data_5CKK # _entry.id 5CKK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 5CKK pdb_00005ckk 10.2210/pdb5ckk/pdb WWPDB D_1000211367 ? ? # 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 2016-01-13 2 'Structure model' 1 1 2016-01-20 3 'Structure model' 1 2 2024-01-10 # _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 ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_dist_value' 4 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 5 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 6 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5CKK _pdbx_database_status.recvd_initial_deposition_date 2015-07-15 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBE _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 'Ponce-Salvatierra, A.' 1 'Hoebartner, C.' 2 'Pena, V.' 3 # _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 Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 1476-4687 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 529 _citation.language ? _citation.page_first 231 _citation.page_last 234 _citation.title 'Crystal structure of a DNA catalyst.' _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/nature16471 _citation.pdbx_database_id_PubMed 26735012 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ponce-Salvatierra, A.' 1 ? primary 'Wawrzyniak-Turek, K.' 2 ? primary 'Steuerwald, U.' 3 ? primary 'Hobartner, C.' 4 ? primary 'Pena, V.' 5 ? # 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 (44-MER)' 13651.733 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(P*GP*CP*AP*CP*UP*AP*GP*AP*UP*CP*GP*GP*AP*UP*G)-3') ; 4831.938 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 3 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no ;(DA)(DT)(DC)(DC)(DG)(DA)(DT)(DG)(DG)(DA)(DT)(DC)(DA)(DT)(DA)(DC)(DG)(DG)(DT)(DC) (DG)(DG)(DA)(DG)(DG)(DG)(DG)(DT)(DT)(DT)(DG)(DC)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG) (DT)(DG)(DC)(DC) ; ATCCGATGGATCATACGGTCGGAGGGGTTTGCCGTTTAAGTGCC Y ? 2 polyribonucleotide no no GCACUAGAUCGGAUG GCACUAGAUCGGAUG D ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name 'MAGNESIUM ION' _pdbx_entity_nonpoly.comp_id MG # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DT n 1 3 DC n 1 4 DC n 1 5 DG n 1 6 DA n 1 7 DT n 1 8 DG n 1 9 DG n 1 10 DA n 1 11 DT n 1 12 DC n 1 13 DA n 1 14 DT n 1 15 DA n 1 16 DC n 1 17 DG n 1 18 DG n 1 19 DT n 1 20 DC n 1 21 DG n 1 22 DG n 1 23 DA n 1 24 DG n 1 25 DG n 1 26 DG n 1 27 DG n 1 28 DT n 1 29 DT n 1 30 DT n 1 31 DG n 1 32 DC n 1 33 DC n 1 34 DG n 1 35 DT n 1 36 DT n 1 37 DT n 1 38 DA n 1 39 DA n 1 40 DG n 1 41 DT n 1 42 DG n 1 43 DC n 1 44 DC n 2 1 G n 2 2 C n 2 3 A n 2 4 C n 2 5 U n 2 6 A n 2 7 G n 2 8 A n 2 9 U n 2 10 C n 2 11 G n 2 12 G n 2 13 A n 2 14 U n 2 15 G n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 44 'synthetic construct' ? 32630 ? 2 1 sample 1 15 'synthetic construct' ? 32630 ? # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 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 DA 1 1 1 DA DA Y . n A 1 2 DT 2 2 2 DT DT Y . n A 1 3 DC 3 3 3 DC DC Y . n A 1 4 DC 4 4 4 DC DC Y . n A 1 5 DG 5 5 5 DG DG Y . n A 1 6 DA 6 6 6 DA DA Y . n A 1 7 DT 7 7 7 DT DT Y . n A 1 8 DG 8 8 8 DG DG Y . n A 1 9 DG 9 9 9 DG DG Y . n A 1 10 DA 10 10 10 DA DA Y . n A 1 11 DT 11 11 11 DT DT Y . n A 1 12 DC 12 12 12 DC DC Y . n A 1 13 DA 13 13 13 DA DA Y . n A 1 14 DT 14 14 14 DT DT Y . n A 1 15 DA 15 15 15 DA DA Y . n A 1 16 DC 16 16 16 DC DC Y . n A 1 17 DG 17 17 17 DG DG Y . n A 1 18 DG 18 18 18 DG DG Y . n A 1 19 DT 19 19 19 DT DT Y . n A 1 20 DC 20 20 20 DC DC Y . n A 1 21 DG 21 21 21 DG DG Y . n A 1 22 DG 22 22 22 DG DG Y . n A 1 23 DA 23 23 23 DA DA Y . n A 1 24 DG 24 24 24 DG DG Y . n A 1 25 DG 25 25 25 DG DG Y . n A 1 26 DG 26 26 26 DG DG Y . n A 1 27 DG 27 27 27 DG DG Y . n A 1 28 DT 28 28 28 DT DT Y . n A 1 29 DT 29 29 29 DT DT Y . n A 1 30 DT 30 30 30 DT DT Y . n A 1 31 DG 31 31 31 DG DG Y . n A 1 32 DC 32 32 32 DC DC Y . n A 1 33 DC 33 33 33 DC DC Y . n A 1 34 DG 34 34 34 DG DG Y . n A 1 35 DT 35 35 35 DT DT Y . n A 1 36 DT 36 36 36 DT DT Y . n A 1 37 DT 37 37 37 DT DT Y . n A 1 38 DA 38 38 38 DA DA Y . n A 1 39 DA 39 39 39 DA DA Y . n A 1 40 DG 40 40 40 DG DG Y . n A 1 41 DT 41 41 41 DT DT Y . n A 1 42 DG 42 42 42 DG DG Y . n A 1 43 DC 43 43 43 DC DC Y . n A 1 44 DC 44 44 44 DC DC Y . n B 2 1 G 1 -6 -6 G G D . n B 2 2 C 2 -5 -5 C C D . n B 2 3 A 3 -4 -4 A A D . n B 2 4 C 4 -3 -3 C C D . n B 2 5 U 5 -2 -2 U U D . n B 2 6 A 6 -1 -1 A A D . n B 2 7 G 7 1 1 G G D . n B 2 8 A 8 2 2 A A D . n B 2 9 U 9 3 3 U U D . n B 2 10 C 10 4 4 C C D . n B 2 11 G 11 5 5 G G D . n B 2 12 G 12 6 6 G G D . n B 2 13 A 13 7 7 A A D . n B 2 14 U 14 8 8 U U D . n B 2 15 G 15 9 9 G G D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 MG 1 101 1 MG MG Y . D 3 MG 1 102 2 MG MG Y . E 3 MG 1 101 3 MG MG D . # 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 ? ? ? '(1.10_2155: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 4 # _cell.entry_id 5CKK _cell.length_a 83.155 _cell.length_b 83.155 _cell.length_c 55.995 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CKK _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # _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 5CKK _exptl.crystals_number ? _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.62 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 53.03 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'MPD, spermine, magnesium chloride, sodium chloride, sodium cacodylate' _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 PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-03-13 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'SLS BEAMLINE X10SA' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline X10SA _diffrn_source.pdbx_synchrotron_site SLS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5CKK _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.8 _reflns.d_resolution_low 41.58 _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 5146 _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 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 4 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 33.87 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.8 _reflns_shell.d_res_low 2.9 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 0.43 _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 97 _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 6.13 _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 25.8 _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5CKK _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 4995 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.33 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 46.446 _refine.ls_d_res_high 2.801 _refine.ls_percent_reflns_obs 96.63 _refine.ls_R_factor_obs 0.2755 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2748 _refine.ls_R_factor_R_free 0.2872 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.98 _refine.ls_number_reflns_R_free 249 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.details ? _refine.pdbx_starting_model 5CKI _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.35 _refine.pdbx_overall_phase_error 33.25 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1232 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1235 _refine_hist.d_res_high 2.801 _refine_hist.d_res_low 46.446 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.015 ? ? 1388 'X-RAY DIFFRACTION' ? f_angle_d 0.659 ? ? 2134 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 30.205 ? ? 614 'X-RAY DIFFRACTION' ? f_chiral_restr 0.033 ? ? 251 'X-RAY DIFFRACTION' ? f_plane_restr 0.004 ? ? 59 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 2.8009 3.5287 2234 0.2797 94.00 0.4024 . . 117 . . . . 'X-RAY DIFFRACTION' . 3.5287 46.4526 2512 0.2742 100.00 0.2734 . . 132 . . . . # _struct.entry_id 5CKK _struct.title 'Crystal structure of 9DB1* deoxyribozyme' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5CKK _struct_keywords.text 'deoxyribozyme, RNA-ligase, catalytic DNA, ligase' _struct_keywords.pdbx_keywords LIGASE # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 3 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 5CKK 5CKK ? 1 ? 1 2 PDB 5CKK 5CKK ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 5CKK Y 1 ? 44 ? 5CKK 1 ? 44 ? 1 44 2 2 5CKK D 1 ? 15 ? 5CKK -6 ? 9 ? -6 9 # _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 # 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)' 2740 ? 1 MORE -29 ? 1 'SSA (A^2)' 9540 ? # _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 # _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 metalc1 metalc ? ? A DT 14 OP1 ? ? ? 1_555 D MG . MG ? ? Y DT 14 Y MG 102 1_555 ? ? ? ? ? ? ? 2.066 ? ? metalc2 metalc ? ? A DT 14 OP2 ? ? ? 1_555 D MG . MG ? ? Y DT 14 Y MG 102 1_555 ? ? ? ? ? ? ? 2.373 ? ? metalc3 metalc ? ? A DA 15 OP2 ? ? ? 1_555 C MG . MG ? ? Y DA 15 Y MG 101 1_555 ? ? ? ? ? ? ? 2.167 ? ? metalc4 metalc ? ? A DA 15 OP1 ? ? ? 1_555 D MG . MG ? ? Y DA 15 Y MG 102 1_555 ? ? ? ? ? ? ? 2.147 ? ? metalc5 metalc ? ? B G 7 O6 ? ? ? 1_555 E MG . MG ? ? D G 1 D MG 101 1_555 ? ? ? ? ? ? ? 2.543 ? ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B U 14 N3 ? ? Y DA 1 D U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B U 14 O4 ? ? Y DA 1 D U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B A 13 N1 ? ? Y DT 2 D A 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B A 13 N6 ? ? Y DT 2 D A 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B G 12 N2 ? ? Y DC 3 D G 6 1_555 ? ? ? ? ? ? 'DC-G PAIR' ? ? ? hydrog6 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B G 11 O6 ? ? Y DC 4 D G 5 1_555 ? ? ? ? ? ? 'DC-G PAIR' ? ? ? hydrog7 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B G 12 N2 ? ? Y DC 4 D G 6 1_555 ? ? ? ? ? ? 'DC-G PAIR' ? ? ? hydrog8 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B C 10 N3 ? ? Y DG 5 D C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B C 10 O2 ? ? Y DG 5 D C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B C 10 N4 ? ? Y DG 5 D C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B U 9 N3 ? ? Y DA 6 D U 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B U 9 O4 ? ? Y DA 6 D U 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B A 8 N1 ? ? Y DT 7 D A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B A 8 N6 ? ? Y DT 7 D A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 8 N3 ? ? ? 1_555 A DA 10 N6 ? ? Y DG 8 Y DA 10 1_555 ? ? ? ? ? ? 'DG-DA MISPAIR' ? ? ? hydrog16 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DG 26 N7 ? ? Y DG 8 Y DG 26 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog17 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DG 26 O6 ? ? Y DG 8 Y DG 26 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog18 hydrog ? ? A DC 12 N3 ? ? ? 1_555 A DG 26 N1 ? ? Y DC 12 Y DG 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 12 N4 ? ? ? 1_555 A DG 26 O6 ? ? Y DC 12 Y DG 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 12 O2 ? ? ? 1_555 A DG 26 N2 ? ? Y DC 12 Y DG 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 14 O4 ? ? ? 1_555 A DG 21 N1 ? ? Y DT 14 Y DG 21 1_555 ? ? ? ? ? ? 'DT-DG MISPAIR' ? ? ? hydrog22 hydrog ? ? A DT 14 N3 ? ? ? 1_555 A DG 25 O6 ? ? Y DT 14 Y DG 25 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A DT 14 O2 ? ? ? 1_555 A DG 25 N1 ? ? Y DT 14 Y DG 25 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog24 hydrog ? ? A DC 16 N3 ? ? ? 1_555 A DG 34 N1 ? ? Y DC 16 Y DG 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 16 N4 ? ? ? 1_555 A DG 34 O6 ? ? Y DC 16 Y DG 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 16 O2 ? ? ? 1_555 A DG 34 N2 ? ? Y DC 16 Y DG 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 17 N1 ? ? ? 1_555 A DC 33 N3 ? ? Y DG 17 Y DC 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 17 N2 ? ? ? 1_555 A DC 33 O2 ? ? Y DG 17 Y DC 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 17 O6 ? ? ? 1_555 A DC 33 N4 ? ? Y DG 17 Y DC 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 18 N2 ? ? ? 1_555 A DG 22 O6 ? ? Y DG 18 Y DG 22 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog31 hydrog ? ? A DG 18 N1 ? ? ? 1_555 A DC 32 N3 ? ? Y DG 18 Y DC 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 18 N2 ? ? ? 1_555 A DC 32 O2 ? ? Y DG 18 Y DC 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DG 18 O6 ? ? ? 1_555 A DC 32 N4 ? ? Y DG 18 Y DC 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DC 20 N3 ? ? ? 1_555 A DG 31 N1 ? ? Y DC 20 Y DG 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DC 20 N4 ? ? ? 1_555 A DG 31 O6 ? ? Y DC 20 Y DG 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DC 20 O2 ? ? ? 1_555 A DG 31 N2 ? ? Y DC 20 Y DG 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DG 21 N3 ? ? ? 1_555 A DA 23 N6 ? ? Y DG 21 Y DA 23 1_555 ? ? ? ? ? ? 'DG-DA MISPAIR' ? ? ? hydrog38 hydrog ? ? A DA 23 N1 ? ? ? 1_555 A DG 31 N2 ? ? Y DA 23 Y DG 31 1_555 ? ? ? ? ? ? 'DA-DG MISPAIR' ? ? ? hydrog39 hydrog ? ? A DG 25 N2 ? ? ? 1_555 A DT 30 O2 ? ? Y DG 25 Y DT 30 1_555 ? ? ? ? ? ? 'DG-DT MISPAIR' ? ? ? hydrog40 hydrog ? ? A DT 29 O2 ? ? ? 1_555 B G 7 N2 ? ? Y DT 29 D G 1 1_555 ? ? ? ? ? ? 'DT-G MISPAIR' ? ? ? hydrog41 hydrog ? ? A DT 35 O4 ? ? ? 1_555 A DT 37 N3 ? ? Y DT 35 Y DT 37 1_555 ? ? ? ? ? ? 'DT-DT MISPAIR' ? ? ? hydrog42 hydrog ? ? A DA 39 N1 ? ? ? 1_555 B U 5 N3 ? ? Y DA 39 D U -2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A DA 39 N6 ? ? ? 1_555 B U 5 O4 ? ? Y DA 39 D U -2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A DG 40 N1 ? ? ? 1_555 B C 4 N3 ? ? Y DG 40 D C -3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A DG 40 N2 ? ? ? 1_555 B C 4 O2 ? ? Y DG 40 D C -3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A DG 40 O6 ? ? ? 1_555 B C 4 N4 ? ? Y DG 40 D C -3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A DT 41 N3 ? ? ? 1_555 B A 3 N1 ? ? Y DT 41 D A -4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A DT 41 O4 ? ? ? 1_555 B A 3 N6 ? ? Y DT 41 D A -4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A DG 42 N1 ? ? ? 1_555 B C 2 N3 ? ? Y DG 42 D C -5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A DG 42 N2 ? ? ? 1_555 B C 2 O2 ? ? Y DG 42 D C -5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A DG 42 O6 ? ? ? 1_555 B C 2 N4 ? ? Y DG 42 D C -5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A DC 43 O2 ? ? ? 1_555 B G 1 N2 ? ? Y DC 43 D G -6 1_555 ? ? ? ? ? ? 'DC-G PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference 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 OP1 ? A DT 14 ? Y DT 14 ? 1_555 MG ? D MG . ? Y MG 102 ? 1_555 OP2 ? A DT 14 ? Y DT 14 ? 1_555 70.0 ? 2 OP1 ? A DT 14 ? Y DT 14 ? 1_555 MG ? D MG . ? Y MG 102 ? 1_555 OP1 ? A DA 15 ? Y DA 15 ? 1_555 91.8 ? 3 OP2 ? A DT 14 ? Y DT 14 ? 1_555 MG ? D MG . ? Y MG 102 ? 1_555 OP1 ? A DA 15 ? Y DA 15 ? 1_555 102.1 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software Y MG 101 ? 1 'binding site for residue MG Y 101' AC2 Software Y MG 102 ? 2 'binding site for residue MG Y 102' AC3 Software D MG 101 ? 2 'binding site for residue MG D 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 1 DA A 15 ? DA Y 15 . ? 1_555 ? 2 AC2 2 DT A 14 ? DT Y 14 . ? 1_555 ? 3 AC2 2 DA A 15 ? DA Y 15 . ? 1_555 ? 4 AC3 2 A B 6 ? A D -1 . ? 1_555 ? 5 AC3 2 G B 7 ? G D 1 . ? 1_555 ? # 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 "O4'" Y DA 15 ? ? "C1'" Y DA 15 ? ? N9 Y DA 15 ? ? 110.57 108.30 2.27 0.30 N 2 1 "O4'" Y DT 35 ? ? "C1'" Y DT 35 ? ? N1 Y DT 35 ? ? 110.32 108.30 2.02 0.30 N # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 4.3772 _pdbx_refine_tls.origin_y -23.6843 _pdbx_refine_tls.origin_z 9.4008 _pdbx_refine_tls.T[1][1] 1.3092 _pdbx_refine_tls.T[2][2] 1.3290 _pdbx_refine_tls.T[3][3] 0.5892 _pdbx_refine_tls.T[1][2] -0.2404 _pdbx_refine_tls.T[1][3] -0.1115 _pdbx_refine_tls.T[2][3] 0.0195 _pdbx_refine_tls.L[1][1] 5.9474 _pdbx_refine_tls.L[2][2] 3.3674 _pdbx_refine_tls.L[3][3] 5.8713 _pdbx_refine_tls.L[1][2] 0.2787 _pdbx_refine_tls.L[1][3] -3.4591 _pdbx_refine_tls.L[2][3] 1.7706 _pdbx_refine_tls.S[1][1] 0.3726 _pdbx_refine_tls.S[1][2] 0.4383 _pdbx_refine_tls.S[1][3] 0.7633 _pdbx_refine_tls.S[2][1] 0.0438 _pdbx_refine_tls.S[2][2] -0.1089 _pdbx_refine_tls.S[2][3] 0.2399 _pdbx_refine_tls.S[3][1] -0.4431 _pdbx_refine_tls.S[3][2] 0.3141 _pdbx_refine_tls.S[3][3] -0.2850 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id ? _pdbx_refine_tls_group.beg_auth_seq_id ? _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id ? _pdbx_refine_tls_group.end_auth_seq_id ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ;chain 'D' or chain 'Y' ; # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 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 DA OP3 O N N 73 DA P P N N 74 DA OP1 O N N 75 DA OP2 O N N 76 DA "O5'" O N N 77 DA "C5'" C N N 78 DA "C4'" C N R 79 DA "O4'" O N N 80 DA "C3'" C N S 81 DA "O3'" O N N 82 DA "C2'" C N N 83 DA "C1'" C N R 84 DA N9 N Y N 85 DA C8 C Y N 86 DA N7 N Y N 87 DA C5 C Y N 88 DA C6 C Y N 89 DA N6 N N N 90 DA N1 N Y N 91 DA C2 C Y N 92 DA N3 N Y N 93 DA C4 C Y N 94 DA HOP3 H N N 95 DA HOP2 H N N 96 DA "H5'" H N N 97 DA "H5''" H N N 98 DA "H4'" H N N 99 DA "H3'" H N N 100 DA "HO3'" H N N 101 DA "H2'" H N N 102 DA "H2''" H N N 103 DA "H1'" H N N 104 DA H8 H N N 105 DA H61 H N N 106 DA H62 H N N 107 DA H2 H N N 108 DC OP3 O N N 109 DC P P N N 110 DC OP1 O N N 111 DC OP2 O N N 112 DC "O5'" O N N 113 DC "C5'" C N N 114 DC "C4'" C N R 115 DC "O4'" O N N 116 DC "C3'" C N S 117 DC "O3'" O N N 118 DC "C2'" C N N 119 DC "C1'" C N R 120 DC N1 N N N 121 DC C2 C N N 122 DC O2 O N N 123 DC N3 N N N 124 DC C4 C N N 125 DC N4 N N N 126 DC C5 C N N 127 DC C6 C N N 128 DC HOP3 H N N 129 DC HOP2 H N N 130 DC "H5'" H N N 131 DC "H5''" H N N 132 DC "H4'" H N N 133 DC "H3'" H N N 134 DC "HO3'" H N N 135 DC "H2'" H N N 136 DC "H2''" H N N 137 DC "H1'" H N N 138 DC H41 H N N 139 DC H42 H N N 140 DC H5 H N N 141 DC H6 H N N 142 DG OP3 O N N 143 DG P P N N 144 DG OP1 O N N 145 DG OP2 O N N 146 DG "O5'" O N N 147 DG "C5'" C N N 148 DG "C4'" C N R 149 DG "O4'" O N N 150 DG "C3'" C N S 151 DG "O3'" O N N 152 DG "C2'" C N N 153 DG "C1'" C N R 154 DG N9 N Y N 155 DG C8 C Y N 156 DG N7 N Y N 157 DG C5 C Y N 158 DG C6 C N N 159 DG O6 O N N 160 DG N1 N N N 161 DG C2 C N N 162 DG N2 N N N 163 DG N3 N N N 164 DG C4 C Y N 165 DG HOP3 H N N 166 DG HOP2 H N N 167 DG "H5'" H N N 168 DG "H5''" H N N 169 DG "H4'" H N N 170 DG "H3'" H N N 171 DG "HO3'" H N N 172 DG "H2'" H N N 173 DG "H2''" H N N 174 DG "H1'" H N N 175 DG H8 H N N 176 DG H1 H N N 177 DG H21 H N N 178 DG H22 H N N 179 DT OP3 O N N 180 DT P P N N 181 DT OP1 O N N 182 DT OP2 O N N 183 DT "O5'" O N N 184 DT "C5'" C N N 185 DT "C4'" C N R 186 DT "O4'" O N N 187 DT "C3'" C N S 188 DT "O3'" O N N 189 DT "C2'" C N N 190 DT "C1'" C N R 191 DT N1 N N N 192 DT C2 C N N 193 DT O2 O N N 194 DT N3 N N N 195 DT C4 C N N 196 DT O4 O N N 197 DT C5 C N N 198 DT C7 C N N 199 DT C6 C N N 200 DT HOP3 H N N 201 DT HOP2 H N N 202 DT "H5'" H N N 203 DT "H5''" H N N 204 DT "H4'" H N N 205 DT "H3'" H N N 206 DT "HO3'" H N N 207 DT "H2'" H N N 208 DT "H2''" H N N 209 DT "H1'" H N N 210 DT H3 H N N 211 DT H71 H N N 212 DT H72 H N N 213 DT H73 H N N 214 DT H6 H N N 215 G OP3 O N N 216 G P P N N 217 G OP1 O N N 218 G OP2 O N N 219 G "O5'" O N N 220 G "C5'" C N N 221 G "C4'" C N R 222 G "O4'" O N N 223 G "C3'" C N S 224 G "O3'" O N N 225 G "C2'" C N R 226 G "O2'" O N N 227 G "C1'" C N R 228 G N9 N Y N 229 G C8 C Y N 230 G N7 N Y N 231 G C5 C Y N 232 G C6 C N N 233 G O6 O N N 234 G N1 N N N 235 G C2 C N N 236 G N2 N N N 237 G N3 N N N 238 G C4 C Y N 239 G HOP3 H N N 240 G HOP2 H N N 241 G "H5'" H N N 242 G "H5''" H N N 243 G "H4'" H N N 244 G "H3'" H N N 245 G "HO3'" H N N 246 G "H2'" H N N 247 G "HO2'" H N N 248 G "H1'" H N N 249 G H8 H N N 250 G H1 H N N 251 G H21 H N N 252 G H22 H N N 253 MG MG MG N N 254 U OP3 O N N 255 U P P N N 256 U OP1 O N N 257 U OP2 O N N 258 U "O5'" O N N 259 U "C5'" C N N 260 U "C4'" C N R 261 U "O4'" O N N 262 U "C3'" C N S 263 U "O3'" O N N 264 U "C2'" C N R 265 U "O2'" O N N 266 U "C1'" C N R 267 U N1 N N N 268 U C2 C N N 269 U O2 O N N 270 U N3 N N N 271 U C4 C N N 272 U O4 O N N 273 U C5 C N N 274 U C6 C N N 275 U HOP3 H N N 276 U HOP2 H N N 277 U "H5'" H N N 278 U "H5''" H N N 279 U "H4'" H N N 280 U "H3'" H N N 281 U "HO3'" H N N 282 U "H2'" H N N 283 U "HO2'" H N N 284 U "H1'" H N N 285 U H3 H N N 286 U H5 H N N 287 U H6 H N N 288 # 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 DA OP3 P sing N N 76 DA OP3 HOP3 sing N N 77 DA P OP1 doub N N 78 DA P OP2 sing N N 79 DA P "O5'" sing N N 80 DA OP2 HOP2 sing N N 81 DA "O5'" "C5'" sing N N 82 DA "C5'" "C4'" sing N N 83 DA "C5'" "H5'" sing N N 84 DA "C5'" "H5''" sing N N 85 DA "C4'" "O4'" sing N N 86 DA "C4'" "C3'" sing N N 87 DA "C4'" "H4'" sing N N 88 DA "O4'" "C1'" sing N N 89 DA "C3'" "O3'" sing N N 90 DA "C3'" "C2'" sing N N 91 DA "C3'" "H3'" sing N N 92 DA "O3'" "HO3'" sing N N 93 DA "C2'" "C1'" sing N N 94 DA "C2'" "H2'" sing N N 95 DA "C2'" "H2''" sing N N 96 DA "C1'" N9 sing N N 97 DA "C1'" "H1'" sing N N 98 DA N9 C8 sing Y N 99 DA N9 C4 sing Y N 100 DA C8 N7 doub Y N 101 DA C8 H8 sing N N 102 DA N7 C5 sing Y N 103 DA C5 C6 sing Y N 104 DA C5 C4 doub Y N 105 DA C6 N6 sing N N 106 DA C6 N1 doub Y N 107 DA N6 H61 sing N N 108 DA N6 H62 sing N N 109 DA N1 C2 sing Y N 110 DA C2 N3 doub Y N 111 DA C2 H2 sing N N 112 DA N3 C4 sing Y N 113 DC OP3 P sing N N 114 DC OP3 HOP3 sing N N 115 DC P OP1 doub N N 116 DC P OP2 sing N N 117 DC P "O5'" sing N N 118 DC OP2 HOP2 sing N N 119 DC "O5'" "C5'" sing N N 120 DC "C5'" "C4'" sing N N 121 DC "C5'" "H5'" sing N N 122 DC "C5'" "H5''" sing N N 123 DC "C4'" "O4'" sing N N 124 DC "C4'" "C3'" sing N N 125 DC "C4'" "H4'" sing N N 126 DC "O4'" "C1'" sing N N 127 DC "C3'" "O3'" sing N N 128 DC "C3'" "C2'" sing N N 129 DC "C3'" "H3'" sing N N 130 DC "O3'" "HO3'" sing N N 131 DC "C2'" "C1'" sing N N 132 DC "C2'" "H2'" sing N N 133 DC "C2'" "H2''" sing N N 134 DC "C1'" N1 sing N N 135 DC "C1'" "H1'" sing N N 136 DC N1 C2 sing N N 137 DC N1 C6 sing N N 138 DC C2 O2 doub N N 139 DC C2 N3 sing N N 140 DC N3 C4 doub N N 141 DC C4 N4 sing N N 142 DC C4 C5 sing N N 143 DC N4 H41 sing N N 144 DC N4 H42 sing N N 145 DC C5 C6 doub N N 146 DC C5 H5 sing N N 147 DC C6 H6 sing N N 148 DG OP3 P sing N N 149 DG OP3 HOP3 sing N N 150 DG P OP1 doub N N 151 DG P OP2 sing N N 152 DG P "O5'" sing N N 153 DG OP2 HOP2 sing N N 154 DG "O5'" "C5'" sing N N 155 DG "C5'" "C4'" sing N N 156 DG "C5'" "H5'" sing N N 157 DG "C5'" "H5''" sing N N 158 DG "C4'" "O4'" sing N N 159 DG "C4'" "C3'" sing N N 160 DG "C4'" "H4'" sing N N 161 DG "O4'" "C1'" sing N N 162 DG "C3'" "O3'" sing N N 163 DG "C3'" "C2'" sing N N 164 DG "C3'" "H3'" sing N N 165 DG "O3'" "HO3'" sing N N 166 DG "C2'" "C1'" sing N N 167 DG "C2'" "H2'" sing N N 168 DG "C2'" "H2''" sing N N 169 DG "C1'" N9 sing N N 170 DG "C1'" "H1'" sing N N 171 DG N9 C8 sing Y N 172 DG N9 C4 sing Y N 173 DG C8 N7 doub Y N 174 DG C8 H8 sing N N 175 DG N7 C5 sing Y N 176 DG C5 C6 sing N N 177 DG C5 C4 doub Y N 178 DG C6 O6 doub N N 179 DG C6 N1 sing N N 180 DG N1 C2 sing N N 181 DG N1 H1 sing N N 182 DG C2 N2 sing N N 183 DG C2 N3 doub N N 184 DG N2 H21 sing N N 185 DG N2 H22 sing N N 186 DG N3 C4 sing N N 187 DT OP3 P sing N N 188 DT OP3 HOP3 sing N N 189 DT P OP1 doub N N 190 DT P OP2 sing N N 191 DT P "O5'" sing N N 192 DT OP2 HOP2 sing N N 193 DT "O5'" "C5'" sing N N 194 DT "C5'" "C4'" sing N N 195 DT "C5'" "H5'" sing N N 196 DT "C5'" "H5''" sing N N 197 DT "C4'" "O4'" sing N N 198 DT "C4'" "C3'" sing N N 199 DT "C4'" "H4'" sing N N 200 DT "O4'" "C1'" sing N N 201 DT "C3'" "O3'" sing N N 202 DT "C3'" "C2'" sing N N 203 DT "C3'" "H3'" sing N N 204 DT "O3'" "HO3'" sing N N 205 DT "C2'" "C1'" sing N N 206 DT "C2'" "H2'" sing N N 207 DT "C2'" "H2''" sing N N 208 DT "C1'" N1 sing N N 209 DT "C1'" "H1'" sing N N 210 DT N1 C2 sing N N 211 DT N1 C6 sing N N 212 DT C2 O2 doub N N 213 DT C2 N3 sing N N 214 DT N3 C4 sing N N 215 DT N3 H3 sing N N 216 DT C4 O4 doub N N 217 DT C4 C5 sing N N 218 DT C5 C7 sing N N 219 DT C5 C6 doub N N 220 DT C7 H71 sing N N 221 DT C7 H72 sing N N 222 DT C7 H73 sing N N 223 DT C6 H6 sing N N 224 G OP3 P sing N N 225 G OP3 HOP3 sing N N 226 G P OP1 doub N N 227 G P OP2 sing N N 228 G P "O5'" sing N N 229 G OP2 HOP2 sing N N 230 G "O5'" "C5'" sing N N 231 G "C5'" "C4'" sing N N 232 G "C5'" "H5'" sing N N 233 G "C5'" "H5''" sing N N 234 G "C4'" "O4'" sing N N 235 G "C4'" "C3'" sing N N 236 G "C4'" "H4'" sing N N 237 G "O4'" "C1'" sing N N 238 G "C3'" "O3'" sing N N 239 G "C3'" "C2'" sing N N 240 G "C3'" "H3'" sing N N 241 G "O3'" "HO3'" sing N N 242 G "C2'" "O2'" sing N N 243 G "C2'" "C1'" sing N N 244 G "C2'" "H2'" sing N N 245 G "O2'" "HO2'" sing N N 246 G "C1'" N9 sing N N 247 G "C1'" "H1'" sing N N 248 G N9 C8 sing Y N 249 G N9 C4 sing Y N 250 G C8 N7 doub Y N 251 G C8 H8 sing N N 252 G N7 C5 sing Y N 253 G C5 C6 sing N N 254 G C5 C4 doub Y N 255 G C6 O6 doub N N 256 G C6 N1 sing N N 257 G N1 C2 sing N N 258 G N1 H1 sing N N 259 G C2 N2 sing N N 260 G C2 N3 doub N N 261 G N2 H21 sing N N 262 G N2 H22 sing N N 263 G N3 C4 sing N N 264 U OP3 P sing N N 265 U OP3 HOP3 sing N N 266 U P OP1 doub N N 267 U P OP2 sing N N 268 U P "O5'" sing N N 269 U OP2 HOP2 sing N N 270 U "O5'" "C5'" sing N N 271 U "C5'" "C4'" sing N N 272 U "C5'" "H5'" sing N N 273 U "C5'" "H5''" sing N N 274 U "C4'" "O4'" sing N N 275 U "C4'" "C3'" sing N N 276 U "C4'" "H4'" sing N N 277 U "O4'" "C1'" sing N N 278 U "C3'" "O3'" sing N N 279 U "C3'" "C2'" sing N N 280 U "C3'" "H3'" sing N N 281 U "O3'" "HO3'" sing N N 282 U "C2'" "O2'" sing N N 283 U "C2'" "C1'" sing N N 284 U "C2'" "H2'" sing N N 285 U "O2'" "HO2'" sing N N 286 U "C1'" N1 sing N N 287 U "C1'" "H1'" sing N N 288 U N1 C2 sing N N 289 U N1 C6 sing N N 290 U C2 O2 doub N N 291 U C2 N3 sing N N 292 U N3 C4 sing N N 293 U N3 H3 sing N N 294 U C4 O4 doub N N 295 U C4 C5 sing N N 296 U C5 C6 doub N N 297 U C5 H5 sing N N 298 U C6 H6 sing N N 299 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5CKK 'double helix' 5CKK 'a-form double helix' 5CKK 'mismatched base pair' 5CKK 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DA 1 1_555 B U 14 1_555 -0.072 -0.189 0.315 5.510 -7.051 -2.561 1 Y_DA1:U8_D Y 1 ? D 8 ? 20 1 1 A DT 2 1_555 B A 13 1_555 0.236 -0.134 0.508 4.130 -11.017 8.796 2 Y_DT2:A7_D Y 2 ? D 7 ? 20 1 1 A DC 3 1_555 B G 12 1_555 0.695 0.234 0.437 -3.135 -9.323 6.435 3 Y_DC3:G6_D Y 3 ? D 6 ? ? 1 1 A DC 4 1_555 B G 11 1_555 0.123 0.230 -1.874 34.106 -17.843 -2.236 4 Y_DC4:G5_D Y 4 ? D 5 ? ? 1 1 A DG 5 1_555 B C 10 1_555 0.477 -0.505 -0.030 14.764 2.778 -5.905 5 Y_DG5:C4_D Y 5 ? D 4 ? 19 1 1 A DA 6 1_555 B U 9 1_555 0.059 -0.230 0.084 19.207 -16.751 1.602 6 Y_DA6:U3_D Y 6 ? D 3 ? 20 1 1 A DT 7 1_555 B A 8 1_555 -0.704 -0.087 -0.391 11.248 -25.234 -6.251 7 Y_DT7:A2_D Y 7 ? D 2 ? 20 1 1 A DG 26 1_555 A DC 12 1_555 0.284 -0.052 0.664 20.954 7.965 7.812 8 Y_DG26:DC12_Y Y 26 ? Y 12 ? 19 1 1 A DT 14 1_555 A DG 25 1_555 2.910 -1.039 0.413 -1.763 13.511 3.645 9 Y_DT14:DG25_Y Y 14 ? Y 25 ? 28 1 1 A DG 21 1_555 A DA 23 1_555 3.847 -4.175 0.937 -32.507 8.367 -53.574 10 Y_DG21:DA23_Y Y 21 ? Y 23 ? ? ? 1 A DG 31 1_555 A DC 20 1_555 0.287 -0.275 -0.067 -6.599 -24.129 -3.825 11 Y_DG31:DC20_Y Y 31 ? Y 20 ? 19 1 1 A DT 29 1_555 B G 7 1_555 -0.795 1.269 0.495 -30.382 -29.511 32.578 12 Y_DT29:G1_D Y 29 ? D 1 ? ? ? 1 A DC 32 1_555 A DG 18 1_555 0.184 -0.136 -0.331 -3.252 -4.269 1.071 13 Y_DC32:DG18_Y Y 32 ? Y 18 ? 19 1 1 A DC 33 1_555 A DG 17 1_555 0.176 -0.165 -0.208 0.796 -2.078 -1.011 14 Y_DC33:DG17_Y Y 33 ? Y 17 ? 19 1 1 A DG 34 1_555 A DC 16 1_555 -0.107 -0.207 0.638 3.318 -9.849 -2.948 15 Y_DG34:DC16_Y Y 34 ? Y 16 ? 19 1 1 A DT 35 1_555 A DT 37 1_555 0.539 -1.798 0.925 31.926 -3.431 78.979 16 Y_DT35:DT37_Y Y 35 ? Y 37 ? ? ? 1 A DA 39 1_555 B U 5 1_555 -0.369 -0.046 0.002 -2.376 -3.063 0.744 17 Y_DA39:U-2_D Y 39 ? D -2 ? 20 1 1 A DG 40 1_555 B C 4 1_555 -0.295 -0.139 -0.033 0.364 -6.723 5.202 18 Y_DG40:C-3_D Y 40 ? D -3 ? 19 1 1 A DT 41 1_555 B A 3 1_555 -1.701 0.124 -0.004 6.042 -8.525 -8.532 19 Y_DT41:A-4_D Y 41 ? D -4 ? 20 1 1 A DG 42 1_555 B C 2 1_555 0.199 -0.151 -0.165 1.906 -5.849 5.457 20 Y_DG42:C-5_D Y 42 ? D -5 ? 19 1 1 A DC 43 1_555 B G 1 1_555 -0.080 0.249 -0.822 -2.772 10.786 3.295 21 Y_DC43:G-6_D Y 43 ? D -6 ? ? 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 DA 1 1_555 B U 14 1_555 A DT 2 1_555 B A 13 1_555 0.916 -1.626 3.226 -0.514 1.659 35.771 -2.876 -1.562 3.137 2.699 0.836 35.812 1 YY_DA1DT2:A7U8_DD Y 1 ? D 8 ? Y 2 ? D 7 ? 1 A DT 2 1_555 B A 13 1_555 A DC 3 1_555 B G 12 1_555 -0.154 -1.662 3.459 1.908 0.714 33.966 -2.961 0.583 3.411 1.221 -3.263 34.025 2 YY_DT2DC3:G6A7_DD Y 2 ? D 7 ? Y 3 ? D 6 ? 1 A DC 3 1_555 B G 12 1_555 A DC 4 1_555 B G 11 1_555 -0.527 -0.739 2.353 21.825 5.980 25.782 -1.870 3.132 1.329 11.069 -40.398 34.178 3 YY_DC3DC4:G5G6_DD Y 3 ? D 6 ? Y 4 ? D 5 ? 1 A DC 4 1_555 B G 11 1_555 A DG 5 1_555 B C 10 1_555 -0.744 -0.475 3.813 -13.078 23.422 34.513 -3.320 -0.490 3.024 33.872 18.913 43.460 4 YY_DC4DG5:C4G5_DD Y 4 ? D 5 ? Y 5 ? D 4 ? 1 A DG 5 1_555 B C 10 1_555 A DA 6 1_555 B U 9 1_555 -0.179 -0.967 3.055 -1.974 6.775 31.195 -2.867 0.002 2.794 12.400 3.613 31.963 5 YY_DG5DA6:U3C4_DD Y 5 ? D 4 ? Y 6 ? D 3 ? 1 A DA 6 1_555 B U 9 1_555 A DT 7 1_555 B A 8 1_555 -0.026 -1.564 3.274 0.535 1.484 32.955 -3.004 0.135 3.201 2.614 -0.942 32.991 6 YY_DA6DT7:A2U3_DD Y 6 ? D 3 ? Y 7 ? D 2 ? 1 A DT 7 1_555 B A 8 1_555 A DG 26 1_555 A DC 12 1_555 4.352 -2.605 -3.450 -48.632 -170.997 -122.209 0.422 2.426 -3.656 85.631 -24.354 -178.926 7 YY_DT7DG26:DC12A2_YD Y 7 ? D 2 ? Y 26 ? Y 12 ? 1 A DG 26 1_555 A DC 12 1_555 A DT 14 1_555 A DG 25 1_555 0.836 2.738 -0.191 -167.431 61.141 -87.936 -1.337 0.505 -0.243 -30.662 -83.968 -178.737 8 YY_DG26DT14:DG25DC12_YY Y 26 ? Y 12 ? Y 14 ? Y 25 ? 1 A DT 14 1_555 A DG 25 1_555 A DG 21 1_555 A DA 23 1_555 4.563 3.165 -2.282 147.011 61.495 -94.958 -1.025 0.938 -5.333 -31.781 75.975 -166.088 9 YY_DT14DG21:DA23DG25_YY Y 14 ? Y 25 ? Y 21 ? Y 23 ? 1 A DG 21 1_555 A DA 23 1_555 A DG 31 1_555 A DC 20 1_555 -0.418 -4.167 1.632 113.888 -105.683 -70.775 2.212 -0.108 -1.085 56.317 60.690 -159.971 10 YY_DG21DG31:DC20DA23_YY Y 21 ? Y 23 ? Y 31 ? Y 20 ? 1 A DC 32 1_555 A DG 18 1_555 A DC 33 1_555 A DG 17 1_555 -0.026 -0.425 3.226 2.654 3.634 34.331 -1.262 0.445 3.155 6.124 -4.473 34.616 11 YY_DC32DC33:DG17DG18_YY Y 32 ? Y 18 ? Y 33 ? Y 17 ? 1 A DC 33 1_555 A DG 17 1_555 A DG 34 1_555 A DC 16 1_555 0.329 -0.381 3.322 -1.402 6.329 38.221 -1.353 -0.669 3.208 9.582 2.122 38.746 12 YY_DC33DG34:DC16DG17_YY Y 33 ? Y 17 ? Y 34 ? Y 16 ? 1 A DG 34 1_555 A DC 16 1_555 A DT 35 1_555 A DT 37 1_555 -0.330 -5.670 4.251 -164.451 20.419 -49.924 2.602 -2.195 2.141 -10.716 -86.310 -167.054 13 YY_DG34DT35:DT37DC16_YY Y 34 ? Y 16 ? Y 35 ? Y 37 ? 1 A DA 39 1_555 B U 5 1_555 A DG 40 1_555 B C 4 1_555 -0.118 -1.787 3.148 -1.856 3.979 33.249 -3.707 -0.080 2.923 6.915 3.226 33.530 14 YY_DA39DG40:C-3U-2_DD Y 39 ? D -2 ? Y 40 ? D -3 ? 1 A DG 40 1_555 B C 4 1_555 A DT 41 1_555 B A 3 1_555 -0.281 -1.636 3.100 1.421 3.990 24.336 -4.927 1.049 2.779 9.375 -3.339 24.697 15 YY_DG40DT41:A-4C-3_DD Y 40 ? D -3 ? Y 41 ? D -4 ? 1 A DT 41 1_555 B A 3 1_555 A DG 42 1_555 B C 2 1_555 0.450 -1.374 3.178 0.384 17.282 40.793 -3.279 -0.566 2.435 23.558 -0.523 44.161 16 YY_DT41DG42:C-5A-4_DD Y 41 ? D -4 ? Y 42 ? D -5 ? 1 A DG 42 1_555 B C 2 1_555 A DC 43 1_555 B G 1 1_555 0.661 -1.028 3.706 8.398 -5.470 34.104 -0.740 0.370 3.869 -9.086 -13.951 35.504 17 YY_DG42DC43:G-6C-5_DD Y 42 ? D -5 ? Y 43 ? D -6 ? # _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 5CKI _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 5CKK _atom_sites.fract_transf_matrix[1][1] 0.012026 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.012026 _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] 0.017859 _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 G MG N O P # loop_