data_1X9K # _entry.id 1X9K # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1X9K pdb_00001x9k 10.2210/pdb1x9k/pdb NDB UR0043 ? ? RCSB RCSB030110 ? ? WWPDB D_1000030110 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1X9C 'Minimal Hairpin Ribozyme (low salt form with GC rich stems in A domain)' unspecified PDB 1M5K 'Four-Way Helical Junction Hairpin Ribozyme with U1A' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1X9K _pdbx_database_status.recvd_initial_deposition_date 2004-08-21 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Alam, S.' 1 'Grum-Tokars, V.' 2 'Krucinska, J.' 3 'Kundracik, M.L.' 4 'Wedekind, J.E.' 5 # 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 ;Conformational Heterogeneity at Position U37 of an All-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn. ; Biochemistry 44 14396 14408 2005 BICHAW US 0006-2960 0033 ? 16262240 10.1021/bi051550i 1 'Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme' 'Acta Crystallogr.,Sect.D' 59 142 145 2003 ABCRE6 DK 0907-4449 0766 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Alam, S.' 1 ? primary 'Grum-Tokars, V.' 2 ? primary 'Krucinska, J.' 3 ? primary 'Kundracik, M.L.' 4 ? primary 'Wedekind, J.E.' 5 ? 1 'Grum-Tokars, V.' 6 ? 1 'Milovanovic, M.' 7 ? 1 'Wedekind, J.E.' 8 ? # _cell.entry_id 1X9K _cell.length_a 94.46 _cell.length_b 94.46 _cell.length_c 129.12 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1X9K _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _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(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3'" 4055.421 1 ? U39C ? ? 2 polymer syn "5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-3'" 4251.654 1 ? ? ? ? 3 polymer syn "5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'" 5535.445 1 ? ? ? ? 4 polymer syn "5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'" 5991.568 1 ? ? ? ? # 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 UCGCAGUCCUAUU UCGCAGUCCUAUU A ? 2 polyribonucleotide no no AAUAGAGAAGCGA AAUAGAGAAGCGA B ? 3 polyribonucleotide no no GGCAGAGAAACACACGA GGCAGAGAAACACACGA C ? 4 polyribonucleotide no no UCGUGGUACAUUACCUGCC UCGUGGUACAUUACCUGCC D ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 C n 1 3 G n 1 4 C n 1 5 A n 1 6 G n 1 7 U n 1 8 C n 1 9 C n 1 10 U n 1 11 A n 1 12 U n 1 13 U n 2 1 A n 2 2 A n 2 3 U n 2 4 A n 2 5 G n 2 6 A n 2 7 G n 2 8 A n 2 9 A n 2 10 G n 2 11 C n 2 12 G n 2 13 A n 3 1 G n 3 2 G n 3 3 C n 3 4 A n 3 5 G n 3 6 A n 3 7 G n 3 8 A n 3 9 A n 3 10 A n 3 11 C n 3 12 A n 3 13 C n 3 14 A n 3 15 C n 3 16 G n 3 17 A n 4 1 U n 4 2 C n 4 3 G n 4 4 U n 4 5 G n 4 6 G n 4 7 U n 4 8 A n 4 9 C n 4 10 A n 4 11 U n 4 12 U n 4 13 A n 4 14 C n 4 15 C n 4 16 U n 4 17 G n 4 18 C n 4 19 C 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 ? _pdbx_entity_src_syn.details 'Solid Phase Chemical Synthesis' # 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 1X9K 1X9K ? ? ? 2 2 PDB 1X9K 1X9K ? ? ? 3 3 PDB 1X9K 1X9K ? ? ? 4 4 PDB 1X9K 1X9K ? ? ? # 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 1X9K A 1 ? 13 ? 1X9K 2 ? 14 ? 2 14 2 2 1X9K B 1 ? 13 ? 1X9K 2 ? 14 ? 2 14 3 3 1X9K C 1 ? 17 ? 1X9K 15 ? 31 ? 15 31 4 4 1X9K D 1 ? 19 ? 1X9K 31 ? 49 ? 31 49 # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 1X9K _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.2 _exptl_crystal.density_percent_sol 70 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details 'ammonium sulfate, spermidine, cobalt hexaamine, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _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 'ammonium sulfate' ? ? ? 1 2 1 spermidine ? ? ? 1 3 1 'cobalt hexaamine' ? ? ? 1 4 1 cacodylate ? ? ? 1 5 1 H2O ? ? ? 1 6 2 'ammonium sulfate' ? ? ? 1 7 2 cacodylate ? ? ? 1 8 2 H2O ? ? ? # _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 MARRESEARCH _diffrn_detector.pdbx_collection_date 2002-07-17 _diffrn_detector.details 'insertion device, double crystal monochromator, vertical focusing mirror' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator Si-220 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 22-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 22-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00 # _reflns.entry_id 1X9K _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 25 _reflns.d_resolution_high 3.17 _reflns.number_obs 6480 _reflns.number_all ? _reflns.percent_possible_obs 98.3 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.064 _reflns.pdbx_netI_over_sigmaI 13.4 _reflns.B_iso_Wilson_estimate 71.5 _reflns.pdbx_redundancy 6.6 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 3.17 _reflns_shell.d_res_low 3.28 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.412 _reflns_shell.meanI_over_sigI_obs 3.9 _reflns_shell.pdbx_redundancy 7.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 594 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1X9K _refine.ls_number_reflns_obs 6161 _refine.ls_number_reflns_all 6192 _refine.pdbx_ls_sigma_I -3 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 13729086.57 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 24.63 _refine.ls_d_res_high 3.17 _refine.ls_percent_reflns_obs 99.5 _refine.ls_R_factor_obs 0.236 _refine.ls_R_factor_all 0.243 _refine.ls_R_factor_R_work 0.236 _refine.ls_R_factor_R_free 0.252 _refine.ls_R_factor_R_free_error 0.010 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.5 _refine.ls_number_reflns_R_free 648 _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 160.9 _refine.aniso_B[1][1] -21.28 _refine.aniso_B[2][2] 13.14 _refine.aniso_B[3][3] 8.13 _refine.aniso_B[1][2] -34.31 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.1 _refine.solvent_model_param_bsol 29.1897 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB entry 1M5K' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Parkinson et al., (1996) Acta Cryst. D52, 57-64' _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.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _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_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1X9K _refine_analyze.Luzzati_coordinate_error_obs 0.72 _refine_analyze.Luzzati_sigma_a_obs 1.03 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.71 _refine_analyze.Luzzati_sigma_a_free 0.75 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 1313 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1313 _refine_hist.d_res_high 3.17 _refine_hist.d_res_low 24.63 # 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 c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.6 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 17.1 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.89 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 4 _refine_ls_shell.d_res_high 3.17 _refine_ls_shell.d_res_low 3.49 _refine_ls_shell.number_reflns_R_work 1346 _refine_ls_shell.R_factor_R_work 0.517 _refine_ls_shell.percent_reflns_obs 99.8 _refine_ls_shell.R_factor_R_free 0.457 _refine_ls_shell.R_factor_R_free_error 0.038 _refine_ls_shell.percent_reflns_R_free 9.8 _refine_ls_shell.number_reflns_R_free 147 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _pdbx_xplor_file.serial_no 1 _pdbx_xplor_file.param_file DNA-RNA_REP.PARAM _pdbx_xplor_file.topol_file DNA-RNA.TOP _pdbx_xplor_file.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 1X9K _struct.title 'An all-RNA Hairpin Ribozyme with mutation U39C' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1X9K _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Hairpin ribozyme, all-RNA, mutation, high salt, S-turn, E-loop, catalytic RNA, 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 4 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 3 B G 13 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog2 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 4 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 4 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 4 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 5 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 5 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 5 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 6 N1 ? ? ? 1_555 C C 11 N3 ? ? A G 7 C C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 6 N2 ? ? ? 1_555 C C 11 O2 ? ? A G 7 C C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 6 O6 ? ? ? 1_555 C C 11 N4 ? ? A G 7 C C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 7 O4 ? ? ? 1_555 B G 7 N2 ? ? A U 8 B G 8 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog12 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 10 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 10 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 10 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 4 N1 ? ? A U 11 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 4 N6 ? ? A U 11 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 11 N1 ? ? ? 1_555 B U 3 N3 ? ? A A 12 B U 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 11 N6 ? ? ? 1_555 B U 3 O4 ? ? A A 12 B U 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 2 N1 ? ? A U 13 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 2 N6 ? ? A U 13 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 13 N3 ? ? ? 1_555 B A 1 N1 ? ? A U 14 B A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 13 O4 ? ? ? 1_555 B A 1 N6 ? ? A U 14 B A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 19 N3 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 19 O2 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 19 N4 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 18 N3 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C G 2 N2 ? ? ? 1_555 D C 18 O2 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C G 2 O6 ? ? ? 1_555 D C 18 N4 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C C 3 O2 ? ? ? 1_555 D G 17 N2 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog30 hydrog ? ? C A 4 N1 ? ? ? 1_555 D U 16 N3 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C A 4 N6 ? ? ? 1_555 D U 16 O4 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C G 5 N1 ? ? ? 1_555 D C 15 N3 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C G 5 N2 ? ? ? 1_555 D C 15 O2 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C G 5 O6 ? ? ? 1_555 D C 15 N4 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C A 6 N1 ? ? ? 1_555 D C 14 N4 ? ? C A 20 D C 44 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog36 hydrog ? ? C G 7 N2 ? ? ? 1_555 D A 13 N7 ? ? C G 21 D A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog37 hydrog ? ? C G 7 N3 ? ? ? 1_555 D A 13 N6 ? ? C G 21 D A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog38 hydrog ? ? C A 8 N6 ? ? ? 1_555 D U 11 O2 ? ? C A 22 D U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog39 hydrog ? ? C A 8 N7 ? ? ? 1_555 D U 11 N3 ? ? C A 22 D U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog40 hydrog ? ? C A 9 N6 ? ? ? 1_555 D A 10 N1 ? ? C A 23 D A 40 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog41 hydrog ? ? C A 10 N6 ? ? ? 1_555 D A 8 N7 ? ? C A 24 D A 38 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog42 hydrog ? ? C A 12 N1 ? ? ? 1_555 D G 6 N1 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog43 hydrog ? ? C A 12 N6 ? ? ? 1_555 D G 6 O6 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog44 hydrog ? ? C C 13 N3 ? ? ? 1_555 D G 5 N1 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C C 13 N4 ? ? ? 1_555 D G 5 O6 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C C 13 O2 ? ? ? 1_555 D G 5 N2 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C A 14 N1 ? ? ? 1_555 D U 4 N3 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C A 14 N6 ? ? ? 1_555 D U 4 O4 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C C 15 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C C 15 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C C 15 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C G 16 N1 ? ? ? 1_555 D C 2 N3 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C G 16 N2 ? ? ? 1_555 D C 2 O2 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C G 16 O6 ? ? ? 1_555 D C 2 N4 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C A 17 N1 ? ? ? 1_555 D U 1 N3 ? ? C A 31 D U 31 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1X9K _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 1X9K _atom_sites.fract_transf_matrix[1][1] 0.010586 _atom_sites.fract_transf_matrix[1][2] 0.006112 _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] 0.012224 _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] 0.007745 _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 U 1 2 2 U U A . n A 1 2 C 2 3 3 C C A . n A 1 3 G 3 4 4 G G A . n A 1 4 C 4 5 5 C C A . n A 1 5 A 5 6 6 A A A . n A 1 6 G 6 7 7 G G A . n A 1 7 U 7 8 8 U U A . n A 1 8 C 8 9 9 C C A . n A 1 9 C 9 10 10 C C A . n A 1 10 U 10 11 11 U U A . n A 1 11 A 11 12 12 A A A . n A 1 12 U 12 13 13 U U A . n A 1 13 U 13 14 14 U U A . n B 2 1 A 1 2 2 A A B . n B 2 2 A 2 3 3 A A B . n B 2 3 U 3 4 4 U U B . n B 2 4 A 4 5 5 A A B . n B 2 5 G 5 6 6 G G B . n B 2 6 A 6 7 7 A A B . n B 2 7 G 7 8 8 G G B . n B 2 8 A 8 9 9 A A B . n B 2 9 A 9 10 10 A A B . n B 2 10 G 10 11 11 G G B . n B 2 11 C 11 12 12 C C B . n B 2 12 G 12 13 13 G G B . n B 2 13 A 13 14 14 A A B . n C 3 1 G 1 15 15 G G C . n C 3 2 G 2 16 16 G G C . n C 3 3 C 3 17 17 C C C . n C 3 4 A 4 18 18 A A C . n C 3 5 G 5 19 19 G G C . n C 3 6 A 6 20 20 A A C . n C 3 7 G 7 21 21 G G C . n C 3 8 A 8 22 22 A A C . n C 3 9 A 9 23 23 A A C . n C 3 10 A 10 24 24 A A C . n C 3 11 C 11 25 25 C C C . n C 3 12 A 12 26 26 A A C . n C 3 13 C 13 27 27 C C C . n C 3 14 A 14 28 28 A A C . n C 3 15 C 15 29 29 C C C . n C 3 16 G 16 30 30 G G C . n C 3 17 A 17 31 31 A A C . n D 4 1 U 1 31 31 U U D . n D 4 2 C 2 32 32 C C D . n D 4 3 G 3 33 33 G G D . n D 4 4 U 4 34 34 U U D . n D 4 5 G 5 35 35 G G D . n D 4 6 G 6 36 36 G G D . n D 4 7 U 7 37 37 U U D . n D 4 8 A 8 38 38 A A D . n D 4 9 C 9 39 39 C C D . n D 4 10 A 10 40 40 A A D . n D 4 11 U 11 41 41 U U D . n D 4 12 U 12 42 42 U U D . n D 4 13 A 13 43 43 A A D . n D 4 14 C 14 44 44 C C D . n D 4 15 C 15 45 45 C C D . n D 4 16 U 16 46 46 U U D . n D 4 17 G 17 47 47 G G D . n D 4 18 C 18 48 48 C C D . n D 4 19 C 19 49 49 C C D . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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 2005-11-22 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-23 # _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' 'Database references' 5 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 # 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' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 CrystalClear 'data reduction' '(MSC/RIGAKU)' ? 2 CrystalClear 'data scaling' '(MSC/RIGAKU)' ? 3 AMoRE phasing . ? 4 # 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 N9 A G 7 ? ? "C1'" A G 7 ? ? "C2'" A G 7 ? ? 125.53 114.00 11.53 1.30 N 2 1 N9 D G 36 ? ? "C1'" D G 36 ? ? "C2'" D G 36 ? ? 121.84 114.00 7.84 1.30 N 3 1 "C1'" D A 38 ? ? "O4'" D A 38 ? ? "C4'" D A 38 ? ? 105.14 109.70 -4.56 0.70 N 4 1 N9 D A 38 ? ? "C1'" D A 38 ? ? "C2'" D A 38 ? ? 124.46 114.00 10.46 1.30 N 5 1 N1 D U 41 ? ? "C1'" D U 41 ? ? "C2'" D U 41 ? ? 122.08 114.00 8.08 1.30 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 A A 6 ? ? 0.055 'SIDE CHAIN' 2 1 U A 8 ? ? 0.129 'SIDE CHAIN' 3 1 U D 31 ? ? 0.075 'SIDE CHAIN' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 U OP3 O N N 111 U P P N N 112 U OP1 O N N 113 U OP2 O N N 114 U "O5'" O N N 115 U "C5'" C N N 116 U "C4'" C N R 117 U "O4'" O N N 118 U "C3'" C N S 119 U "O3'" O N N 120 U "C2'" C N R 121 U "O2'" O N N 122 U "C1'" C N R 123 U N1 N N N 124 U C2 C N N 125 U O2 O N N 126 U N3 N N N 127 U C4 C N N 128 U O4 O N N 129 U C5 C N N 130 U C6 C N N 131 U HOP3 H N N 132 U HOP2 H N N 133 U "H5'" H N N 134 U "H5''" H N N 135 U "H4'" H N N 136 U "H3'" H N N 137 U "HO3'" H N N 138 U "H2'" H N N 139 U "HO2'" H N N 140 U "H1'" H N N 141 U H3 H N N 142 U H5 H N N 143 U H6 H N N 144 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1X9K 'double helix' 1X9K 'a-form double helix' 1X9K 'bulge loop' 1X9K 'mismatched base pair' 1X9K '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 C 2 1_555 B G 12 1_555 -0.043 0.061 0.733 4.328 -30.730 9.940 1 A_C3:G13_B A 3 ? B 13 ? ? 1 1 A G 3 1_555 B C 11 1_555 -0.109 -0.443 -0.518 4.771 -24.108 7.215 2 A_G4:C12_B A 4 ? B 12 ? 19 1 1 A C 4 1_555 B G 10 1_555 -0.659 -0.178 -1.286 8.429 -14.157 9.030 3 A_C5:G11_B A 5 ? B 11 ? 19 1 1 A U 7 1_555 B G 7 1_555 -7.799 -2.689 -1.310 21.523 3.547 -4.228 4 A_U8:G8_B A 8 ? B 8 ? ? ? 1 A C 9 1_555 B G 5 1_555 0.377 0.197 0.414 -7.155 11.470 4.296 5 A_C10:G6_B A 10 ? B 6 ? 19 1 1 A U 10 1_555 B A 4 1_555 1.226 -0.236 0.385 3.607 -0.208 -3.495 6 A_U11:A5_B A 11 ? B 5 ? 20 1 1 A A 11 1_555 B U 3 1_555 -0.352 -0.046 0.163 2.243 0.779 -2.087 7 A_A12:U4_B A 12 ? B 4 ? 20 1 1 A U 12 1_555 B A 2 1_555 0.356 -0.080 0.112 15.036 -2.738 -0.344 8 A_U13:A3_B A 13 ? B 3 ? 20 1 1 A U 13 1_555 B A 1 1_555 -0.735 -0.331 1.715 -35.961 8.897 -11.764 9 A_U14:A2_B A 14 ? B 2 ? 20 1 1 C G 1 1_555 D C 19 1_555 -0.407 0.226 0.314 -9.465 -3.485 1.673 10 C_G15:C49_D C 15 ? D 49 ? 19 1 1 C G 2 1_555 D C 18 1_555 0.129 -0.061 0.464 -8.898 -10.245 -2.504 11 C_G16:C48_D C 16 ? D 48 ? 19 1 1 C C 3 1_555 D G 17 1_555 0.562 0.376 0.063 10.983 -13.203 15.884 12 C_C17:G47_D C 17 ? D 47 ? ? 1 1 C A 4 1_555 D U 16 1_555 0.452 -0.364 -1.176 -9.867 -9.663 0.428 13 C_A18:U46_D C 18 ? D 46 ? 20 1 1 C G 5 1_555 D C 15 1_555 0.033 -0.433 -0.248 -11.137 -8.496 2.987 14 C_G19:C45_D C 19 ? D 45 ? 19 1 1 C A 6 1_555 D C 14 1_555 1.452 0.156 -0.219 -10.550 -10.217 8.309 15 C_A20:C44_D C 20 ? D 44 ? ? 1 1 C G 7 1_555 D A 13 1_555 6.851 -4.203 -0.076 -5.797 -10.198 -7.027 16 C_G21:A43_D C 21 ? D 43 ? 11 10 1 C A 8 1_555 D U 11 1_555 -3.692 -1.248 0.334 -15.748 9.115 -107.821 17 C_A22:U41_D C 22 ? D 41 ? 24 4 1 C A 9 1_555 D A 10 1_555 -4.099 1.495 -0.158 -2.312 -19.566 -99.117 18 C_A23:A40_D C 23 ? D 40 ? ? ? 1 C A 10 1_555 D A 8 1_555 4.850 2.790 -0.034 -6.550 -0.890 -142.092 19 C_A24:A38_D C 24 ? D 38 ? ? ? 1 C C 11 1_555 A G 6 1_555 -0.662 -0.409 0.352 5.221 -11.702 -10.875 20 C_C25:G7_A C 25 ? A 7 ? 19 1 1 C A 12 1_555 D G 6 1_555 -1.468 1.294 -0.491 -17.078 -26.114 -19.122 21 C_A26:G36_D C 26 ? D 36 ? 8 1 1 C C 13 1_555 D G 5 1_555 0.624 -0.042 -0.087 8.287 -13.790 -9.820 22 C_C27:G35_D C 27 ? D 35 ? 19 1 1 C A 14 1_555 D U 4 1_555 -0.103 0.096 0.289 11.370 -12.801 -5.894 23 C_A28:U34_D C 28 ? D 34 ? 20 1 1 C C 15 1_555 D G 3 1_555 -0.156 0.025 0.240 4.499 -10.319 9.053 24 C_C29:G33_D C 29 ? D 33 ? 19 1 1 C G 16 1_555 D C 2 1_555 -1.185 -0.064 0.477 -0.044 13.359 1.700 25 C_G30:C32_D C 30 ? D 32 ? 19 1 1 C A 17 1_555 D U 1 1_555 1.527 0.347 -0.312 -18.771 4.871 5.986 26 C_A31:U31_D C 31 ? D 31 ? ? ? # 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 2 1_555 B G 12 1_555 A G 3 1_555 B C 11 1_555 -0.551 -1.298 3.497 6.380 5.882 35.200 -2.935 1.804 3.104 9.549 -10.356 36.221 1 AA_C3G4:C12G13_BB A 3 ? B 13 ? A 4 ? B 12 ? 1 A G 3 1_555 B C 11 1_555 A C 4 1_555 B G 10 1_555 0.693 -0.463 3.127 6.789 15.244 21.619 -4.597 0.138 2.404 34.738 -15.470 27.249 2 AA_G4C5:G11C12_BB A 4 ? B 12 ? A 5 ? B 11 ? 1 A C 9 1_555 B G 5 1_555 A U 10 1_555 B A 4 1_555 -1.323 -2.525 2.788 0.457 -4.247 30.886 -3.971 2.540 3.079 -7.926 -0.854 31.173 3 AA_C10U11:A5G6_BB A 10 ? B 6 ? A 11 ? B 5 ? 1 A U 10 1_555 B A 4 1_555 A A 11 1_555 B U 3 1_555 0.247 -1.493 3.138 3.887 11.398 28.648 -4.725 0.198 2.396 21.856 -7.452 31.027 4 AA_U11A12:U4A5_BB A 11 ? B 5 ? A 12 ? B 4 ? 1 A A 11 1_555 B U 3 1_555 A U 12 1_555 B A 2 1_555 0.421 -1.382 3.323 2.983 -5.325 34.701 -1.451 -0.229 3.513 -8.844 -4.954 35.218 5 AA_A12U13:A3U4_BB A 12 ? B 4 ? A 13 ? B 3 ? 1 A U 12 1_555 B A 2 1_555 A U 13 1_555 B A 1 1_555 0.326 -3.068 4.790 -2.982 21.666 33.596 -7.507 -0.892 2.415 33.448 4.604 39.914 6 AA_U13U14:A2A3_BB A 13 ? B 3 ? A 14 ? B 2 ? 1 C G 1 1_555 D C 19 1_555 C G 2 1_555 D C 18 1_555 -1.271 -1.176 3.082 -3.664 6.434 37.152 -2.581 1.521 2.952 9.977 5.681 37.857 7 CC_G15G16:C48C49_DD C 15 ? D 49 ? C 16 ? D 48 ? 1 C G 2 1_555 D C 18 1_555 C C 3 1_555 D G 17 1_555 0.932 -1.503 2.622 3.922 2.746 34.502 -2.845 -1.080 2.586 4.601 -6.573 34.823 8 CC_G16C17:G47C48_DD C 16 ? D 48 ? C 17 ? D 47 ? 1 C C 3 1_555 D G 17 1_555 C A 4 1_555 D U 16 1_555 -0.914 -1.122 3.470 2.612 24.088 30.785 -4.444 1.669 2.024 38.735 -4.201 38.994 9 CC_C17A18:U46G47_DD C 17 ? D 47 ? C 18 ? D 46 ? 1 C A 4 1_555 D U 16 1_555 C G 5 1_555 D C 15 1_555 -0.343 -1.900 3.205 -12.801 6.148 26.287 -4.903 -1.855 2.592 12.431 25.883 29.818 10 CC_A18G19:C45U46_DD C 18 ? D 46 ? C 19 ? D 45 ? 1 C G 5 1_555 D C 15 1_555 C A 6 1_555 D C 14 1_555 0.463 -1.589 3.530 -0.635 -0.528 33.551 -2.659 -0.914 3.545 -0.915 1.100 33.561 11 CC_G19A20:C44C45_DD C 19 ? D 45 ? C 20 ? D 44 ? 1 C A 6 1_555 D C 14 1_555 C G 7 1_555 D A 13 1_555 -0.415 -0.958 3.376 9.001 7.183 67.327 -1.129 0.714 3.201 6.431 -8.058 68.191 12 CC_A20G21:A43C44_DD C 20 ? D 44 ? C 21 ? D 43 ? 1 C G 7 1_555 D A 13 1_555 C A 8 1_555 D U 11 1_555 -2.738 -0.525 3.747 1.936 4.229 12.108 -7.285 14.395 2.922 19.149 -8.765 12.968 13 CC_G21A22:U41A43_DD C 21 ? D 43 ? C 22 ? D 41 ? 1 C A 8 1_555 D U 11 1_555 C A 9 1_555 D A 10 1_555 -0.008 -2.570 3.529 -16.022 6.195 44.007 -3.744 -1.351 2.991 7.919 20.478 47.085 14 CC_A22A23:A40U41_DD C 22 ? D 41 ? C 23 ? D 40 ? 1 C A 9 1_555 D A 10 1_555 C A 10 1_555 D A 8 1_555 -3.551 -2.712 3.282 -3.064 -4.656 68.958 -2.211 3.011 3.572 -4.105 2.702 69.155 15 CC_A23A24:A38A40_DD C 23 ? D 40 ? C 24 ? D 38 ? 1 C A 10 1_555 D A 8 1_555 C C 11 1_555 A G 6 1_555 1.994 0.174 3.120 -4.549 0.855 -33.861 -0.430 2.679 3.346 -1.460 -7.765 -34.166 16 CC_A24C25:G7A38_AD C 24 ? D 38 ? C 25 ? A 7 ? 1 C C 11 1_555 A G 6 1_555 C A 12 1_555 D G 6 1_555 0.610 -2.292 3.326 6.966 11.110 45.018 -3.767 -0.216 2.776 14.158 -8.878 46.793 17 CC_C25A26:G36G7_DA C 25 ? A 7 ? C 26 ? D 36 ? 1 C A 12 1_555 D G 6 1_555 C C 13 1_555 D G 5 1_555 0.617 -0.538 2.918 -8.141 -5.274 43.018 -0.278 -1.502 2.806 -7.085 10.937 44.048 18 CC_A26C27:G35G36_DD C 26 ? D 36 ? C 27 ? D 35 ? 1 C C 13 1_555 D G 5 1_555 C A 14 1_555 D U 4 1_555 0.333 -1.488 3.189 0.851 4.789 30.509 -3.669 -0.470 2.935 9.029 -1.604 30.885 19 CC_C27A28:U34G35_DD C 27 ? D 35 ? C 28 ? D 34 ? 1 C A 14 1_555 D U 4 1_555 C C 15 1_555 D G 3 1_555 1.229 -1.858 3.237 5.750 6.450 30.671 -4.526 -1.224 2.971 11.900 -10.609 31.837 20 CC_A28C29:G33U34_DD C 28 ? D 34 ? C 29 ? D 33 ? 1 C C 15 1_555 D G 3 1_555 C G 16 1_555 D C 2 1_555 0.543 -1.762 2.828 -2.760 6.302 30.365 -4.254 -1.436 2.366 11.841 5.186 31.117 21 CC_C29G30:C32G33_DD C 29 ? D 33 ? C 30 ? D 32 ? 1 C G 16 1_555 D C 2 1_555 C A 17 1_555 D U 1 1_555 0.250 -1.711 3.496 7.221 12.534 46.306 -3.073 0.262 2.970 15.501 -8.930 48.394 22 CC_G30A31:U31C32_DD C 30 ? D 32 ? C 31 ? D 31 ? # _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 1M5K _pdbx_initial_refinement_model.details 'PDB entry 1M5K' #