data_6UGJ # _entry.id 6UGJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 6UGJ pdb_00006ugj 10.2210/pdb6ugj/pdb WWPDB D_1000244561 ? ? # 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 2020-01-01 2 'Structure model' 1 1 2020-03-04 3 'Structure model' 1 2 2024-03-13 4 'Structure model' 1 3 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' database_2 6 4 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.year' 5 2 'Structure model' '_citation_author.identifier_ORCID' 6 3 'Structure model' '_database_2.pdbx_DOI' 7 3 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6UGJ _pdbx_database_status.recvd_initial_deposition_date 2019-09-26 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Chan, C.W.' 1 0000-0001-5472-4803 'Mondragon, A.' 2 0000-0002-0423-6323 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Rna _citation.journal_id_ASTM RNARFU _citation.journal_id_CSD 2122 _citation.journal_id_ISSN 1469-9001 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 26 _citation.language ? _citation.page_first 278 _citation.page_last 289 _citation.title ;Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs. ; _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1261/rna.073478.119 _citation.pdbx_database_id_PubMed 31848215 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chan, C.W.' 1 ? primary 'Badong, D.' 2 ? primary 'Rajan, R.' 3 ? primary 'Mondragon, A.' 4 ? # 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 'tRNA(Asp) acceptor stem/T stem-loop' 9989.942 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 non-polymer syn URACIL 112.087 1 ? ? ? ? 4 non-polymer syn DIPHOSPHATE 173.943 1 ? ? ? ? 5 water nat water 18.015 70 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGAGCGGGCGGGUUCGAGUCCCGUCCGUUCC _entity_poly.pdbx_seq_one_letter_code_can GGAGCGGGCGGGUUCGAGUCCCGUCCGUUCC _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 'SULFATE ION' SO4 3 URACIL URA 4 DIPHOSPHATE DPO 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 A n 1 4 G n 1 5 C n 1 6 G n 1 7 G n 1 8 G n 1 9 C n 1 10 G n 1 11 G n 1 12 G n 1 13 U n 1 14 U n 1 15 C n 1 16 G n 1 17 A n 1 18 G n 1 19 U n 1 20 C n 1 21 C n 1 22 C n 1 23 G n 1 24 U n 1 25 C n 1 26 C n 1 27 G n 1 28 U n 1 29 U n 1 30 C n 1 31 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 31 _pdbx_entity_src_syn.organism_scientific 'Escherichia coli' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 562 _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 DPO non-polymer . DIPHOSPHATE ? 'O7 P2 -4' 173.943 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 URA non-polymer . URACIL ? 'C4 H4 N2 O2' 112.087 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 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 C 5 5 5 C C A . n A 1 6 G 6 6 6 G G A . n A 1 7 G 7 7 7 G G A . n A 1 8 G 8 8 8 G G A . n A 1 9 C 9 9 9 C C A . n A 1 10 G 10 10 10 G G A . n A 1 11 G 11 11 11 G G A . n A 1 12 G 12 12 12 G G A . n A 1 13 U 13 13 13 U U A . n A 1 14 U 14 14 ? ? ? A . n A 1 15 C 15 15 ? ? ? A . n A 1 16 G 16 16 ? ? ? A . n A 1 17 A 17 17 17 A A A . n A 1 18 G 18 18 18 G G A . n A 1 19 U 19 19 19 U U A . n A 1 20 C 20 20 20 C C A . n A 1 21 C 21 21 21 C C A . n A 1 22 C 22 22 22 C C A . n A 1 23 G 23 23 23 G G A . n A 1 24 U 24 24 24 U U A . n A 1 25 C 25 25 25 C C A . n A 1 26 C 26 26 26 C C A . n A 1 27 G 27 27 27 G G A . n A 1 28 U 28 28 28 U U A . n A 1 29 U 29 29 29 U U A . n A 1 30 C 30 30 30 C C A . n A 1 31 C 31 31 31 C C 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 SO4 1 101 1 SO4 SO4 A . C 3 URA 1 102 1 URA URA A . D 4 DPO 1 103 1 DPO 3PO A . E 5 HOH 1 201 73 HOH HOH A . E 5 HOH 2 202 68 HOH HOH A . E 5 HOH 3 203 59 HOH HOH A . E 5 HOH 4 204 64 HOH HOH A . E 5 HOH 5 205 7 HOH HOH A . E 5 HOH 6 206 72 HOH HOH A . E 5 HOH 7 207 26 HOH HOH A . E 5 HOH 8 208 6 HOH HOH A . E 5 HOH 9 209 65 HOH HOH A . E 5 HOH 10 210 12 HOH HOH A . E 5 HOH 11 211 58 HOH HOH A . E 5 HOH 12 212 55 HOH HOH A . E 5 HOH 13 213 67 HOH HOH A . E 5 HOH 14 214 16 HOH HOH A . E 5 HOH 15 215 25 HOH HOH A . E 5 HOH 16 216 54 HOH HOH A . E 5 HOH 17 217 21 HOH HOH A . E 5 HOH 18 218 52 HOH HOH A . E 5 HOH 19 219 20 HOH HOH A . E 5 HOH 20 220 5 HOH HOH A . E 5 HOH 21 221 23 HOH HOH A . E 5 HOH 22 222 29 HOH HOH A . E 5 HOH 23 223 66 HOH HOH A . E 5 HOH 24 224 71 HOH HOH A . E 5 HOH 25 225 11 HOH HOH A . E 5 HOH 26 226 39 HOH HOH A . E 5 HOH 27 227 69 HOH HOH A . E 5 HOH 28 228 31 HOH HOH A . E 5 HOH 29 229 56 HOH HOH A . E 5 HOH 30 230 36 HOH HOH A . E 5 HOH 31 231 51 HOH HOH A . E 5 HOH 32 232 19 HOH HOH A . E 5 HOH 33 233 9 HOH HOH A . E 5 HOH 34 234 32 HOH HOH A . E 5 HOH 35 235 2 HOH HOH A . E 5 HOH 36 236 53 HOH HOH A . E 5 HOH 37 237 57 HOH HOH A . E 5 HOH 38 238 44 HOH HOH A . E 5 HOH 39 239 38 HOH HOH A . E 5 HOH 40 240 37 HOH HOH A . E 5 HOH 41 241 42 HOH HOH A . E 5 HOH 42 242 10 HOH HOH A . E 5 HOH 43 243 3 HOH HOH A . E 5 HOH 44 244 28 HOH HOH A . E 5 HOH 45 245 34 HOH HOH A . E 5 HOH 46 246 60 HOH HOH A . E 5 HOH 47 247 13 HOH HOH A . E 5 HOH 48 248 24 HOH HOH A . E 5 HOH 49 249 50 HOH HOH A . E 5 HOH 50 250 43 HOH HOH A . E 5 HOH 51 251 17 HOH HOH A . E 5 HOH 52 252 8 HOH HOH A . E 5 HOH 53 253 45 HOH HOH A . E 5 HOH 54 254 1 HOH HOH A . E 5 HOH 55 255 4 HOH HOH A . E 5 HOH 56 256 62 HOH HOH A . E 5 HOH 57 257 41 HOH HOH A . E 5 HOH 58 258 49 HOH HOH A . E 5 HOH 59 259 15 HOH HOH A . E 5 HOH 60 260 35 HOH HOH A . E 5 HOH 61 261 14 HOH HOH A . E 5 HOH 62 262 63 HOH HOH A . E 5 HOH 63 263 46 HOH HOH A . E 5 HOH 64 264 70 HOH HOH A . E 5 HOH 65 265 27 HOH HOH A . E 5 HOH 66 266 30 HOH HOH A . E 5 HOH 67 267 33 HOH HOH A . E 5 HOH 68 268 40 HOH HOH A . E 5 HOH 69 269 48 HOH HOH A . E 5 HOH 70 270 47 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 ? ? ? 5.8.0238 1 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.25 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? STARANISO ? ? ? . 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 6UGJ _cell.details ? _cell.formula_units_Z ? _cell.length_a 43.845 _cell.length_a_esd ? _cell.length_b 43.845 _cell.length_b_esd ? _cell.length_c 259.285 _cell.length_c_esd ? _cell.volume ? _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 ? # _symmetry.entry_id 6UGJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _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 6UGJ _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 2.40 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 48.76 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 287 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '2 M ammonium sulfate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ;Crystals were flash frozen with liquid nitrogen in crystallization well solution supplemented with either increased ammonium sulfate concentration or with 20% (v/v) glycerol for cryo-protection ; _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 Monochromator _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 9M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-03-01 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97620 _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 'APS BEAMLINE 21-ID-D' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97620 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 21-ID-D _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6UGJ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 43.25 _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 9777 _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 92 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 21.7 _reflns.pdbx_Rmerge_I_obs 0.156 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 11.5 _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 0.160 _reflns.pdbx_Rpim_I_all 0.034 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.60 _reflns_shell.d_res_low 1.691 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.0 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 6865 _reflns_shell.percent_possible_all 68.8 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 4.054 _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 14.3 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all 4.2 _reflns_shell.pdbx_Rpim_I_all 1.089 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.492 _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] -0.1000 _refine.aniso_B[1][2] -0.0500 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][2] -0.1000 _refine.aniso_B[2][3] -0.0000 _refine.aniso_B[3][3] 0.3200 _refine.B_iso_max 118.830 _refine.B_iso_mean 35.7430 _refine.B_iso_min 19.570 _refine.correlation_coeff_Fo_to_Fc 0.9600 _refine.correlation_coeff_Fo_to_Fc_free 0.9400 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _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 6UGJ _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 1.6000 _refine.ls_d_res_low 43.2500 _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 9077 _refine.ls_number_reflns_R_free 492 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 72.1900 _refine.ls_percent_reflns_R_free 5.1000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2165 _refine.ls_R_factor_R_free 0.2724 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2136 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model '5 base pair A-form RNA helix' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.1290 _refine.pdbx_overall_ESU_R_Free 0.1370 _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B 2.2750 _refine.overall_SU_ML 0.0750 _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 final _refine_hist.details ? _refine_hist.d_res_high 1.6000 _refine_hist.d_res_low 43.2500 _refine_hist.number_atoms_solvent 70 _refine_hist.number_atoms_total 692 _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 28 _refine_hist.pdbx_B_iso_mean_ligand 79.68 _refine_hist.pdbx_B_iso_mean_solvent 38.20 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 600 _refine_hist.pdbx_number_atoms_ligand 22 _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' ? 0.009 0.011 689 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.002 0.020 279 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.615 1.292 1071 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 1.593 2.985 675 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? 0.075 0.200 112 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.015 0.020 346 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.002 0.020 157 ? r_gen_planes_other ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.6020 _refine_ls_shell.d_res_low 1.6440 _refine_ls_shell.number_reflns_all 194 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 7 _refine_ls_shell.number_reflns_R_work 187 _refine_ls_shell.percent_reflns_obs 20.1000 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.2990 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.3990 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 6UGJ _struct.title 'Crystal structure of a fragment of E. coli tRNA(Asp) consisting of its acceptor stem/T stem-loop. Short unit cell.' _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 6UGJ _struct_keywords.text 'tRNA RNA unmodified T-loop acceptor stem, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6UGJ _struct_ref.pdbx_db_accession 6UGJ _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 6UGJ _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 31 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6UGJ _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 31 _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 31 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 440 ? 1 MORE -2 ? 1 'SSA (A^2)' 5610 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? A G 1 P ? ? ? 1_555 D DPO . O7 ? ? A G 1 A DPO 103 1_555 ? ? ? ? ? ? ? 1.576 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 31 N3 ? ? A G 1 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 31 O2 ? ? A G 1 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 31 N4 ? ? A G 1 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 2 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 2 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 2 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 29 N3 ? ? A A 3 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 29 O4 ? ? A A 3 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A U 28 O2 ? ? A G 4 A U 28 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 A U 28 N3 ? ? A G 4 A U 28 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 27 N1 ? ? A C 5 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 27 O6 ? ? A C 5 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 27 N2 ? ? A C 5 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 6 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 6 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 6 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 25 N3 ? ? A G 7 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 25 O2 ? ? A G 7 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 25 N4 ? ? A G 7 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 A U 24 O2 ? ? A G 8 A U 24 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A G 8 O6 ? ? ? 1_555 A U 24 N3 ? ? A G 8 A U 24 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 9 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 9 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 9 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 10 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 10 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 10 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 11 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 11 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 11 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 12 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 20 O2 ? ? A G 12 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 20 N4 ? ? A G 12 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 13 N3 ? ? ? 1_555 A A 17 N7 ? ? A U 13 A A 17 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog35 hydrog ? ? A U 13 O2 ? ? ? 1_555 A A 17 N6 ? ? A U 13 A A 17 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SO4 101 ? 8 'binding site for residue SO4 A 101' AC2 Software A URA 102 ? 2 'binding site for residue URA A 102' AC3 Software A DPO 103 ? 3 'binding site for residue DPO A 103' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 8 G A 8 ? G A 8 . ? 3_545 ? 2 AC1 8 G A 8 ? G A 8 . ? 1_555 ? 3 AC1 8 G A 8 ? G A 8 . ? 2_445 ? 4 AC1 8 C A 9 ? C A 9 . ? 1_555 ? 5 AC1 8 C A 9 ? C A 9 . ? 2_445 ? 6 AC1 8 C A 9 ? C A 9 . ? 3_545 ? 7 AC1 8 HOH E . ? HOH A 212 . ? 2_445 ? 8 AC1 8 HOH E . ? HOH A 212 . ? 1_555 ? 9 AC2 2 U A 13 ? U A 13 . ? 1_555 ? 10 AC2 2 A A 17 ? A A 17 . ? 1_555 ? 11 AC3 3 G A 1 ? G A 1 . ? 1_555 ? 12 AC3 3 C A 31 ? C A 31 . ? 16_544 ? 13 AC3 3 HOH E . ? HOH A 223 . ? 16_544 ? # 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 204 ? ? 1_555 O A HOH 256 ? ? 2_555 1.91 2 1 O A HOH 203 ? ? 1_555 O A HOH 255 ? ? 2_555 2.19 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O5'" A G 4 ? ? P A G 4 ? ? OP1 A G 4 ? ? 119.88 110.70 9.18 1.20 N 2 1 "O5'" A G 4 ? ? P A G 4 ? ? OP2 A G 4 ? ? 92.27 105.70 -13.43 0.90 N # 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 SO4 101 ? B SO4 . 2 1 A HOH 215 ? E HOH . 3 1 A HOH 220 ? E HOH . 4 1 A HOH 243 ? E HOH . 5 1 A HOH 247 ? E HOH . 6 1 A HOH 248 ? E HOH . 7 1 A HOH 252 ? E HOH . 8 1 A HOH 254 ? E HOH . 9 1 A HOH 261 ? E HOH . 10 1 A HOH 266 ? E HOH . 11 1 A HOH 270 ? E HOH . # _pdbx_entry_details.entry_id 6UGJ _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A U 14 ? A U 14 2 1 Y 1 A C 15 ? A C 15 3 1 Y 1 A G 16 ? A G 16 # 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 DPO P1 P N N 73 DPO O1 O N N 74 DPO O2 O N N 75 DPO O3 O N N 76 DPO O4 O N N 77 DPO P2 P N N 78 DPO O5 O N N 79 DPO O6 O N N 80 DPO O7 O N N 81 G OP3 O N N 82 G P P N N 83 G OP1 O N N 84 G OP2 O N N 85 G "O5'" O N N 86 G "C5'" C N N 87 G "C4'" C N R 88 G "O4'" O N N 89 G "C3'" C N S 90 G "O3'" O N N 91 G "C2'" C N R 92 G "O2'" O N N 93 G "C1'" C N R 94 G N9 N Y N 95 G C8 C Y N 96 G N7 N Y N 97 G C5 C Y N 98 G C6 C N N 99 G O6 O N N 100 G N1 N N N 101 G C2 C N N 102 G N2 N N N 103 G N3 N N N 104 G C4 C Y N 105 G HOP3 H N N 106 G HOP2 H N N 107 G "H5'" H N N 108 G "H5''" H N N 109 G "H4'" H N N 110 G "H3'" H N N 111 G "HO3'" H N N 112 G "H2'" H N N 113 G "HO2'" H N N 114 G "H1'" H N N 115 G H8 H N N 116 G H1 H N N 117 G H21 H N N 118 G H22 H N N 119 HOH O O N N 120 HOH H1 H N N 121 HOH H2 H N N 122 SO4 S S N N 123 SO4 O1 O N N 124 SO4 O2 O N N 125 SO4 O3 O N N 126 SO4 O4 O N N 127 U OP3 O N N 128 U P P N N 129 U OP1 O N N 130 U OP2 O N N 131 U "O5'" O N N 132 U "C5'" C N N 133 U "C4'" C N R 134 U "O4'" O N N 135 U "C3'" C N S 136 U "O3'" O N N 137 U "C2'" C N R 138 U "O2'" O N N 139 U "C1'" C N R 140 U N1 N N N 141 U C2 C N N 142 U O2 O N N 143 U N3 N N N 144 U C4 C N N 145 U O4 O N N 146 U C5 C N N 147 U C6 C N N 148 U HOP3 H N N 149 U HOP2 H N N 150 U "H5'" H N N 151 U "H5''" H N N 152 U "H4'" H N N 153 U "H3'" H N N 154 U "HO3'" H N N 155 U "H2'" H N N 156 U "HO2'" H N N 157 U "H1'" H N N 158 U H3 H N N 159 U H5 H N N 160 U H6 H N N 161 URA N1 N N N 162 URA C2 C N N 163 URA O2 O N N 164 URA N3 N N N 165 URA C4 C N N 166 URA O4 O N N 167 URA C5 C N N 168 URA C6 C N N 169 URA HN1 H N N 170 URA HN3 H N N 171 URA H5 H N N 172 URA H6 H N N 173 # 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 DPO P1 O1 doub N N 76 DPO P1 O2 sing N N 77 DPO P1 O3 sing N N 78 DPO P1 O4 sing N N 79 DPO O4 P2 sing N N 80 DPO P2 O5 doub N N 81 DPO P2 O6 sing N N 82 DPO P2 O7 sing N N 83 G OP3 P sing N N 84 G OP3 HOP3 sing N N 85 G P OP1 doub N N 86 G P OP2 sing N N 87 G P "O5'" sing N N 88 G OP2 HOP2 sing N N 89 G "O5'" "C5'" sing N N 90 G "C5'" "C4'" sing N N 91 G "C5'" "H5'" sing N N 92 G "C5'" "H5''" sing N N 93 G "C4'" "O4'" sing N N 94 G "C4'" "C3'" sing N N 95 G "C4'" "H4'" sing N N 96 G "O4'" "C1'" sing N N 97 G "C3'" "O3'" sing N N 98 G "C3'" "C2'" sing N N 99 G "C3'" "H3'" sing N N 100 G "O3'" "HO3'" sing N N 101 G "C2'" "O2'" sing N N 102 G "C2'" "C1'" sing N N 103 G "C2'" "H2'" sing N N 104 G "O2'" "HO2'" sing N N 105 G "C1'" N9 sing N N 106 G "C1'" "H1'" sing N N 107 G N9 C8 sing Y N 108 G N9 C4 sing Y N 109 G C8 N7 doub Y N 110 G C8 H8 sing N N 111 G N7 C5 sing Y N 112 G C5 C6 sing N N 113 G C5 C4 doub Y N 114 G C6 O6 doub N N 115 G C6 N1 sing N N 116 G N1 C2 sing N N 117 G N1 H1 sing N N 118 G C2 N2 sing N N 119 G C2 N3 doub N N 120 G N2 H21 sing N N 121 G N2 H22 sing N N 122 G N3 C4 sing N N 123 HOH O H1 sing N N 124 HOH O H2 sing N N 125 SO4 S O1 doub N N 126 SO4 S O2 doub N N 127 SO4 S O3 sing N N 128 SO4 S O4 sing N N 129 U OP3 P sing N N 130 U OP3 HOP3 sing N N 131 U P OP1 doub N N 132 U P OP2 sing N N 133 U P "O5'" sing N N 134 U OP2 HOP2 sing N N 135 U "O5'" "C5'" sing N N 136 U "C5'" "C4'" sing N N 137 U "C5'" "H5'" sing N N 138 U "C5'" "H5''" sing N N 139 U "C4'" "O4'" sing N N 140 U "C4'" "C3'" sing N N 141 U "C4'" "H4'" sing N N 142 U "O4'" "C1'" sing N N 143 U "C3'" "O3'" sing N N 144 U "C3'" "C2'" sing N N 145 U "C3'" "H3'" sing N N 146 U "O3'" "HO3'" sing N N 147 U "C2'" "O2'" sing N N 148 U "C2'" "C1'" sing N N 149 U "C2'" "H2'" sing N N 150 U "O2'" "HO2'" sing N N 151 U "C1'" N1 sing N N 152 U "C1'" "H1'" sing N N 153 U N1 C2 sing N N 154 U N1 C6 sing N N 155 U C2 O2 doub N N 156 U C2 N3 sing N N 157 U N3 C4 sing N N 158 U N3 H3 sing N N 159 U C4 O4 doub N N 160 U C4 C5 sing N N 161 U C5 C6 doub N N 162 U C5 H5 sing N N 163 U C6 H6 sing N N 164 URA N1 C2 sing N N 165 URA N1 C6 sing N N 166 URA N1 HN1 sing N N 167 URA C2 O2 doub N N 168 URA C2 N3 sing N N 169 URA N3 C4 sing N N 170 URA N3 HN3 sing N N 171 URA C4 O4 doub N N 172 URA C4 C5 sing N N 173 URA C5 C6 doub N N 174 URA C5 H5 sing N N 175 URA C6 H6 sing N N 176 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6UGJ 'double helix' 6UGJ 'a-form double helix' 6UGJ 'bulge loop' 6UGJ '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 G 1 1_555 A C 31 1_555 -0.322 -0.070 -0.369 -10.884 0.710 1.746 1 A_G1:C31_A A 1 ? A 31 ? 19 1 1 A G 2 1_555 A C 30 1_555 -0.445 -0.142 -0.437 -10.397 -8.366 0.193 2 A_G2:C30_A A 2 ? A 30 ? 19 1 1 A A 3 1_555 A U 29 1_555 0.058 -0.168 -0.026 -7.454 -7.247 4.343 3 A_A3:U29_A A 3 ? A 29 ? 20 1 1 A G 4 1_555 A U 28 1_555 -2.356 -0.609 -0.034 -4.997 -14.848 -1.706 4 A_G4:U28_A A 4 ? A 28 ? 28 1 1 A C 5 1_555 A G 27 1_555 0.220 -0.122 0.034 0.657 -11.075 -0.006 5 A_C5:G27_A A 5 ? A 27 ? 19 1 1 A G 6 1_555 A C 26 1_555 -0.242 -0.170 -0.131 -4.202 -7.135 -1.564 6 A_G6:C26_A A 6 ? A 26 ? 19 1 1 A G 7 1_555 A C 25 1_555 -0.140 -0.087 -0.194 -9.476 -15.014 3.719 7 A_G7:C25_A A 7 ? A 25 ? 19 1 1 A G 8 1_555 A U 24 1_555 -2.366 -0.581 -0.102 -4.836 -9.427 -0.118 8 A_G8:U24_A A 8 ? A 24 ? 28 1 1 A C 9 1_555 A G 23 1_555 0.241 -0.168 -0.039 0.796 -12.990 -0.762 9 A_C9:G23_A A 9 ? A 23 ? 19 1 1 A G 10 1_555 A C 22 1_555 -0.055 -0.082 -0.076 -5.404 -10.287 1.031 10 A_G10:C22_A A 10 ? A 22 ? 19 1 1 A G 11 1_555 A C 21 1_555 -0.090 -0.114 0.023 -7.198 -14.355 3.651 11 A_G11:C21_A A 11 ? A 21 ? 19 1 1 A G 12 1_555 A C 20 1_555 -0.380 -0.259 -0.032 -10.325 -12.140 2.904 12 A_G12:C20_A A 12 ? A 20 ? 19 1 1 A U 13 1_555 A A 17 1_555 3.987 -2.065 0.002 -5.462 -1.388 -95.123 13 A_U13:A17_A A 13 ? A 17 ? 24 4 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 31 1_555 A G 2 1_555 A C 30 1_555 -0.430 -2.172 3.469 0.888 4.318 26.961 -5.681 1.133 3.074 9.184 -1.889 27.313 1 AA_G1G2:C30C31_AA A 1 ? A 31 ? A 2 ? A 30 ? 1 A G 2 1_555 A C 30 1_555 A A 3 1_555 A U 29 1_555 0.107 -1.758 3.213 -2.723 5.673 31.996 -4.055 -0.635 2.849 10.169 4.880 32.593 2 AA_G2A3:U29C30_AA A 2 ? A 30 ? A 3 ? A 29 ? 1 A A 3 1_555 A U 29 1_555 A G 4 1_555 A U 28 1_555 0.496 -2.214 3.100 1.257 9.750 20.487 -8.454 -0.895 1.887 25.596 -3.300 22.700 3 AA_A3G4:U28U29_AA A 3 ? A 29 ? A 4 ? A 28 ? 1 A G 4 1_555 A U 28 1_555 A C 5 1_555 A G 27 1_555 0.019 -1.430 3.222 -0.275 2.268 41.346 -2.259 -0.056 3.142 3.209 0.389 41.407 4 AA_G4C5:G27U28_AA A 4 ? A 28 ? A 5 ? A 27 ? 1 A C 5 1_555 A G 27 1_555 A G 6 1_555 A C 26 1_555 0.077 -1.947 3.373 1.793 6.454 28.310 -5.246 0.227 2.867 12.966 -3.603 29.076 5 AA_C5G6:C26G27_AA A 5 ? A 27 ? A 6 ? A 26 ? 1 A G 6 1_555 A C 26 1_555 A G 7 1_555 A C 25 1_555 0.690 -1.754 3.444 1.035 8.653 30.036 -4.870 -1.089 2.861 16.271 -1.945 31.247 6 AA_G6G7:C25C26_AA A 6 ? A 26 ? A 7 ? A 25 ? 1 A G 7 1_555 A C 25 1_555 A G 8 1_555 A U 24 1_555 -0.596 -1.960 2.957 -5.824 8.776 24.857 -6.055 0.048 2.229 19.317 12.821 26.964 7 AA_G7G8:U24C25_AA A 7 ? A 25 ? A 8 ? A 24 ? 1 A G 8 1_555 A U 24 1_555 A C 9 1_555 A G 23 1_555 0.077 -1.497 3.145 -0.442 5.110 39.311 -2.765 -0.161 2.934 7.557 0.654 39.631 8 AA_G8C9:G23U24_AA A 8 ? A 24 ? A 9 ? A 23 ? 1 A C 9 1_555 A G 23 1_555 A G 10 1_555 A C 22 1_555 0.644 -1.962 3.363 2.244 11.040 29.161 -5.598 -0.800 2.513 20.966 -4.261 31.217 9 AA_C9G10:C22G23_AA A 9 ? A 23 ? A 10 ? A 22 ? 1 A G 10 1_555 A C 22 1_555 A G 11 1_555 A C 21 1_555 -0.043 -2.076 3.327 0.207 6.432 28.760 -5.387 0.126 2.806 12.748 -0.409 29.457 10 AA_G10G11:C21C22_AA A 10 ? A 22 ? A 11 ? A 21 ? 1 A G 11 1_555 A C 21 1_555 A G 12 1_555 A C 20 1_555 0.757 -2.106 3.270 3.115 7.128 29.948 -5.247 -0.853 2.770 13.508 -5.903 30.919 11 AA_G11G12:C20C21_AA A 11 ? A 21 ? A 12 ? A 20 ? 1 A G 12 1_555 A C 20 1_555 A U 13 1_555 A A 17 1_555 -1.920 -1.934 3.191 -0.163 1.921 87.619 -1.436 1.383 3.160 1.387 0.118 87.636 12 AA_G12U13:A17C20_AA A 12 ? A 20 ? A 13 ? A 17 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)' 'United States' 'R01 GM058443' 1 'National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)' 'United States' 'R35 GM118108' 2 'National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)' 'United States' 'T32 GM008152' 3 'National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)' 'United States' 'T32 GM008382' 4 # _pdbx_initial_refinement_model.accession_code 1EHZ _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.details 'homology model' # _atom_sites.entry_id 6UGJ _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.fract_transf_matrix[1][1] 0.022808 _atom_sites.fract_transf_matrix[1][2] 0.013168 _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] 0.026336 _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] 0.003857 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O P S # loop_