data_5TGP # _entry.id 5TGP # _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 5TGP pdb_00005tgp 10.2210/pdb5tgp/pdb WWPDB D_1000224227 ? ? # _pdbx_database_related.content_type unspecified _pdbx_database_related.db_id 5TGR _pdbx_database_related.db_name PDB _pdbx_database_related.details . # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5TGP _pdbx_database_status.recvd_initial_deposition_date 2016-09-28 _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 'Zhang, W.' 1 'Huang, Z.' 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 ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'DNA 8mer containing two 2SeT modifications' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhang, W.' 1 ? primary 'Huang, Z.' 2 ? # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 5TGP _cell.details ? _cell.formula_units_Z ? _cell.length_a 44.861 _cell.length_a_esd ? _cell.length_b 44.861 _cell.length_b_esd ? _cell.length_c 41.736 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TGP _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' _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 ;DNA/RNA (5'-R(*G)-D(P*(2ST))-R(P*G)-D(P*(2ST))-R(P*AP*CP*AP*C)-3') ; 2648.537 2 ? ? ? ? 2 water nat water 18.015 25 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'G(US3)G(US3)ACAC' _entity_poly.pdbx_seq_one_letter_code_can GTGTACAC _entity_poly.pdbx_strand_id A,C _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 US3 n 1 3 G n 1 4 US3 n 1 5 A n 1 6 C n 1 7 A n 1 8 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 8 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5TGP _struct_ref.pdbx_db_accession 5TGP _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 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 5TGP A 1 ? 8 ? 5TGP 1 ? 8 ? 1 8 2 1 5TGP C 1 ? 8 ? 5TGP 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 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 US3 'DNA linking' n '1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one' "2-Se-Thymidine-5'-phosphate" 'C10 H15 N2 O7 P Se' 385.169 # _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 5TGP _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 2.29 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 46.26 _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 7.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 294 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate, 0.012 M Spermine tetrahydrochloride, 0.080 M Sodium chloride, 0.020 M Magnesium chloride hexahydrate ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _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 'MAR CCD 130 mm' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-10-01 # _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 0.98 _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 8.2.1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.98 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 8.2.1 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5TGP _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 38.85 _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 6189 _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 97.1 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.5 _reflns.pdbx_Rmerge_I_obs 0.057 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 30.9 _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 0.788 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.6 _reflns_shell.d_res_low 1.66 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.13 _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 92.7 _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 0.351 _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 2.6 _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] 0.00 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][2] 0.00 _refine.aniso_B[2][3] 0.00 _refine.aniso_B[3][3] -0.01 _refine.B_iso_max ? _refine.B_iso_mean 24.167 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.969 _refine.correlation_coeff_Fo_to_Fc_free 0.954 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _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 5TGP _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 1.60 _refine.ls_d_res_low 38.85 _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 5882 _refine.ls_number_reflns_R_free 307 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 97.36 _refine.ls_percent_reflns_R_free 5.0 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.18948 _refine.ls_R_factor_R_free 0.20811 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.18848 _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 ? _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 1dns _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.086 _refine.pdbx_overall_ESU_R_Free 0.083 _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 1.930 _refine.overall_SU_ML 0.065 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _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 322 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 25 _refine_hist.number_atoms_total 347 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 38.85 # 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' ? 0.026 0.013 352 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.002 0.020 174 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 3.505 1.576 520 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 2.950 3.000 406 ? 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' ? 0.623 0.200 56 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.024 0.020 184 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.003 0.020 76 ? 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' ? 2.165 2.527 352 ? r_scbond_it ? ? 'X-RAY DIFFRACTION' ? 2.167 2.527 351 ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? 2.944 3.780 520 ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? 3.603 25.908 527 ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? 3.530 25.822 516 ? 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 1.601 _refine_ls_shell.d_res_low 1.643 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 19 _refine_ls_shell.number_reflns_R_work 381 _refine_ls_shell.percent_reflns_obs 89.89 _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 0.292 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.254 _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 ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 5TGP _struct.title 'DNA 8mer containing two 2SeT modifications' _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 5TGP _struct_keywords.text 'DNA, selenium, modification' _struct_keywords.pdbx_keywords DNA # 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 1 ? C N N 2 ? D N N 2 ? # 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 1 "O3'" ? ? ? 1_555 A US3 2 P ? ? A G 1 A US3 2 1_555 ? ? ? ? ? ? ? 1.547 ? ? covale2 covale one ? A US3 2 "O3'" ? ? ? 1_555 A G 3 P ? ? A US3 2 A G 3 1_555 ? ? ? ? ? ? ? 1.702 ? ? covale3 covale both ? A G 3 "O3'" ? ? ? 1_555 A US3 4 P ? ? A G 3 A US3 4 1_555 ? ? ? ? ? ? ? 1.589 ? ? covale4 covale one ? A US3 4 "O3'" ? ? ? 1_555 A A 5 P ? ? A US3 4 A A 5 1_555 ? ? ? ? ? ? ? 1.681 ? ? covale5 covale both ? B G 1 "O3'" ? ? ? 1_555 B US3 2 P ? ? C G 1 C US3 2 1_555 ? ? ? ? ? ? ? 1.675 ? ? covale6 covale one ? B US3 2 "O3'" ? ? ? 1_555 B G 3 P ? ? C US3 2 C G 3 1_555 ? ? ? ? ? ? ? 1.638 ? ? covale7 covale both ? B G 3 "O3'" ? ? ? 1_555 B US3 4 P ? ? C G 3 C US3 4 1_555 ? ? ? ? ? ? ? 1.446 ? ? covale8 covale one ? B US3 4 "O3'" ? ? ? 1_555 B A 5 P ? ? C US3 4 C A 5 1_555 ? ? ? ? ? ? ? 1.595 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 1 C C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 1 C C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 1 C C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A US3 2 N3 ? ? ? 1_555 B A 7 N1 ? ? A US3 2 C A 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A US3 2 O4 ? ? ? 1_555 B A 7 N6 ? ? A US3 2 C A 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 3 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 3 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 3 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A US3 4 N3 ? ? ? 1_555 B A 5 N1 ? ? A US3 4 C A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A US3 4 O4 ? ? ? 1_555 B A 5 N6 ? ? A US3 4 C A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 B US3 4 N3 ? ? A A 5 C US3 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 B US3 4 O4 ? ? A A 5 C US3 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 6 C G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 6 C G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 6 C G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 7 N1 ? ? ? 1_555 B US3 2 N3 ? ? A A 7 C US3 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 7 N6 ? ? ? 1_555 B US3 2 O4 ? ? A A 7 C US3 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 8 C G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 8 C G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 8 C G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 5TGP _atom_sites.fract_transf_matrix[1][1] 0.022291 _atom_sites.fract_transf_matrix[1][2] 0.012870 _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] 0.025740 _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] 0.023960 _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 SE # 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 G 1 1 1 G G A . n A 1 2 US3 2 2 2 US3 2ST A . n A 1 3 G 3 3 3 G G A . n A 1 4 US3 4 4 4 US3 2ST A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 A 7 7 7 A A A . n A 1 8 C 8 8 8 C C A . n B 1 1 G 1 1 1 G G C . n B 1 2 US3 2 2 2 US3 2ST C . n B 1 3 G 3 3 3 G G C . n B 1 4 US3 4 4 4 US3 2ST C . n B 1 5 A 5 5 5 A A C . n B 1 6 C 6 6 6 C C C . n B 1 7 A 7 7 7 A A C . n B 1 8 C 8 8 8 C C C . 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 2 HOH 1 101 23 HOH HOH A . C 2 HOH 2 102 18 HOH HOH A . C 2 HOH 3 103 4 HOH HOH A . C 2 HOH 4 104 22 HOH HOH A . C 2 HOH 5 105 1 HOH HOH A . C 2 HOH 6 106 8 HOH HOH A . C 2 HOH 7 107 3 HOH HOH A . C 2 HOH 8 108 6 HOH HOH A . C 2 HOH 9 109 20 HOH HOH A . C 2 HOH 10 110 9 HOH HOH A . C 2 HOH 11 111 12 HOH HOH A . C 2 HOH 12 112 2 HOH HOH A . C 2 HOH 13 113 21 HOH HOH A . D 2 HOH 1 101 7 HOH HOH C . D 2 HOH 2 102 14 HOH HOH C . D 2 HOH 3 103 17 HOH HOH C . D 2 HOH 4 104 5 HOH HOH C . D 2 HOH 5 105 13 HOH HOH C . D 2 HOH 6 106 10 HOH HOH C . D 2 HOH 7 107 25 HOH HOH C . D 2 HOH 8 108 11 HOH HOH C . D 2 HOH 9 109 16 HOH HOH C . D 2 HOH 10 110 24 HOH HOH C . D 2 HOH 11 111 26 HOH HOH C . D 2 HOH 12 112 15 HOH HOH C . # _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)' 780 ? 1 MORE -0 ? 1 'SSA (A^2)' 3080 ? # _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 2017-10-18 2 'Structure model' 1 1 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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 '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' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 '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' '_database_2.pdbx_DOI' 2 2 '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 ? ? ? 5.8.0069 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? 1.0 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? 1.0 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? 1.0 4 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 "O5'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 G _pdbx_validate_close_contact.auth_seq_id_1 1 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 101 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.11 # 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 US3 2 ? ? P A G 3 ? ? 1.702 1.607 0.095 0.012 Y 2 1 "O3'" A US3 4 ? ? P A A 5 ? ? 1.681 1.607 0.074 0.012 Y 3 1 "O3'" C G 3 ? ? P C US3 4 ? ? 1.446 1.607 -0.161 0.012 Y # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A G 1 ? ? "O3'" A G 1 ? ? P A US3 2 ? ? 133.73 119.70 14.03 1.20 Y 2 1 "O3'" A G 1 ? ? P A US3 2 ? ? OP2 A US3 2 ? ? 87.06 105.20 -18.14 2.20 Y 3 1 "C3'" A US3 2 ? ? "O3'" A US3 2 ? ? P A G 3 ? ? 109.02 119.70 -10.68 1.20 Y 4 1 "O3'" A US3 2 ? ? P A G 3 ? ? OP2 A G 3 ? ? 122.47 110.50 11.97 1.10 Y 5 1 "C3'" A G 3 ? ? "O3'" A G 3 ? ? P A US3 4 ? ? 127.10 119.70 7.40 1.20 Y 6 1 "O3'" A US3 4 ? ? P A A 5 ? ? OP2 A A 5 ? ? 117.63 110.50 7.13 1.10 Y 7 1 "O5'" A A 7 ? ? P A A 7 ? ? OP2 A A 7 ? ? 95.20 105.70 -10.50 0.90 N 8 1 "O5'" A C 8 ? ? P A C 8 ? ? OP1 A C 8 ? ? 97.93 105.70 -7.77 0.90 N 9 1 "C3'" C US3 2 ? ? "O3'" C US3 2 ? ? P C G 3 ? ? 133.50 119.70 13.80 1.20 Y 10 1 "O3'" C US3 2 ? ? P C G 3 ? ? "O5'" C G 3 ? ? 92.20 104.00 -11.80 1.90 Y 11 1 "C3'" C G 3 ? ? "O3'" C G 3 ? ? P C US3 4 ? ? 132.49 119.70 12.79 1.20 Y 12 1 "O3'" C G 3 ? ? P C US3 4 ? ? OP1 C US3 4 ? ? 81.52 105.20 -23.68 2.20 Y # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A G 1 ? "O2'" ? A G 1 "O2'" 2 1 Y 1 A G 3 ? "O2'" ? A G 3 "O2'" 3 1 Y 1 A A 5 ? "O2'" ? A A 5 "O2'" 4 1 Y 1 A C 6 ? "O2'" ? A C 6 "O2'" 5 1 Y 1 A A 7 ? "O2'" ? A A 7 "O2'" 6 1 Y 1 A C 8 ? "O2'" ? A C 8 "O2'" 7 1 Y 1 C G 1 ? "O2'" ? B G 1 "O2'" 8 1 Y 1 C G 3 ? "O2'" ? B G 3 "O2'" 9 1 Y 1 C A 5 ? "O2'" ? B A 5 "O2'" 10 1 Y 1 C C 6 ? "O2'" ? B C 6 "O2'" 11 1 Y 1 C A 7 ? "O2'" ? B A 7 "O2'" 12 1 Y 1 C C 8 ? "O2'" ? B C 8 "O2'" # 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 US3 P P N N 114 US3 N1 N N N 115 US3 C2 C N N 116 US3 SE2 SE N N 117 US3 N3 N N N 118 US3 C4 C N N 119 US3 O4 O N N 120 US3 C5 C N N 121 US3 C6 C N N 122 US3 "C1'" C N R 123 US3 OP3 O N N 124 US3 "C2'" C N N 125 US3 OP2 O N N 126 US3 "C3'" C N S 127 US3 "O3'" O N N 128 US3 "C4'" C N R 129 US3 "O4'" O N N 130 US3 "C5'" C N N 131 US3 "O5'" O N N 132 US3 C5A C N N 133 US3 H6 H N N 134 US3 "H1'" H N N 135 US3 HOP3 H N N 136 US3 "H2'" H N N 137 US3 "H2'A" H N N 138 US3 HOP2 H N N 139 US3 "H3'" H N N 140 US3 "HO3'" H N N 141 US3 "H4'" H N N 142 US3 "H5'" H N N 143 US3 "H5'A" H N N 144 US3 H5A H N N 145 US3 H5AA H N N 146 US3 H5AB H N N 147 US3 HSE2 H N N 148 US3 OP1 O N N 149 # 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 US3 P OP2 sing N N 118 US3 N1 "C1'" sing N N 119 US3 N1 C6 sing N N 120 US3 C2 N1 sing N N 121 US3 C2 N3 doub N N 122 US3 SE2 C2 sing N N 123 US3 SE2 HSE2 sing N N 124 US3 N3 C4 sing N N 125 US3 C4 O4 doub N N 126 US3 C4 C5 sing N N 127 US3 C5 C5A sing N N 128 US3 C6 C5 doub N N 129 US3 C6 H6 sing N N 130 US3 "C1'" "O4'" sing N N 131 US3 "C1'" "H1'" sing N N 132 US3 OP3 P sing N N 133 US3 OP3 HOP3 sing N N 134 US3 "C2'" "C1'" sing N N 135 US3 "C2'" "C3'" sing N N 136 US3 "C2'" "H2'" sing N N 137 US3 "C2'" "H2'A" sing N N 138 US3 OP2 HOP2 sing N N 139 US3 "C3'" "C4'" sing N N 140 US3 "C3'" "H3'" sing N N 141 US3 "O3'" "C3'" sing N N 142 US3 "O3'" "HO3'" sing N N 143 US3 "C4'" "O4'" sing N N 144 US3 "C4'" "C5'" sing N N 145 US3 "C4'" "H4'" sing N N 146 US3 "C5'" "O5'" sing N N 147 US3 "C5'" "H5'" sing N N 148 US3 "C5'" "H5'A" sing N N 149 US3 "O5'" P sing N N 150 US3 C5A H5A sing N N 151 US3 C5A H5AA sing N N 152 US3 C5A H5AB sing N N 153 US3 P OP1 doub N N 154 # _ndb_struct_conf_na.entry_id 5TGP _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 G 1 1_555 B C 8 1_555 -0.265 -0.087 -0.018 -12.200 -4.682 0.502 1 A_G1:C8_C A 1 ? C 8 ? 19 1 1 A US3 2 1_555 B A 7 1_555 -0.294 -0.115 0.126 -10.780 -12.192 -3.841 2 A_US32:A7_C A 2 ? C 7 ? 20 1 1 A G 3 1_555 B C 6 1_555 -0.168 -0.140 0.029 -6.652 -8.494 0.156 3 A_G3:C6_C A 3 ? C 6 ? 19 1 1 A US3 4 1_555 B A 5 1_555 -0.214 -0.109 -0.082 -2.719 -9.800 -5.796 4 A_US34:A5_C A 4 ? C 5 ? 20 1 1 A A 5 1_555 B US3 4 1_555 0.359 -0.076 0.025 1.288 -8.919 -5.229 5 A_A5:US34_C A 5 ? C 4 ? 20 1 1 A C 6 1_555 B G 3 1_555 0.249 -0.165 0.192 5.304 -9.978 -1.985 6 A_C6:G3_C A 6 ? C 3 ? 19 1 1 A A 7 1_555 B US3 2 1_555 0.154 -0.172 0.143 7.673 -12.070 -2.550 7 A_A7:US32_C A 7 ? C 2 ? 20 1 1 A C 8 1_555 B G 1 1_555 0.212 -0.192 0.072 2.324 -0.128 -1.937 8 A_C8:G1_C A 8 ? C 1 ? 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 G 1 1_555 B C 8 1_555 A US3 2 1_555 B A 7 1_555 -0.054 -2.055 3.340 1.401 5.194 33.554 -4.328 0.312 2.993 8.926 -2.408 33.970 1 AA_G1US32:A7C8_CC A 1 ? C 8 ? A 2 ? C 7 ? 1 A US3 2 1_555 B A 7 1_555 A G 3 1_555 B C 6 1_555 0.360 -1.443 3.129 1.960 10.659 28.072 -4.714 -0.339 2.448 21.010 -3.863 30.052 2 AA_US32G3:C6A7_CC A 2 ? C 7 ? A 3 ? C 6 ? 1 A G 3 1_555 B C 6 1_555 A US3 4 1_555 B A 5 1_555 -0.819 -1.396 3.266 0.123 6.378 33.421 -3.363 1.419 2.954 10.965 -0.211 34.007 3 AA_G3US34:A5C6_CC A 3 ? C 6 ? A 4 ? C 5 ? 1 A US3 4 1_555 B A 5 1_555 A A 5 1_555 B US3 4 1_555 0.163 -1.200 3.216 -0.441 9.945 31.580 -3.670 -0.356 2.720 17.731 0.786 33.073 4 AA_US34A5:US34A5_CC A 4 ? C 5 ? A 5 ? C 4 ? 1 A A 5 1_555 B US3 4 1_555 A C 6 1_555 B G 3 1_555 0.614 -1.492 3.308 -0.715 4.683 34.004 -3.247 -1.150 3.068 7.960 1.215 34.322 5 AA_A5C6:G3US34_CC A 5 ? C 4 ? A 6 ? C 3 ? 1 A C 6 1_555 B G 3 1_555 A A 7 1_555 B US3 2 1_555 0.026 -1.642 3.084 -1.131 8.929 28.719 -4.755 -0.252 2.470 17.467 2.212 30.068 6 AA_C6A7:US32G3_CC A 6 ? C 3 ? A 7 ? C 2 ? 1 A A 7 1_555 B US3 2 1_555 A C 8 1_555 B G 1 1_555 -0.089 -2.275 3.486 -1.826 4.098 35.292 -4.338 -0.127 3.210 6.726 2.997 35.567 7 AA_A7C8:G1US32_CC A 7 ? C 2 ? A 8 ? C 1 ? # _pdbx_entity_nonpoly.entity_id 2 _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 1DNS _pdbx_initial_refinement_model.details ? #