data_6C8E # _entry.id 6C8E # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 6C8E pdb_00006c8e 10.2210/pdb6c8e/pdb WWPDB D_1000232278 ? ? # 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 2018-05-30 2 'Structure model' 1 1 2018-10-31 3 'Structure model' 1 2 2019-11-20 4 'Structure model' 1 3 2023-10-04 5 'Structure model' 2 0 2024-05-01 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 3 'Structure model' 'Author supporting evidence' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Refinement description' 7 5 'Structure model' 'Derived calculations' 8 5 'Structure model' 'Non-polymer description' 9 5 'Structure model' 'Structure summary' # 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' pdbx_audit_support 4 4 'Structure model' chem_comp_atom 5 4 'Structure model' chem_comp_bond 6 4 'Structure model' database_2 7 4 'Structure model' pdbx_initial_refinement_model 8 5 'Structure model' chem_comp 9 5 'Structure model' entity 10 5 'Structure model' pdbx_entity_nonpoly # 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.page_first' 2 2 'Structure model' '_citation.pdbx_database_id_PubMed' 3 2 'Structure model' '_citation.title' 4 2 'Structure model' '_citation_author.identifier_ORCID' 5 3 'Structure model' '_pdbx_audit_support.funding_organization' 6 4 'Structure model' '_database_2.pdbx_DOI' 7 4 'Structure model' '_database_2.pdbx_database_accession' 8 5 'Structure model' '_chem_comp.formula' 9 5 'Structure model' '_chem_comp.name' 10 5 'Structure model' '_entity.pdbx_description' 11 5 'Structure model' '_pdbx_entity_nonpoly.name' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6C8E _pdbx_database_status.recvd_initial_deposition_date 2018-01-24 _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 'Zhang, W.' 1 ? 'Szostak, J.W.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Elife _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2050-084X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 7 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Crystallographic observation of nonenzymatic RNA primer extension.' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.7554/eLife.36422 _citation.pdbx_database_id_PubMed 29851379 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhang, W.' 1 0000-0003-4811-4384 primary 'Walton, T.' 2 0000-0001-6812-1579 primary 'Li, L.' 3 0000-0003-4766-5782 primary 'Szostak, J.W.' 4 0000-0003-4131-1203 # 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 (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') ; 4512.804 2 ? ? ? ? 2 non-polymer syn ;2-amino-1-[(R)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-3-[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-1H-imidazol-3-ium ; 774.511 2 ? ? ? ? 3 water nat water 18.015 4 ? ? ? ? # _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 '(LCC)(LCC)(LCC)(LCG)ACUUAAGUCG' _entity_poly.pdbx_seq_one_letter_code_can NNNGACUUAAGUCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 ;2-amino-1-[(R)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-3-[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-1H-imidazol-3-ium ; EQ1 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LCC n 1 2 LCC n 1 3 LCC n 1 4 LCG n 1 5 A n 1 6 C n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 G n 1 12 U n 1 13 C n 1 14 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 14 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 EQ1 non-polymer . ;2-amino-1-[(R)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-3-[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-1H-imidazol-3-ium ; ? 'C23 H30 N13 O14 P2 1' 774.511 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 LCC 'RNA linking' . '[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' ? 'C11 H16 N3 O8 P' 349.234 LCG 'RNA linking' n '[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' ? 'C11 H14 N5 O8 P' 375.231 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 LCC 1 1 1 LCC LCC A . n A 1 2 LCC 2 2 2 LCC LCC A . n A 1 3 LCC 3 3 3 LCC LCC A . n A 1 4 LCG 4 4 4 LCG LCG A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C 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 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n B 1 1 LCC 1 1 1 LCC LCC B . n B 1 2 LCC 2 2 2 LCC LCC B . n B 1 3 LCC 3 3 3 LCC LCC B . n B 1 4 LCG 4 4 4 LCG LCG B . n B 1 5 A 5 5 5 A A B . n B 1 6 C 6 6 6 C C B . n B 1 7 U 7 7 7 U U B . n B 1 8 U 8 8 8 U U B . n B 1 9 A 9 9 9 A A B . n B 1 10 A 10 10 10 A A B . n B 1 11 G 11 11 11 G G B . n B 1 12 U 12 12 12 U U B . n B 1 13 C 13 13 13 C C B . n B 1 14 G 14 14 14 G G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 EQ1 1 101 2 EQ1 GIM A . D 2 EQ1 1 101 1 EQ1 GIM B . E 3 HOH 1 201 1 HOH HOH A . E 3 HOH 2 202 2 HOH HOH A . E 3 HOH 3 203 4 HOH HOH A . F 3 HOH 1 201 3 HOH HOH B . # 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 ? ? ? 5.8.0158 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.entry_id 6C8E _cell.length_a 49.023 _cell.length_b 49.023 _cell.length_c 81.317 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C8E _symmetry.space_group_name_H-M 'P 3 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 # _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 6C8E _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 2.91 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 57.75 _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 7.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate pH 7.0, 0.012 M Spermine tetrahydrochloride, 0.080 M Sodium chloride ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 99 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MAR CCD 130 mm' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-04-04 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6C8E _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.80 _reflns.d_resolution_low 50 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 10695 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 97.7 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.1 _reflns.pdbx_Rmerge_I_obs 0.098 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 20.6 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.357 _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 0.103 _reflns.pdbx_Rpim_I_all 0.033 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.979 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.80 _reflns_shell.d_res_low 1.86 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.95 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 1051 _reflns_shell.percent_possible_all 100 _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 0.713 _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 9.9 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 0.612 _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all 0.752 _reflns_shell.pdbx_Rpim_I_all 0.236 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.984 _reflns_shell.pdbx_R_split ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 6C8E _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 10123 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 42.46 _refine.ls_d_res_high 1.80 _refine.ls_percent_reflns_obs 97.41 _refine.ls_R_factor_obs 0.26822 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.26709 _refine.ls_R_factor_R_free 0.28970 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.3 _refine.ls_number_reflns_R_free 565 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.948 _refine.correlation_coeff_Fo_to_Fc_free 0.942 _refine.B_iso_mean 52.894 _refine.aniso_B[1][1] 1.23 _refine.aniso_B[2][2] 1.23 _refine.aniso_B[3][3] -2.46 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 5DHC _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.033 _refine.pdbx_overall_ESU_R_Free 0.030 _refine.overall_SU_ML 0.134 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 4.996 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id 1 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 598 _refine_hist.pdbx_number_atoms_ligand 104 _refine_hist.number_atoms_solvent 4 _refine_hist.number_atoms_total 706 _refine_hist.d_res_high 1.80 _refine_hist.d_res_low 42.46 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.028 0.017 ? 780 'X-RAY DIFFRACTION' ? r_bond_other_d 0.058 0.024 ? 320 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.250 1.999 ? 1210 'X-RAY DIFFRACTION' ? r_angle_other_deg 4.224 3.228 ? 792 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.192 0.200 ? 138 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.018 0.020 ? 380 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.003 0.020 ? 124 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 6.606 5.777 ? 778 'X-RAY DIFFRACTION' ? r_scbond_other 6.603 5.778 ? 779 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other 8.202 8.679 ? 1210 'X-RAY DIFFRACTION' ? r_long_range_B_refined 9.453 54.580 ? 1124 'X-RAY DIFFRACTION' ? r_long_range_B_other 9.457 54.564 ? 1125 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.800 _refine_ls_shell.d_res_low 1.847 _refine_ls_shell.number_reflns_R_work 756 _refine_ls_shell.R_factor_R_work 0.316 _refine_ls_shell.percent_reflns_obs 99.87 _refine_ls_shell.R_factor_R_free 0.353 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 37 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 6C8E _struct.title 'RNA-imidazolium-bridged intermediate complex, 4h soaking' _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 6C8E _struct_keywords.text 'RNA, intermediate, dinucleotide' _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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6C8E _struct_ref.pdbx_db_accession 6C8E _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 6C8E A 1 ? 14 ? 6C8E 1 ? 14 ? 1 14 2 1 6C8E B 1 ? 14 ? 6C8E 1 ? 14 ? 1 14 # _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)' 2700 ? 1 MORE 9 ? 1 'SSA (A^2)' 5800 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A LCC 1 "O3'" ? ? ? 1_555 A LCC 2 P ? ? A LCC 1 A LCC 2 1_555 ? ? ? ? ? ? ? 1.645 ? ? covale2 covale both ? A LCC 2 "O3'" ? ? ? 1_555 A LCC 3 P ? ? A LCC 2 A LCC 3 1_555 ? ? ? ? ? ? ? 1.659 ? ? covale3 covale both ? A LCC 3 "O3'" ? ? ? 1_555 A LCG 4 P ? ? A LCC 3 A LCG 4 1_555 ? ? ? ? ? ? ? 1.684 ? ? covale4 covale both ? A LCG 4 "O3'" ? ? ? 1_555 A A 5 P ? ? A LCG 4 A A 5 1_555 ? ? ? ? ? ? ? 1.701 ? ? covale5 covale both ? B LCC 1 "O3'" ? ? ? 1_555 B LCC 2 P ? ? B LCC 1 B LCC 2 1_555 ? ? ? ? ? ? ? 1.698 ? ? covale6 covale both ? B LCC 2 "O3'" ? ? ? 1_555 B LCC 3 P ? ? B LCC 2 B LCC 3 1_555 ? ? ? ? ? ? ? 1.681 ? ? covale7 covale both ? B LCC 3 "O3'" ? ? ? 1_555 B LCG 4 P ? ? B LCC 3 B LCG 4 1_555 ? ? ? ? ? ? ? 1.696 ? ? covale8 covale both ? B LCG 4 "O3'" ? ? ? 1_555 B A 5 P ? ? B LCG 4 B A 5 1_555 ? ? ? ? ? ? ? 1.706 ? ? hydrog1 hydrog ? ? A LCG 4 N1 ? ? ? 1_555 B C 13 N3 ? ? A LCG 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A LCG 4 N2 ? ? ? 1_555 B C 13 O2 ? ? A LCG 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A LCG 4 O6 ? ? ? 1_555 B C 13 N4 ? ? A LCG 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 12 N3 ? ? A A 5 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 12 O4 ? ? A A 5 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 6 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 6 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 6 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 7 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 7 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 8 B A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 8 O4 ? ? ? 1_555 B A 9 N6 ? ? A U 8 B A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 9 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 9 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 10 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 10 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 11 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 11 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 11 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 12 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 12 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 13 N3 ? ? ? 1_555 B LCG 4 N1 ? ? A C 13 B LCG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 13 N4 ? ? ? 1_555 B LCG 4 O6 ? ? A C 13 B LCG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 13 O2 ? ? ? 1_555 B LCG 4 N2 ? ? A C 13 B LCG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # 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 EQ1 101 ? 6 'binding site for residue EQ1 A 101' AC2 Software B EQ1 101 ? 5 'binding site for residue EQ1 B 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 LCC A 1 ? LCC A 1 . ? 5_557 ? 2 AC1 6 LCC A 1 ? LCC A 1 . ? 1_555 ? 3 AC1 6 LCC A 2 ? LCC A 2 . ? 1_555 ? 4 AC1 6 LCC A 3 ? LCC A 3 . ? 1_555 ? 5 AC1 6 G B 14 ? G B 14 . ? 2_545 ? 6 AC1 6 G B 14 ? G B 14 . ? 1_555 ? 7 AC2 5 G A 14 ? G A 14 . ? 3_655 ? 8 AC2 5 G A 14 ? G A 14 . ? 1_555 ? 9 AC2 5 LCC B 1 ? LCC B 1 . ? 1_555 ? 10 AC2 5 LCC B 2 ? LCC B 2 . ? 1_555 ? 11 AC2 5 LCC B 3 ? LCC B 3 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A LCC 3 ? ? P A LCG 4 ? ? 1.684 1.607 0.077 0.012 Y 2 1 "O3'" A LCG 4 ? ? P A A 5 ? ? 1.701 1.607 0.094 0.012 Y 3 1 "O3'" A C 13 ? ? P A G 14 ? ? 1.528 1.607 -0.079 0.012 Y 4 1 "O3'" B LCC 1 ? ? P B LCC 2 ? ? 1.698 1.607 0.091 0.012 Y 5 1 "O3'" B LCC 2 ? ? P B LCC 3 ? ? 1.681 1.607 0.074 0.012 Y 6 1 "O3'" B LCC 3 ? ? P B LCG 4 ? ? 1.696 1.607 0.089 0.012 Y 7 1 "O3'" B LCG 4 ? ? P B A 5 ? ? 1.706 1.607 0.099 0.012 Y # 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 "C3'" A LCC 1 ? ? "O3'" A LCC 1 ? ? P A LCC 2 ? ? 144.89 119.70 25.19 1.20 Y 2 1 "C3'" A LCC 2 ? ? "O3'" A LCC 2 ? ? P A LCC 3 ? ? 110.38 119.70 -9.32 1.20 Y 3 1 "O3'" A LCC 2 ? ? P A LCC 3 ? ? "O5'" A LCC 3 ? ? 115.62 104.00 11.62 1.90 Y 4 1 "C3'" A LCC 3 ? ? "O3'" A LCC 3 ? ? P A LCG 4 ? ? 130.15 119.70 10.45 1.20 Y 5 1 "C3'" A LCG 4 ? ? "O3'" A LCG 4 ? ? P A A 5 ? ? 101.72 119.70 -17.98 1.20 Y 6 1 "C3'" B LCC 1 ? ? "O3'" B LCC 1 ? ? P B LCC 2 ? ? 143.06 119.70 23.36 1.20 Y 7 1 "C3'" B LCC 2 ? ? "O3'" B LCC 2 ? ? P B LCC 3 ? ? 111.22 119.70 -8.48 1.20 Y 8 1 "O3'" B LCC 3 ? ? P B LCG 4 ? ? "O5'" B LCG 4 ? ? 120.05 104.00 16.05 1.90 Y 9 1 "C3'" B LCG 4 ? ? "O3'" B LCG 4 ? ? P B A 5 ? ? 111.99 119.70 -7.71 1.20 Y 10 1 "O3'" B LCG 4 ? ? P B A 5 ? ? OP2 B A 5 ? ? 118.44 110.50 7.94 1.10 Y # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 203 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance . _pdbx_distant_solvent_atoms.neighbor_ligand_distance 6.14 # 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 EQ1 PA P N N 73 EQ1 PG P N N 74 EQ1 C1C C Y N 75 EQ1 C1D C N R 76 EQ1 C1E C N R 77 EQ1 N1A N N N 78 EQ1 N1B N N N 79 EQ1 N1C N Y N 80 EQ1 O1A O N N 81 EQ1 O1G O N N 82 EQ1 C2A C N N 83 EQ1 C2B C N N 84 EQ1 C2C C Y N 85 EQ1 C2D C N R 86 EQ1 C2E C N R 87 EQ1 N2A N N N 88 EQ1 N2B N N N 89 EQ1 N2C N Y N 90 EQ1 O2A O N N 91 EQ1 O2D O N N 92 EQ1 O2E O N N 93 EQ1 O2G O N N 94 EQ1 C3C C Y N 95 EQ1 C3D C N S 96 EQ1 C3E C N S 97 EQ1 N3A N N N 98 EQ1 N3B N N N 99 EQ1 N3C N N N 100 EQ1 O3D O N N 101 EQ1 O3E O N N 102 EQ1 C4A C Y N 103 EQ1 C4B C Y N 104 EQ1 C4D C N R 105 EQ1 C4E C N R 106 EQ1 O4D O N N 107 EQ1 O4E O N N 108 EQ1 C5A C Y N 109 EQ1 C5B C Y N 110 EQ1 C5D C N N 111 EQ1 C5E C N N 112 EQ1 O5D O N N 113 EQ1 O5E O N N 114 EQ1 C6A C N N 115 EQ1 C6B C N N 116 EQ1 O6A O N N 117 EQ1 O6B O N N 118 EQ1 N7A N Y N 119 EQ1 N7B N Y N 120 EQ1 C8A C Y N 121 EQ1 C8B C Y N 122 EQ1 N9A N Y N 123 EQ1 N9B N Y N 124 EQ1 H1 H N N 125 EQ1 H2 H N N 126 EQ1 H3 H N N 127 EQ1 H4 H N N 128 EQ1 H5 H N N 129 EQ1 H6 H N N 130 EQ1 H7 H N N 131 EQ1 H8 H N N 132 EQ1 H9 H N N 133 EQ1 H10 H N N 134 EQ1 H11 H N N 135 EQ1 H12 H N N 136 EQ1 H13 H N N 137 EQ1 H14 H N N 138 EQ1 H15 H N N 139 EQ1 H16 H N N 140 EQ1 H17 H N N 141 EQ1 H18 H N N 142 EQ1 H19 H N N 143 EQ1 H20 H N N 144 EQ1 H21 H N N 145 EQ1 H22 H N N 146 EQ1 H23 H N N 147 EQ1 H24 H N N 148 EQ1 H25 H N N 149 EQ1 H26 H N N 150 EQ1 H27 H N N 151 EQ1 H28 H N N 152 EQ1 H29 H N N 153 EQ1 H30 H N N 154 G OP3 O N N 155 G P P N N 156 G OP1 O N N 157 G OP2 O N N 158 G "O5'" O N N 159 G "C5'" C N N 160 G "C4'" C N R 161 G "O4'" O N N 162 G "C3'" C N S 163 G "O3'" O N N 164 G "C2'" C N R 165 G "O2'" O N N 166 G "C1'" C N R 167 G N9 N Y N 168 G C8 C Y N 169 G N7 N Y N 170 G C5 C Y N 171 G C6 C N N 172 G O6 O N N 173 G N1 N N N 174 G C2 C N N 175 G N2 N N N 176 G N3 N N N 177 G C4 C Y N 178 G HOP3 H N N 179 G HOP2 H N N 180 G "H5'" H N N 181 G "H5''" H N N 182 G "H4'" H N N 183 G "H3'" H N N 184 G "HO3'" H N N 185 G "H2'" H N N 186 G "HO2'" H N N 187 G "H1'" H N N 188 G H8 H N N 189 G H1 H N N 190 G H21 H N N 191 G H22 H N N 192 HOH O O N N 193 HOH H1 H N N 194 HOH H2 H N N 195 LCC "O5'" O N N 196 LCC "C5'" C N N 197 LCC "C4'" C N R 198 LCC "O4'" O N N 199 LCC "C1'" C N R 200 LCC N1 N N N 201 LCC C6 C N N 202 LCC C5 C N N 203 LCC C5M C N N 204 LCC C4 C N N 205 LCC N4 N N N 206 LCC N3 N N N 207 LCC C2 C N N 208 LCC O2 O N N 209 LCC "C3'" C N S 210 LCC "C2'" C N R 211 LCC "O2'" O N N 212 LCC "O3'" O N N 213 LCC "C6'" C N N 214 LCC P P N N 215 LCC O1P O N N 216 LCC O2P O N N 217 LCC OXT O N N 218 LCC "H5'1" H N N 219 LCC "H5'2" H N N 220 LCC "H1'" H N N 221 LCC H6 H N N 222 LCC H5M1 H N N 223 LCC H5M2 H N N 224 LCC H5M3 H N N 225 LCC H41 H N N 226 LCC H42 H N N 227 LCC "H3'" H N N 228 LCC "H2'1" H N N 229 LCC H3T H N N 230 LCC "H6'1" H N N 231 LCC "H6'2" H N N 232 LCC H1P H N N 233 LCC HXT H N N 234 LCG P P N N 235 LCG OP1 O N N 236 LCG "O5'" O N N 237 LCG "C5'" C N N 238 LCG "C3'" C N S 239 LCG "C6'" C N N 240 LCG N9 N Y N 241 LCG C8 C Y N 242 LCG C4 C Y N 243 LCG N7 N Y N 244 LCG C5 C Y N 245 LCG C6 C N N 246 LCG "C2'" C N R 247 LCG O6 O N N 248 LCG "C4'" C N R 249 LCG "C1'" C N R 250 LCG C2 C N N 251 LCG N1 N N N 252 LCG "O4'" O N N 253 LCG OP2 O N N 254 LCG N2 N N N 255 LCG N3 N N N 256 LCG "O2'" O N N 257 LCG "O3'" O N N 258 LCG OP3 O N N 259 LCG "H5'" H N N 260 LCG "H5''" H N N 261 LCG "H3'" H N N 262 LCG "H6'1" H N N 263 LCG "H6'2" H N N 264 LCG H8 H N N 265 LCG "H2'" H N N 266 LCG "H1'" H N N 267 LCG H1 H N N 268 LCG HOP2 H N N 269 LCG H21 H N N 270 LCG H22 H N N 271 LCG "HO3'" H N N 272 LCG HOP3 H N N 273 U OP3 O N N 274 U P P N N 275 U OP1 O N N 276 U OP2 O N N 277 U "O5'" O N N 278 U "C5'" C N N 279 U "C4'" C N R 280 U "O4'" O N N 281 U "C3'" C N S 282 U "O3'" O N N 283 U "C2'" C N R 284 U "O2'" O N N 285 U "C1'" C N R 286 U N1 N N N 287 U C2 C N N 288 U O2 O N N 289 U N3 N N N 290 U C4 C N N 291 U O4 O N N 292 U C5 C N N 293 U C6 C N N 294 U HOP3 H N N 295 U HOP2 H N N 296 U "H5'" H N N 297 U "H5''" H N N 298 U "H4'" H N N 299 U "H3'" H N N 300 U "HO3'" H N N 301 U "H2'" H N N 302 U "HO2'" H N N 303 U "H1'" H N N 304 U H3 H N N 305 U H5 H N N 306 U H6 H N N 307 # 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 EQ1 O2G PG doub N N 76 EQ1 PG O1G sing N N 77 EQ1 PG O5E sing N N 78 EQ1 PG N2C sing N N 79 EQ1 C2C N2C sing Y N 80 EQ1 C2C C3C doub Y N 81 EQ1 O5E C5E sing N N 82 EQ1 C5E C4E sing N N 83 EQ1 N2C C1C doub Y N 84 EQ1 O3E C3E sing N N 85 EQ1 C3C N1C sing Y N 86 EQ1 C3E C4E sing N N 87 EQ1 C3E C2E sing N N 88 EQ1 C1C N1C sing Y N 89 EQ1 C1C N3C sing N N 90 EQ1 C4E O4E sing N N 91 EQ1 N1C PA sing N N 92 EQ1 C2E O2E sing N N 93 EQ1 C2E C1E sing N N 94 EQ1 O4E C1E sing N N 95 EQ1 O3D C3D sing N N 96 EQ1 PA O2A doub N N 97 EQ1 PA O1A sing N N 98 EQ1 PA O5D sing N N 99 EQ1 C8B N7B doub Y N 100 EQ1 C8B N9B sing Y N 101 EQ1 C1E N9B sing N N 102 EQ1 N7B C5B sing Y N 103 EQ1 N9B C4B sing Y N 104 EQ1 C5B C4B doub Y N 105 EQ1 C5B C6B sing N N 106 EQ1 C4B N3B sing N N 107 EQ1 C3D C4D sing N N 108 EQ1 C3D C2D sing N N 109 EQ1 O6B C6B doub N N 110 EQ1 C6B N1B sing N N 111 EQ1 N3B C2B doub N N 112 EQ1 C5D O5D sing N N 113 EQ1 C5D C4D sing N N 114 EQ1 N1B C2B sing N N 115 EQ1 C2B N2B sing N N 116 EQ1 C4D O4D sing N N 117 EQ1 C2D O2D sing N N 118 EQ1 C2D C1D sing N N 119 EQ1 C8A N7A doub Y N 120 EQ1 C8A N9A sing Y N 121 EQ1 N7A C5A sing Y N 122 EQ1 O4D C1D sing N N 123 EQ1 N9A C1D sing N N 124 EQ1 N9A C4A sing Y N 125 EQ1 C5A C4A doub Y N 126 EQ1 C5A C6A sing N N 127 EQ1 C4A N3A sing N N 128 EQ1 O6A C6A doub N N 129 EQ1 C6A N1A sing N N 130 EQ1 N3A C2A doub N N 131 EQ1 N1A C2A sing N N 132 EQ1 C2A N2A sing N N 133 EQ1 C1D H1 sing N N 134 EQ1 C1E H2 sing N N 135 EQ1 N1A H3 sing N N 136 EQ1 N1B H4 sing N N 137 EQ1 O1A H5 sing N N 138 EQ1 O1G H6 sing N N 139 EQ1 C2C H7 sing N N 140 EQ1 C2D H8 sing N N 141 EQ1 C2E H9 sing N N 142 EQ1 N2A H10 sing N N 143 EQ1 N2A H11 sing N N 144 EQ1 N2B H12 sing N N 145 EQ1 N2B H13 sing N N 146 EQ1 O2D H14 sing N N 147 EQ1 O2E H15 sing N N 148 EQ1 C3C H16 sing N N 149 EQ1 C3D H17 sing N N 150 EQ1 C3E H18 sing N N 151 EQ1 N3C H19 sing N N 152 EQ1 N3C H20 sing N N 153 EQ1 O3D H21 sing N N 154 EQ1 O3E H22 sing N N 155 EQ1 C4D H23 sing N N 156 EQ1 C4E H24 sing N N 157 EQ1 C5D H25 sing N N 158 EQ1 C5D H26 sing N N 159 EQ1 C5E H27 sing N N 160 EQ1 C5E H28 sing N N 161 EQ1 C8A H29 sing N N 162 EQ1 C8B H30 sing N N 163 G OP3 P sing N N 164 G OP3 HOP3 sing N N 165 G P OP1 doub N N 166 G P OP2 sing N N 167 G P "O5'" sing N N 168 G OP2 HOP2 sing N N 169 G "O5'" "C5'" sing N N 170 G "C5'" "C4'" sing N N 171 G "C5'" "H5'" sing N N 172 G "C5'" "H5''" sing N N 173 G "C4'" "O4'" sing N N 174 G "C4'" "C3'" sing N N 175 G "C4'" "H4'" sing N N 176 G "O4'" "C1'" sing N N 177 G "C3'" "O3'" sing N N 178 G "C3'" "C2'" sing N N 179 G "C3'" "H3'" sing N N 180 G "O3'" "HO3'" sing N N 181 G "C2'" "O2'" sing N N 182 G "C2'" "C1'" sing N N 183 G "C2'" "H2'" sing N N 184 G "O2'" "HO2'" sing N N 185 G "C1'" N9 sing N N 186 G "C1'" "H1'" sing N N 187 G N9 C8 sing Y N 188 G N9 C4 sing Y N 189 G C8 N7 doub Y N 190 G C8 H8 sing N N 191 G N7 C5 sing Y N 192 G C5 C6 sing N N 193 G C5 C4 doub Y N 194 G C6 O6 doub N N 195 G C6 N1 sing N N 196 G N1 C2 sing N N 197 G N1 H1 sing N N 198 G C2 N2 sing N N 199 G C2 N3 doub N N 200 G N2 H21 sing N N 201 G N2 H22 sing N N 202 G N3 C4 sing N N 203 HOH O H1 sing N N 204 HOH O H2 sing N N 205 LCC "O5'" "C5'" sing N N 206 LCC "O5'" P sing N N 207 LCC "C5'" "C4'" sing N N 208 LCC "C5'" "H5'1" sing N N 209 LCC "C5'" "H5'2" sing N N 210 LCC "C4'" "O4'" sing N N 211 LCC "C4'" "C3'" sing N N 212 LCC "C4'" "C6'" sing N N 213 LCC "O4'" "C1'" sing N N 214 LCC "C1'" N1 sing N N 215 LCC "C1'" "C2'" sing N N 216 LCC "C1'" "H1'" sing N N 217 LCC N1 C6 sing N N 218 LCC N1 C2 sing N N 219 LCC C6 C5 doub N N 220 LCC C6 H6 sing N N 221 LCC C5 C5M sing N N 222 LCC C5 C4 sing N N 223 LCC C5M H5M1 sing N N 224 LCC C5M H5M2 sing N N 225 LCC C5M H5M3 sing N N 226 LCC C4 N4 sing N N 227 LCC C4 N3 doub N N 228 LCC N4 H41 sing N N 229 LCC N4 H42 sing N N 230 LCC N3 C2 sing N N 231 LCC C2 O2 doub N N 232 LCC "C3'" "C2'" sing N N 233 LCC "C3'" "O3'" sing N N 234 LCC "C3'" "H3'" sing N N 235 LCC "C2'" "O2'" sing N N 236 LCC "C2'" "H2'1" sing N N 237 LCC "O2'" "C6'" sing N N 238 LCC "O3'" H3T sing N N 239 LCC "C6'" "H6'1" sing N N 240 LCC "C6'" "H6'2" sing N N 241 LCC P O1P sing N N 242 LCC P O2P doub N N 243 LCC P OXT sing N N 244 LCC O1P H1P sing N N 245 LCC OXT HXT sing N N 246 LCG P OP1 doub N N 247 LCG P "O5'" sing N N 248 LCG P OP2 sing N N 249 LCG P OP3 sing N N 250 LCG "O5'" "C5'" sing N N 251 LCG "C5'" "C4'" sing N N 252 LCG "C5'" "H5'" sing N N 253 LCG "C5'" "H5''" sing N N 254 LCG "C3'" "C2'" sing N N 255 LCG "C3'" "C4'" sing N N 256 LCG "C3'" "O3'" sing N N 257 LCG "C3'" "H3'" sing N N 258 LCG "C6'" "C4'" sing N N 259 LCG "C6'" "O2'" sing N N 260 LCG "C6'" "H6'1" sing N N 261 LCG "C6'" "H6'2" sing N N 262 LCG N9 C8 sing Y N 263 LCG N9 C4 sing Y N 264 LCG N9 "C1'" sing N N 265 LCG C8 N7 doub Y N 266 LCG C8 H8 sing N N 267 LCG C4 C5 doub Y N 268 LCG C4 N3 sing N N 269 LCG N7 C5 sing Y N 270 LCG C5 C6 sing N N 271 LCG C6 O6 doub N N 272 LCG C6 N1 sing N N 273 LCG "C2'" "C1'" sing N N 274 LCG "C2'" "O2'" sing N N 275 LCG "C2'" "H2'" sing N N 276 LCG "C4'" "O4'" sing N N 277 LCG "C1'" "O4'" sing N N 278 LCG "C1'" "H1'" sing N N 279 LCG C2 N1 sing N N 280 LCG C2 N2 sing N N 281 LCG C2 N3 doub N N 282 LCG N1 H1 sing N N 283 LCG OP2 HOP2 sing N N 284 LCG N2 H21 sing N N 285 LCG N2 H22 sing N N 286 LCG "O3'" "HO3'" sing N N 287 LCG OP3 HOP3 sing N N 288 U OP3 P sing N N 289 U OP3 HOP3 sing N N 290 U P OP1 doub N N 291 U P OP2 sing N N 292 U P "O5'" sing N N 293 U OP2 HOP2 sing N N 294 U "O5'" "C5'" sing N N 295 U "C5'" "C4'" sing N N 296 U "C5'" "H5'" sing N N 297 U "C5'" "H5''" sing N N 298 U "C4'" "O4'" sing N N 299 U "C4'" "C3'" sing N N 300 U "C4'" "H4'" sing N N 301 U "O4'" "C1'" sing N N 302 U "C3'" "O3'" sing N N 303 U "C3'" "C2'" sing N N 304 U "C3'" "H3'" sing N N 305 U "O3'" "HO3'" sing N N 306 U "C2'" "O2'" sing N N 307 U "C2'" "C1'" sing N N 308 U "C2'" "H2'" sing N N 309 U "O2'" "HO2'" sing N N 310 U "C1'" N1 sing N N 311 U "C1'" "H1'" sing N N 312 U N1 C2 sing N N 313 U N1 C6 sing N N 314 U C2 O2 doub N N 315 U C2 N3 sing N N 316 U N3 C4 sing N N 317 U N3 H3 sing N N 318 U C4 O4 doub N N 319 U C4 C5 sing N N 320 U C5 C6 doub N N 321 U C5 H5 sing N N 322 U C6 H6 sing N N 323 # _ndb_struct_conf_na.entry_id 6C8E _ndb_struct_conf_na.feature 'a-form double helix' # 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 LCG 4 1_555 B C 13 1_555 -0.443 -0.215 0.395 2.819 -8.092 -0.715 1 A_LCG4:C13_B A 4 ? B 13 ? 19 1 1 A A 5 1_555 B U 12 1_555 0.026 -0.192 0.027 2.086 -15.645 -3.163 2 A_A5:U12_B A 5 ? B 12 ? 20 1 1 A C 6 1_555 B G 11 1_555 0.346 -0.219 0.199 8.043 -14.946 0.653 3 A_C6:G11_B A 6 ? B 11 ? 19 1 1 A U 7 1_555 B A 10 1_555 0.386 -0.229 -0.115 -1.492 -16.204 4.739 4 A_U7:A10_B A 7 ? B 10 ? 20 1 1 A U 8 1_555 B A 9 1_555 -0.031 -0.209 0.551 -1.772 -9.817 -2.191 5 A_U8:A9_B A 8 ? B 9 ? 20 1 1 A A 9 1_555 B U 8 1_555 -0.142 -0.120 -0.013 3.079 -17.372 2.073 6 A_A9:U8_B A 9 ? B 8 ? 20 1 1 A A 10 1_555 B U 7 1_555 -0.326 -0.249 -0.187 -2.706 -17.009 4.873 7 A_A10:U7_B A 10 ? B 7 ? 20 1 1 A G 11 1_555 B C 6 1_555 -0.484 -0.157 0.094 -6.351 -17.370 1.616 8 A_G11:C6_B A 11 ? B 6 ? 19 1 1 A U 12 1_555 B A 5 1_555 -0.116 -0.093 0.175 -4.326 -6.222 -5.087 9 A_U12:A5_B A 12 ? B 5 ? 20 1 1 A C 13 1_555 B LCG 4 1_555 0.470 -0.271 0.075 1.079 -13.579 -4.199 10 A_C13:LCG4_B A 13 ? B 4 ? 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 LCG 4 1_555 B C 13 1_555 A A 5 1_555 B U 12 1_555 -0.422 -1.387 3.308 2.376 8.814 34.013 -3.551 1.036 2.837 14.741 -3.974 35.182 1 AA_LCG4A5:U12C13_BB A 4 ? B 13 ? A 5 ? B 12 ? 1 A A 5 1_555 B U 12 1_555 A C 6 1_555 B G 11 1_555 0.457 -1.474 3.118 -2.504 2.070 33.475 -2.864 -1.173 2.983 3.583 4.335 33.628 2 AA_A5C6:G11U12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A C 6 1_555 B G 11 1_555 A U 7 1_555 B A 10 1_555 -0.263 -1.573 3.416 2.550 12.064 31.165 -4.638 0.860 2.615 21.434 -4.530 33.459 3 AA_C6U7:A10G11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A U 7 1_555 B A 10 1_555 A U 8 1_555 B A 9 1_555 -0.320 -1.291 3.255 -7.631 8.481 29.465 -3.881 -0.768 2.781 15.941 14.343 31.551 4 AA_U7U8:A9A10_BB A 7 ? B 10 ? A 8 ? B 9 ? 1 A U 8 1_555 B A 9 1_555 A A 9 1_555 B U 8 1_555 0.174 -1.524 3.102 5.315 14.116 30.404 -4.566 0.436 2.200 25.071 -9.440 33.861 5 AA_U8A9:U8A9_BB A 8 ? B 9 ? A 9 ? B 8 ? 1 A A 9 1_555 B U 8 1_555 A A 10 1_555 B U 7 1_555 0.347 -1.262 3.424 1.621 13.830 29.696 -4.554 -0.345 2.609 25.307 -2.965 32.732 6 AA_A9A10:U7U8_BB A 9 ? B 8 ? A 10 ? B 7 ? 1 A A 10 1_555 B U 7 1_555 A G 11 1_555 B C 6 1_555 0.238 -1.524 3.270 -0.615 9.515 31.525 -4.208 -0.518 2.703 17.031 1.100 32.900 7 AA_A10G11:C6U7_BB A 10 ? B 7 ? A 11 ? B 6 ? 1 A G 11 1_555 B C 6 1_555 A U 12 1_555 B A 5 1_555 -0.537 -1.441 3.264 -0.892 3.961 33.328 -3.127 0.788 3.090 6.874 1.548 33.568 8 AA_G11U12:A5C6_BB A 11 ? B 6 ? A 12 ? B 5 ? 1 A U 12 1_555 B A 5 1_555 A C 13 1_555 B LCG 4 1_555 0.460 -1.485 3.147 2.533 4.449 34.506 -3.113 -0.407 2.964 7.450 -4.242 34.872 9 AA_U12C13:LCG4A5_BB A 12 ? B 5 ? A 13 ? B 4 ? # _pdbx_audit_support.funding_organization 'Howard Hughes Medical Institute (HHMI)' _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 5DHC _pdbx_initial_refinement_model.details ? # loop_ _pdbx_reflns_twin.domain_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.type _pdbx_reflns_twin.operator _pdbx_reflns_twin.fraction 1 1 1 ? 'H, K, L' 0.514 2 1 1 ? -h,-k,l 0.486 # _atom_sites.entry_id 6C8E _atom_sites.fract_transf_matrix[1][1] 0.020399 _atom_sites.fract_transf_matrix[1][2] 0.011777 _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] 0.023554 _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] 0.012298 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_