data_8KED # _entry.id 8KED # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.404 _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 8KED pdb_00008ked 10.2210/pdb8ked/pdb WWPDB D_1300040181 ? ? # 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 _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2025-02-19 ? 2 'Structure model' 1 1 2025-09-10 ? # _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 ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.journal_volume' 7 2 'Structure model' '_citation.pdbx_database_id_DOI' 8 2 'Structure model' '_citation.pdbx_database_id_PubMed' 9 2 'Structure model' '_citation.title' 10 2 'Structure model' '_citation.year' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8KED _pdbx_database_status.recvd_initial_deposition_date 2023-08-11 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBC _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email huanglin36@mail.sysu.edu.cn _pdbx_contact_author.name_first Lin _pdbx_contact_author.name_last Huang _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-2121-365X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Liao, W.' 1 ? 'Huang, L.' 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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 53 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title ;Crystal structures reveal the distinct features of the 2'-dG-III riboswitch in the purine riboswitch family. ; _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkaf702 _citation.pdbx_database_id_PubMed 40694847 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chen, K.' 1 0009-0005-1868-1056 primary 'Liao, W.' 2 0000-0001-9823-9949 primary 'Wang, J.' 3 ? primary 'Ren, Y.' 4 0009-0006-0959-2008 primary 'Lu, Z.' 5 ? primary 'Peng, X.' 6 ? primary 'Wang, J.' 7 ? primary 'Huang, L.' 8 0000-0002-2121-365X # 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 (72-MER)' 23024.611 1 ? ? ? ? 2 non-polymer syn "GUANOSINE-5'-TRIPHOSPHATE" 523.180 1 ? ? ? ? 3 non-polymer syn GUANINE 151.126 1 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 4 ? ? ? ? 5 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGAUUCGUAUAUCCUUAAUGAUAUGGUUUAAGGGCAAUACAUAGAGACCACAAAUUUCUUACUGCGAAUUCU _entity_poly.pdbx_seq_one_letter_code_can GGAUUCGUAUAUCCUUAAUGAUAUGGUUUAAGGGCAAUACAUAGAGACCACAAAUUUCUUACUGCGAAUUCU _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "GUANOSINE-5'-TRIPHOSPHATE" GTP 3 GUANINE GUN 4 'MAGNESIUM ION' MG 5 'SODIUM ION' NA # 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 G n 1 3 A n 1 4 U n 1 5 U n 1 6 C n 1 7 G n 1 8 U n 1 9 A n 1 10 U n 1 11 A n 1 12 U n 1 13 C n 1 14 C n 1 15 U n 1 16 U n 1 17 A n 1 18 A n 1 19 U n 1 20 G n 1 21 A n 1 22 U n 1 23 A n 1 24 U n 1 25 G n 1 26 G n 1 27 U n 1 28 U n 1 29 U n 1 30 A n 1 31 A n 1 32 G n 1 33 G n 1 34 G n 1 35 C n 1 36 A n 1 37 A n 1 38 U n 1 39 A n 1 40 C n 1 41 A n 1 42 U n 1 43 A n 1 44 G n 1 45 A n 1 46 G n 1 47 A n 1 48 C n 1 49 C n 1 50 A n 1 51 C n 1 52 A n 1 53 A n 1 54 A n 1 55 U n 1 56 U n 1 57 U n 1 58 C n 1 59 U n 1 60 U n 1 61 A n 1 62 C n 1 63 U n 1 64 G n 1 65 C n 1 66 G n 1 67 A n 1 68 A n 1 69 U n 1 70 U n 1 71 C n 1 72 U 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 72 _pdbx_entity_src_syn.organism_scientific 'Bacillus sp.' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 1409 _pdbx_entity_src_syn.details ? # 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 GTP non-polymer n "GUANOSINE-5'-TRIPHOSPHATE" ? 'C10 H16 N5 O14 P3' 523.180 GUN non-polymer . GUANINE ? 'C5 H5 N5 O' 151.126 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 ? ? ? A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 U 4 4 4 U U A . n A 1 5 U 5 5 5 U U A . n A 1 6 C 6 6 6 C C A . n A 1 7 G 7 7 7 G G A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 U 10 10 10 U U A . n A 1 11 A 11 11 11 A A A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 C 14 14 14 C C A . n A 1 15 U 15 15 15 U U A . n A 1 16 U 16 16 16 U U A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 U 19 19 19 U U A . n A 1 20 G 20 20 20 G G A . n A 1 21 A 21 21 21 A A A . n A 1 22 U 22 22 22 U U A . n A 1 23 A 23 23 23 A A A . n A 1 24 U 24 24 24 U U A . n A 1 25 G 25 25 25 G G A . n A 1 26 G 26 26 26 G G A . n A 1 27 U 27 27 27 U U A . n A 1 28 U 28 28 28 U U A . n A 1 29 U 29 29 29 U U A . n A 1 30 A 30 30 30 A A A . n A 1 31 A 31 31 31 A A A . n A 1 32 G 32 32 32 G G A . n A 1 33 G 33 33 33 G G A . n A 1 34 G 34 34 34 G G A . n A 1 35 C 35 35 35 C C A . n A 1 36 A 36 36 36 A A A . n A 1 37 A 37 37 37 A A A . n A 1 38 U 38 38 38 U U A . n A 1 39 A 39 39 39 A A A . n A 1 40 C 40 40 40 C C A . n A 1 41 A 41 41 41 A A A . n A 1 42 U 42 42 42 U U A . n A 1 43 A 43 43 43 A A A . n A 1 44 G 44 44 44 G G A . n A 1 45 A 45 45 45 A A A . n A 1 46 G 46 46 46 G G A . n A 1 47 A 47 47 47 A A A . n A 1 48 C 48 48 48 C C A . n A 1 49 C 49 49 49 C C A . n A 1 50 A 50 50 50 A A A . n A 1 51 C 51 51 51 C C A . n A 1 52 A 52 52 52 A A A . n A 1 53 A 53 53 53 A A A . n A 1 54 A 54 54 54 A A A . n A 1 55 U 55 55 55 U U A . n A 1 56 U 56 56 56 U U A . n A 1 57 U 57 57 57 U U A . n A 1 58 C 58 58 58 C C A . n A 1 59 U 59 59 59 U U A . n A 1 60 U 60 60 60 U U A . n A 1 61 A 61 61 61 A A A . n A 1 62 C 62 62 62 C C A . n A 1 63 U 63 63 63 U U A . n A 1 64 G 64 64 64 G G A . n A 1 65 C 65 65 65 C C A . n A 1 66 G 66 66 66 G G A . n A 1 67 A 67 67 67 A A A . n A 1 68 A 68 68 68 A A A . n A 1 69 U 69 69 69 U U A . n A 1 70 U 70 70 70 U U A . n A 1 71 C 71 71 71 C C A . n A 1 72 U 72 72 72 U U A . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id GUN _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id GUN _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # 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 B 2 GTP 1 101 1 GTP GTP A . C 3 GUN 1 102 99 GUN GUN A . D 4 MG 1 103 1 MG MG A . E 4 MG 1 104 2 MG MG A . F 4 MG 1 105 3 MG MG A . G 4 MG 1 106 4 MG MG A . H 5 NA 1 107 1 NA NA A . # 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 ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 113.380 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 8KED _cell.details ? _cell.formula_units_Z ? _cell.length_a 138.674 _cell.length_a_esd ? _cell.length_b 26.182 _cell.length_b_esd ? _cell.length_c 65.524 _cell.length_c_esd ? _cell.volume 218368.714 _cell.volume_esd ? _cell.Z_PDB 4 _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 ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8KED _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # _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 8KED _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 2.37 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 48.12 _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.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_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 6.4 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;0.08 M Sodium chloride, 0.01 M Potassium chloride, 0.01 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 6.4, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride, 0.1M Glycine. ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 291 # _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.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2023-01-08 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _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 0.97918 _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 'SSRF BEAMLINE BL10U2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97918 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL10U2 _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate 69.84 _reflns.entry_id 8KED _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.10 _reflns.d_resolution_low 63.64 _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 12561 _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 96.7 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 5.3 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 10.9 _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 0.024 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.998 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.050 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 2.10 _reflns_shell.d_res_low 2.21 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 0.6 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 1654 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _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 3.4 _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 1.157 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.450 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all 91.7 _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 1.883 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 105.86 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _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 8KED _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 2.11 _refine.ls_d_res_low 24.30 _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 12345 _refine.ls_number_reflns_R_free 552 _refine.ls_number_reflns_R_work 11793 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 95.03 _refine.ls_percent_reflns_R_free 4.47 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2143 _refine.ls_R_factor_R_free 0.2531 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2123 _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 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _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 1.33 _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 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _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 49.6578 _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 ? _refine.overall_SU_ML 0.3376 _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 LAST _refine_hist.details ? _refine_hist.d_res_high 2.11 _refine_hist.d_res_low 24.30 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1550 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1502 _refine_hist.pdbx_number_atoms_ligand 48 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # 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' ? 0.0031 ? 1724 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.7486 ? 2680 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0332 ? 359 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0046 ? 73 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 13.7839 ? 863 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _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_error _refine_ls_shell.R_factor_R_work _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_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 2.11 2.32 . . 115 2639 86.22 . . . . 0.5613 . . . . . . . . . . . 0.6029 'X-RAY DIFFRACTION' 2.32 2.65 . . 132 3061 99.38 . . . . 0.4388 . . . . . . . . . . . 0.4804 'X-RAY DIFFRACTION' 2.65 3.34 . . 145 2988 96.70 . . . . 0.2849 . . . . . . . . . . . 0.3271 'X-RAY DIFFRACTION' 3.34 24.30 . . 160 3105 97.64 . . . . 0.1556 . . . . . . . . . . . 0.2028 # _struct.entry_id 8KED _struct.title ;Crystal structure of 2'-dG-III riboswitch with guanine ; _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 8KED _struct_keywords.text ;Riboswitch, 2'-Deoxyguanosine, 2'-dG, Guanine, Aptamer, RNA ; _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 4 ? G N N 4 ? H N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8KED _struct_ref.pdbx_db_accession 8KED _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8KED _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 72 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 8KED _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 72 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 72 # _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # 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)' 490 ? 1 MORE -11 ? 1 'SSA (A^2)' 12190 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _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_ _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 2 P ? ? ? 1_555 B GTP . "O3'" ? ? A G 2 A GTP 101 1_555 ? ? ? ? ? ? ? 1.562 ? ? metalc1 metalc ? ? A G 2 O6 ? ? ? 1_555 H NA . NA ? ? A G 2 A NA 107 1_555 ? ? ? ? ? ? ? 2.881 ? ? metalc2 metalc ? ? A U 8 O4 ? ? ? 1_555 D MG . MG ? ? A U 8 A MG 103 1_555 ? ? ? ? ? ? ? 2.713 ? ? metalc3 metalc ? ? A A 9 OP2 ? ? ? 1_555 G MG . MG ? ? A A 9 A MG 106 1_555 ? ? ? ? ? ? ? 2.155 ? ? metalc4 metalc ? ? A U 10 "O3'" ? ? ? 1_555 F MG . MG ? ? A U 10 A MG 105 1_555 ? ? ? ? ? ? ? 2.753 ? ? metalc5 metalc ? ? A U 10 "O2'" ? ? ? 1_555 F MG . MG ? ? A U 10 A MG 105 1_555 ? ? ? ? ? ? ? 2.570 ? ? metalc6 metalc ? ? A A 11 OP1 ? ? ? 1_555 G MG . MG ? ? A A 11 A MG 106 1_555 ? ? ? ? ? ? ? 2.757 ? ? metalc7 metalc ? ? A U 63 O4 ? ? ? 1_555 D MG . MG ? ? A U 63 A MG 103 1_555 ? ? ? ? ? ? ? 2.850 ? ? metalc8 metalc ? ? A G 64 O6 ? ? ? 1_555 D MG . MG ? ? A G 64 A MG 103 1_555 ? ? ? ? ? ? ? 2.497 ? ? metalc9 metalc ? ? A U 70 O4 ? ? ? 1_555 H NA . NA ? ? A U 70 A NA 107 1_555 ? ? ? ? ? ? ? 3.000 ? ? metalc10 metalc ? ? B GTP . O6 ? ? ? 1_555 H NA . NA ? ? A GTP 101 A NA 107 1_555 ? ? ? ? ? ? ? 3.140 ? ? metalc11 metalc ? ? C GUN . O6 ? ? ? 1_555 F MG . MG ? ? A GUN 102 A MG 105 1_555 ? ? ? ? ? ? ? 2.796 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 70 O2 ? ? A G 2 A U 70 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 70 N3 ? ? A G 2 A U 70 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 69 N3 ? ? A A 3 A U 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 69 O4 ? ? A A 3 A U 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 68 N1 ? ? A U 4 A A 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 68 N6 ? ? A U 4 A A 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 5 N3 ? ? ? 1_555 A A 67 N1 ? ? A U 5 A A 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 5 O4 ? ? ? 1_555 A A 67 N6 ? ? A U 5 A A 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 66 N1 ? ? A C 6 A G 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 66 O6 ? ? A C 6 A G 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 66 N2 ? ? A C 6 A G 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 65 N3 ? ? A G 7 A C 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 65 O2 ? ? A G 7 A C 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 65 N4 ? ? A G 7 A C 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 8 N3 ? ? ? 1_555 A G 64 O6 ? ? A U 8 A G 64 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog16 hydrog ? ? A U 8 O2 ? ? ? 1_555 A G 64 N1 ? ? A U 8 A G 64 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog17 hydrog ? ? A A 9 N1 ? ? ? 1_555 A U 63 N3 ? ? A A 9 A U 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 9 N6 ? ? ? 1_555 A U 63 O4 ? ? A A 9 A U 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 39 N1 ? ? A U 10 A A 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 10 O4 ? ? ? 1_555 A A 39 N6 ? ? A U 10 A A 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 11 N1 ? ? ? 1_555 A G 34 N2 ? ? A A 11 A G 34 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog22 hydrog ? ? A A 11 N6 ? ? ? 1_555 A G 34 N3 ? ? A A 11 A G 34 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog23 hydrog ? ? A U 12 N3 ? ? ? 1_555 A A 41 N7 ? ? A U 12 A A 41 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog24 hydrog ? ? A U 12 O4 ? ? ? 1_555 A A 41 N6 ? ? A U 12 A A 41 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog25 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 13 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 13 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 13 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 14 N3 ? ? ? 1_555 A G 32 N1 ? ? A C 14 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 14 N4 ? ? ? 1_555 A G 32 O6 ? ? A C 14 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 32 N2 ? ? A C 14 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 15 N3 ? ? ? 1_555 A A 31 N1 ? ? A U 15 A A 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 15 O4 ? ? ? 1_555 A A 31 N6 ? ? A U 15 A A 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 30 N1 ? ? A U 16 A A 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 30 N6 ? ? A U 16 A A 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A A 17 N1 ? ? ? 1_555 A U 29 N3 ? ? A A 17 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A A 17 N6 ? ? ? 1_555 A U 29 O4 ? ? A A 17 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A A 18 N1 ? ? ? 1_555 A U 28 N3 ? ? A A 18 A U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A A 18 N6 ? ? ? 1_555 A U 28 O4 ? ? A A 18 A U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 19 N3 ? ? ? 1_555 A U 27 O4 ? ? A U 19 A U 27 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog40 hydrog ? ? A U 19 O2 ? ? ? 1_555 A U 27 N3 ? ? A U 19 A U 27 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog41 hydrog ? ? A A 21 N1 ? ? ? 1_555 A A 54 N6 ? ? A A 21 A A 54 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog42 hydrog ? ? A A 21 N6 ? ? ? 1_555 A A 54 N7 ? ? A A 21 A A 54 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog43 hydrog ? ? A U 22 O2 ? ? ? 1_555 A G 25 N2 ? ? A U 22 A G 25 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog44 hydrog ? ? A U 22 N3 ? ? ? 1_555 A A 53 N7 ? ? A U 22 A A 53 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog45 hydrog ? ? A U 22 O2 ? ? ? 1_555 A A 53 N6 ? ? A U 22 A A 53 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog46 hydrog ? ? A A 23 N6 ? ? ? 1_555 A A 52 N1 ? ? A A 23 A A 52 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog47 hydrog ? ? A A 23 N7 ? ? ? 1_555 A A 52 N6 ? ? A A 23 A A 52 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog48 hydrog ? ? A G 25 N1 ? ? ? 1_555 A C 49 N3 ? ? A G 25 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 25 N2 ? ? ? 1_555 A C 49 O2 ? ? A G 25 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A G 25 O6 ? ? ? 1_555 A C 49 N4 ? ? A G 25 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A G 26 N1 ? ? ? 1_555 A C 48 N3 ? ? A G 26 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A G 26 N2 ? ? ? 1_555 A C 48 O2 ? ? A G 26 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A G 26 O6 ? ? ? 1_555 A C 48 N4 ? ? A G 26 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A G 26 N2 ? ? ? 1_555 A A 54 N1 ? ? A G 26 A A 54 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog55 hydrog ? ? A G 26 N3 ? ? ? 1_555 A A 54 N6 ? ? A G 26 A A 54 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog56 hydrog ? ? A G 34 N1 ? ? ? 1_555 A C 40 N3 ? ? A G 34 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A G 34 N2 ? ? ? 1_555 A C 40 O2 ? ? A G 34 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A G 34 O6 ? ? ? 1_555 A C 40 N4 ? ? A G 34 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A A 37 N6 ? ? ? 1_555 A U 63 O2 ? ? A A 37 A U 63 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog60 hydrog ? ? A U 42 N3 ? ? ? 1_555 A U 60 O2 ? ? A U 42 A U 60 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog61 hydrog ? ? A U 42 O4 ? ? ? 1_555 A U 60 N3 ? ? A U 42 A U 60 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog62 hydrog ? ? A A 43 N1 ? ? ? 1_555 A U 59 N3 ? ? A A 43 A U 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A A 43 N6 ? ? ? 1_555 A U 59 O4 ? ? A A 43 A U 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A G 44 N1 ? ? ? 1_555 A C 58 N3 ? ? A G 44 A C 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A G 44 N2 ? ? ? 1_555 A C 58 O2 ? ? A G 44 A C 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A G 44 O6 ? ? ? 1_555 A C 58 N4 ? ? A G 44 A C 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A A 45 N1 ? ? ? 1_555 A U 57 N3 ? ? A A 45 A U 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A A 45 N6 ? ? ? 1_555 A U 57 O4 ? ? A A 45 A U 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A G 46 N1 ? ? ? 1_555 A U 56 O2 ? ? A G 46 A U 56 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog70 hydrog ? ? A G 46 O6 ? ? ? 1_555 A U 56 N3 ? ? A G 46 A U 56 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog71 hydrog ? ? A A 47 N1 ? ? ? 1_555 A U 55 N3 ? ? A A 47 A U 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A A 47 N6 ? ? ? 1_555 A U 55 O4 ? ? A A 47 A U 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A C 49 O2 ? ? ? 1_555 A A 53 N6 ? ? A C 49 A A 53 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O6 ? A G 2 ? A G 2 ? 1_555 NA ? H NA . ? A NA 107 ? 1_555 O4 ? A U 70 ? A U 70 ? 1_555 70.1 ? 2 O6 ? A G 2 ? A G 2 ? 1_555 NA ? H NA . ? A NA 107 ? 1_555 O6 ? B GTP . ? A GTP 101 ? 1_555 64.6 ? 3 O4 ? A U 70 ? A U 70 ? 1_555 NA ? H NA . ? A NA 107 ? 1_555 O6 ? B GTP . ? A GTP 101 ? 1_555 85.6 ? 4 O4 ? A U 8 ? A U 8 ? 1_555 MG ? D MG . ? A MG 103 ? 1_555 O4 ? A U 63 ? A U 63 ? 1_555 110.5 ? 5 O4 ? A U 8 ? A U 8 ? 1_555 MG ? D MG . ? A MG 103 ? 1_555 O6 ? A G 64 ? A G 64 ? 1_555 83.2 ? 6 O4 ? A U 63 ? A U 63 ? 1_555 MG ? D MG . ? A MG 103 ? 1_555 O6 ? A G 64 ? A G 64 ? 1_555 81.5 ? 7 OP2 ? A A 9 ? A A 9 ? 1_555 MG ? G MG . ? A MG 106 ? 1_555 OP1 ? A A 11 ? A A 11 ? 1_555 90.5 ? 8 "O3'" ? A U 10 ? A U 10 ? 1_555 MG ? F MG . ? A MG 105 ? 1_555 "O2'" ? A U 10 ? A U 10 ? 1_555 61.3 ? 9 "O3'" ? A U 10 ? A U 10 ? 1_555 MG ? F MG . ? A MG 105 ? 1_555 O6 ? C GUN . ? A GUN 102 ? 1_555 138.7 ? 10 "O2'" ? A U 10 ? A U 10 ? 1_555 MG ? F MG . ? A MG 105 ? 1_555 O6 ? C GUN . ? A GUN 102 ? 1_555 79.9 ? # _pdbx_entry_details.entry_id 8KED _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_protein_modification N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -x,y,-z 3 x+1/2,y+1/2,z 4 -x+1/2,y+1/2,-z # 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 -31.1480113503 -4.3721019725 22.4853229811 0.746369931678 ? 0.0572223257693 ? -0.000655710957814 ? 1.01054139983 ? 0.0396774912511 ? 0.812576144962 ? 1.30997290237 ? -0.060415065561 ? 0.768007679702 ? 0.668254124429 ? -1.20164095952 ? 1.23096067913 ? 0.165645120522 ? -0.472673393554 ? 0.037509054502 ? 0.0571830320395 ? 0.325581629715 ? -0.0766819730284 ? -0.283102422091 ? -0.664538645989 ? -0.00300284848389 ? 2 'X-RAY DIFFRACTION' ? refined -31.663469212 -9.48841033604 40.0364650383 0.895107017312 ? 0.0522475641084 ? -0.0284141759036 ? 1.85497503351 ? 0.206604673599 ? 0.946776021035 ? 0.0764416764733 ? -0.0155605703981 ? -0.0133745185883 ? 0.209331132634 ? 0.0882445147778 ? 0.0746514856439 ? -0.148094131079 ? -0.275030236086 ? 0.120304039804 ? 0.176787895493 ? 0.355193459393 ? -0.00836498637761 ? -0.26074928177 ? 0.155233096677 ? -0.00100565434517 ? 3 'X-RAY DIFFRACTION' ? refined -41.5677602591 2.50927999633 19.0451119872 0.967674672797 ? 0.325596263395 ? 0.127349639155 ? 1.18006141096 ? 0.119523334818 ? 0.781755686331 ? 0.158624092944 ? 0.0775217597747 ? 0.101520016922 ? 0.133668508033 ? 0.00678991221712 ? 0.0929084254235 ? 0.192994584379 ? -0.846834130162 ? 0.0647190312694 ? -0.622545622656 ? -0.00156340514119 ? -0.378534038889 ? 0.293183076217 ? -0.0822568137036 ? 0.00415678492907 ? 4 'X-RAY DIFFRACTION' ? refined -26.3688777605 -5.42388835288 35.34050858 0.758636501344 ? 0.237717175055 ? -0.111603282237 ? 1.08276733753 ? -0.00177375662089 ? 0.821569744075 ? 0.234251338169 ? -0.158549781227 ? 0.378616369044 ? 1.03096691071 ? -0.577573673731 ? 0.898477681159 ? -0.00715730710949 ? -1.61381908952 ? -0.477757539234 ? 0.32337787149 ? 0.504765644394 ? -0.142199659736 ? 0.41372823627 ? -1.67892908005 ? 0.0495060176445 ? 5 'X-RAY DIFFRACTION' ? refined -23.6492704093 -8.0440001284 8.41445275568 0.816795343451 ? -0.00431153158443 ? 0.0232069255345 ? 0.729424664591 ? -0.0552574687419 ? 0.866082117482 ? 0.116085361516 ? -0.366916305223 ? 0.195172199828 ? 0.44690981611 ? -0.269293558439 ? 0.202229810208 ? 0.265026187254 ? 0.347888715684 ? 0.195224137024 ? 0.0810213182396 ? 0.138232587078 ? -0.302995451413 ? -0.0369390803643 ? -0.35024601653 ? -0.00036194516583 ? # 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.beg_PDB_ins_code _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.end_PDB_ins_code _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 B ? A 2 ? B ? A 21 ? ? ;chain 'A' and (resid 2 through 21 ) ; 2 'X-RAY DIFFRACTION' 2 B ? A 22 ? B ? A 31 ? ? ;chain 'A' and (resid 22 through 31 ) ; 3 'X-RAY DIFFRACTION' 3 B ? A 32 ? B ? A 36 ? ? ;chain 'A' and (resid 32 through 36 ) ; 4 'X-RAY DIFFRACTION' 4 B ? A 37 ? B ? A 56 ? ? ;chain 'A' and (resid 37 through 56 ) ; 5 'X-RAY DIFFRACTION' 5 B ? A 57 ? B ? A 72 ? ? ;chain 'A' and (resid 57 through 72 ) ; # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id G _pdbx_unobs_or_zero_occ_residues.auth_seq_id 1 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id G _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 # 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 GTP PG P N N 111 GTP O1G O N N 112 GTP O2G O N N 113 GTP O3G O N N 114 GTP O3B O N N 115 GTP PB P N N 116 GTP O1B O N N 117 GTP O2B O N N 118 GTP O3A O N N 119 GTP PA P N N 120 GTP O1A O N N 121 GTP O2A O N N 122 GTP "O5'" O N N 123 GTP "C5'" C N N 124 GTP "C4'" C N R 125 GTP "O4'" O N N 126 GTP "C3'" C N S 127 GTP "O3'" O N N 128 GTP "C2'" C N R 129 GTP "O2'" O N N 130 GTP "C1'" C N R 131 GTP N9 N Y N 132 GTP C8 C Y N 133 GTP N7 N Y N 134 GTP C5 C Y N 135 GTP C6 C N N 136 GTP O6 O N N 137 GTP N1 N N N 138 GTP C2 C N N 139 GTP N2 N N N 140 GTP N3 N N N 141 GTP C4 C Y N 142 GTP HOG2 H N N 143 GTP HOG3 H N N 144 GTP HOB2 H N N 145 GTP HOA2 H N N 146 GTP "H5'" H N N 147 GTP "H5''" H N N 148 GTP "H4'" H N N 149 GTP "H3'" H N N 150 GTP "HO3'" H N N 151 GTP "H2'" H N N 152 GTP "HO2'" H N N 153 GTP "H1'" H N N 154 GTP H8 H N N 155 GTP HN1 H N N 156 GTP HN21 H N N 157 GTP HN22 H N N 158 GUN N9 N Y N 159 GUN C8 C Y N 160 GUN N7 N Y N 161 GUN C5 C Y N 162 GUN C6 C N N 163 GUN O6 O N N 164 GUN N1 N N N 165 GUN C2 C N N 166 GUN N2 N N N 167 GUN N3 N N N 168 GUN C4 C Y N 169 GUN HN9 H N N 170 GUN H8 H N N 171 GUN HN1 H N N 172 GUN HN21 H N N 173 GUN HN22 H N N 174 MG MG MG N N 175 NA NA NA N N 176 U OP3 O N N 177 U P P N N 178 U OP1 O N N 179 U OP2 O N N 180 U "O5'" O N N 181 U "C5'" C N N 182 U "C4'" C N R 183 U "O4'" O N N 184 U "C3'" C N S 185 U "O3'" O N N 186 U "C2'" C N R 187 U "O2'" O N N 188 U "C1'" C N R 189 U N1 N N N 190 U C2 C N N 191 U O2 O N N 192 U N3 N N N 193 U C4 C N N 194 U O4 O N N 195 U C5 C N N 196 U C6 C N N 197 U HOP3 H N N 198 U HOP2 H N N 199 U "H5'" H N N 200 U "H5''" H N N 201 U "H4'" H N N 202 U "H3'" H N N 203 U "HO3'" H N N 204 U "H2'" H N N 205 U "HO2'" H N N 206 U "H1'" H N N 207 U H3 H N N 208 U H5 H N N 209 U H6 H N N 210 # 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 GTP PG O1G doub N N 116 GTP PG O2G sing N N 117 GTP PG O3G sing N N 118 GTP PG O3B sing N N 119 GTP O2G HOG2 sing N N 120 GTP O3G HOG3 sing N N 121 GTP O3B PB sing N N 122 GTP PB O1B doub N N 123 GTP PB O2B sing N N 124 GTP PB O3A sing N N 125 GTP O2B HOB2 sing N N 126 GTP O3A PA sing N N 127 GTP PA O1A doub N N 128 GTP PA O2A sing N N 129 GTP PA "O5'" sing N N 130 GTP O2A HOA2 sing N N 131 GTP "O5'" "C5'" sing N N 132 GTP "C5'" "C4'" sing N N 133 GTP "C5'" "H5'" sing N N 134 GTP "C5'" "H5''" sing N N 135 GTP "C4'" "O4'" sing N N 136 GTP "C4'" "C3'" sing N N 137 GTP "C4'" "H4'" sing N N 138 GTP "O4'" "C1'" sing N N 139 GTP "C3'" "O3'" sing N N 140 GTP "C3'" "C2'" sing N N 141 GTP "C3'" "H3'" sing N N 142 GTP "O3'" "HO3'" sing N N 143 GTP "C2'" "O2'" sing N N 144 GTP "C2'" "C1'" sing N N 145 GTP "C2'" "H2'" sing N N 146 GTP "O2'" "HO2'" sing N N 147 GTP "C1'" N9 sing N N 148 GTP "C1'" "H1'" sing N N 149 GTP N9 C8 sing Y N 150 GTP N9 C4 sing Y N 151 GTP C8 N7 doub Y N 152 GTP C8 H8 sing N N 153 GTP N7 C5 sing Y N 154 GTP C5 C6 sing N N 155 GTP C5 C4 doub Y N 156 GTP C6 O6 doub N N 157 GTP C6 N1 sing N N 158 GTP N1 C2 sing N N 159 GTP N1 HN1 sing N N 160 GTP C2 N2 sing N N 161 GTP C2 N3 doub N N 162 GTP N2 HN21 sing N N 163 GTP N2 HN22 sing N N 164 GTP N3 C4 sing N N 165 GUN N9 C8 sing Y N 166 GUN N9 C4 sing Y N 167 GUN N9 HN9 sing N N 168 GUN C8 N7 doub Y N 169 GUN C8 H8 sing N N 170 GUN N7 C5 sing Y N 171 GUN C5 C6 sing N N 172 GUN C5 C4 doub Y N 173 GUN C6 O6 doub N N 174 GUN C6 N1 sing N N 175 GUN N1 C2 sing N N 176 GUN N1 HN1 sing N N 177 GUN C2 N2 sing N N 178 GUN C2 N3 doub N N 179 GUN N2 HN21 sing N N 180 GUN N2 HN22 sing N N 181 GUN N3 C4 sing N N 182 U OP3 P sing N N 183 U OP3 HOP3 sing N N 184 U P OP1 doub N N 185 U P OP2 sing N N 186 U P "O5'" sing N N 187 U OP2 HOP2 sing N N 188 U "O5'" "C5'" sing N N 189 U "C5'" "C4'" sing N N 190 U "C5'" "H5'" sing N N 191 U "C5'" "H5''" sing N N 192 U "C4'" "O4'" sing N N 193 U "C4'" "C3'" sing N N 194 U "C4'" "H4'" sing N N 195 U "O4'" "C1'" sing N N 196 U "C3'" "O3'" sing N N 197 U "C3'" "C2'" sing N N 198 U "C3'" "H3'" sing N N 199 U "O3'" "HO3'" sing N N 200 U "C2'" "O2'" sing N N 201 U "C2'" "C1'" sing N N 202 U "C2'" "H2'" sing N N 203 U "O2'" "HO2'" sing N N 204 U "C1'" N1 sing N N 205 U "C1'" "H1'" sing N N 206 U N1 C2 sing N N 207 U N1 C6 sing N N 208 U C2 O2 doub N N 209 U C2 N3 sing N N 210 U N3 C4 sing N N 211 U N3 H3 sing N N 212 U C4 O4 doub N N 213 U C4 C5 sing N N 214 U C5 C6 doub N N 215 U C5 H5 sing N N 216 U C6 H6 sing N N 217 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8KED 'double helix' 8KED 'a-form double helix' 8KED 'mismatched base pair' 8KED 'three-way junction' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 2 1_555 A U 70 1_555 -1.803 -0.473 0.473 5.628 -8.655 -2.614 1 A_G2:U70_A A 2 ? A 70 ? 28 1 1 A A 3 1_555 A U 69 1_555 0.008 -0.057 0.296 2.489 -10.193 3.609 2 A_A3:U69_A A 3 ? A 69 ? 20 1 1 A U 4 1_555 A A 68 1_555 -0.184 -0.140 0.451 -2.021 -8.986 -2.221 3 A_U4:A68_A A 4 ? A 68 ? 20 1 1 A U 5 1_555 A A 67 1_555 -0.103 -0.102 0.245 -0.819 -6.936 2.398 4 A_U5:A67_A A 5 ? A 67 ? 20 1 1 A C 6 1_555 A G 66 1_555 0.198 -0.177 0.177 -0.285 -8.092 1.511 5 A_C6:G66_A A 6 ? A 66 ? 19 1 1 A G 7 1_555 A C 65 1_555 -0.194 -0.102 -0.046 -13.551 -16.008 0.796 6 A_G7:C65_A A 7 ? A 65 ? 19 1 1 A U 8 1_555 A G 64 1_555 1.866 -0.452 0.357 -9.323 -12.104 0.935 7 A_U8:G64_A A 8 ? A 64 ? 28 1 1 A A 9 1_555 A U 63 1_555 0.048 -0.053 0.435 -1.806 -7.470 -2.744 8 A_A9:U63_A A 9 ? A 63 ? 20 1 1 A U 27 1_555 A U 19 1_555 -2.440 -1.991 0.481 0.110 -15.613 15.349 9 A_U27:U19_A A 27 ? A 19 ? 16 1 1 A U 28 1_555 A A 18 1_555 -0.118 -0.156 0.431 -7.898 -5.975 6.197 10 A_U28:A18_A A 28 ? A 18 ? 20 1 1 A U 29 1_555 A A 17 1_555 -0.098 -0.096 0.198 -3.225 0.402 3.095 11 A_U29:A17_A A 29 ? A 17 ? 20 1 1 A A 30 1_555 A U 16 1_555 0.118 -0.052 0.426 2.528 -3.617 -1.084 12 A_A30:U16_A A 30 ? A 16 ? 20 1 1 A A 31 1_555 A U 15 1_555 0.158 -0.033 0.014 0.503 -1.210 -1.071 13 A_A31:U15_A A 31 ? A 15 ? 20 1 1 A G 32 1_555 A C 14 1_555 -0.122 -0.027 0.165 0.931 -5.251 -0.292 14 A_G32:C14_A A 32 ? A 14 ? 19 1 1 A G 33 1_555 A C 13 1_555 -0.156 -0.168 0.110 -4.527 -3.344 0.522 15 A_G33:C13_A A 33 ? A 13 ? 19 1 1 A G 34 1_555 A C 40 1_555 -0.202 -0.114 0.138 2.034 9.054 0.462 16 A_G34:C40_A A 34 ? A 40 ? 19 1 1 A U 10 1_555 A A 39 1_555 -0.013 -0.109 0.075 16.442 -3.378 2.448 17 A_U10:A39_A A 10 ? A 39 ? 20 1 1 A U 12 1_555 A A 41 1_555 -0.407 3.506 -0.398 -0.745 7.177 -65.831 18 A_U12:A41_A A 12 ? A 41 ? 23 3 1 A U 60 1_555 A U 42 1_555 2.317 -1.755 0.300 12.443 -3.076 16.417 19 A_U60:U42_A A 60 ? A 42 ? 16 1 1 A U 59 1_555 A A 43 1_555 0.098 -0.135 0.092 1.676 1.910 3.629 20 A_U59:A43_A A 59 ? A 43 ? 20 1 1 A C 58 1_555 A G 44 1_555 0.186 -0.141 0.259 -3.324 -0.845 1.482 21 A_C58:G44_A A 58 ? A 44 ? 19 1 1 A U 57 1_555 A A 45 1_555 0.015 -0.075 0.401 -4.972 3.999 4.443 22 A_U57:A45_A A 57 ? A 45 ? 20 1 1 A U 56 1_555 A G 46 1_555 1.906 -0.426 -0.323 3.684 -5.378 7.208 23 A_U56:G46_A A 56 ? A 46 ? 28 1 1 A U 55 1_555 A A 47 1_555 0.047 -0.004 -0.070 7.046 -5.362 2.110 24 A_U55:A47_A A 55 ? A 47 ? 20 1 1 A G 26 1_555 A C 48 1_555 0.040 -0.097 0.912 18.934 -8.089 -1.785 25 A_G26:C48_A A 26 ? A 48 ? 19 1 1 A G 25 1_555 A C 49 1_555 -0.061 -0.234 0.840 4.906 -7.552 -4.090 26 A_G25:C49_A A 25 ? A 49 ? 19 1 1 A A 52 1_555 A A 23 1_555 3.713 2.224 0.207 21.409 6.870 -109.959 27 A_A52:A23_A A 52 ? A 23 ? 5 4 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 2 1_555 A U 70 1_555 A A 3 1_555 A U 69 1_555 -0.042 -1.193 3.299 -2.685 3.703 42.211 -2.022 -0.213 3.185 5.124 3.715 42.447 1 AA_G2A3:U69U70_AA A 2 ? A 70 ? A 3 ? A 69 ? 1 A A 3 1_555 A U 69 1_555 A U 4 1_555 A A 68 1_555 -0.450 -1.583 3.232 -2.778 4.919 31.656 -3.703 0.336 2.986 8.928 5.041 32.144 2 AA_A3U4:A68U69_AA A 3 ? A 69 ? A 4 ? A 68 ? 1 A U 4 1_555 A A 68 1_555 A U 5 1_555 A A 67 1_555 0.209 -1.213 3.062 1.243 4.475 34.040 -2.693 -0.176 2.889 7.599 -2.111 34.347 3 AA_U4U5:A67A68_AA A 4 ? A 68 ? A 5 ? A 67 ? 1 A U 5 1_555 A A 67 1_555 A C 6 1_555 A G 66 1_555 0.442 -1.249 3.225 1.038 2.393 36.059 -2.342 -0.570 3.149 3.859 -1.675 36.150 4 AA_U5C6:G66A67_AA A 5 ? A 67 ? A 6 ? A 66 ? 1 A C 6 1_555 A G 66 1_555 A G 7 1_555 A C 65 1_555 0.001 -1.807 3.334 1.907 16.513 29.938 -5.394 0.266 2.079 29.297 -3.384 34.151 5 AA_C6G7:C65G66_AA A 6 ? A 66 ? A 7 ? A 65 ? 1 A G 7 1_555 A C 65 1_555 A U 8 1_555 A G 64 1_555 0.014 -1.084 3.162 -1.310 2.861 40.538 -1.864 -0.159 3.080 4.121 1.887 40.655 6 AA_G7U8:G64C65_AA A 7 ? A 65 ? A 8 ? A 64 ? 1 A U 8 1_555 A G 64 1_555 A A 9 1_555 A U 63 1_555 -0.387 -1.423 2.756 4.117 11.863 26.325 -4.764 1.441 1.873 24.363 -8.456 29.119 7 AA_U8A9:U63G64_AA A 8 ? A 64 ? A 9 ? A 63 ? 1 A U 27 1_555 A U 19 1_555 A U 28 1_555 A A 18 1_555 -0.562 -1.243 3.491 -1.024 1.839 46.068 -1.754 0.624 3.453 2.348 1.308 46.113 8 AA_U27U28:A18U19_AA A 27 ? A 19 ? A 28 ? A 18 ? 1 A U 28 1_555 A A 18 1_555 A U 29 1_555 A A 17 1_555 -0.541 -1.826 3.077 2.281 3.824 25.968 -4.922 1.734 2.727 8.431 -5.029 26.340 9 AA_U28U29:A17A18_AA A 28 ? A 18 ? A 29 ? A 17 ? 1 A U 29 1_555 A A 17 1_555 A A 30 1_555 A U 16 1_555 -0.312 -1.805 2.871 -1.894 7.971 31.083 -4.425 0.288 2.361 14.559 3.460 32.118 10 AA_U29A30:U16A17_AA A 29 ? A 17 ? A 30 ? A 16 ? 1 A A 30 1_555 A U 16 1_555 A A 31 1_555 A U 15 1_555 -0.431 -1.824 3.319 0.979 3.850 30.496 -4.178 1.001 3.057 7.281 -1.850 30.748 11 AA_A30A31:U15U16_AA A 30 ? A 16 ? A 31 ? A 15 ? 1 A A 31 1_555 A U 15 1_555 A G 32 1_555 A C 14 1_555 0.272 -1.797 3.192 -0.924 7.050 29.758 -4.682 -0.683 2.696 13.486 1.769 30.577 12 AA_A31G32:C14U15_AA A 31 ? A 15 ? A 32 ? A 14 ? 1 A G 32 1_555 A C 14 1_555 A G 33 1_555 A C 13 1_555 0.403 -2.090 3.286 1.522 6.368 34.118 -4.428 -0.454 2.876 10.731 -2.565 34.722 13 AA_G32G33:C13C14_AA A 32 ? A 14 ? A 33 ? A 13 ? 1 A G 33 1_555 A C 13 1_555 A G 34 1_555 A C 40 1_555 2.630 -0.980 2.977 3.932 -2.116 51.381 -0.990 -2.771 3.192 -2.435 -4.525 51.562 14 AA_G33G34:C40C13_AA A 33 ? A 13 ? A 34 ? A 40 ? 1 A G 34 1_555 A C 40 1_555 A U 10 1_555 A A 39 1_555 -1.925 -0.556 3.015 0.472 6.501 46.039 -1.202 2.476 2.897 8.263 -0.600 46.473 15 AA_G34U10:A39C40_AA A 34 ? A 40 ? A 10 ? A 39 ? 1 A U 12 1_555 A A 41 1_555 A U 60 1_555 A U 42 1_555 3.848 -1.213 -2.317 -128.767 -113.997 110.806 -1.164 -1.296 -3.086 -57.468 64.913 175.447 16 AA_U12U60:U42A41_AA A 12 ? A 41 ? A 60 ? A 42 ? 1 A U 60 1_555 A U 42 1_555 A U 59 1_555 A A 43 1_555 -0.434 1.610 -2.923 2.086 -6.803 -34.488 -3.518 -0.980 -2.540 11.326 3.473 -35.192 17 AA_U60U59:A43U42_AA A 60 ? A 42 ? A 59 ? A 43 ? 1 A U 59 1_555 A A 43 1_555 A C 58 1_555 A G 44 1_555 -0.174 1.867 -3.073 0.666 -4.167 -28.713 -4.551 -0.479 -2.775 8.346 1.334 -29.015 18 AA_U59C58:G44A43_AA A 59 ? A 43 ? A 58 ? A 44 ? 1 A C 58 1_555 A G 44 1_555 A U 57 1_555 A A 45 1_555 0.199 2.147 -3.111 -1.889 -5.589 -29.588 -5.139 0.724 -2.653 10.808 -3.654 -30.158 19 AA_C58U57:A45G44_AA A 58 ? A 44 ? A 57 ? A 45 ? 1 A U 57 1_555 A A 45 1_555 A U 56 1_555 A G 46 1_555 1.045 2.696 -3.327 6.341 -10.308 -21.891 -8.950 0.745 -2.084 24.849 15.287 -24.978 20 AA_U57U56:G46A45_AA A 57 ? A 45 ? A 56 ? A 46 ? 1 A U 56 1_555 A G 46 1_555 A U 55 1_555 A A 47 1_555 -0.482 1.808 -3.458 -3.113 -0.484 -39.167 -2.750 -0.325 -3.463 0.720 -4.635 -39.288 21 AA_U56U55:A47G46_AA A 56 ? A 46 ? A 55 ? A 47 ? 1 A U 55 1_555 A A 47 1_555 A G 26 1_555 A C 48 1_555 2.129 1.047 -3.153 2.154 -7.270 -53.022 -1.600 2.235 -3.073 8.096 2.399 -53.522 22 AA_U55G26:C48A47_AA A 55 ? A 47 ? A 26 ? A 48 ? 1 A G 26 1_555 A C 48 1_555 A G 25 1_555 A C 49 1_555 -0.704 1.085 -3.015 -1.130 -5.900 -27.378 -3.486 -1.215 -2.752 12.279 -2.351 -28.017 23 AA_G26G25:C49C48_AA A 26 ? A 48 ? A 25 ? A 49 ? 1 A G 25 1_555 A C 49 1_555 A A 52 1_555 A A 23 1_555 -3.964 0.598 -3.965 -4.388 3.865 132.170 0.359 2.204 -3.888 2.113 2.399 132.237 24 AA_G25A52:A23C49_AA A 25 ? A 49 ? A 52 ? A 23 ? # _pdbx_audit_support.funding_organization 'National Natural Science Foundation of China (NSFC)' _pdbx_audit_support.country China _pdbx_audit_support.grant_number 32171191 _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list 8KEB _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 8KEB _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'C 1 2 1' _space_group.name_Hall 'C 2y' _space_group.IT_number 5 _space_group.crystal_system monoclinic _space_group.id 1 # _atom_sites.entry_id 8KED _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.007211 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.003118 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.038194 _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] 0.016627 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? MG ? ? 9.41153 2.53737 ? ? 2.59044 63.03566 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? NA ? ? 9.38062 1.54875 ? ? 3.38349 72.32734 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ # loop_ #