data_5V9Z # _entry.id 5V9Z # _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 5V9Z pdb_00005v9z 10.2210/pdb5v9z/pdb WWPDB D_1000227104 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5V9Z _pdbx_database_status.recvd_initial_deposition_date 2017-03-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 _audit_author.identifier_ORCID 'Zhang, W.' 1 ? 'Szostak, J.W.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'J. Am. Chem. Soc.' _citation.journal_id_ASTM JACSAT _citation.journal_id_CSD ? _citation.journal_id_ISSN 1520-5126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 140 _citation.language ? _citation.page_first 2829 _citation.page_last 2840 _citation.title 'Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacs.7b11750 _citation.pdbx_database_id_PubMed 29411978 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhang, W.' 1 ? primary 'Tam, C.P.' 2 ? primary 'Zhou, L.' 3 ? primary 'Oh, S.S.' 4 ? primary 'Wang, J.' 5 ? primary 'Szostak, J.W.' 6 ? # _cell.entry_id 5V9Z _cell.length_a 45.275 _cell.length_b 45.275 _cell.length_c 154.573 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V9Z _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # 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 (25-MER)' 8159.974 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(P*GP*CP*AP*CP*CP*UP*CP*A)-3') ; 2485.553 1 ? ? ? ? 3 non-polymer syn "5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine" 427.309 1 ? ? ? ? 4 water nat water 18.015 12 ? ? ? ? # 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 yes 'UGAGGUG(LCC)(LCC)GAGCGCGAAAGCGCUC' UGAGGUGNNGAGCGCGAAAGCGCUC A ? 2 polyribonucleotide no no GCACCUCA GCACCUCA B ? # 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 G n 1 3 A n 1 4 G n 1 5 G n 1 6 U n 1 7 G n 1 8 LCC n 1 9 LCC n 1 10 G n 1 11 A n 1 12 G n 1 13 C n 1 14 G n 1 15 C n 1 16 G n 1 17 A n 1 18 A n 1 19 A n 1 20 G n 1 21 C n 1 22 G n 1 23 C n 1 24 U n 1 25 C n 2 1 G n 2 2 C n 2 3 A n 2 4 C n 2 5 C n 2 6 U n 2 7 C n 2 8 A n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample 1 25 'synthetic construct' ? 32630 ? 2 1 sample 1 8 'synthetic construct' ? 32630 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 5V9Z 5V9Z ? 1 ? 1 2 PDB 5V9Z 5V9Z ? 2 ? 1 # 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 5V9Z A 1 ? 25 ? 5V9Z 1 ? 25 ? 1 25 2 2 5V9Z B 1 ? 8 ? 5V9Z 1 ? 8 ? 1 8 # 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 8OS 'RNA linking' n "5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine" ? 'C14 H18 N7 O7 P' 427.309 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 LCC 'RNA linking' . '[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' ? 'C11 H16 N3 O8 P' 349.234 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5V9Z _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 3.64 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 66.2 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '50 mM MgCl2, 3 M ammonia sulfate, 100 mM HEPES 7.5' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 99 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-01-26 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5V9Z _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.5 _reflns.d_resolution_low 50 _reflns.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.number_all ? _reflns.number_obs 5769 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 95.4 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.6 _reflns.pdbx_Rmerge_I_obs 0.1 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value 0.089 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 16.3 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.226 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.976 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.5 _reflns_shell.d_res_low 2.59 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.7 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 418 _reflns_shell.percent_possible_all 73.1 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.710 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 7.2 _reflns_shell.pdbx_Rsym_value 0.486 _reflns_shell.pdbx_chi_squared 0.678 _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.912 _reflns_shell.pdbx_R_split ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5V9Z _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 5466 _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 43.45 _refine.ls_d_res_high 2.51 _refine.ls_percent_reflns_obs 95.51 _refine.ls_R_factor_obs 0.22161 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21812 _refine.ls_R_factor_R_free 0.28106 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.2 _refine.ls_number_reflns_R_free 302 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.945 _refine.correlation_coeff_Fo_to_Fc_free 0.921 _refine.B_iso_mean 73.171 _refine.aniso_B[1][1] 0.03 _refine.aniso_B[2][2] 0.03 _refine.aniso_B[3][3] -0.07 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 4fnj _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.312 _refine.pdbx_overall_ESU_R_Free 0.270 _refine.overall_SU_ML 0.227 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 11.619 _refine.overall_SU_R_Cruickshank_DPI ? _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 1 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 709 _refine_hist.pdbx_number_atoms_ligand 29 _refine_hist.number_atoms_solvent 12 _refine_hist.number_atoms_total 750 _refine_hist.d_res_high 2.51 _refine_hist.d_res_low 43.45 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.013 0.012 ? 822 'X-RAY DIFFRACTION' ? r_bond_other_d 0.022 0.021 ? 350 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.438 1.442 ? 1276 'X-RAY DIFFRACTION' ? r_angle_other_deg 2.541 3.070 ? 841 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.244 0.200 ? 139 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.013 0.020 ? 425 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.002 0.020 ? 186 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 7.261 7.790 ? 822 'X-RAY DIFFRACTION' ? r_scbond_other 7.257 7.791 ? 823 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other 8.982 11.629 ? 1277 'X-RAY DIFFRACTION' ? r_long_range_B_refined 9.754 79.079 ? 1123 'X-RAY DIFFRACTION' ? r_long_range_B_other 9.749 79.087 ? 1124 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.508 _refine_ls_shell.d_res_low 2.573 _refine_ls_shell.number_reflns_R_work 279 _refine_ls_shell.R_factor_R_work 0.491 _refine_ls_shell.percent_reflns_obs 69.76 _refine_ls_shell.R_factor_R_free 0.554 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 14 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 5V9Z _struct.title 'RNA hairpin structure containing 2-MeImpG analogue bound' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 5V9Z _struct_keywords.text 'RNA, molecular evolution' _struct_keywords.pdbx_keywords 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 ? E 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 covale1 covale both ? A G 7 "O3'" ? ? ? 1_555 A LCC 8 P ? ? A G 7 A LCC 8 1_555 ? ? ? ? ? ? ? 1.656 ? ? covale2 covale both ? A LCC 8 "O3'" ? ? ? 1_555 A LCC 9 P ? ? A LCC 8 A LCC 9 1_555 ? ? ? ? ? ? ? 1.680 ? ? covale3 covale both ? A LCC 9 "O3'" ? ? ? 1_555 A G 10 P ? ? A LCC 9 A G 10 1_555 ? ? ? ? ? ? ? 1.658 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 2 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 2 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 2 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 3 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 3 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 4 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 4 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 4 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 5 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 5 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 5 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 6 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 6 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 25 N3 ? ? A G 10 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 25 O2 ? ? A G 10 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 25 N4 ? ? A G 10 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 11 N1 ? ? ? 1_555 A U 24 N3 ? ? A A 11 A U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 11 N6 ? ? ? 1_555 A U 24 O4 ? ? A A 11 A U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 12 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 12 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 12 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 13 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 13 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 13 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 14 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 14 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 14 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 14 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 14 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 16 N2 ? ? ? 1_555 A A 19 N7 ? ? A G 16 A A 19 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog35 hydrog ? ? A G 16 N3 ? ? ? 1_555 A A 19 N6 ? ? A G 16 A A 19 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 8OS 101 ? 8 'binding site for residue 8OS A 101' AC2 Software A LCC 8 ? 5 'binding site for residues LCC A 8 and LCC A 9' # 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 8 G A 2 ? G A 2 . ? 5_446 ? 2 AC1 8 A A 3 ? A A 3 . ? 5_446 ? 3 AC1 8 LCC A 9 ? LCC A 9 . ? 1_555 ? 4 AC1 8 G A 10 ? G A 10 . ? 1_555 ? 5 AC1 8 A A 17 ? A A 17 . ? 3_554 ? 6 AC1 8 C A 25 ? C A 25 . ? 1_555 ? 7 AC1 8 G B 1 ? G B 1 . ? 1_555 ? 8 AC1 8 C B 7 ? C B 7 . ? 5_446 ? 9 AC2 5 G A 2 ? G A 2 . ? 5_446 ? 10 AC2 5 G A 7 ? G A 7 . ? 1_555 ? 11 AC2 5 G A 10 ? G A 10 . ? 1_555 ? 12 AC2 5 8OS C . ? 8OS A 101 . ? 1_555 ? 13 AC2 5 G B 1 ? G B 1 . ? 1_555 ? # _atom_sites.entry_id 5V9Z _atom_sites.fract_transf_matrix[1][1] 0.022087 _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] 0.022087 _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] 0.006469 _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 1 1 U U A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 G 7 7 7 G G A . n A 1 8 LCC 8 8 8 LCC LCC A . n A 1 9 LCC 9 9 9 LCC LCC A . n A 1 10 G 10 10 10 G G A . n A 1 11 A 11 11 11 A A A . n A 1 12 G 12 12 12 G G A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 G 16 16 16 G G A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 A 19 19 19 A A A . n A 1 20 G 20 20 20 G G A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n A 1 24 U 24 24 24 U U A . n A 1 25 C 25 25 25 C C A . n B 2 1 G 1 1 1 G G B . n B 2 2 C 2 2 2 C C B . n B 2 3 A 3 3 3 A A B . n B 2 4 C 4 4 4 C C B . n B 2 5 C 5 5 5 C C B . n B 2 6 U 6 6 6 U U B . n B 2 7 C 7 7 7 C C B . n B 2 8 A 8 8 8 A A 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 8OS 1 101 1 8OS rG A . D 4 HOH 1 201 10 HOH HOH A . D 4 HOH 2 202 4 HOH HOH A . D 4 HOH 3 203 2 HOH HOH A . D 4 HOH 4 204 8 HOH HOH A . D 4 HOH 5 205 5 HOH HOH A . D 4 HOH 6 206 9 HOH HOH A . D 4 HOH 7 207 3 HOH HOH A . E 4 HOH 1 101 11 HOH HOH B . E 4 HOH 2 102 14 HOH HOH B . E 4 HOH 3 103 12 HOH HOH B . E 4 HOH 4 104 13 HOH HOH B . E 4 HOH 5 105 1 HOH HOH B . # _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 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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)' 1000 ? 1 MORE -2 ? 1 'SSA (A^2)' 6440 ? # _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 2018-02-21 2 'Structure model' 1 1 2018-03-14 3 'Structure model' 1 2 2023-10-04 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 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' citation 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 # 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 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.title' 5 3 'Structure model' '_database_2.pdbx_DOI' 6 3 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0135 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? 3.1 4 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 N3 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 A _pdbx_validate_symm_contact.auth_seq_id_1 11 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 "O2'" _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 A _pdbx_validate_symm_contact.auth_seq_id_2 8 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 5_446 _pdbx_validate_symm_contact.dist 1.91 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A LCC 8 ? ? P A LCC 9 ? ? 1.680 1.607 0.073 0.012 Y 2 1 P B G 1 ? ? OP3 B G 1 ? ? 1.511 1.607 -0.096 0.012 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 "O3'" A G 7 ? ? P A LCC 8 ? ? "O5'" A LCC 8 ? ? 86.77 104.00 -17.23 1.90 Y 2 1 "O3'" A LCC 8 ? ? P A LCC 9 ? ? "O5'" A LCC 9 ? ? 129.47 104.00 25.47 1.90 Y 3 1 "C3'" A LCC 9 ? ? "O3'" A LCC 9 ? ? P A G 10 ? ? 144.59 119.70 24.89 1.20 Y 4 1 "O3'" A LCC 9 ? ? P A G 10 ? ? "O5'" A G 10 ? ? 116.61 104.00 12.61 1.90 Y # 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 8OS O1 O N N 1 8OS C1 C N N 2 8OS N1 N N N 3 8OS C2 C N N 4 8OS N2 N N N 5 8OS N3 N N N 6 8OS C3 C Y N 7 8OS C4 C Y N 8 8OS N4 N Y N 9 8OS C5 C Y N 10 8OS N5 N Y N 11 8OS C6 C N R 12 8OS O2 O N N 13 8OS C7 C N R 14 8OS O3 O N N 15 8OS C8 C N S 16 8OS O4 O N N 17 8OS C9 C N R 18 8OS C10 C N N 19 8OS O5 O N N 20 8OS P1 P N N 21 8OS O6 O N N 22 8OS O7 O N N 23 8OS C11 C Y N 24 8OS N6 N Y N 25 8OS C12 C Y N 26 8OS N7 N Y N 27 8OS C13 C Y N 28 8OS C14 C N N 29 8OS H1 H N N 30 8OS H2 H N N 31 8OS H3 H N N 32 8OS H4 H N N 33 8OS H5 H N N 34 8OS H6 H N N 35 8OS H7 H N N 36 8OS H8 H N N 37 8OS H9 H N N 38 8OS H10 H N N 39 8OS H11 H N N 40 8OS H12 H N N 41 8OS H13 H N N 42 8OS H14 H N N 43 8OS H15 H N N 44 8OS H17 H N N 45 8OS H18 H N N 46 8OS H19 H N N 47 A OP3 O N N 48 A P P N N 49 A OP1 O N N 50 A OP2 O N N 51 A "O5'" O N N 52 A "C5'" C N N 53 A "C4'" C N R 54 A "O4'" O N N 55 A "C3'" C N S 56 A "O3'" O N N 57 A "C2'" C N R 58 A "O2'" O N N 59 A "C1'" C N R 60 A N9 N Y N 61 A C8 C Y N 62 A N7 N Y N 63 A C5 C Y N 64 A C6 C Y N 65 A N6 N N N 66 A N1 N Y N 67 A C2 C Y N 68 A N3 N Y N 69 A C4 C Y N 70 A HOP3 H N N 71 A HOP2 H N N 72 A "H5'" H N N 73 A "H5''" H N N 74 A "H4'" H N N 75 A "H3'" H N N 76 A "HO3'" H N N 77 A "H2'" H N N 78 A "HO2'" H N N 79 A "H1'" H N N 80 A H8 H N N 81 A H61 H N N 82 A H62 H N N 83 A H2 H N N 84 C OP3 O N N 85 C P P N N 86 C OP1 O N N 87 C OP2 O N N 88 C "O5'" O N N 89 C "C5'" C N N 90 C "C4'" C N R 91 C "O4'" O N N 92 C "C3'" C N S 93 C "O3'" O N N 94 C "C2'" C N R 95 C "O2'" O N N 96 C "C1'" C N R 97 C N1 N N N 98 C C2 C N N 99 C O2 O N N 100 C N3 N N N 101 C C4 C N N 102 C N4 N N N 103 C C5 C N N 104 C C6 C N N 105 C HOP3 H N N 106 C HOP2 H N N 107 C "H5'" H N N 108 C "H5''" H N N 109 C "H4'" H N N 110 C "H3'" H N N 111 C "HO3'" H N N 112 C "H2'" H N N 113 C "HO2'" H N N 114 C "H1'" H N N 115 C H41 H N N 116 C H42 H N N 117 C H5 H N N 118 C H6 H N N 119 G OP3 O N N 120 G P P N N 121 G OP1 O N N 122 G OP2 O N N 123 G "O5'" O N N 124 G "C5'" C N N 125 G "C4'" C N R 126 G "O4'" O N N 127 G "C3'" C N S 128 G "O3'" O N N 129 G "C2'" C N R 130 G "O2'" O N N 131 G "C1'" C N R 132 G N9 N Y N 133 G C8 C Y N 134 G N7 N Y N 135 G C5 C Y N 136 G C6 C N N 137 G O6 O N N 138 G N1 N N N 139 G C2 C N N 140 G N2 N N N 141 G N3 N N N 142 G C4 C Y N 143 G HOP3 H N N 144 G HOP2 H N N 145 G "H5'" H N N 146 G "H5''" H N N 147 G "H4'" H N N 148 G "H3'" H N N 149 G "HO3'" H N N 150 G "H2'" H N N 151 G "HO2'" H N N 152 G "H1'" H N N 153 G H8 H N N 154 G H1 H N N 155 G H21 H N N 156 G H22 H N N 157 HOH O O N N 158 HOH H1 H N N 159 HOH H2 H N N 160 LCC "O5'" O N N 161 LCC "C5'" C N N 162 LCC "C4'" C N R 163 LCC "O4'" O N N 164 LCC "C1'" C N R 165 LCC N1 N N N 166 LCC C6 C N N 167 LCC C5 C N N 168 LCC C5M C N N 169 LCC C4 C N N 170 LCC N4 N N N 171 LCC N3 N N N 172 LCC C2 C N N 173 LCC O2 O N N 174 LCC "C3'" C N S 175 LCC "C2'" C N R 176 LCC "O2'" O N N 177 LCC "O3'" O N N 178 LCC "C6'" C N N 179 LCC P P N N 180 LCC O1P O N N 181 LCC O2P O N N 182 LCC OXT O N N 183 LCC "H5'1" H N N 184 LCC "H5'2" H N N 185 LCC "H1'" H N N 186 LCC H6 H N N 187 LCC H5M1 H N N 188 LCC H5M2 H N N 189 LCC H5M3 H N N 190 LCC H41 H N N 191 LCC H42 H N N 192 LCC "H3'" H N N 193 LCC "H2'1" H N N 194 LCC H3T H N N 195 LCC "H6'1" H N N 196 LCC "H6'2" H N N 197 LCC H1P H N N 198 LCC HXT H N N 199 U OP3 O N N 200 U P P N N 201 U OP1 O N N 202 U OP2 O N N 203 U "O5'" O N N 204 U "C5'" C N N 205 U "C4'" C N R 206 U "O4'" O N N 207 U "C3'" C N S 208 U "O3'" O N N 209 U "C2'" C N R 210 U "O2'" O N N 211 U "C1'" C N R 212 U N1 N N N 213 U C2 C N N 214 U O2 O N N 215 U N3 N N N 216 U C4 C N N 217 U O4 O N N 218 U C5 C N N 219 U C6 C N N 220 U HOP3 H N N 221 U HOP2 H N N 222 U "H5'" H N N 223 U "H5''" H N N 224 U "H4'" H N N 225 U "H3'" H N N 226 U "HO3'" H N N 227 U "H2'" H N N 228 U "HO2'" H N N 229 U "H1'" H N N 230 U H3 H N N 231 U H5 H N N 232 U H6 H N N 233 # 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 8OS C14 C13 sing N N 1 8OS O7 P1 doub N N 2 8OS C13 N7 sing Y N 3 8OS C13 C11 doub Y N 4 8OS C10 C9 sing N N 5 8OS C10 O5 sing N N 6 8OS N7 C12 doub Y N 7 8OS O4 C8 sing N N 8 8OS P1 C11 sing N N 9 8OS P1 O5 sing N N 10 8OS P1 O6 sing N N 11 8OS C11 N6 sing Y N 12 8OS C9 C8 sing N N 13 8OS C9 O2 sing N N 14 8OS C8 C7 sing N N 15 8OS C12 N6 sing Y N 16 8OS O2 C6 sing N N 17 8OS O3 C7 sing N N 18 8OS C7 C6 sing N N 19 8OS C6 N5 sing N N 20 8OS C5 N5 sing Y N 21 8OS C5 N4 doub Y N 22 8OS N5 C3 sing Y N 23 8OS N4 C4 sing Y N 24 8OS C3 N3 sing N N 25 8OS C3 C4 doub Y N 26 8OS N3 C2 doub N N 27 8OS C4 C1 sing N N 28 8OS C2 N2 sing N N 29 8OS C2 N1 sing N N 30 8OS C1 N1 sing N N 31 8OS C1 O1 doub N N 32 8OS N1 H1 sing N N 33 8OS N2 H2 sing N N 34 8OS N2 H3 sing N N 35 8OS C5 H4 sing N N 36 8OS C6 H5 sing N N 37 8OS C7 H6 sing N N 38 8OS O3 H7 sing N N 39 8OS C8 H8 sing N N 40 8OS O4 H9 sing N N 41 8OS C9 H10 sing N N 42 8OS C10 H11 sing N N 43 8OS C10 H12 sing N N 44 8OS O6 H13 sing N N 45 8OS N6 H14 sing N N 46 8OS C12 H15 sing N N 47 8OS C14 H17 sing N N 48 8OS C14 H18 sing N N 49 8OS C14 H19 sing N N 50 A OP3 P sing N N 51 A OP3 HOP3 sing N N 52 A P OP1 doub N N 53 A P OP2 sing N N 54 A P "O5'" sing N N 55 A OP2 HOP2 sing N N 56 A "O5'" "C5'" sing N N 57 A "C5'" "C4'" sing N N 58 A "C5'" "H5'" sing N N 59 A "C5'" "H5''" sing N N 60 A "C4'" "O4'" sing N N 61 A "C4'" "C3'" sing N N 62 A "C4'" "H4'" sing N N 63 A "O4'" "C1'" sing N N 64 A "C3'" "O3'" sing N N 65 A "C3'" "C2'" sing N N 66 A "C3'" "H3'" sing N N 67 A "O3'" "HO3'" sing N N 68 A "C2'" "O2'" sing N N 69 A "C2'" "C1'" sing N N 70 A "C2'" "H2'" sing N N 71 A "O2'" "HO2'" sing N N 72 A "C1'" N9 sing N N 73 A "C1'" "H1'" sing N N 74 A N9 C8 sing Y N 75 A N9 C4 sing Y N 76 A C8 N7 doub Y N 77 A C8 H8 sing N N 78 A N7 C5 sing Y N 79 A C5 C6 sing Y N 80 A C5 C4 doub Y N 81 A C6 N6 sing N N 82 A C6 N1 doub Y N 83 A N6 H61 sing N N 84 A N6 H62 sing N N 85 A N1 C2 sing Y N 86 A C2 N3 doub Y N 87 A C2 H2 sing N N 88 A N3 C4 sing Y N 89 C OP3 P sing N N 90 C OP3 HOP3 sing N N 91 C P OP1 doub N N 92 C P OP2 sing N N 93 C P "O5'" sing N N 94 C OP2 HOP2 sing N N 95 C "O5'" "C5'" sing N N 96 C "C5'" "C4'" sing N N 97 C "C5'" "H5'" sing N N 98 C "C5'" "H5''" sing N N 99 C "C4'" "O4'" sing N N 100 C "C4'" "C3'" sing N N 101 C "C4'" "H4'" sing N N 102 C "O4'" "C1'" sing N N 103 C "C3'" "O3'" sing N N 104 C "C3'" "C2'" sing N N 105 C "C3'" "H3'" sing N N 106 C "O3'" "HO3'" sing N N 107 C "C2'" "O2'" sing N N 108 C "C2'" "C1'" sing N N 109 C "C2'" "H2'" sing N N 110 C "O2'" "HO2'" sing N N 111 C "C1'" N1 sing N N 112 C "C1'" "H1'" sing N N 113 C N1 C2 sing N N 114 C N1 C6 sing N N 115 C C2 O2 doub N N 116 C C2 N3 sing N N 117 C N3 C4 doub N N 118 C C4 N4 sing N N 119 C C4 C5 sing N N 120 C N4 H41 sing N N 121 C N4 H42 sing N N 122 C C5 C6 doub N N 123 C C5 H5 sing N N 124 C C6 H6 sing N N 125 G OP3 P sing N N 126 G OP3 HOP3 sing N N 127 G P OP1 doub N N 128 G P OP2 sing N N 129 G P "O5'" sing N N 130 G OP2 HOP2 sing N N 131 G "O5'" "C5'" sing N N 132 G "C5'" "C4'" sing N N 133 G "C5'" "H5'" sing N N 134 G "C5'" "H5''" sing N N 135 G "C4'" "O4'" sing N N 136 G "C4'" "C3'" sing N N 137 G "C4'" "H4'" sing N N 138 G "O4'" "C1'" sing N N 139 G "C3'" "O3'" sing N N 140 G "C3'" "C2'" sing N N 141 G "C3'" "H3'" sing N N 142 G "O3'" "HO3'" sing N N 143 G "C2'" "O2'" sing N N 144 G "C2'" "C1'" sing N N 145 G "C2'" "H2'" sing N N 146 G "O2'" "HO2'" sing N N 147 G "C1'" N9 sing N N 148 G "C1'" "H1'" sing N N 149 G N9 C8 sing Y N 150 G N9 C4 sing Y N 151 G C8 N7 doub Y N 152 G C8 H8 sing N N 153 G N7 C5 sing Y N 154 G C5 C6 sing N N 155 G C5 C4 doub Y N 156 G C6 O6 doub N N 157 G C6 N1 sing N N 158 G N1 C2 sing N N 159 G N1 H1 sing N N 160 G C2 N2 sing N N 161 G C2 N3 doub N N 162 G N2 H21 sing N N 163 G N2 H22 sing N N 164 G N3 C4 sing N N 165 HOH O H1 sing N N 166 HOH O H2 sing N N 167 LCC "O5'" "C5'" sing N N 168 LCC "O5'" P sing N N 169 LCC "C5'" "C4'" sing N N 170 LCC "C5'" "H5'1" sing N N 171 LCC "C5'" "H5'2" sing N N 172 LCC "C4'" "O4'" sing N N 173 LCC "C4'" "C3'" sing N N 174 LCC "C4'" "C6'" sing N N 175 LCC "O4'" "C1'" sing N N 176 LCC "C1'" N1 sing N N 177 LCC "C1'" "C2'" sing N N 178 LCC "C1'" "H1'" sing N N 179 LCC N1 C6 sing N N 180 LCC N1 C2 sing N N 181 LCC C6 C5 doub N N 182 LCC C6 H6 sing N N 183 LCC C5 C5M sing N N 184 LCC C5 C4 sing N N 185 LCC C5M H5M1 sing N N 186 LCC C5M H5M2 sing N N 187 LCC C5M H5M3 sing N N 188 LCC C4 N4 sing N N 189 LCC C4 N3 doub N N 190 LCC N4 H41 sing N N 191 LCC N4 H42 sing N N 192 LCC N3 C2 sing N N 193 LCC C2 O2 doub N N 194 LCC "C3'" "C2'" sing N N 195 LCC "C3'" "O3'" sing N N 196 LCC "C3'" "H3'" sing N N 197 LCC "C2'" "O2'" sing N N 198 LCC "C2'" "H2'1" sing N N 199 LCC "O2'" "C6'" sing N N 200 LCC "O3'" H3T sing N N 201 LCC "C6'" "H6'1" sing N N 202 LCC "C6'" "H6'2" sing N N 203 LCC P O1P sing N N 204 LCC P O2P doub N N 205 LCC P OXT sing N N 206 LCC O1P H1P sing N N 207 LCC OXT HXT sing N N 208 U OP3 P sing N N 209 U OP3 HOP3 sing N N 210 U P OP1 doub N N 211 U P OP2 sing N N 212 U P "O5'" sing N N 213 U OP2 HOP2 sing N N 214 U "O5'" "C5'" sing N N 215 U "C5'" "C4'" sing N N 216 U "C5'" "H5'" sing N N 217 U "C5'" "H5''" sing N N 218 U "C4'" "O4'" sing N N 219 U "C4'" "C3'" sing N N 220 U "C4'" "H4'" sing N N 221 U "O4'" "C1'" sing N N 222 U "C3'" "O3'" sing N N 223 U "C3'" "C2'" sing N N 224 U "C3'" "H3'" sing N N 225 U "O3'" "HO3'" sing N N 226 U "C2'" "O2'" sing N N 227 U "C2'" "C1'" sing N N 228 U "C2'" "H2'" sing N N 229 U "O2'" "HO2'" sing N N 230 U "C1'" N1 sing N N 231 U "C1'" "H1'" sing N N 232 U N1 C2 sing N N 233 U N1 C6 sing N N 234 U C2 O2 doub N N 235 U C2 N3 sing N N 236 U N3 C4 sing N N 237 U N3 H3 sing N N 238 U C4 O4 doub N N 239 U C4 C5 sing N N 240 U C5 C6 doub N N 241 U C5 H5 sing N N 242 U C6 H6 sing N N 243 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5V9Z 'double helix' 5V9Z 'a-form double helix' 5V9Z tetraloop 5V9Z '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 G 2 1_555 B C 7 1_555 -0.152 -0.160 0.246 -4.880 2.052 -3.124 1 A_G2:C7_B A 2 ? B 7 ? 19 1 1 A A 3 1_555 B U 6 1_555 0.023 -0.172 -0.033 3.326 -12.184 2.064 2 A_A3:U6_B A 3 ? B 6 ? 20 1 1 A G 4 1_555 B C 5 1_555 -0.095 -0.138 -0.130 -4.141 -16.171 -1.246 3 A_G4:C5_B A 4 ? B 5 ? 19 1 1 A G 5 1_555 B C 4 1_555 -0.151 -0.015 -0.225 -13.093 -20.259 2.811 4 A_G5:C4_B A 5 ? B 4 ? 19 1 1 A U 6 1_555 B A 3 1_555 0.170 -0.079 0.198 -5.704 -10.662 0.833 5 A_U6:A3_B A 6 ? B 3 ? 20 1 1 A G 7 1_555 B C 2 1_555 -0.150 0.041 0.066 -12.236 -19.150 -1.380 6 A_G7:C2_B A 7 ? B 2 ? 19 1 1 A G 10 1_555 A C 25 1_555 0.031 -0.080 -0.134 -5.758 -16.376 1.399 7 A_G10:C25_A A 10 ? A 25 ? 19 1 1 A A 11 1_555 A U 24 1_555 0.152 -0.192 -0.041 -0.181 -13.609 1.001 8 A_A11:U24_A A 11 ? A 24 ? 20 1 1 A G 12 1_555 A C 23 1_555 -0.030 -0.046 -0.327 -2.443 -20.908 0.743 9 A_G12:C23_A A 12 ? A 23 ? 19 1 1 A C 13 1_555 A G 22 1_555 0.283 -0.110 -0.229 3.773 -14.202 -0.727 10 A_C13:G22_A A 13 ? A 22 ? 19 1 1 A G 14 1_555 A C 21 1_555 -0.040 -0.010 -0.269 -3.801 -7.090 0.232 11 A_G14:C21_A A 14 ? A 21 ? 19 1 1 A C 15 1_555 A G 20 1_555 0.689 0.068 -0.105 3.166 4.189 1.995 12 A_C15:G20_A A 15 ? A 20 ? 19 1 1 A G 16 1_555 A A 19 1_555 6.998 -5.015 0.667 11.913 2.430 -12.266 13 A_G16:A19_A A 16 ? A 19 ? 11 10 # 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 G 2 1_555 B C 7 1_555 A A 3 1_555 B U 6 1_555 0.393 -1.408 3.213 0.815 9.910 31.020 -4.106 -0.571 2.659 17.960 -1.478 32.538 1 AA_G2A3:U6C7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A A 3 1_555 B U 6 1_555 A G 4 1_555 B C 5 1_555 -0.359 -1.460 3.429 0.505 11.952 32.923 -4.186 0.671 2.743 20.274 -0.857 34.972 2 AA_A3G4:C5U6_BB A 3 ? B 6 ? A 4 ? B 5 ? 1 A G 4 1_555 B C 5 1_555 A G 5 1_555 B C 4 1_555 1.007 -2.222 3.513 3.772 8.000 29.470 -5.770 -1.156 2.926 15.297 -7.214 30.740 3 AA_G4G5:C4C5_BB A 4 ? B 5 ? A 5 ? B 4 ? 1 A G 5 1_555 B C 4 1_555 A U 6 1_555 B A 3 1_555 -0.601 -1.413 3.077 -3.992 0.118 34.291 -2.399 0.425 3.120 0.199 6.742 34.516 4 AA_G5U6:A3C4_BB A 5 ? B 4 ? A 6 ? B 3 ? 1 A U 6 1_555 B A 3 1_555 A G 7 1_555 B C 2 1_555 0.037 -1.680 3.309 1.325 7.077 30.952 -4.312 0.164 2.863 13.040 -2.441 31.758 5 AA_U6G7:C2A3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A G 10 1_555 A C 25 1_555 A A 11 1_555 A U 24 1_555 -0.294 -1.018 3.213 -3.835 5.937 31.420 -2.855 -0.127 2.989 10.793 6.972 32.185 6 AA_G10A11:U24C25_AA A 10 ? A 25 ? A 11 ? A 24 ? 1 A A 11 1_555 A U 24 1_555 A G 12 1_555 A C 23 1_555 -0.080 -1.300 3.380 2.309 12.094 31.661 -4.101 0.494 2.704 21.191 -4.046 33.913 7 AA_A11G12:C23U24_AA A 11 ? A 24 ? A 12 ? A 23 ? 1 A G 12 1_555 A C 23 1_555 A C 13 1_555 A G 22 1_555 0.472 -1.381 3.203 0.468 1.609 31.484 -2.832 -0.784 3.136 2.963 -0.861 31.527 8 AA_G12C13:G22C23_AA A 12 ? A 23 ? A 13 ? A 22 ? 1 A C 13 1_555 A G 22 1_555 A G 14 1_555 A C 21 1_555 0.793 -1.963 3.412 3.560 9.949 28.078 -5.766 -0.829 2.655 19.648 -7.029 29.963 9 AA_C13G14:C21G22_AA A 13 ? A 22 ? A 14 ? A 21 ? 1 A G 14 1_555 A C 21 1_555 A C 15 1_555 A G 20 1_555 0.362 -2.258 3.223 0.249 -0.138 31.914 -4.081 -0.614 3.235 -0.251 -0.454 31.916 10 AA_G14C15:G20C21_AA A 14 ? A 21 ? A 15 ? A 20 ? 1 A C 15 1_555 A G 20 1_555 A G 16 1_555 A A 19 1_555 -1.843 -1.274 3.005 0.572 11.065 49.627 -2.167 2.185 2.663 12.996 -0.672 50.772 11 AA_C15G16:A19G20_AA A 15 ? A 20 ? A 16 ? A 19 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 "5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine" 8OS 4 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 4FNJ _pdbx_initial_refinement_model.details ? # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #