data_8TDY # _entry.id 8TDY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.395 _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 8TDY pdb_00008tdy 10.2210/pdb8tdy/pdb WWPDB D_1000275652 ? ? # 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 2024-06-12 2 'Structure model' 1 1 2024-06-26 # _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.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation_author.identifier_ORCID' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8TDY _pdbx_database_status.recvd_initial_deposition_date 2023-07-05 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.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 jwszostak@uchicago.edu _pdbx_contact_author.name_first Jack _pdbx_contact_author.name_last Szostak _pdbx_contact_author.name_mi W. _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-4131-1203 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Fang, Z.' 1 0000-0001-8679-6633 'Jia, X.' 2 0000-0001-9094-9882 'Szostak, J.W.' 3 0000-0003-4131-1203 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_id_ASTM JACSAT _citation.journal_id_CSD ? _citation.journal_id_ISSN 1520-5126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 146 _citation.language ? _citation.page_first 15897 _citation.page_last 15907 _citation.title 'Diaminopurine in Nonenzymatic RNA Template Copying.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacs.4c02560 _citation.pdbx_database_id_PubMed 38818863 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Jia, X.' 1 ? primary 'Fang, Z.' 2 ? primary 'Kim, S.C.' 3 ? primary 'Ding, D.' 4 ? primary 'Zhou, L.' 5 ? primary 'Szostak, J.W.' 6 ? # 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 5098.078 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 water nat water 18.015 60 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'AGAG(N6G)AGAUCUUCUCU' _entity_poly.pdbx_seq_one_letter_code_can AGAGGAGAUCUUCUCU _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 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 A n 1 2 G n 1 3 A n 1 4 G n 1 5 N6G n 1 6 A n 1 7 G n 1 8 A n 1 9 U n 1 10 C n 1 11 U n 1 12 U n 1 13 C n 1 14 U n 1 15 C n 1 16 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 16 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 N6G 'RNA linking' n '((2R,3S,4R,5S)-5-(2,6-DIAMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE' ? 'C10 H15 N6 O7 P' 362.236 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 A 1 1 1 A A A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 N6G 5 5 5 N6G DAP A . n A 1 6 A 6 6 6 A A A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 U 9 9 9 U U A . n A 1 10 C 10 10 10 C C A . n A 1 11 U 11 11 11 U U 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 U 14 14 14 U U A . n A 1 15 C 15 15 15 C C A . n A 1 16 U 16 16 16 U U A . 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 B 2 MG 1 101 1 MG MG A . C 2 MG 1 102 2 MG MG A . D 3 HOH 1 201 35 HOH HOH A . D 3 HOH 2 202 41 HOH HOH A . D 3 HOH 3 203 28 HOH HOH A . D 3 HOH 4 204 50 HOH HOH A . D 3 HOH 5 205 5 HOH HOH A . D 3 HOH 6 206 51 HOH HOH A . D 3 HOH 7 207 56 HOH HOH A . D 3 HOH 8 208 22 HOH HOH A . D 3 HOH 9 209 3 HOH HOH A . D 3 HOH 10 210 9 HOH HOH A . D 3 HOH 11 211 20 HOH HOH A . D 3 HOH 12 212 49 HOH HOH A . D 3 HOH 13 213 26 HOH HOH A . D 3 HOH 14 214 55 HOH HOH A . D 3 HOH 15 215 52 HOH HOH A . D 3 HOH 16 216 24 HOH HOH A . D 3 HOH 17 217 18 HOH HOH A . D 3 HOH 18 218 54 HOH HOH A . D 3 HOH 19 219 4 HOH HOH A . D 3 HOH 20 220 45 HOH HOH A . D 3 HOH 21 221 31 HOH HOH A . D 3 HOH 22 222 13 HOH HOH A . D 3 HOH 23 223 43 HOH HOH A . D 3 HOH 24 224 61 HOH HOH A . D 3 HOH 25 225 36 HOH HOH A . D 3 HOH 26 226 19 HOH HOH A . D 3 HOH 27 227 46 HOH HOH A . D 3 HOH 28 228 2 HOH HOH A . D 3 HOH 29 229 25 HOH HOH A . D 3 HOH 30 230 59 HOH HOH A . D 3 HOH 31 231 58 HOH HOH A . D 3 HOH 32 232 15 HOH HOH A . D 3 HOH 33 233 44 HOH HOH A . D 3 HOH 34 234 1 HOH HOH A . D 3 HOH 35 235 29 HOH HOH A . D 3 HOH 36 236 30 HOH HOH A . D 3 HOH 37 237 10 HOH HOH A . D 3 HOH 38 238 27 HOH HOH A . D 3 HOH 39 239 32 HOH HOH A . D 3 HOH 40 240 16 HOH HOH A . D 3 HOH 41 241 39 HOH HOH A . D 3 HOH 42 242 17 HOH HOH A . D 3 HOH 43 243 6 HOH HOH A . D 3 HOH 44 244 23 HOH HOH A . D 3 HOH 45 245 47 HOH HOH A . D 3 HOH 46 246 57 HOH HOH A . D 3 HOH 47 247 40 HOH HOH A . D 3 HOH 48 248 21 HOH HOH A . D 3 HOH 49 249 53 HOH HOH A . D 3 HOH 50 250 48 HOH HOH A . D 3 HOH 51 251 34 HOH HOH A . D 3 HOH 52 252 33 HOH HOH A . D 3 HOH 53 253 8 HOH HOH A . D 3 HOH 54 254 12 HOH HOH A . D 3 HOH 55 255 38 HOH HOH A . D 3 HOH 56 256 11 HOH HOH A . D 3 HOH 57 257 7 HOH HOH A . D 3 HOH 58 258 42 HOH HOH A . D 3 HOH 59 259 60 HOH HOH A . D 3 HOH 60 260 37 HOH HOH 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 ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0267 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 8TDY _cell.details ? _cell.formula_units_Z ? _cell.length_a 41.146 _cell.length_a_esd ? _cell.length_b 41.146 _cell.length_b_esd ? _cell.length_c 125.047 _cell.length_c_esd ? _cell.volume 183340.813 _cell.volume_esd ? _cell.Z_PDB 18 _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 8TDY _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ;R 3 2" ; _symmetry.space_group_name_H-M 'H 3 2' _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 8TDY _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 2.00 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 38.44 _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, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;80 mM Strontium chloride hexahydrate, 20 mM Magnesium chloride hexahydrate, 40 mM Sodium cacodylate trihydrate pH 7.0, 20% v/v (+/-)-2-Methyl-2,4-pentanediol, 12 mM Spermine ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _diffrn.ambient_environment ? _diffrn.ambient_temp 99 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _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 2023-03-01 _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 1.038413 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'ALS BEAMLINE 2.0.1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.038413 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 2.0.1 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.B_iso_Wilson_estimate 10.08 _reflns.entry_id 8TDY _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.65 _reflns.d_resolution_low 50 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 5058 _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 99.6 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 8.5 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 4.2 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.951 _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 0.104 _reflns.pdbx_Rpim_I_all 0.035 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1.000 _reflns.pdbx_CC_star 1.000 _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.097 _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 1.65 _reflns_shell.d_res_low 1.71 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 4.2 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 483 _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 6.1 _reflns_shell.pdbx_chi_squared 1.021 _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all 0.569 _reflns_shell.pdbx_Rpim_I_all 0.225 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.902 _reflns_shell.pdbx_CC_star 0.974 _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all 99.2 _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.520 _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 13.06 _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 8TDY _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.66 _refine.ls_d_res_low 41.68 _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 4946 _refine.ls_number_reflns_R_free 235 _refine.ls_number_reflns_R_work 4711 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.85 _refine.ls_percent_reflns_R_free 4.75 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1975 _refine.ls_R_factor_R_free 0.2238 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1962 _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 1.38 _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 18.6202 _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 0.1547 _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 1.66 _refine_hist.d_res_low 41.68 _refine_hist.number_atoms_solvent 60 _refine_hist.number_atoms_total 399 _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 337 _refine_hist.pdbx_number_atoms_ligand 2 _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' ? 0.0049 ? 376 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.9549 ? 584 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0421 ? 78 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0091 ? 16 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 5.6062 ? 180 ? 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' 1.66 1.72 . . 16 383 79 . . . . 0.2283 . . . . . . . . . . . 0.2676 'X-RAY DIFFRACTION' 1.72 1.79 . . 29 444 95 . . . . 0.2004 . . . . . . . . . . . 0.2466 'X-RAY DIFFRACTION' 1.79 1.87 . . 22 477 99 . . . . 0.2038 . . . . . . . . . . . 0.2076 'X-RAY DIFFRACTION' 1.87 1.97 . . 26 463 99 . . . . 0.2100 . . . . . . . . . . . 0.2849 'X-RAY DIFFRACTION' 1.97 2.09 . . 24 483 100 . . . . 0.2149 . . . . . . . . . . . 0.2533 'X-RAY DIFFRACTION' 2.09 2.25 . . 21 471 100 . . . . 0.2129 . . . . . . . . . . . 0.2881 'X-RAY DIFFRACTION' 2.25 2.48 . . 30 480 100 . . . . 0.2218 . . . . . . . . . . . 0.3298 'X-RAY DIFFRACTION' 2.48 2.84 . . 20 495 100 . . . . 0.2176 . . . . . . . . . . . 0.1637 'X-RAY DIFFRACTION' 2.84 3.57 . . 23 484 97 . . . . 0.1876 . . . . . . . . . . . 0.1687 'X-RAY DIFFRACTION' 3.58 41.68 . . 24 531 98 . . . . 0.1579 . . . . . . . . . . . 0.1737 # _struct.entry_id 8TDY _struct.title '16mer self-complementary duplex RNA with D:U pair sequence 1' _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 8TDY _struct_keywords.text 'Diaminopurine, RNA, Non-canonical base pair' _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 2 ? D N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8TDY _struct_ref.pdbx_db_accession 8TDY _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 8TDY _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 16 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 8TDY _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 16 _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 16 # _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)' 3190 ? 1 MORE -26 ? 1 'SSA (A^2)' 5580 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 4_555 y,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 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 4 "O3'" ? ? ? 1_555 A N6G 5 P ? ? A G 4 A N6G 5 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale2 covale both ? A N6G 5 "O3'" ? ? ? 1_555 A A 6 P ? ? A N6G 5 A A 6 1_555 ? ? ? ? ? ? ? 1.608 ? ? metalc1 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 204 1_555 ? ? ? ? ? ? ? 2.536 ? ? metalc2 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 210 1_555 ? ? ? ? ? ? ? 2.616 ? ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 215 1_555 ? ? ? ? ? ? ? 2.595 ? ? metalc4 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 243 1_555 ? ? ? ? ? ? ? 1.716 ? ? metalc5 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 253 1_555 ? ? ? ? ? ? ? 2.467 ? ? metalc6 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 257 1_555 ? ? ? ? ? ? ? 2.090 ? ? metalc7 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 222 1_555 ? ? ? ? ? ? ? 2.433 ? ? metalc8 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 246 1_555 ? ? ? ? ? ? ? 2.539 ? ? metalc9 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 251 1_555 ? ? ? ? ? ? ? 2.472 ? ? metalc10 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 254 1_555 ? ? ? ? ? ? ? 2.472 ? ? metalc11 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 256 1_555 ? ? ? ? ? ? ? 2.123 ? ? hydrog1 hydrog ? ? A A 1 N1 ? ? ? 1_555 A U 16 N3 ? ? A A 1 A U 16 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 1 N6 ? ? ? 1_555 A U 16 O4 ? ? A A 1 A U 16 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 2 A C 15 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 2 A C 15 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 2 A C 15 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 14 N3 ? ? A A 3 A U 14 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 14 O4 ? ? A A 3 A U 14 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 4 A C 13 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 4 A C 13 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 4 A C 13 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A N6G 5 N2 ? ? ? 1_555 A U 12 O2 ? ? A N6G 5 A U 12 4_555 ? ? ? ? ? ? 'N6G-U MISPAIR' ? ? ? hydrog12 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 11 N3 ? ? A A 6 A U 11 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 11 O4 ? ? A A 6 A U 11 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 10 N3 ? ? A G 7 A C 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 10 O2 ? ? A G 7 A C 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 10 N4 ? ? A G 7 A C 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 9 N3 ? ? A A 8 A U 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 9 O4 ? ? A A 8 A U 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 9 N3 ? ? ? 1_555 A A 8 N1 ? ? A U 9 A A 8 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 9 O4 ? ? ? 1_555 A A 8 N6 ? ? A U 9 A A 8 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 7 N1 ? ? A C 10 A G 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 7 O6 ? ? A C 10 A G 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 7 N2 ? ? A C 10 A G 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A U 11 N3 ? ? ? 1_555 A A 6 N1 ? ? A U 11 A A 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 6 N6 ? ? A U 11 A A 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 12 O2 ? ? ? 1_555 A N6G 5 N2 ? ? A U 12 A N6G 5 4_555 ? ? ? ? ? ? 'U-N6G MISPAIR' ? ? ? hydrog27 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 4 N1 ? ? A C 13 A G 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 4 O6 ? ? A C 13 A G 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 4 N2 ? ? A C 13 A G 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 3 N1 ? ? A U 14 A A 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 3 N6 ? ? A U 14 A A 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 2 N1 ? ? A C 15 A G 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 2 O6 ? ? A C 15 A G 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 2 N2 ? ? A C 15 A G 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 1 N1 ? ? A U 16 A A 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 1 N6 ? ? A U 16 A A 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # 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 O ? D HOH . ? A HOH 204 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 210 ? 1_555 118.9 ? 2 O ? D HOH . ? A HOH 204 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 215 ? 1_555 78.3 ? 3 O ? D HOH . ? A HOH 210 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 215 ? 1_555 158.7 ? 4 O ? D HOH . ? A HOH 204 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 243 ? 1_555 157.3 ? 5 O ? D HOH . ? A HOH 210 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 243 ? 1_555 78.1 ? 6 O ? D HOH . ? A HOH 215 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 243 ? 1_555 82.2 ? 7 O ? D HOH . ? A HOH 204 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 253 ? 1_555 66.5 ? 8 O ? D HOH . ? A HOH 210 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 253 ? 1_555 62.1 ? 9 O ? D HOH . ? A HOH 215 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 253 ? 1_555 139.2 ? 10 O ? D HOH . ? A HOH 243 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 253 ? 1_555 135.7 ? 11 O ? D HOH . ? A HOH 204 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 257 ? 1_555 133.5 ? 12 O ? D HOH . ? A HOH 210 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 257 ? 1_555 57.7 ? 13 O ? D HOH . ? A HOH 215 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 257 ? 1_555 121.0 ? 14 O ? D HOH . ? A HOH 243 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 257 ? 1_555 67.4 ? 15 O ? D HOH . ? A HOH 253 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 257 ? 1_555 75.1 ? 16 O ? D HOH . ? A HOH 222 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 246 ? 1_555 87.3 ? 17 O ? D HOH . ? A HOH 222 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 251 ? 1_555 69.0 ? 18 O ? D HOH . ? A HOH 246 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 251 ? 1_555 119.8 ? 19 O ? D HOH . ? A HOH 222 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 254 ? 1_555 135.3 ? 20 O ? D HOH . ? A HOH 246 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 254 ? 1_555 90.0 ? 21 O ? D HOH . ? A HOH 251 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 254 ? 1_555 74.0 ? 22 O ? D HOH . ? A HOH 222 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 256 ? 1_555 83.7 ? 23 O ? D HOH . ? A HOH 246 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 256 ? 1_555 62.6 ? 24 O ? D HOH . ? A HOH 251 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 256 ? 1_555 60.4 ? 25 O ? D HOH . ? A HOH 254 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 256 ? 1_555 56.1 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 243 ? ? O A HOH 257 ? ? 2.13 2 1 O A HOH 254 ? ? O A HOH 256 ? ? 2.18 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 221 ? D HOH . 2 1 A HOH 235 ? D HOH . 3 1 A HOH 236 ? D HOH . 4 1 A HOH 239 ? D HOH . 5 1 A HOH 252 ? D HOH . # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x-y,z 3 -x+y,-x,z 4 x-y,-y,-z 5 -x,-x+y,-z 6 y,x,-z 7 x+1/3,y+2/3,z+2/3 8 -y+1/3,x-y+2/3,z+2/3 9 -x+y+1/3,-x+2/3,z+2/3 10 x-y+1/3,-y+2/3,-z+2/3 11 -x+1/3,-x+y+2/3,-z+2/3 12 y+1/3,x+2/3,-z+2/3 13 x+2/3,y+1/3,z+1/3 14 -y+2/3,x-y+1/3,z+1/3 15 -x+y+2/3,-x+1/3,z+1/3 16 x-y+2/3,-y+1/3,-z+1/3 17 -x+2/3,-x+y+1/3,-z+1/3 18 y+2/3,x+1/3,-z+1/3 # _pdbx_entry_details.entry_id 8TDY _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 MG MG MG N N 114 N6G P P N N 115 N6G OP1 O N N 116 N6G OP2 O N N 117 N6G "O5'" O N N 118 N6G "C5'" C N N 119 N6G "C4'" C N R 120 N6G "O4'" O N N 121 N6G "C1'" C N R 122 N6G N9 N Y N 123 N6G C4 C Y N 124 N6G N3 N Y N 125 N6G C2 C Y N 126 N6G N2 N N N 127 N6G N1 N Y N 128 N6G C6 C Y N 129 N6G N6 N N N 130 N6G C5 C Y N 131 N6G N7 N Y N 132 N6G C8 C Y N 133 N6G "C2'" C N R 134 N6G "O2'" O N N 135 N6G "C3'" C N S 136 N6G "O3'" O N N 137 N6G OP3 O N N 138 N6G HOP2 H N N 139 N6G "H5'" H N N 140 N6G "H5''" H N N 141 N6G "H4'" H N N 142 N6G "H1'" H N N 143 N6G HN21 H N N 144 N6G HN22 H N N 145 N6G HN61 H N N 146 N6G HN62 H N N 147 N6G H8 H N N 148 N6G "H2'" H N N 149 N6G "HO2'" H N N 150 N6G "H3'" H N N 151 N6G "HO3'" H N N 152 N6G HOP3 H N N 153 U OP3 O N N 154 U P P N N 155 U OP1 O N N 156 U OP2 O N N 157 U "O5'" O N N 158 U "C5'" C N N 159 U "C4'" C N R 160 U "O4'" O N N 161 U "C3'" C N S 162 U "O3'" O N N 163 U "C2'" C N R 164 U "O2'" O N N 165 U "C1'" C N R 166 U N1 N N N 167 U C2 C N N 168 U O2 O N N 169 U N3 N N N 170 U C4 C N N 171 U O4 O N N 172 U C5 C N N 173 U C6 C N N 174 U HOP3 H N N 175 U HOP2 H N N 176 U "H5'" H N N 177 U "H5''" H N N 178 U "H4'" H N N 179 U "H3'" H N N 180 U "HO3'" H N N 181 U "H2'" H N N 182 U "HO2'" H N N 183 U "H1'" H N N 184 U H3 H N N 185 U H5 H N N 186 U H6 H N N 187 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 N6G P OP1 doub N N 118 N6G P OP2 sing N N 119 N6G P "O5'" sing N N 120 N6G P OP3 sing N N 121 N6G OP2 HOP2 sing N N 122 N6G "O5'" "C5'" sing N N 123 N6G "C5'" "C4'" sing N N 124 N6G "C5'" "H5'" sing N N 125 N6G "C5'" "H5''" sing N N 126 N6G "C4'" "O4'" sing N N 127 N6G "C4'" "C3'" sing N N 128 N6G "C4'" "H4'" sing N N 129 N6G "O4'" "C1'" sing N N 130 N6G "C1'" N9 sing N N 131 N6G "C1'" "C2'" sing N N 132 N6G "C1'" "H1'" sing N N 133 N6G N9 C4 sing Y N 134 N6G N9 C8 sing Y N 135 N6G C4 N3 sing Y N 136 N6G C4 C5 doub Y N 137 N6G N3 C2 doub Y N 138 N6G C2 N2 sing N N 139 N6G C2 N1 sing Y N 140 N6G N2 HN21 sing N N 141 N6G N2 HN22 sing N N 142 N6G N1 C6 doub Y N 143 N6G C6 N6 sing N N 144 N6G C6 C5 sing Y N 145 N6G N6 HN61 sing N N 146 N6G N6 HN62 sing N N 147 N6G C5 N7 sing Y N 148 N6G N7 C8 doub Y N 149 N6G C8 H8 sing N N 150 N6G "C2'" "O2'" sing N N 151 N6G "C2'" "C3'" sing N N 152 N6G "C2'" "H2'" sing N N 153 N6G "O2'" "HO2'" sing N N 154 N6G "C3'" "O3'" sing N N 155 N6G "C3'" "H3'" sing N N 156 N6G "O3'" "HO3'" sing N N 157 N6G OP3 HOP3 sing N N 158 U OP3 P sing N N 159 U OP3 HOP3 sing N N 160 U P OP1 doub N N 161 U P OP2 sing N N 162 U P "O5'" sing N N 163 U OP2 HOP2 sing N N 164 U "O5'" "C5'" sing N N 165 U "C5'" "C4'" sing N N 166 U "C5'" "H5'" sing N N 167 U "C5'" "H5''" sing N N 168 U "C4'" "O4'" sing N N 169 U "C4'" "C3'" sing N N 170 U "C4'" "H4'" sing N N 171 U "O4'" "C1'" sing N N 172 U "C3'" "O3'" sing N N 173 U "C3'" "C2'" sing N N 174 U "C3'" "H3'" sing N N 175 U "O3'" "HO3'" sing N N 176 U "C2'" "O2'" sing N N 177 U "C2'" "C1'" sing N N 178 U "C2'" "H2'" sing N N 179 U "O2'" "HO2'" sing N N 180 U "C1'" N1 sing N N 181 U "C1'" "H1'" sing N N 182 U N1 C2 sing N N 183 U N1 C6 sing N N 184 U C2 O2 doub N N 185 U C2 N3 sing N N 186 U N3 C4 sing N N 187 U N3 H3 sing N N 188 U C4 O4 doub N N 189 U C4 C5 sing N N 190 U C5 C6 doub N N 191 U C5 H5 sing N N 192 U C6 H6 sing N N 193 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8TDY 'a-form double helix' 8TDY 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A A 1 1_555 A U 16 4_555 -0.102 -0.098 0.253 0.464 -12.260 0.502 1 A_A1:U16_A A 1 ? A 16 ? 20 1 1 A G 2 1_555 A C 15 4_555 -0.184 -0.196 0.117 -1.334 -16.700 -0.736 2 A_G2:C15_A A 2 ? A 15 ? 19 1 1 A A 3 1_555 A U 14 4_555 0.140 -0.178 0.152 0.490 -13.210 1.266 3 A_A3:U14_A A 3 ? A 14 ? 20 1 1 A G 4 1_555 A C 13 4_555 -0.423 -0.178 0.083 -1.428 -9.329 -2.238 4 A_G4:C13_A A 4 ? A 13 ? 19 1 1 A N6G 5 1_555 A U 12 4_555 0.000 -0.136 -0.168 -6.406 -10.007 -1.658 5 A_N6G5:U12_A A 5 ? A 12 ? ? 1 1 A A 6 1_555 A U 11 4_555 -0.036 -0.112 -0.106 -4.520 -13.601 1.545 6 A_A6:U11_A A 6 ? A 11 ? 20 1 1 A G 7 1_555 A C 10 4_555 -0.176 -0.111 0.038 -3.869 -10.538 0.200 7 A_G7:C10_A A 7 ? A 10 ? 19 1 1 A A 8 1_555 A U 9 4_555 -0.026 -0.093 -0.024 -1.049 -15.281 0.526 8 A_A8:U9_A A 8 ? A 9 ? 20 1 1 A U 9 1_555 A A 8 4_555 0.026 -0.093 -0.024 1.049 -15.281 0.526 9 A_U9:A8_A A 9 ? A 8 ? 20 1 1 A C 10 1_555 A G 7 4_555 0.176 -0.111 0.038 3.869 -10.538 0.200 10 A_C10:G7_A A 10 ? A 7 ? 19 1 1 A U 11 1_555 A A 6 4_555 0.036 -0.112 -0.106 4.520 -13.601 1.545 11 A_U11:A6_A A 11 ? A 6 ? 20 1 1 A U 12 1_555 A N6G 5 4_555 0.000 -0.136 -0.168 6.406 -10.007 -1.658 12 A_U12:N6G5_A A 12 ? A 5 ? ? 1 1 A C 13 1_555 A G 4 4_555 0.423 -0.178 0.083 1.428 -9.329 -2.238 13 A_C13:G4_A A 13 ? A 4 ? 19 1 1 A U 14 1_555 A A 3 4_555 -0.140 -0.178 0.152 -0.490 -13.210 1.266 14 A_U14:A3_A A 14 ? A 3 ? 20 1 1 A C 15 1_555 A G 2 4_555 0.184 -0.196 0.117 1.334 -16.700 -0.736 15 A_C15:G2_A A 15 ? A 2 ? 19 1 1 A U 16 1_555 A A 1 4_555 0.102 -0.098 0.253 -0.464 -12.260 0.502 16 A_U16:A1_A A 16 ? A 1 ? 20 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 A 1 1_555 A U 16 4_555 A G 2 1_555 A C 15 4_555 -0.610 -1.158 3.245 -1.401 6.399 35.563 -2.738 0.792 3.020 10.368 2.271 36.142 1 AA_A1G2:C15U16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A G 2 1_555 A C 15 4_555 A A 3 1_555 A U 14 4_555 0.546 -1.187 3.145 0.923 4.010 33.448 -2.663 -0.800 3.001 6.935 -1.596 33.693 2 AA_G2A3:U14C15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A A 3 1_555 A U 14 4_555 A G 4 1_555 A C 13 4_555 -0.261 -1.481 3.211 -1.204 10.343 31.819 -4.139 0.272 2.622 18.264 2.127 33.437 3 AA_A3G4:C13U14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A C 13 4_555 A N6G 5 1_555 A U 12 4_555 0.145 -1.859 3.393 1.677 13.534 30.941 -5.235 0.002 2.398 23.963 -2.970 33.746 4 AA_G4N6G5:U12C13_AA A 4 ? A 13 ? A 5 ? A 12 ? 1 A N6G 5 1_555 A U 12 4_555 A A 6 1_555 A U 11 4_555 0.857 -1.709 3.203 1.800 10.808 30.662 -4.757 -1.246 2.517 19.667 -3.276 32.516 5 AA_N6G5A6:U11U12_AA A 5 ? A 12 ? A 6 ? A 11 ? 1 A A 6 1_555 A U 11 4_555 A G 7 1_555 A C 10 4_555 -0.183 -2.093 3.155 0.067 9.589 26.737 -6.163 0.386 2.281 19.940 -0.139 28.375 6 AA_A6G7:C10U11_AA A 6 ? A 11 ? A 7 ? A 10 ? 1 A G 7 1_555 A C 10 4_555 A A 8 1_555 A U 9 4_555 -0.447 -1.426 3.201 0.016 5.298 32.568 -3.362 0.790 2.939 9.370 -0.027 32.985 7 AA_G7A8:U9C10_AA A 7 ? A 10 ? A 8 ? A 9 ? 1 A A 8 1_555 A U 9 4_555 A U 9 1_555 A A 8 4_555 0.000 -1.173 3.142 0.000 8.454 31.898 -3.385 0.000 2.750 15.056 0.000 32.971 8 AA_A8U9:A8U9_AA A 8 ? A 9 ? A 9 ? A 8 ? 1 A U 9 1_555 A A 8 4_555 A C 10 1_555 A G 7 4_555 0.447 -1.426 3.201 -0.016 5.298 32.568 -3.362 -0.790 2.939 9.370 0.027 32.985 9 AA_U9C10:G7A8_AA A 9 ? A 8 ? A 10 ? A 7 ? 1 A C 10 1_555 A G 7 4_555 A U 11 1_555 A A 6 4_555 0.183 -2.093 3.155 -0.067 9.589 26.737 -6.163 -0.386 2.281 19.940 0.139 28.375 10 AA_C10U11:A6G7_AA A 10 ? A 7 ? A 11 ? A 6 ? 1 A U 11 1_555 A A 6 4_555 A U 12 1_555 A N6G 5 4_555 -0.857 -1.709 3.203 -1.800 10.808 30.662 -4.757 1.246 2.517 19.667 3.276 32.516 11 AA_U11U12:N6G5A6_AA A 11 ? A 6 ? A 12 ? A 5 ? 1 A U 12 1_555 A N6G 5 4_555 A C 13 1_555 A G 4 4_555 -0.145 -1.859 3.393 -1.677 13.534 30.941 -5.235 -0.002 2.398 23.963 2.970 33.746 12 AA_U12C13:G4N6G5_AA A 12 ? A 5 ? A 13 ? A 4 ? 1 A C 13 1_555 A G 4 4_555 A U 14 1_555 A A 3 4_555 0.261 -1.481 3.211 1.204 10.343 31.819 -4.139 -0.272 2.622 18.264 -2.127 33.437 13 AA_C13U14:A3G4_AA A 13 ? A 4 ? A 14 ? A 3 ? 1 A U 14 1_555 A A 3 4_555 A C 15 1_555 A G 2 4_555 -0.546 -1.187 3.145 -0.923 4.010 33.448 -2.663 0.800 3.001 6.935 1.596 33.693 14 AA_U14C15:G2A3_AA A 14 ? A 3 ? A 15 ? A 2 ? 1 A C 15 1_555 A G 2 4_555 A U 16 1_555 A A 1 4_555 0.610 -1.158 3.245 1.401 6.399 35.563 -2.738 -0.792 3.020 10.368 -2.271 36.142 15 AA_C15U16:A1G2_AA A 15 ? A 2 ? A 16 ? A 1 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Science Foundation (NSF, United States)' 'United States' 2104708 1 'Simons Foundation' 'United States' 290363 2 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id N6G _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id N6G _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 ? # _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 3ND4 _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'R 3 2 :H' _space_group.name_Hall ;R 3 2" ; _space_group.IT_number 155 _space_group.crystal_system trigonal _space_group.id 1 # _atom_sites.entry_id 8TDY _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] 0.024304 _atom_sites.fract_transf_matrix[1][2] 0.014032 _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] 0.028063 _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] 0.007997 _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. ; ? 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_