data_9YDK # _entry.id 9YDK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.416 _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 9YDK pdb_00009ydk 10.2210/pdb9ydk/pdb WWPDB D_1000300215 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2026-08-05 _pdbx_audit_revision_history.part_number ? # _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_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9YDK _pdbx_database_status.recvd_initial_deposition_date 2025-09-22 _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 N # _pdbx_contact_author.id 2 _pdbx_contact_author.email martin.egli@vanderbilt.edu _pdbx_contact_author.name_first Martin _pdbx_contact_author.name_last Egli _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-4145-356X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Harp, J.M.' 1 0000-0002-9116-5606 'Egli, M.' 2 0000-0003-4145-356X # _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 Org.Lett. _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1523-7060 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 28 _citation.language ? _citation.page_first 9133 _citation.page_last 9138 _citation.title 'A Postsynthetic Strategy for Oligonucleotides Containing 2-Fluoro-adenine and Isoguanine Nucleobases.' _citation.year 2026 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.orglett.6c01203 _citation.pdbx_database_id_PubMed 42455745 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Madaoui, M.' 1 ? primary 'Kundu, J.' 2 0000-0003-2669-8112 primary 'Datta, D.' 3 0000-0003-2077-1294 primary 'Harp, J.M.' 4 ? primary 'Egli, M.' 5 0000-0003-4145-356X primary 'Manoharan, M.' 6 0000-0002-7931-1172 # 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 12-mer' 3869.351 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 91 ? ? ? ? # _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 'CGCGAAUU(A1CU1)GCG' _entity_poly.pdbx_seq_one_letter_code_can CGCGAAUUXGCG _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 C n 1 2 G n 1 3 C n 1 4 G n 1 5 A n 1 6 A n 1 7 U n 1 8 U n 1 9 A1CU1 n 1 10 G n 1 11 C n 1 12 G 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 12 _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 A1CU1 'RNA linking' n ;(2~{R},3~{R},4~{S},5~{R})-2-(6-azanyl-2-fluoranyl-purin-9-yl)-5-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]oxolane-3,4-diol ; ? 'C10 H13 F N5 O7 P' 365.212 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 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 C 1 1 1 C C A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 A 6 6 6 A A A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A1CU1 9 13 9 A1CU1 2FR A . n A 1 10 G 10 14 10 G G A . n A 1 11 C 11 15 11 C C A . n A 1 12 G 12 16 12 G G A . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id A1CU1 _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id A1CU1 _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 MG 1 101 1 MG MG A . C 3 HOH 1 201 14 HOH HOH A . C 3 HOH 2 202 33 HOH HOH A . C 3 HOH 3 203 10 HOH HOH A . C 3 HOH 4 204 70 HOH HOH A . C 3 HOH 5 205 38 HOH HOH A . C 3 HOH 6 206 16 HOH HOH A . C 3 HOH 7 207 57 HOH HOH A . C 3 HOH 8 208 77 HOH HOH A . C 3 HOH 9 209 90 HOH HOH A . C 3 HOH 10 210 13 HOH HOH A . C 3 HOH 11 211 1 HOH HOH A . C 3 HOH 12 212 52 HOH HOH A . C 3 HOH 13 213 19 HOH HOH A . C 3 HOH 14 214 58 HOH HOH A . C 3 HOH 15 215 8 HOH HOH A . C 3 HOH 16 216 7 HOH HOH A . C 3 HOH 17 217 22 HOH HOH A . C 3 HOH 18 218 55 HOH HOH A . C 3 HOH 19 219 56 HOH HOH A . C 3 HOH 20 220 27 HOH HOH A . C 3 HOH 21 221 23 HOH HOH A . C 3 HOH 22 222 3 HOH HOH A . C 3 HOH 23 223 50 HOH HOH A . C 3 HOH 24 224 82 HOH HOH A . C 3 HOH 25 225 64 HOH HOH A . C 3 HOH 26 226 17 HOH HOH A . C 3 HOH 27 227 51 HOH HOH A . C 3 HOH 28 228 69 HOH HOH A . C 3 HOH 29 229 67 HOH HOH A . C 3 HOH 30 230 54 HOH HOH A . C 3 HOH 31 231 59 HOH HOH A . C 3 HOH 32 232 15 HOH HOH A . C 3 HOH 33 233 28 HOH HOH A . C 3 HOH 34 234 48 HOH HOH A . C 3 HOH 35 235 9 HOH HOH A . C 3 HOH 36 236 83 HOH HOH A . C 3 HOH 37 237 66 HOH HOH A . C 3 HOH 38 238 25 HOH HOH A . C 3 HOH 39 239 79 HOH HOH A . C 3 HOH 40 240 24 HOH HOH A . C 3 HOH 41 241 46 HOH HOH A . C 3 HOH 42 242 6 HOH HOH A . C 3 HOH 43 243 61 HOH HOH A . C 3 HOH 44 244 2 HOH HOH A . C 3 HOH 45 245 12 HOH HOH A . C 3 HOH 46 246 11 HOH HOH A . C 3 HOH 47 247 20 HOH HOH A . C 3 HOH 48 248 5 HOH HOH A . C 3 HOH 49 249 26 HOH HOH A . C 3 HOH 50 250 53 HOH HOH A . C 3 HOH 51 251 73 HOH HOH A . C 3 HOH 52 252 32 HOH HOH A . C 3 HOH 53 253 43 HOH HOH A . C 3 HOH 54 254 40 HOH HOH A . C 3 HOH 55 255 4 HOH HOH A . C 3 HOH 56 256 39 HOH HOH A . C 3 HOH 57 257 42 HOH HOH A . C 3 HOH 58 258 37 HOH HOH A . C 3 HOH 59 259 44 HOH HOH A . C 3 HOH 60 260 30 HOH HOH A . C 3 HOH 61 261 41 HOH HOH A . C 3 HOH 62 262 29 HOH HOH A . C 3 HOH 63 263 80 HOH HOH A . C 3 HOH 64 264 35 HOH HOH A . C 3 HOH 65 265 88 HOH HOH A . C 3 HOH 66 266 21 HOH HOH A . C 3 HOH 67 267 49 HOH HOH A . C 3 HOH 68 268 34 HOH HOH A . C 3 HOH 69 269 91 HOH HOH A . C 3 HOH 70 270 18 HOH HOH A . C 3 HOH 71 271 72 HOH HOH A . C 3 HOH 72 272 89 HOH HOH A . C 3 HOH 73 273 85 HOH HOH A . C 3 HOH 74 274 45 HOH HOH A . C 3 HOH 75 275 75 HOH HOH A . C 3 HOH 76 276 78 HOH HOH A . C 3 HOH 77 277 31 HOH HOH A . C 3 HOH 78 278 36 HOH HOH A . C 3 HOH 79 279 76 HOH HOH A . C 3 HOH 80 280 86 HOH HOH A . C 3 HOH 81 281 71 HOH HOH A . C 3 HOH 82 282 84 HOH HOH A . C 3 HOH 83 283 62 HOH HOH A . C 3 HOH 84 284 60 HOH HOH A . C 3 HOH 85 285 47 HOH HOH A . C 3 HOH 86 286 63 HOH HOH A . C 3 HOH 87 287 65 HOH HOH A . C 3 HOH 88 288 87 HOH HOH A . C 3 HOH 89 289 74 HOH HOH A . C 3 HOH 90 290 81 HOH HOH A . C 3 HOH 91 291 68 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_reference_DOI _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.21.1_5286 ? 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? SAINT ? ? ? . ? 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? 'PROTEUM PLUS' ? ? ? . ? 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? MOLREP ? ? ? . ? 4 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 128.091 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 9YDK _cell.details ? _cell.formula_units_Z ? _cell.length_a 40.156 _cell.length_a_esd ? _cell.length_b 35.022 _cell.length_b_esd ? _cell.length_c 31.212 _cell.length_c_esd ? _cell.volume 34546.602 _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9YDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9YDK _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 2.33 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 44.89 _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 ? _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 ;drops containing 300nl 1 mM RNA and 300nl 10% 2-methyl-2,4-pentanediol (MPD), 40 mM sodium cacodylate, pH 7.0, 12 mM spermine 4HCl, 80 mM potassium chloride, 20 mM magnesium chloride and reservoir containing 40% MPD ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'Bruker PHOTON III' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2022-07-14 _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 'confocal multilayer' _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 1.3412 _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 'LIQUID ANODE' _diffrn_source.target ? _diffrn_source.type 'BRUKER METALJET' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.3412 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_synchrotron_site ? # _reflns.B_iso_Wilson_estimate 10.42 _reflns.entry_id 9YDK _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.12 _reflns.d_resolution_low 15.8 _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 13040 _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 98.59 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 8.7 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 12.46 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.998 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs ? _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 1.12 _reflns_shell.d_res_low 1.16 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 1233 _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 ? _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 0.603 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _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 16.10 _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 9YDK _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 1.12 _refine.ls_d_res_low 15.80 _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 13001 _refine.ls_number_reflns_R_free 1282 _refine.ls_number_reflns_R_work 23928 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 97.89 _refine.ls_percent_reflns_R_free 5.09 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1653 _refine.ls_R_factor_R_free 0.1855 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1642 _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.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _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 0.00 _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 1.1100 _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 26.1728 _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 0.1475 _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 1.12 _refine_hist.d_res_low 15.80 _refine_hist.number_atoms_solvent 91 _refine_hist.number_atoms_total 348 _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 167 _refine_hist.pdbx_number_atoms_ligand 90 _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_Zscore _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0116 ? 286 ? f_bond_d ? ? ? 'X-RAY DIFFRACTION' ? 1.5093 ? 445 ? f_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 0.0514 ? 58 ? f_chiral_restr ? ? ? 'X-RAY DIFFRACTION' ? 0.0244 ? 12 ? f_plane_restr ? ? ? 'X-RAY DIFFRACTION' ? 20.8960 ? 166 ? 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.correlation_coeff_Fo_to_Fc _refine_ls_shell.correlation_coeff_Fo_to_Fc_free _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free _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' 1.12 1.16 . . 118 2427 89.08 . . . . 0.3203 . . . . . . . . . . . . . . . 0.3963 'X-RAY DIFFRACTION' 1.16 1.22 . . 134 2615 95.88 . . . . 0.2672 . . . . . . . . . . . . . . . 0.3114 'X-RAY DIFFRACTION' 1.22 1.28 . . 144 2690 99.44 . . . . 0.2078 . . . . . . . . . . . . . . . 0.2232 'X-RAY DIFFRACTION' 1.28 1.36 . . 130 2697 99.82 . . . . 0.1983 . . . . . . . . . . . . . . . 0.2391 'X-RAY DIFFRACTION' 1.36 1.47 . . 187 2705 99.76 . . . . 0.1632 . . . . . . . . . . . . . . . 0.2238 'X-RAY DIFFRACTION' 1.47 1.61 . . 116 2722 99.86 . . . . 0.1513 . . . . . . . . . . . . . . . 0.1272 'X-RAY DIFFRACTION' 1.62 1.85 . . 165 2681 99.34 . . . . 0.1429 . . . . . . . . . . . . . . . 0.1439 'X-RAY DIFFRACTION' 1.85 2.33 . . 145 2722 99.62 . . . . 0.1572 . . . . . . . . . . . . . . . 0.1388 'X-RAY DIFFRACTION' 2.33 15.80 . . 143 2669 98.22 . . . . 0.1423 . . . . . . . . . . . . . . . 0.1915 # _struct.entry_id 9YDK _struct.title 'Dickerson dodecamer RNA duplex containing a modified base with a 2-F-6-aminopurine/G mismatch.' _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 9YDK _struct_keywords.text 'Dickerson dodecamer, RNA oligonucleotide, 2-F-6-aminopurine, A/G mismatch, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9YDK _struct_ref.pdbx_db_accession 9YDK _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 9YDK _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 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 9YDK _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)' 2560 ? 1 MORE -13 ? 1 'SSA (A^2)' 4200 ? # _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 # 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' 2_656 -x+1,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 20.9009346637 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 24.5648407871 # 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 U 8 "O3'" ? ? ? 1_555 A A1CU1 9 P ? ? A U 8 A A1CU1 13 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale2 covale one ? A A1CU1 9 "O3'" ? ? ? 1_555 A G 10 P ? ? A A1CU1 13 A G 14 1_555 ? ? ? ? ? ? ? 1.581 ? ? metalc1 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 101 A HOH 232 2_656 ? ? ? ? ? ? ? 2.207 ? ? metalc2 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 101 A HOH 242 1_555 ? ? ? ? ? ? ? 2.029 ? ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 101 A HOH 244 1_555 ? ? ? ? ? ? ? 2.131 ? ? metalc4 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 101 A HOH 270 1_555 ? ? ? ? ? ? ? 2.086 ? ? metalc5 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 101 A HOH 282 2_656 ? ? ? ? ? ? ? 2.240 ? ? metalc6 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? A MG 101 A HOH 283 1_555 ? ? ? ? ? ? ? 2.166 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 12 N1 ? ? A C 1 A G 16 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 12 O6 ? ? A C 1 A G 16 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 12 N2 ? ? A C 1 A G 16 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 11 N3 ? ? A G 2 A C 15 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 11 O2 ? ? A G 2 A C 15 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 11 N4 ? ? A G 2 A C 15 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 10 N1 ? ? A C 3 A G 14 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 10 O6 ? ? A C 3 A G 14 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 10 N2 ? ? A C 3 A G 14 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 A A1CU1 9 N1 ? ? A G 4 A A1CU1 13 2_656 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A A1CU1 9 N6 ? ? A G 4 A A1CU1 13 2_656 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 8 N3 ? ? A A 5 A U 8 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 8 O4 ? ? A A 5 A U 8 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 7 N3 ? ? A A 6 A U 7 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 7 O4 ? ? A A 6 A U 7 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 6 N1 ? ? A U 7 A A 6 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 6 N6 ? ? A U 7 A A 6 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 5 N1 ? ? A U 8 A A 5 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 5 N6 ? ? A U 8 A A 5 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A1CU1 9 N1 ? ? ? 1_555 A G 4 N1 ? ? A A1CU1 13 A G 4 2_656 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog21 hydrog ? ? A A1CU1 9 N6 ? ? ? 1_555 A G 4 O6 ? ? A A1CU1 13 A G 4 2_656 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog22 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 3 N3 ? ? A G 14 A C 3 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 3 O2 ? ? A G 14 A C 3 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 3 N4 ? ? A G 14 A C 3 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 2 N1 ? ? A C 15 A G 2 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 2 O6 ? ? A C 15 A G 2 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 2 N2 ? ? A C 15 A G 2 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 1 N3 ? ? A G 16 A C 1 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 1 O2 ? ? A G 16 A C 1 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 1 N4 ? ? A G 16 A C 1 2_656 ? ? ? ? ? ? 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 ? C HOH . ? A HOH 232 ? 2_656 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 242 ? 1_555 89.0 ? 2 O ? C HOH . ? A HOH 232 ? 2_656 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 244 ? 1_555 173.1 ? 3 O ? C HOH . ? A HOH 242 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 244 ? 1_555 88.6 ? 4 O ? C HOH . ? A HOH 232 ? 2_656 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 270 ? 1_555 85.8 ? 5 O ? C HOH . ? A HOH 242 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 270 ? 1_555 96.2 ? 6 O ? C HOH . ? A HOH 244 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 270 ? 1_555 88.0 ? 7 O ? C HOH . ? A HOH 232 ? 2_656 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 282 ? 2_656 95.4 ? 8 O ? C HOH . ? A HOH 242 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 282 ? 2_656 163.1 ? 9 O ? C HOH . ? A HOH 244 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 282 ? 2_656 88.8 ? 10 O ? C HOH . ? A HOH 270 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 282 ? 2_656 100.4 ? 11 O ? C HOH . ? A HOH 232 ? 2_656 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 283 ? 1_555 97.1 ? 12 O ? C HOH . ? A HOH 242 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 283 ? 1_555 85.5 ? 13 O ? C HOH . ? A HOH 244 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 283 ? 1_555 89.2 ? 14 O ? C HOH . ? A HOH 270 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 283 ? 1_555 176.7 ? 15 O ? C HOH . ? A HOH 282 ? 2_656 MG ? B MG . ? A MG 101 ? 1_555 O ? C HOH . ? A HOH 283 ? 1_555 77.8 ? # _pdbx_entry_details.entry_id 9YDK _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 N # 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 229 ? ? O A HOH 237 ? ? 1.80 2 1 O A HOH 209 ? ? O A HOH 237 ? ? 2.07 3 1 O A HOH 204 ? ? O A HOH 275 ? ? 2.19 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 273 ? ? 1_555 O A HOH 273 ? ? 2_656 1.88 2 1 O A HOH 236 ? ? 1_555 O A HOH 259 ? ? 3_555 1.94 3 1 O A HOH 209 ? ? 1_555 O A HOH 275 ? ? 2_656 2.08 # 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 285 ? C HOH . 2 1 A HOH 290 ? C HOH . # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -x,y,-z 3 x+1/2,y+1/2,z 4 -x+1/2,y+1/2,-z # loop_ _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 A1CU1 C4 C Y N 38 A1CU1 C5 C Y N 39 A1CU1 C6 C Y N 40 A1CU1 C2 C Y N 41 A1CU1 N9 N Y N 42 A1CU1 N1 N Y N 43 A1CU1 N7 N Y N 44 A1CU1 "C1'" C N R 45 A1CU1 "C2'" C N R 46 A1CU1 "C3'" C N S 47 A1CU1 "C4'" C N R 48 A1CU1 "C5'" C N N 49 A1CU1 C8 C Y N 50 A1CU1 F F N N 51 A1CU1 N3 N Y N 52 A1CU1 N6 N N N 53 A1CU1 "O2'" O N N 54 A1CU1 "O3'" O N N 55 A1CU1 "O4'" O N N 56 A1CU1 "O5'" O N N 57 A1CU1 OP1 O N N 58 A1CU1 OP2 O N N 59 A1CU1 P P N N 60 A1CU1 "H1'" H N N 61 A1CU1 "H2'" H N N 62 A1CU1 "H3'" H N N 63 A1CU1 "H4'" H N N 64 A1CU1 "H5'" H N N 65 A1CU1 "H5''" H N N 66 A1CU1 H8 H N N 67 A1CU1 H62 H N N 68 A1CU1 H61 H N N 69 A1CU1 "HO2'" H N N 70 A1CU1 "HO3'" H N N 71 A1CU1 HOP2 H N N 72 A1CU1 OP3 O N N 73 A1CU1 HOP3 H N N 74 C OP3 O N N 75 C P P N N 76 C OP1 O N N 77 C OP2 O N N 78 C "O5'" O N N 79 C "C5'" C N N 80 C "C4'" C N R 81 C "O4'" O N N 82 C "C3'" C N S 83 C "O3'" O N N 84 C "C2'" C N R 85 C "O2'" O N N 86 C "C1'" C N R 87 C N1 N N N 88 C C2 C N N 89 C O2 O N N 90 C N3 N N N 91 C C4 C N N 92 C N4 N N N 93 C C5 C N N 94 C C6 C N N 95 C HOP3 H N N 96 C HOP2 H N N 97 C "H5'" H N N 98 C "H5''" H N N 99 C "H4'" H N N 100 C "H3'" H N N 101 C "HO3'" H N N 102 C "H2'" H N N 103 C "HO2'" H N N 104 C "H1'" H N N 105 C H41 H N N 106 C H42 H N N 107 C H5 H N N 108 C H6 H N N 109 G OP3 O N N 110 G P P N N 111 G OP1 O N N 112 G OP2 O N N 113 G "O5'" O N N 114 G "C5'" C N N 115 G "C4'" C N R 116 G "O4'" O N N 117 G "C3'" C N S 118 G "O3'" O N N 119 G "C2'" C N R 120 G "O2'" O N N 121 G "C1'" C N R 122 G N9 N Y N 123 G C8 C Y N 124 G N7 N Y N 125 G C5 C Y N 126 G C6 C N N 127 G O6 O N N 128 G N1 N N N 129 G C2 C N N 130 G N2 N N N 131 G N3 N N N 132 G C4 C Y N 133 G HOP3 H N N 134 G HOP2 H N N 135 G "H5'" H N N 136 G "H5''" H N N 137 G "H4'" H N N 138 G "H3'" H N N 139 G "HO3'" H N N 140 G "H2'" H N N 141 G "HO2'" H N N 142 G "H1'" H N N 143 G H8 H N N 144 G H1 H N N 145 G H21 H N N 146 G H22 H N N 147 HOH O O N N 148 HOH H1 H N N 149 HOH H2 H N N 150 MG MG MG N N 151 U OP3 O N N 152 U P P N N 153 U OP1 O N N 154 U OP2 O N N 155 U "O5'" O N N 156 U "C5'" C N N 157 U "C4'" C N R 158 U "O4'" O N N 159 U "C3'" C N S 160 U "O3'" O N N 161 U "C2'" C N R 162 U "O2'" O N N 163 U "C1'" C N R 164 U N1 N N N 165 U C2 C N N 166 U O2 O N N 167 U N3 N N N 168 U C4 C N N 169 U O4 O N N 170 U C5 C N N 171 U C6 C N N 172 U HOP3 H N N 173 U HOP2 H N N 174 U "H5'" H N N 175 U "H5''" H N N 176 U "H4'" H N N 177 U "H3'" H N N 178 U "HO3'" H N N 179 U "H2'" H N N 180 U "HO2'" H N N 181 U "H1'" H N N 182 U H3 H N N 183 U H5 H N N 184 U H6 H N N 185 # 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 A1CU1 C6 N6 sing N N 40 A1CU1 C5 C6 doub Y N 41 A1CU1 C8 N7 doub Y N 42 A1CU1 N7 C5 sing Y N 43 A1CU1 C4 C5 sing Y N 44 A1CU1 "C1'" N9 sing N N 45 A1CU1 "C2'" "C1'" sing N N 46 A1CU1 "O2'" "C2'" sing N N 47 A1CU1 "C3'" "C2'" sing N N 48 A1CU1 "O3'" "C3'" sing N N 49 A1CU1 "C4'" "C3'" sing N N 50 A1CU1 "O5'" "C5'" sing N N 51 A1CU1 P "O5'" sing N N 52 A1CU1 OP1 P doub N N 53 A1CU1 OP2 P sing N N 54 A1CU1 "C5'" "C4'" sing N N 55 A1CU1 "O4'" "C4'" sing N N 56 A1CU1 N9 C4 sing Y N 57 A1CU1 N3 C4 doub Y N 58 A1CU1 C2 N3 sing Y N 59 A1CU1 F C2 sing N N 60 A1CU1 N1 C2 doub Y N 61 A1CU1 C6 N1 sing Y N 62 A1CU1 C8 N9 sing Y N 63 A1CU1 "C1'" "O4'" sing N N 64 A1CU1 "C1'" "H1'" sing N N 65 A1CU1 "C2'" "H2'" sing N N 66 A1CU1 "C3'" "H3'" sing N N 67 A1CU1 "C4'" "H4'" sing N N 68 A1CU1 "C5'" "H5'" sing N N 69 A1CU1 "C5'" "H5''" sing N N 70 A1CU1 C8 H8 sing N N 71 A1CU1 N6 H62 sing N N 72 A1CU1 N6 H61 sing N N 73 A1CU1 "O2'" "HO2'" sing N N 74 A1CU1 "O3'" "HO3'" sing N N 75 A1CU1 OP2 HOP2 sing N N 76 A1CU1 P OP3 sing N N 77 A1CU1 OP3 HOP3 sing N N 78 C OP3 P sing N N 79 C OP3 HOP3 sing N N 80 C P OP1 doub N N 81 C P OP2 sing N N 82 C P "O5'" sing N N 83 C OP2 HOP2 sing N N 84 C "O5'" "C5'" sing N N 85 C "C5'" "C4'" sing N N 86 C "C5'" "H5'" sing N N 87 C "C5'" "H5''" sing N N 88 C "C4'" "O4'" sing N N 89 C "C4'" "C3'" sing N N 90 C "C4'" "H4'" sing N N 91 C "O4'" "C1'" sing N N 92 C "C3'" "O3'" sing N N 93 C "C3'" "C2'" sing N N 94 C "C3'" "H3'" sing N N 95 C "O3'" "HO3'" sing N N 96 C "C2'" "O2'" sing N N 97 C "C2'" "C1'" sing N N 98 C "C2'" "H2'" sing N N 99 C "O2'" "HO2'" sing N N 100 C "C1'" N1 sing N N 101 C "C1'" "H1'" sing N N 102 C N1 C2 sing N N 103 C N1 C6 sing N N 104 C C2 O2 doub N N 105 C C2 N3 sing N N 106 C N3 C4 doub N N 107 C C4 N4 sing N N 108 C C4 C5 sing N N 109 C N4 H41 sing N N 110 C N4 H42 sing N N 111 C C5 C6 doub N N 112 C C5 H5 sing N N 113 C C6 H6 sing N N 114 G OP3 P sing N N 115 G OP3 HOP3 sing N N 116 G P OP1 doub N N 117 G P OP2 sing N N 118 G P "O5'" sing N N 119 G OP2 HOP2 sing N N 120 G "O5'" "C5'" sing N N 121 G "C5'" "C4'" sing N N 122 G "C5'" "H5'" sing N N 123 G "C5'" "H5''" sing N N 124 G "C4'" "O4'" sing N N 125 G "C4'" "C3'" sing N N 126 G "C4'" "H4'" sing N N 127 G "O4'" "C1'" sing N N 128 G "C3'" "O3'" sing N N 129 G "C3'" "C2'" sing N N 130 G "C3'" "H3'" sing N N 131 G "O3'" "HO3'" sing N N 132 G "C2'" "O2'" sing N N 133 G "C2'" "C1'" sing N N 134 G "C2'" "H2'" sing N N 135 G "O2'" "HO2'" sing N N 136 G "C1'" N9 sing N N 137 G "C1'" "H1'" sing N N 138 G N9 C8 sing Y N 139 G N9 C4 sing Y N 140 G C8 N7 doub Y N 141 G C8 H8 sing N N 142 G N7 C5 sing Y N 143 G C5 C6 sing N N 144 G C5 C4 doub Y N 145 G C6 O6 doub N N 146 G C6 N1 sing N N 147 G N1 C2 sing N N 148 G N1 H1 sing N N 149 G C2 N2 sing N N 150 G C2 N3 doub N N 151 G N2 H21 sing N N 152 G N2 H22 sing N N 153 G N3 C4 sing N N 154 HOH O H1 sing N N 155 HOH O H2 sing N N 156 U OP3 P sing N N 157 U OP3 HOP3 sing N N 158 U P OP1 doub N N 159 U P OP2 sing N N 160 U P "O5'" sing N N 161 U OP2 HOP2 sing N N 162 U "O5'" "C5'" sing N N 163 U "C5'" "C4'" sing N N 164 U "C5'" "H5'" sing N N 165 U "C5'" "H5''" sing N N 166 U "C4'" "O4'" sing N N 167 U "C4'" "C3'" sing N N 168 U "C4'" "H4'" sing N N 169 U "O4'" "C1'" sing N N 170 U "C3'" "O3'" sing N N 171 U "C3'" "C2'" sing N N 172 U "C3'" "H3'" sing N N 173 U "O3'" "HO3'" sing N N 174 U "C2'" "O2'" sing N N 175 U "C2'" "C1'" sing N N 176 U "C2'" "H2'" sing N N 177 U "O2'" "HO2'" sing N N 178 U "C1'" N1 sing N N 179 U "C1'" "H1'" sing N N 180 U N1 C2 sing N N 181 U N1 C6 sing N N 182 U C2 O2 doub N N 183 U C2 N3 sing N N 184 U N3 C4 sing N N 185 U N3 H3 sing N N 186 U C4 O4 doub N N 187 U C4 C5 sing N N 188 U C5 C6 doub N N 189 U C5 H5 sing N N 190 U C6 H6 sing N N 191 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9YDK 'double helix' 9YDK 'a-form double helix' 9YDK '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 C 1 1_555 A G 12 2_656 0.114 -0.138 -0.032 7.465 -16.608 0.430 1 A_C1:G16_A A 1 ? A 16 ? 19 1 1 A G 2 1_555 A C 11 2_656 -0.257 -0.170 -0.024 -6.084 -17.613 1.057 2 A_G2:C15_A A 2 ? A 15 ? 19 1 1 A C 3 1_555 A G 10 2_656 0.143 -0.168 0.182 -2.816 -14.237 -2.776 3 A_C3:G14_A A 3 ? A 14 ? 19 1 1 A G 4 1_555 A A1CU1 9 2_656 -0.037 1.563 -0.208 4.366 -4.875 -21.431 4 A_G4:A1CU113_A A 4 ? A 13 ? 8 1 1 A A 5 1_555 A U 8 2_656 0.028 -0.031 0.131 5.314 -14.416 -4.539 5 A_A5:U8_A A 5 ? A 8 ? 20 1 1 A A 6 1_555 A U 7 2_656 0.083 -0.093 -0.031 4.076 -24.932 -1.942 6 A_A6:U7_A A 6 ? A 7 ? 20 1 1 A U 7 1_555 A A 6 2_656 -0.083 -0.093 -0.031 -4.076 -24.932 -1.942 7 A_U7:A6_A A 7 ? A 6 ? 20 1 1 A U 8 1_555 A A 5 2_656 -0.028 -0.031 0.131 -5.314 -14.416 -4.539 8 A_U8:A5_A A 8 ? A 5 ? 20 1 1 A A1CU1 9 1_555 A G 4 2_656 0.037 1.563 -0.208 -4.366 -4.875 -21.431 9 A_A1CU113:G4_A A 13 ? A 4 ? 8 1 1 A G 10 1_555 A C 3 2_656 -0.143 -0.168 0.182 2.816 -14.237 -2.776 10 A_G14:C3_A A 14 ? A 3 ? 19 1 1 A C 11 1_555 A G 2 2_656 0.257 -0.170 -0.024 6.084 -17.613 1.057 11 A_C15:G2_A A 15 ? A 2 ? 19 1 1 A G 12 1_555 A C 1 2_656 -0.114 -0.138 -0.032 -7.465 -16.608 0.430 12 A_G16:C1_A A 16 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 A G 12 2_656 A G 2 1_555 A C 11 2_656 -0.493 -1.707 3.410 -2.688 13.508 32.101 -4.798 0.435 2.541 23.142 4.604 34.859 1 AA_C1G2:C15G16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A G 2 1_555 A C 11 2_656 A C 3 1_555 A G 10 2_656 -0.536 -1.160 3.138 -2.218 4.027 35.192 -2.461 0.572 3.019 6.625 3.650 35.482 2 AA_G2C3:G14C15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A C 3 1_555 A G 10 2_656 A G 4 1_555 A A1CU1 9 2_656 -0.906 -1.294 3.104 2.282 8.421 27.862 -4.188 2.237 2.532 16.968 -4.598 29.170 3 AA_C3G4:A1CU113G14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A A1CU1 9 2_656 A A 5 1_555 A U 8 2_656 0.651 -1.469 3.164 -2.613 12.610 28.897 -4.736 -1.618 2.274 23.831 4.939 31.581 4 AA_G4A5:U8A1CU113_AA A 4 ? A 13 ? A 5 ? A 8 ? 1 A A 5 1_555 A U 8 2_656 A A 6 1_555 A U 7 2_656 0.088 -0.959 3.228 1.860 9.269 35.272 -2.755 0.105 2.893 14.967 -3.004 36.478 5 AA_A5A6:U7U8_AA A 5 ? A 8 ? A 6 ? A 7 ? 1 A A 6 1_555 A U 7 2_656 A U 7 1_555 A A 6 2_656 0.000 -1.149 3.422 0.000 11.826 32.504 -3.745 0.000 2.844 20.308 0.000 34.533 6 AA_A6U7:A6U7_AA A 6 ? A 7 ? A 7 ? A 6 ? 1 A U 7 1_555 A A 6 2_656 A U 8 1_555 A A 5 2_656 -0.088 -0.959 3.228 -1.860 9.269 35.272 -2.755 -0.105 2.893 14.967 3.004 36.478 7 AA_U7U8:A5A6_AA A 7 ? A 6 ? A 8 ? A 5 ? 1 A U 8 1_555 A A 5 2_656 A A1CU1 9 1_555 A G 4 2_656 -0.651 -1.469 3.164 2.613 12.610 28.897 -4.736 1.618 2.274 23.831 -4.939 31.581 8 AA_U8A1CU113:G4A5_AA A 8 ? A 5 ? A 13 ? A 4 ? 1 A A1CU1 9 1_555 A G 4 2_656 A G 10 1_555 A C 3 2_656 0.906 -1.294 3.104 -2.282 8.421 27.862 -4.188 -2.237 2.532 16.968 4.598 29.170 9 AA_A1CU113G14:C3G4_AA A 13 ? A 4 ? A 14 ? A 3 ? 1 A G 10 1_555 A C 3 2_656 A C 11 1_555 A G 2 2_656 0.536 -1.160 3.138 2.218 4.027 35.192 -2.461 -0.572 3.019 6.625 -3.650 35.482 10 AA_G14C15:G2C3_AA A 14 ? A 3 ? A 15 ? A 2 ? 1 A C 11 1_555 A G 2 2_656 A G 12 1_555 A C 1 2_656 0.493 -1.707 3.410 2.688 13.508 32.101 -4.798 -0.435 2.541 23.142 -4.604 34.859 11 AA_C15G16:C1G2_AA A 15 ? A 2 ? A 16 ? A 1 ? # _pdbx_audit_support.funding_organization 'Other private' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _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 2Q1R _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'C 1 2 1' _space_group.name_Hall 'C 2y' _space_group.IT_number 5 _space_group.crystal_system monoclinic _space_group.id 1 # _atom_sites.entry_id 9YDK _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] 0.024903 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.019520 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.028553 _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] 0.040709 _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. ; ? F ? ? 4.90428 4.07044 ? ? 12.99538 1.63651 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? H ? ? 0.51345 0.48472 ? ? 24.73122 6.32584 ? ? 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. ; ? O1- ? ? 4.31557 2.79156 1.86576 ? 8.03600 32.36470 0.29580 ? 0.0 ;3-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ # loop_ #