data_4U34 # _entry.id 4U34 # _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 4U34 pdb_00004u34 10.2210/pdb4u34/pdb WWPDB D_1000202726 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 4U35 PDB . unspecified 4U37 PDB . unspecified 4U38 PDB . # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 4U34 _pdbx_database_status.recvd_initial_deposition_date 2014-07-18 _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 'Sheng, J.' 1 'Larsen, A.' 2 'Heuberger, B.' 3 'Blain, J.C.' 4 'Szostak, J.W.' 5 # _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 136 _citation.language ? _citation.page_first 13916 _citation.page_last 13924 _citation.title 'Crystal Structure Studies of RNA Duplexes Containing s(2)U:A and s(2)U:U Base Pairs.' _citation.year 2014 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/ja508015a _citation.pdbx_database_id_PubMed 25188906 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sheng, J.' 1 ? primary 'Larsen, A.' 2 ? primary 'Heuberger, B.D.' 3 ? primary 'Blain, J.C.' 4 ? primary 'Szostak, J.W.' 5 ? # _cell.entry_id 4U34 _cell.length_a 37.385 _cell.length_b 38.683 _cell.length_c 30.072 _cell.angle_alpha 90.00 _cell.angle_beta 109.18 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U34 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(*UP*AP*GP*CP*(SUR)P*CP*C-3') ; 2173.397 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3') ; 2260.419 1 ? ? ? ? 3 water nat water 18.015 97 ? ? ? ? # 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 'UAGC(SUR)CC' UAGCUCC A ? 2 polyribonucleotide no no GGAGCUA GGAGCUA 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 A n 1 3 G n 1 4 C n 1 5 SUR n 1 6 C n 1 7 C n 2 1 G n 2 2 G n 2 3 A n 2 4 G n 2 5 C n 2 6 U n 2 7 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 7 'synthetic construct' ? 32630 ? 2 1 sample 1 7 '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 4U34 4U34 ? 1 ? 1 2 PDB 4U34 4U34 ? 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 4U34 A 1 ? 7 ? 4U34 1 ? 7 ? 1 7 2 2 4U34 B 1 ? 7 ? 4U34 8 ? 14 ? 8 14 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SUR 'RNA linking' n "1-(BETA-D-RIBOFURANOSYL)-2-THIO-URACIL-5'-PHOSPHATE" ? 'C9 H13 N2 O8 P S' 340.247 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 4U34 _exptl.crystals_number ? _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.45 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 49.7 _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, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '10% MPD, 40 mM Na cacodylate pH 6.0, 12 mM spermine tetra-HCl and 80 mM NaCl' _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 2012-04-17 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Double crystal, Si(111)' _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 1.0 _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 1.0 _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 4U34 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.35 _reflns.d_resolution_low 30 _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 8436 _reflns.number_obs 8031 _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 93.5 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.7 _reflns.pdbx_Rmerge_I_obs 0.065 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 24.3 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _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 ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.35 _reflns_shell.d_res_low 1.40 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 11.1 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 66.6 _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 0.129 _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 4.0 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _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 ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] -0.01 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] -0.02 _refine.aniso_B[2][2] 0.01 _refine.aniso_B[2][3] 0.00 _refine.aniso_B[3][3] -0.02 _refine.B_iso_max ? _refine.B_iso_mean 11.115 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.949 _refine.correlation_coeff_Fo_to_Fc_free 0.951 _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 4U34 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.35 _refine.ls_d_res_low 22.06 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 8031 _refine.ls_number_reflns_R_free 404 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 93.35 _refine.ls_percent_reflns_R_free 4.8 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.18807 _refine.ls_R_factor_R_free 0.19788 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.18756 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details MASK _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 434D _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.064 _refine.pdbx_overall_ESU_R_Free 0.061 _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_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B 1.725 _refine.overall_SU_ML 0.036 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _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 292 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 97 _refine_hist.number_atoms_total 389 _refine_hist.d_res_high 1.35 _refine_hist.d_res_low 22.06 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.005 0.012 325 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.412 1.538 503 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_angle_other_deg ? ? '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' ? 0.080 0.200 56 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.010 0.020 144 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_gen_planes_other ? ? '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 ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_long_range_B_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.347 _refine_ls_shell.d_res_low 1.381 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 23 _refine_ls_shell.number_reflns_R_work 373 _refine_ls_shell.percent_reflns_obs 61.68 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.262 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.259 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? # _struct.entry_id 4U34 _struct.title 'Crystal Structures of RNA Duplexes Containing 2-thio-Uridine' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 4U34 _struct_keywords.text 'RNA, 2-thio-uridine' _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 3 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A C 4 "O3'" ? ? ? 1_555 A SUR 5 P ? ? A C 4 A SUR 5 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale2 covale both ? A SUR 5 "O3'" ? ? ? 1_555 A C 6 P ? ? A SUR 5 A C 6 1_555 ? ? ? ? ? ? ? 1.591 ? ? hydrog1 hydrog ? ? A U 1 N3 ? ? ? 1_555 B A 7 N1 ? ? A U 1 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A U 1 O4 ? ? ? 1_555 B A 7 N6 ? ? A U 1 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A A 2 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 2 B U 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 2 B U 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 3 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 3 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 3 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A SUR 5 N3 ? ? ? 1_555 B A 3 N1 ? ? A SUR 5 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A SUR 5 O4 ? ? ? 1_555 B A 3 N6 ? ? A SUR 5 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 6 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 6 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 6 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 7 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 7 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 7 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 4U34 _atom_sites.fract_transf_matrix[1][1] 0.026749 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009302 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.025851 _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] 0.035207 _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 S # 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 A 2 2 2 A A A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 SUR 5 5 5 SUR 2sU A . n A 1 6 C 6 6 6 C C A . n A 1 7 C 7 7 7 C C A . n B 2 1 G 1 8 8 G G B . n B 2 2 G 2 9 9 G G B . n B 2 3 A 3 10 10 A A B . n B 2 4 G 4 11 11 G G B . n B 2 5 C 5 12 12 C C B . n B 2 6 U 6 13 13 U U B . n B 2 7 A 7 14 14 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 HOH 1 101 97 HOH HOH A . C 3 HOH 2 102 44 HOH HOH A . C 3 HOH 3 103 37 HOH HOH A . C 3 HOH 4 104 42 HOH HOH A . C 3 HOH 5 105 4 HOH HOH A . C 3 HOH 6 106 83 HOH HOH A . C 3 HOH 7 107 24 HOH HOH A . C 3 HOH 8 108 90 HOH HOH A . C 3 HOH 9 109 66 HOH HOH A . C 3 HOH 10 110 72 HOH HOH A . C 3 HOH 11 111 96 HOH HOH A . C 3 HOH 12 112 39 HOH HOH A . C 3 HOH 13 113 1 HOH HOH A . C 3 HOH 14 114 25 HOH HOH A . C 3 HOH 15 115 2 HOH HOH A . C 3 HOH 16 116 51 HOH HOH A . C 3 HOH 17 117 47 HOH HOH A . C 3 HOH 18 118 26 HOH HOH A . C 3 HOH 19 119 31 HOH HOH A . C 3 HOH 20 120 67 HOH HOH A . C 3 HOH 21 121 11 HOH HOH A . C 3 HOH 22 122 75 HOH HOH A . C 3 HOH 23 123 14 HOH HOH A . C 3 HOH 24 124 48 HOH HOH A . C 3 HOH 25 125 15 HOH HOH A . C 3 HOH 26 126 3 HOH HOH A . C 3 HOH 27 127 58 HOH HOH A . C 3 HOH 28 128 65 HOH HOH A . C 3 HOH 29 129 86 HOH HOH A . C 3 HOH 30 130 69 HOH HOH A . C 3 HOH 31 131 57 HOH HOH A . C 3 HOH 32 132 5 HOH HOH A . C 3 HOH 33 133 12 HOH HOH A . C 3 HOH 34 134 16 HOH HOH A . C 3 HOH 35 135 17 HOH HOH A . C 3 HOH 36 136 29 HOH HOH A . C 3 HOH 37 137 32 HOH HOH A . C 3 HOH 38 138 34 HOH HOH A . C 3 HOH 39 139 35 HOH HOH A . C 3 HOH 40 140 38 HOH HOH A . C 3 HOH 41 141 41 HOH HOH A . C 3 HOH 42 142 45 HOH HOH A . C 3 HOH 43 143 49 HOH HOH A . C 3 HOH 44 144 52 HOH HOH A . C 3 HOH 45 145 54 HOH HOH A . C 3 HOH 46 146 56 HOH HOH A . C 3 HOH 47 147 59 HOH HOH A . C 3 HOH 48 148 63 HOH HOH A . C 3 HOH 49 149 64 HOH HOH A . C 3 HOH 50 150 81 HOH HOH A . C 3 HOH 51 151 85 HOH HOH A . C 3 HOH 52 152 94 HOH HOH A . D 3 HOH 1 101 74 HOH HOH B . D 3 HOH 2 102 22 HOH HOH B . D 3 HOH 3 103 77 HOH HOH B . D 3 HOH 4 104 36 HOH HOH B . D 3 HOH 5 105 30 HOH HOH B . D 3 HOH 6 106 33 HOH HOH B . D 3 HOH 7 107 71 HOH HOH B . D 3 HOH 8 108 9 HOH HOH B . D 3 HOH 9 109 6 HOH HOH B . D 3 HOH 10 110 23 HOH HOH B . D 3 HOH 11 111 18 HOH HOH B . D 3 HOH 12 112 40 HOH HOH B . D 3 HOH 13 113 19 HOH HOH B . D 3 HOH 14 114 73 HOH HOH B . D 3 HOH 15 115 43 HOH HOH B . D 3 HOH 16 116 10 HOH HOH B . D 3 HOH 17 117 82 HOH HOH B . D 3 HOH 18 118 21 HOH HOH B . D 3 HOH 19 119 8 HOH HOH B . D 3 HOH 20 120 55 HOH HOH B . D 3 HOH 21 121 95 HOH HOH B . D 3 HOH 22 122 13 HOH HOH B . D 3 HOH 23 123 84 HOH HOH B . D 3 HOH 24 124 79 HOH HOH B . D 3 HOH 25 125 60 HOH HOH B . D 3 HOH 26 126 46 HOH HOH B . D 3 HOH 27 127 68 HOH HOH B . D 3 HOH 28 128 92 HOH HOH B . D 3 HOH 29 129 7 HOH HOH B . D 3 HOH 30 130 20 HOH HOH B . D 3 HOH 31 131 27 HOH HOH B . D 3 HOH 32 132 28 HOH HOH B . D 3 HOH 33 133 50 HOH HOH B . D 3 HOH 34 134 53 HOH HOH B . D 3 HOH 35 135 61 HOH HOH B . D 3 HOH 36 136 62 HOH HOH B . D 3 HOH 37 137 70 HOH HOH B . D 3 HOH 38 138 76 HOH HOH B . D 3 HOH 39 139 78 HOH HOH B . D 3 HOH 40 140 80 HOH HOH B . D 3 HOH 41 141 87 HOH HOH B . D 3 HOH 42 142 88 HOH HOH B . D 3 HOH 43 143 89 HOH HOH B . D 3 HOH 44 144 91 HOH HOH B . D 3 HOH 45 145 93 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 # 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)' 1250 ? 1 MORE -1 ? 1 'SSA (A^2)' 2630 ? # _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 2014-08-13 2 'Structure model' 1 1 2014-09-17 3 'Structure model' 1 2 2014-10-01 4 'Structure model' 1 3 2014-10-15 5 'Structure model' 1 4 2015-01-14 6 'Structure model' 1 5 2015-08-26 7 'Structure model' 1 6 2017-09-27 8 'Structure model' 1 7 2019-11-20 9 'Structure model' 1 8 2023-09-27 # _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' 'Database references' 3 4 'Structure model' 'Database references' 4 5 'Structure model' 'Database references' 5 6 'Structure model' 'Data collection' 6 7 'Structure model' 'Derived calculations' 7 7 'Structure model' 'Refinement description' 8 8 'Structure model' 'Author supporting evidence' 9 9 'Structure model' 'Data collection' 10 9 'Structure model' 'Database references' 11 9 '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 7 'Structure model' pdbx_struct_oper_list 2 7 'Structure model' software 3 8 'Structure model' pdbx_audit_support 4 9 'Structure model' chem_comp_atom 5 9 'Structure model' chem_comp_bond 6 9 'Structure model' database_2 7 9 '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 7 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 2 7 'Structure model' '_software.classification' 3 8 'Structure model' '_pdbx_audit_support.funding_organization' 4 9 'Structure model' '_database_2.pdbx_DOI' 5 9 'Structure model' '_database_2.pdbx_database_accession' # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[1][1]_esd _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][2]_esd _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[1][3]_esd _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[2][2]_esd _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.T[2][3]_esd _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[3][3]_esd _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[1][1]_esd _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][2]_esd _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[1][3]_esd _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[2][2]_esd _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.L[2][3]_esd _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[3][3]_esd _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][1]_esd _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][2]_esd _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[1][3]_esd _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][1]_esd _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][2]_esd _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][3]_esd _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][1]_esd _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][2]_esd _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[3][3]_esd 1 'X-RAY DIFFRACTION' ? refined -2.0012 -3.1276 -9.4296 0.0242 ? -0.0048 ? -0.0058 ? 0.0501 ? -0.0042 ? 0.0360 ? 1.2079 ? 0.7771 ? -0.0840 ? 0.6724 ? 0.2576 ? 0.5891 ? 0.0209 ? -0.0746 ? -0.0114 ? -0.0121 ? -0.0426 ? -0.0041 ? -0.0393 ? -0.0229 ? 0.0217 ? 2 'X-RAY DIFFRACTION' ? refined -4.2865 1.9318 -11.7522 0.0285 ? -0.0048 ? -0.0102 ? 0.0354 ? 0.0175 ? 0.0283 ? 0.4063 ? 0.1384 ? -0.3073 ? 1.6079 ? 1.1842 ? 1.3015 ? 0.0388 ? -0.0013 ? -0.0502 ? -0.0503 ? -0.0455 ? -0.0488 ? -0.0743 ? -0.0501 ? 0.0067 ? # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 ? ? A 1 ? ? A 7 ? ? 2 'X-RAY DIFFRACTION' 2 ? ? B 8 ? ? B 14 ? ? # 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 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.6.0117 2 # 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 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 SUR P P N N 114 SUR OP1 O N N 115 SUR OP2 O N N 116 SUR OP3 O N N 117 SUR "O5'" O N N 118 SUR "C5'" C N N 119 SUR "C4'" C N R 120 SUR "O4'" O N N 121 SUR "C3'" C N S 122 SUR "C1'" C N R 123 SUR N1 N N N 124 SUR "C2'" C N R 125 SUR C6 C N N 126 SUR C2 C N N 127 SUR C5 C N N 128 SUR S2 S N N 129 SUR N3 N N N 130 SUR C4 C N N 131 SUR O4 O N N 132 SUR "O2'" O N N 133 SUR "O3'" O N N 134 SUR HOP1 H N N 135 SUR HOP3 H N N 136 SUR "H5'1" H N N 137 SUR "H5'2" H N N 138 SUR "H4'" H N N 139 SUR "H3'" H N N 140 SUR "H1'" H N N 141 SUR "H2'" H N N 142 SUR HC6 H N N 143 SUR HC5 H N N 144 SUR HN3 H N N 145 SUR HO2 H N N 146 SUR HO3 H N N 147 U OP3 O N N 148 U P P N N 149 U OP1 O N N 150 U OP2 O N N 151 U "O5'" O N N 152 U "C5'" C N N 153 U "C4'" C N R 154 U "O4'" O N N 155 U "C3'" C N S 156 U "O3'" O N N 157 U "C2'" C N R 158 U "O2'" O N N 159 U "C1'" C N R 160 U N1 N N N 161 U C2 C N N 162 U O2 O N N 163 U N3 N N N 164 U C4 C N N 165 U O4 O N N 166 U C5 C N N 167 U C6 C N N 168 U HOP3 H N N 169 U HOP2 H N N 170 U "H5'" H N N 171 U "H5''" H N N 172 U "H4'" H N N 173 U "H3'" H N N 174 U "HO3'" H N N 175 U "H2'" H N N 176 U "HO2'" H N N 177 U "H1'" H N N 178 U H3 H N N 179 U H5 H N N 180 U H6 H N N 181 # 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 HOH O H1 sing N N 116 HOH O H2 sing N N 117 SUR P OP1 sing N N 118 SUR P OP2 doub N N 119 SUR P OP3 sing N N 120 SUR P "O5'" sing N N 121 SUR OP1 HOP1 sing N N 122 SUR OP3 HOP3 sing N N 123 SUR "O5'" "C5'" sing N N 124 SUR "C5'" "C4'" sing N N 125 SUR "C5'" "H5'1" sing N N 126 SUR "C5'" "H5'2" sing N N 127 SUR "C4'" "O4'" sing N N 128 SUR "C4'" "C3'" sing N N 129 SUR "C4'" "H4'" sing N N 130 SUR "O4'" "C1'" sing N N 131 SUR "C3'" "C2'" sing N N 132 SUR "C3'" "O3'" sing N N 133 SUR "C3'" "H3'" sing N N 134 SUR "C1'" N1 sing N N 135 SUR "C1'" "C2'" sing N N 136 SUR "C1'" "H1'" sing N N 137 SUR N1 C6 sing N N 138 SUR N1 C2 sing N N 139 SUR "C2'" "O2'" sing N N 140 SUR "C2'" "H2'" sing N N 141 SUR C6 C5 doub N N 142 SUR C6 HC6 sing N N 143 SUR C2 S2 doub N N 144 SUR C2 N3 sing N N 145 SUR C5 C4 sing N N 146 SUR C5 HC5 sing N N 147 SUR N3 C4 sing N N 148 SUR N3 HN3 sing N N 149 SUR C4 O4 doub N N 150 SUR "O2'" HO2 sing N N 151 SUR "O3'" HO3 sing N N 152 U OP3 P sing N N 153 U OP3 HOP3 sing N N 154 U P OP1 doub N N 155 U P OP2 sing N N 156 U P "O5'" sing N N 157 U OP2 HOP2 sing N N 158 U "O5'" "C5'" sing N N 159 U "C5'" "C4'" sing N N 160 U "C5'" "H5'" sing N N 161 U "C5'" "H5''" sing N N 162 U "C4'" "O4'" sing N N 163 U "C4'" "C3'" sing N N 164 U "C4'" "H4'" sing N N 165 U "O4'" "C1'" sing N N 166 U "C3'" "O3'" sing N N 167 U "C3'" "C2'" sing N N 168 U "C3'" "H3'" sing N N 169 U "O3'" "HO3'" sing N N 170 U "C2'" "O2'" sing N N 171 U "C2'" "C1'" sing N N 172 U "C2'" "H2'" sing N N 173 U "O2'" "HO2'" sing N N 174 U "C1'" N1 sing N N 175 U "C1'" "H1'" sing N N 176 U N1 C2 sing N N 177 U N1 C6 sing N N 178 U C2 O2 doub N N 179 U C2 N3 sing N N 180 U N3 C4 sing N N 181 U N3 H3 sing N N 182 U C4 O4 doub N N 183 U C4 C5 sing N N 184 U C5 C6 doub N N 185 U C5 H5 sing N N 186 U C6 H6 sing N N 187 # _ndb_struct_conf_na.entry_id 4U34 _ndb_struct_conf_na.feature 'a-form double helix' # 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 U 1 1_555 B A 7 1_555 -0.116 -0.027 0.061 -0.983 -3.485 2.611 1 A_U1:A14_B A 1 ? B 14 ? 20 1 1 A A 2 1_555 B U 6 1_555 0.071 -0.051 0.174 2.702 -12.134 3.369 2 A_A2:U13_B A 2 ? B 13 ? 20 1 1 A G 3 1_555 B C 5 1_555 -0.031 -0.179 0.100 3.405 -11.057 -2.318 3 A_G3:C12_B A 3 ? B 12 ? 19 1 1 A C 4 1_555 B G 4 1_555 0.241 -0.101 0.063 3.970 -16.667 3.147 4 A_C4:G11_B A 4 ? B 11 ? 19 1 1 A SUR 5 1_555 B A 3 1_555 -0.183 -0.126 -0.068 -1.967 -9.277 -3.060 5 A_SUR5:A10_B A 5 ? B 10 ? 20 1 1 A C 6 1_555 B G 2 1_555 0.201 -0.139 -0.032 2.832 -11.764 1.144 6 A_C6:G9_B A 6 ? B 9 ? 19 1 1 A C 7 1_555 B G 1 1_555 0.223 -0.163 -0.116 4.816 -2.587 -1.247 7 A_C7:G8_B A 7 ? B 8 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A U 1 1_555 B A 7 1_555 A A 2 1_555 B U 6 1_555 0.182 -1.442 3.124 0.547 6.735 31.309 -3.722 -0.241 2.764 12.300 -0.999 32.012 1 AA_U1A2:U13A14_BB A 1 ? B 14 ? A 2 ? B 13 ? 1 A A 2 1_555 B U 6 1_555 A G 3 1_555 B C 5 1_555 -0.898 -1.190 3.215 -1.413 4.984 32.875 -2.879 1.342 3.042 8.740 2.477 33.269 2 AA_A2G3:C12U13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A G 3 1_555 B C 5 1_555 A C 4 1_555 B G 4 1_555 0.909 -1.506 3.157 2.038 6.280 34.139 -3.417 -1.231 2.890 10.575 -3.432 34.753 3 AA_G3C4:G11C12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A C 4 1_555 B G 4 1_555 A SUR 5 1_555 B A 3 1_555 -1.031 -1.770 3.347 -2.443 10.617 29.866 -5.080 1.460 2.652 19.791 4.553 31.749 4 AA_C4SUR5:A10G11_BB A 4 ? B 11 ? A 5 ? B 10 ? 1 A SUR 5 1_555 B A 3 1_555 A C 6 1_555 B G 2 1_555 0.554 -1.205 3.199 0.614 4.722 33.366 -2.812 -0.860 3.014 8.172 -1.062 33.695 5 AA_SUR5C6:G9A10_BB A 5 ? B 10 ? A 6 ? B 9 ? 1 A C 6 1_555 B G 2 1_555 A C 7 1_555 B G 1 1_555 -0.238 -1.745 3.243 -1.068 4.301 31.810 -3.894 0.246 2.994 7.799 1.937 32.109 6 AA_C6C7:G8G9_BB A 6 ? B 9 ? A 7 ? B 8 ? # _pdbx_audit_support.funding_organization 'Howard Hughes Medical Institute (HHMI)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 434D _pdbx_initial_refinement_model.details ? #