 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 3 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 3 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 4 B G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 4 B G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 4 B G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 5 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 5 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 5 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 6 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 6 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 6 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 7 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 7 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 7 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 5 O2 ? ? A G 8 B C 17 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog20 hydrog ? ? A U 9 O2 ? ? ? 1_555 B G 4 N2 ? ? A U 9 B G 16 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog21 hydrog ? ? A G 10 N1 ? ? ? 1_555 B U 3 O2 ? ? A G 10 B U 15 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A G 10 O6 ? ? ? 1_555 B U 3 N3 ? ? A G 10 B U 15 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog24 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 12 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 12 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 12 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 353D _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 353D _atom_sites.fract_transf_matrix[1][1] 0.033220 _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] 0.033220 _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] 0.011520 _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 A 1 1 1 A A A . n A 1 2 U 2 2 2 U U A . n A 1 3 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 C 5 5 5 C C A . n A 1 6 C 6 6 6 C C A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G A . n A 1 9 U 9 9 9 U U A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n B 2 1 G 1 13 13 G G B . n B 2 2 G 2 14 14 G G B . n B 2 3 U 3 15 15 U U B . n B 2 4 G 4 16 16 G G B . n B 2 5 C 5 17 17 C C B . n B 2 6 G 6 18 18 G G B . n B 2 7 G 7 19 19 G G B . n B 2 8 G 8 20 20 G G B . n B 2 9 G 9 21 21 G G B . n B 2 10 G 10 22 22 G G B . n B 2 11 A 11 23 23 A A B . n B 2 12 U 12 24 24 U U 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 13 1 HOH HOH A . C 3 HOH 2 14 2 HOH HOH A . C 3 HOH 3 15 3 HOH HOH A . C 3 HOH 4 16 4 HOH HOH A . C 3 HOH 5 17 5 HOH HOH A . C 3 HOH 6 18 6 HOH HOH A . C 3 HOH 7 19 7 HOH HOH A . C 3 HOH 8 20 8 HOH HOH A . C 3 HOH 9 21 9 HOH HOH A . C 3 HOH 10 22 10 HOH HOH A . C 3 HOH 11 23 12 HOH HOH A . C 3 HOH 12 24 13 HOH HOH A . C 3 HOH 13 25 15 HOH HOH A . C 3 HOH 14 26 19 HOH HOH A . C 3 HOH 15 27 25 HOH HOH A . C 3 HOH 16 28 28 HOH HOH A . C 3 HOH 17 29 33 HOH HOH A . C 3 HOH 18 30 34 HOH HOH A . C 3 HOH 19 31 41 HOH HOH A . C 3 HOH 20 32 43 HOH HOH A . C 3 HOH 21 33 44 HOH HOH A . C 3 HOH 22 34 45 HOH HOH A . C 3 HOH 23 35 46 HOH HOH A . C 3 HOH 24 36 47 HOH HOH A . C 3 HOH 25 37 2 HOH HOH A . C 3 HOH 26 38 4 HOH HOH A . C 3 HOH 27 39 6 HOH HOH A . C 3 HOH 28 40 7 HOH HOH A . C 3 HOH 29 41 9 HOH HOH A . C 3 HOH 30 42 10 HOH HOH A . C 3 HOH 31 43 12 HOH HOH A . C 3 HOH 32 44 13 HOH HOH A . C 3 HOH 33 45 14 HOH HOH A . C 3 HOH 34 46 20 HOH HOH A . C 3 HOH 35 47 22 HOH HOH A . C 3 HOH 36 48 26 HOH HOH A . C 3 HOH 37 49 28 HOH HOH A . C 3 HOH 38 50 32 HOH HOH A . C 3 HOH 39 51 34 HOH HOH A . C 3 HOH 40 52 35 HOH HOH A . C 3 HOH 41 53 38 HOH HOH A . C 3 HOH 42 54 40 HOH HOH A . C 3 HOH 43 55 1 HOH HOH A . C 3 HOH 44 56 2 HOH HOH A . C 3 HOH 45 57 3 HOH HOH A . C 3 HOH 46 58 4 HOH HOH A . C 3 HOH 47 59 5 HOH HOH A . C 3 HOH 48 60 6 HOH HOH A . C 3 HOH 49 61 13 HOH HOH A . C 3 HOH 50 62 14 HOH HOH A . C 3 HOH 51 63 18 HOH HOH A . C 3 HOH 52 64 19 HOH HOH A . C 3 HOH 53 65 20 HOH HOH A . C 3 HOH 54 66 21 HOH HOH A . C 3 HOH 55 67 22 HOH HOH A . C 3 HOH 56 68 23 HOH HOH A . C 3 HOH 57 69 27 HOH HOH A . C 3 HOH 58 70 28 HOH HOH A . C 3 HOH 59 71 32 HOH HOH A . C 3 HOH 60 72 33 HOH HOH A . C 3 HOH 61 73 34 HOH HOH A . C 3 HOH 62 74 35 HOH HOH A . C 3 HOH 63 75 36 HOH HOH A . C 3 HOH 64 76 37 HOH HOH A . C 3 HOH 65 77 38 HOH HOH A . C 3 HOH 66 78 39 HOH HOH A . C 3 HOH 67 79 40 HOH HOH A . C 3 HOH 68 80 41 HOH HOH A . C 3 HOH 69 81 42 HOH HOH A . C 3 HOH 70 82 53 HOH HOH A . C 3 HOH 71 83 55 HOH HOH A . C 3 HOH 72 84 59 HOH HOH A . C 3 HOH 73 85 60 HOH HOH A . C 3 HOH 74 86 61 HOH HOH A . C 3 HOH 75 87 63 HOH HOH A . C 3 HOH 76 88 64 HOH HOH A . C 3 HOH 77 89 67 HOH HOH A . D 3 HOH 1 25 11 HOH HOH B . D 3 HOH 2 26 14 HOH HOH B . D 3 HOH 3 27 16 HOH HOH B . D 3 HOH 4 28 17 HOH HOH B . D 3 HOH 5 29 18 HOH HOH B . D 3 HOH 6 30 20 HOH HOH B . D 3 HOH 7 31 21 HOH HOH B . D 3 HOH 8 32 22 HOH HOH B . D 3 HOH 9 33 23 HOH HOH B . D 3 HOH 10 34 24 HOH HOH B . D 3 HOH 11 35 26 HOH HOH B . D 3 HOH 12 36 27 HOH HOH B . D 3 HOH 13 37 29 HOH HOH B . D 3 HOH 14 38 30 HOH HOH B . D 3 HOH 15 39 31 HOH HOH B . D 3 HOH 16 40 32 HOH HOH B . D 3 HOH 17 41 35 HOH HOH B . D 3 HOH 18 42 36 HOH HOH B . D 3 HOH 19 43 37 HOH HOH B . D 3 HOH 20 44 38 HOH HOH B . D 3 HOH 21 45 39 HOH HOH B . D 3 HOH 22 46 40 HOH HOH B . D 3 HOH 23 47 42 HOH HOH B . D 3 HOH 24 48 48 HOH HOH B . D 3 HOH 25 49 1 HOH HOH B . D 3 HOH 26 50 3 HOH HOH B . D 3 HOH 27 51 5 HOH HOH B . D 3 HOH 28 52 8 HOH HOH B . D 3 HOH 29 53 11 HOH HOH B . D 3 HOH 30 54 15 HOH HOH B . D 3 HOH 31 55 16 HOH HOH B . D 3 HOH 32 56 17 HOH HOH B . D 3 HOH 33 57 18 HOH HOH B . D 3 HOH 34 58 19 HOH HOH B . D 3 HOH 35 59 21 HOH HOH B . D 3 HOH 36 60 23 HOH HOH B . D 3 HOH 37 61 24 HOH HOH B . D 3 HOH 38 62 25 HOH HOH B . D 3 HOH 39 63 27 HOH HOH B . D 3 HOH 40 64 29 HOH HOH B . D 3 HOH 41 65 30 HOH HOH B . D 3 HOH 42 66 31 HOH HOH B . D 3 HOH 43 67 33 HOH HOH B . D 3 HOH 44 68 36 HOH HOH B . D 3 HOH 45 69 37 HOH HOH B . D 3 HOH 46 70 49 HOH HOH B . D 3 HOH 47 71 41 HOH HOH B . D 3 HOH 48 72 42 HOH HOH B . D 3 HOH 49 73 7 HOH HOH B . D 3 HOH 50 74 8 HOH HOH B . D 3 HOH 51 75 9 HOH HOH B . D 3 HOH 52 76 10 HOH HOH B . D 3 HOH 53 77 11 HOH HOH B . D 3 HOH 54 78 12 HOH HOH B . D 3 HOH 55 79 15 HOH HOH B . D 3 HOH 56 80 16 HOH HOH B . D 3 HOH 57 81 17 HOH HOH B . D 3 HOH 58 82 24 HOH HOH B . D 3 HOH 59 83 25 HOH HOH B . D 3 HOH 60 84 26 HOH HOH B . D 3 HOH 61 85 29 HOH HOH B . D 3 HOH 62 86 30 HOH HOH B . D 3 HOH 63 87 31 HOH HOH B . D 3 HOH 64 88 43 HOH HOH B . D 3 HOH 65 89 44 HOH HOH B . D 3 HOH 66 90 45 HOH HOH B . D 3 HOH 67 91 46 HOH HOH B . D 3 HOH 68 92 47 HOH HOH B . D 3 HOH 69 93 48 HOH HOH B . D 3 HOH 70 94 49 HOH HOH B . D 3 HOH 71 95 50 HOH HOH B . D 3 HOH 72 96 51 HOH HOH B . D 3 HOH 73 97 52 HOH HOH B . D 3 HOH 74 98 54 HOH HOH B . D 3 HOH 75 99 56 HOH HOH B . D 3 HOH 76 100 57 HOH HOH B . D 3 HOH 77 101 58 HOH HOH B . D 3 HOH 78 102 62 HOH HOH B . D 3 HOH 79 103 65 HOH HOH B . D 3 HOH 80 104 66 HOH HOH B . D 3 HOH 81 105 68 HOH HOH B . # _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 # 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 1997-11-10 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-02-14 5 'Structure model' 1 4 2023-08-02 # _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' 'Data collection' 4 4 'Structure model' 'Experimental preparation' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 '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' diffrn 2 4 'Structure model' exptl_crystal_grow 3 5 'Structure model' database_2 4 5 'Structure model' diffrn_source 5 5 '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 4 'Structure model' '_diffrn.ambient_temp' 2 4 'Structure model' '_exptl_crystal_grow.pdbx_details' 3 4 'Structure model' '_exptl_crystal_grow.temp' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' 6 5 'Structure model' '_diffrn_source.pdbx_synchrotron_site' # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language AMoRE phasing . ? 1 ? ? ? ? NUCLSQ refinement . ? 2 ? ? ? ? XDS 'data reduction' . ? 3 ? ? ? ? DENZO 'data reduction' . ? 4 ? ? ? ? # 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 "C5'" A C 7 ? ? "C4'" A C 7 ? ? 1.583 1.509 0.074 0.012 N 2 1 N7 A G 8 ? ? C8 A G 8 ? ? 1.492 1.305 0.187 0.006 N 3 1 C8 A G 8 ? ? N9 A G 8 ? ? 1.479 1.374 0.105 0.007 N 4 1 "O3'" B G 13 ? ? P B G 14 ? ? 1.810 1.607 0.203 0.012 Y 5 1 P B G 14 ? ? OP2 B G 14 ? ? 1.595 1.485 0.110 0.017 N 6 1 P B G 14 ? ? "O5'" B G 14 ? ? 1.749 1.593 0.156 0.010 N 7 1 "C5'" B G 14 ? ? "C4'" B G 14 ? ? 1.466 1.508 -0.042 0.007 N 8 1 "C5'" B U 15 ? ? "C4'" B U 15 ? ? 1.589 1.509 0.080 0.012 N 9 1 N7 B G 16 ? ? C8 B G 16 ? ? 1.458 1.305 0.153 0.006 N 10 1 C8 B G 16 ? ? N9 B G 16 ? ? 1.422 1.374 0.048 0.007 N 11 1 N7 B G 18 ? ? C8 B G 18 ? ? 1.378 1.305 0.073 0.006 N 12 1 "O4'" B G 19 ? ? "C1'" B G 19 ? ? 1.574 1.415 0.159 0.012 N 13 1 "C1'" B G 19 ? ? N9 B G 19 ? ? 1.280 1.464 -0.184 0.014 N 14 1 N7 B G 19 ? ? C8 B G 19 ? ? 1.464 1.305 0.159 0.006 N 15 1 C8 B G 19 ? ? N9 B G 19 ? ? 1.451 1.374 0.077 0.007 N 16 1 N7 B A 23 ? ? C8 B A 23 ? ? 1.473 1.311 0.162 0.007 N 17 1 C8 B A 23 ? ? N9 B A 23 ? ? 1.473 1.373 0.100 0.008 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 "C3'" A A 1 ? ? "C2'" A A 1 ? ? "C1'" A A 1 ? ? 95.15 101.30 -6.15 0.70 N 2 1 "O4'" A A 1 ? ? "C1'" A A 1 ? ? N9 A A 1 ? ? 113.88 108.50 5.38 0.70 N 3 1 "C5'" A U 2 ? ? "C4'" A U 2 ? ? "O4'" A U 2 ? ? 118.19 109.80 8.39 0.90 N 4 1 N1 A U 2 ? ? C2 A U 2 ? ? O2 A U 2 ? ? 129.45 122.80 6.65 0.70 N 5 1 N3 A U 2 ? ? C2 A U 2 ? ? O2 A U 2 ? ? 113.84 122.20 -8.36 0.70 N 6 1 "C3'" A C 3 ? ? "O3'" A C 3 ? ? P A C 4 ? ? 129.32 119.70 9.62 1.20 Y 7 1 "O3'" A C 5 ? ? P A C 6 ? ? "O5'" A C 6 ? ? 90.99 104.00 -13.01 1.90 Y 8 1 "O4'" A C 6 ? ? "C4'" A C 6 ? ? "C3'" A C 6 ? ? 96.80 104.00 -7.20 1.00 N 9 1 N1 A C 6 ? ? C2 A C 6 ? ? O2 A C 6 ? ? 126.39 118.90 7.49 0.60 N 10 1 N3 A C 6 ? ? C2 A C 6 ? ? O2 A C 6 ? ? 115.54 121.90 -6.36 0.70 N 11 1 P A C 7 ? ? "O5'" A C 7 ? ? "C5'" A C 7 ? ? 130.54 120.90 9.64 1.60 N 12 1 N1 A C 7 ? ? C2 A C 7 ? ? O2 A C 7 ? ? 123.38 118.90 4.48 0.60 N 13 1 N3 A C 7 ? ? C2 A C 7 ? ? O2 A C 7 ? ? 117.33 121.90 -4.57 0.70 N 14 1 "C5'" A G 8 ? ? "C4'" A G 8 ? ? "C3'" A G 8 ? ? 103.08 115.20 -12.12 1.40 N 15 1 "C5'" A G 8 ? ? "C4'" A G 8 ? ? "O4'" A G 8 ? ? 116.49 109.80 6.69 0.90 N 16 1 "C1'" A G 8 ? ? "O4'" A G 8 ? ? "C4'" A G 8 ? ? 105.30 109.70 -4.40 0.70 N 17 1 C5 A G 8 ? ? N7 A G 8 ? ? C8 A G 8 ? ? 109.50 104.30 5.20 0.50 N 18 1 N7 A G 8 ? ? C8 A G 8 ? ? N9 A G 8 ? ? 97.89 113.10 -15.21 0.50 N 19 1 C8 A G 8 ? ? N9 A G 8 ? ? C4 A G 8 ? ? 115.25 106.40 8.85 0.40 N 20 1 "C3'" A G 8 ? ? "O3'" A G 8 ? ? P A U 9 ? ? 127.16 119.70 7.46 1.20 Y 21 1 "C3'" A U 9 ? ? "C2'" A U 9 ? ? "C1'" A U 9 ? ? 96.39 101.30 -4.91 0.70 N 22 1 "O4'" A U 9 ? ? "C1'" A U 9 ? ? N1 A U 9 ? ? 115.82 108.50 7.32 0.70 N 23 1 N1 A U 9 ? ? C2 A U 9 ? ? N3 A U 9 ? ? 118.71 114.90 3.81 0.60 N 24 1 N3 A U 9 ? ? C2 A U 9 ? ? O2 A U 9 ? ? 116.74 122.20 -5.46 0.70 N 25 1 C5 A U 9 ? ? C4 A U 9 ? ? O4 A U 9 ? ? 129.79 125.90 3.89 0.60 N 26 1 "C5'" A G 10 ? ? "C4'" A G 10 ? ? "O4'" A G 10 ? ? 117.88 109.80 8.08 0.90 N 27 1 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 117.16 108.50 8.66 0.70 N 28 1 N1 A C 11 ? ? C2 A C 11 ? ? O2 A C 11 ? ? 123.64 118.90 4.74 0.60 N 29 1 "C5'" A C 12 ? ? "C4'" A C 12 ? ? "C3'" A C 12 ? ? 105.48 115.20 -9.72 1.40 N 30 1 N1 A C 12 ? ? C2 A C 12 ? ? O2 A C 12 ? ? 122.84 118.90 3.94 0.60 N 31 1 "O3'" B G 13 ? ? P B G 14 ? ? "O5'" B G 14 ? ? 88.25 104.00 -15.75 1.90 Y 32 1 "O3'" B G 13 ? ? P B G 14 ? ? OP2 B G 14 ? ? 124.21 110.50 13.71 1.10 Y 33 1 "O3'" B G 13 ? ? P B G 14 ? ? OP1 B G 14 ? ? 82.18 105.20 -23.02 2.20 Y 34 1 "O5'" B G 14 ? ? P B G 14 ? ? OP1 B G 14 ? ? 87.82 105.70 -17.88 0.90 N 35 1 "O5'" B G 14 ? ? P B G 14 ? ? OP2 B G 14 ? ? 142.82 110.70 32.12 1.20 N 36 1 P B G 14 ? ? "O5'" B G 14 ? ? "C5'" B G 14 ? ? 100.43 120.90 -20.47 1.60 N 37 1 "C5'" B G 14 ? ? "C4'" B G 14 ? ? "C3'" B G 14 ? ? 101.69 115.20 -13.51 1.40 N 38 1 N3 B U 15 ? ? C2 B U 15 ? ? O2 B U 15 ? ? 117.47 122.20 -4.73 0.70 N 39 1 "C4'" B G 16 ? ? "C3'" B G 16 ? ? "C2'" B G 16 ? ? 95.07 102.60 -7.53 1.00 N 40 1 C5 B G 16 ? ? N7 B G 16 ? ? C8 B G 16 ? ? 107.32 104.30 3.02 0.50 N 41 1 N7 B G 16 ? ? C8 B G 16 ? ? N9 B G 16 ? ? 103.76 113.10 -9.34 0.50 N 42 1 C8 B G 16 ? ? N9 B G 16 ? ? C4 B G 16 ? ? 111.11 106.40 4.71 0.40 N 43 1 N1 B C 17 ? ? C2 B C 17 ? ? O2 B C 17 ? ? 123.48 118.90 4.58 0.60 N 44 1 N3 B C 17 ? ? C2 B C 17 ? ? O2 B C 17 ? ? 116.54 121.90 -5.36 0.70 N 45 1 P B G 18 ? ? "O5'" B G 18 ? ? "C5'" B G 18 ? ? 133.93 120.90 13.03 1.60 N 46 1 "C4'" B G 18 ? ? "C3'" B G 18 ? ? "O3'" B G 18 ? ? 126.80 113.00 13.80 2.00 N 47 1 "O4'" B G 18 ? ? "C1'" B G 18 ? ? N9 B G 18 ? ? 98.27 108.20 -9.93 0.80 N 48 1 N7 B G 18 ? ? C8 B G 18 ? ? N9 B G 18 ? ? 107.14 113.10 -5.96 0.50 N 49 1 C8 B G 18 ? ? N9 B G 18 ? ? C4 B G 18 ? ? 109.24 106.40 2.84 0.40 N 50 1 C4 B G 18 ? ? N9 B G 18 ? ? "C1'" B G 18 ? ? 112.49 126.50 -14.01 1.30 N 51 1 "C3'" B G 18 ? ? "O3'" B G 18 ? ? P B G 19 ? ? 132.44 119.70 12.74 1.20 Y 52 1 "C1'" B G 19 ? ? "O4'" B G 19 ? ? "C4'" B G 19 ? ? 98.03 109.70 -11.67 0.70 N 53 1 "O4'" B G 19 ? ? "C1'" B G 19 ? ? N9 B G 19 ? ? 99.74 108.20 -8.46 0.80 N 54 1 C5 B G 19 ? ? N7 B G 19 ? ? C8 B G 19 ? ? 109.19 104.30 4.89 0.50 N 55 1 N7 B G 19 ? ? C8 B G 19 ? ? N9 B G 19 ? ? 99.05 113.10 -14.05 0.50 N 56 1 C8 B G 19 ? ? N9 B G 19 ? ? C4 B G 19 ? ? 115.12 106.40 8.72 0.40 N 57 1 C4 B G 19 ? ? N9 B G 19 ? ? "C1'" B G 19 ? ? 116.44 126.50 -10.06 1.30 N 58 1 "O4'" B G 21 ? ? "C1'" B G 21 ? ? N9 B G 21 ? ? 114.42 108.50 5.92 0.70 N 59 1 N1 B G 21 ? ? C6 B G 21 ? ? O6 B G 21 ? ? 115.87 119.90 -4.03 0.60 N 60 1 "C5'" B G 22 ? ? "C4'" B G 22 ? ? "O4'" B G 22 ? ? 116.81 109.80 7.01 0.90 N 61 1 "O3'" B G 22 ? ? P B A 23 ? ? "O5'" B A 23 ? ? 91.84 104.00 -12.16 1.90 Y 62 1 "C5'" B A 23 ? ? "C4'" B A 23 ? ? "C3'" B A 23 ? ? 103.33 115.20 -11.87 1.40 N 63 1 C5 B A 23 ? ? N7 B A 23 ? ? C8 B A 23 ? ? 107.95 103.90 4.05 0.50 N 64 1 N7 B A 23 ? ? C8 B A 23 ? ? N9 B A 23 ? ? 100.12 113.80 -13.68 0.50 N 65 1 C8 B A 23 ? ? N9 B A 23 ? ? C4 B A 23 ? ? 113.80 105.80 8.00 0.40 N 66 1 N1 B U 24 ? ? C2 B U 24 ? ? O2 B U 24 ? ? 127.11 122.80 4.31 0.70 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 U A 2 ? ? 0.077 'SIDE CHAIN' 2 1 C A 3 ? ? 0.082 'SIDE CHAIN' 3 1 C A 4 ? ? 0.079 'SIDE CHAIN' 4 1 C A 6 ? ? 0.142 'SIDE CHAIN' 5 1 C A 7 ? ? 0.091 'SIDE CHAIN' 6 1 G A 8 ? ? 0.080 'SIDE CHAIN' 7 1 U A 9 ? ? 0.110 'SIDE CHAIN' 8 1 G A 10 ? ? 0.075 'SIDE CHAIN' 9 1 C A 11 ? ? 0.075 'SIDE CHAIN' 10 1 C A 12 ? ? 0.175 'SIDE CHAIN' 11 1 G B 13 ? ? 0.086 'SIDE CHAIN' 12 1 G B 14 ? ? 0.102 'SIDE CHAIN' 13 1 G B 16 ? ? 0.146 'SIDE CHAIN' 14 1 C B 17 ? ? 0.085 'SIDE CHAIN' 15 1 G B 18 ? ? 0.176 'SIDE CHAIN' 16 1 G B 19 ? ? 0.079 'SIDE CHAIN' 17 1 G B 20 ? ? 0.095 'SIDE CHAIN' 18 1 G B 21 ? ? 0.157 'SIDE CHAIN' 19 1 G B 22 ? ? 0.181 'SIDE CHAIN' 20 1 A B 23 ? ? 0.078 'SIDE CHAIN' 21 1 U B 24 ? ? 0.130 'SIDE CHAIN' # _pdbx_validate_polymer_linkage.id 1 _pdbx_validate_polymer_linkage.PDB_model_num 1 _pdbx_validate_polymer_linkage.auth_atom_id_1 "O3'" _pdbx_validate_polymer_linkage.auth_asym_id_1 B _pdbx_validate_polymer_linkage.auth_comp_id_1 G _pdbx_validate_polymer_linkage.auth_seq_id_1 13 _pdbx_validate_polymer_linkage.PDB_ins_code_1 ? _pdbx_validate_polymer_linkage.label_alt_id_1 ? _pdbx_validate_polymer_linkage.auth_atom_id_2 P _pdbx_validate_polymer_linkage.auth_asym_id_2 B _pdbx_validate_polymer_linkage.auth_comp_id_2 G _pdbx_validate_polymer_linkage.auth_seq_id_2 14 _pdbx_validate_polymer_linkage.PDB_ins_code_2 ? _pdbx_validate_polymer_linkage.label_alt_id_2 ? _pdbx_validate_polymer_linkage.dist 1.81 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 353D 'a-form double helix' 353D '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 A 1 1_555 B U 12 1_555 -0.834 0.224 0.700 12.584 -19.414 6.454 1 A_A1:U24_B A 1 ? B 24 ? ? 1 1 A U 2 1_555 B A 11 1_555 -1.006 -0.446 -0.498 4.704 -11.716 -4.572 2 A_U2:A23_B A 2 ? B 23 ? 20 1 1 A C 3 1_555 B G 10 1_555 1.743 -0.638 -0.043 -2.974 -13.361 -2.211 3 A_C3:G22_B A 3 ? B 22 ? 19 1 1 A C 4 1_555 B G 9 1_555 0.595 -0.615 -0.380 7.129 -12.435 -5.848 4 A_C4:G21_B A 4 ? B 21 ? 19 1 1 A C 5 1_555 B G 8 1_555 0.693 0.098 0.208 -7.370 -28.220 8.151 5 A_C5:G20_B A 5 ? B 20 ? 19 1 1 A C 6 1_555 B G 7 1_555 0.146 -0.074 -0.697 11.417 -12.279 -0.156 6 A_C6:G19_B A 6 ? B 19 ? 19 1 1 A C 7 1_555 B G 6 1_555 -0.145 -0.300 0.136 3.916 -16.858 -3.364 7 A_C7:G18_B A 7 ? B 18 ? 19 1 1 A G 8 1_555 B C 5 1_555 -1.698 -0.144 -0.073 4.827 -4.223 1.852 8 A_G8:C17_B A 8 ? B 17 ? ? 1 1 A U 9 1_555 B G 4 1_555 -1.178 -0.120 -0.613 3.979 -13.928 1.928 9 A_U9:G16_B A 9 ? B 16 ? ? 1 1 A G 10 1_555 B U 3 1_555 -1.410 -0.429 -0.340 -6.614 -19.636 -6.501 10 A_G10:U15_B A 10 ? B 15 ? 28 1 1 A C 11 1_555 B G 2 1_555 0.780 -0.472 -0.322 0.433 -6.809 -15.858 11 A_C11:G14_B A 11 ? B 14 ? ? 1 1 A C 12 1_555 B G 1 1_555 0.778 -0.404 -0.357 7.697 -19.154 3.176 12 A_C12:G13_B A 12 ? B 13 ? 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 A 1 1_555 B U 12 1_555 A U 2 1_555 B A 11 1_555 -0.943 -2.292 3.569 3.875 5.471 31.223 -5.176 2.429 2.998 10.020 -7.097 31.917 1 AA_A1U2:A23U24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A U 2 1_555 B A 11 1_555 A C 3 1_555 B G 10 1_555 0.613 -0.235 3.632 -0.038 8.003 39.987 -1.314 -0.885 3.522 11.563 0.055 40.748 2 AA_U2C3:G22A23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A C 3 1_555 B G 10 1_555 A C 4 1_555 B G 9 1_555 0.624 -1.763 2.729 9.645 14.596 36.679 -3.794 -0.077 2.010 21.741 -14.367 40.507 3 AA_C3C4:G21G22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A C 4 1_555 B G 9 1_555 A C 5 1_555 B G 8 1_555 0.623 -1.798 3.674 0.859 10.485 26.005 -6.251 -1.078 2.772 22.180 -1.818 28.018 4 AA_C4C5:G20G21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A C 5 1_555 B G 8 1_555 A C 6 1_555 B G 7 1_555 -0.309 -2.014 2.782 7.415 15.627 30.261 -5.044 1.310 1.483 27.312 -12.960 34.755 5 AA_C5C6:G19G20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A C 6 1_555 B G 7 1_555 A C 7 1_555 B G 6 1_555 -0.416 -1.530 3.609 -13.632 21.305 27.592 -5.204 -1.147 1.985 36.436 23.314 37.264 6 AA_C6C7:G18G19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A C 7 1_555 B G 6 1_555 A G 8 1_555 B C 5 1_555 0.538 -1.074 2.999 -0.469 11.454 26.677 -4.298 -1.163 2.339 23.493 0.963 28.994 7 AA_C7G8:C17G18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A G 8 1_555 B C 5 1_555 A U 9 1_555 B G 4 1_555 0.472 -2.179 3.434 5.806 3.570 30.099 -4.811 0.272 3.193 6.766 -11.003 30.844 8 AA_G8U9:G16C17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A U 9 1_555 B G 4 1_555 A G 10 1_555 B U 3 1_555 0.152 -1.420 3.618 -3.849 15.707 31.550 -4.680 -0.823 2.608 26.798 6.566 35.360 9 AA_U9G10:U15G16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A G 10 1_555 B U 3 1_555 A C 11 1_555 B G 2 1_555 -0.285 -1.456 3.198 -0.587 5.571 44.871 -2.368 0.320 3.009 7.265 0.765 45.201 10 AA_G10C11:G14U15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A C 11 1_555 B G 2 1_555 A C 12 1_555 B G 1 1_555 1.258 -1.203 3.173 6.492 2.846 29.929 -2.824 -1.108 3.242 5.415 -12.354 30.739 11 AA_C11C12:G13G14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _pdbx_entity_nonpoly.entity_id 3 _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 1RNA _pdbx_initial_refinement_model.details 'NDB ENTRY ARN035 (PDB ENTRY 1RNA)' #