data_6YML # _entry.id 6YML # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 6YML pdb_00006yml 10.2210/pdb6yml/pdb WWPDB D_1292107858 ? ? # 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 2020-07-22 2 'Structure model' 1 1 2020-07-29 3 'Structure model' 1 2 2024-01-24 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' '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 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 5 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 6YML _pdbx_database_status.recvd_initial_deposition_date 2020-04-08 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Huang, L.' 1 ? 'Lilley, D.M.J.' 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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 48 _citation.language ? _citation.page_first 7545 _citation.page_last 7556 _citation.title 'Crystal structure and ligand-induced folding of the SAM/SAH riboswitch.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkaa493 _citation.pdbx_database_id_PubMed 32520325 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Huang, L.' 1 ? primary 'Liao, T.W.' 2 ? primary 'Wang, J.' 3 ? primary 'Ha, T.' 4 ? primary 'Lilley, D.M.J.' 5 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'Chains: A,C' 8389.874 2 ? ? ? ? 2 polymer syn 'Chains: B,D' 2895.791 2 ? ? ? ? 3 non-polymer syn 'ADENOSINE MONOPHOSPHATE' 347.221 1 ? ? ? ? 4 non-polymer syn "5'-S-(3-aminopropyl)-5'-thioadenosine" 340.401 2 ? ? ? ? 5 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 6 water nat water 18.015 5 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes 'GGU(CBV)ACAACGGCUUCCUGGCGUGACC' GGUCACAACGGCUUCCUGGCGUGACC A,C ? 2 polyribonucleotide no no AUUGGAGCA AUUGGAGCA B,D ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'ADENOSINE MONOPHOSPHATE' AMP 4 "5'-S-(3-aminopropyl)-5'-thioadenosine" DSH 5 'SULFATE ION' SO4 6 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 U n 1 4 CBV n 1 5 A n 1 6 C n 1 7 A n 1 8 A n 1 9 C n 1 10 G n 1 11 G n 1 12 C n 1 13 U n 1 14 U n 1 15 C n 1 16 C n 1 17 U n 1 18 G n 1 19 G n 1 20 C n 1 21 G n 1 22 U n 1 23 G n 1 24 A n 1 25 C n 1 26 C n 2 1 A n 2 2 U n 2 3 U n 2 4 G n 2 5 G n 2 6 A n 2 7 G n 2 8 C n 2 9 A n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 26 'Roseobacter sp.' ? 1907202 ? 2 1 sample 1 9 'Roseobacter sp.' ? 1907202 ? # 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 AMP non-polymer . 'ADENOSINE MONOPHOSPHATE' ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CBV 'RNA linking' n ;5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C9 H13 Br N3 O8 P' 402.093 DSH non-polymer . "5'-S-(3-aminopropyl)-5'-thioadenosine" ? 'C13 H20 N6 O3 S' 340.401 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 # 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 7 7 G G A . n A 1 2 G 2 8 8 G G A . n A 1 3 U 3 9 9 U U A . n A 1 4 CBV 4 10 10 CBV CBV A . n A 1 5 A 5 11 11 A A A . n A 1 6 C 6 12 12 C C A . n A 1 7 A 7 13 13 A A A . n A 1 8 A 8 14 14 A A A . n A 1 9 C 9 15 15 C C A . n A 1 10 G 10 16 16 G G A . n A 1 11 G 11 17 17 G G A . n A 1 12 C 12 18 18 C C A . n A 1 13 U 13 19 19 U U A . n A 1 14 U 14 20 20 U U A . n A 1 15 C 15 21 21 C C A . n A 1 16 C 16 22 22 C C A . n A 1 17 U 17 23 23 U U A . n A 1 18 G 18 24 24 G G A . n A 1 19 G 19 25 25 G G A . n A 1 20 C 20 26 26 C C A . n A 1 21 G 21 27 27 G G A . n A 1 22 U 22 28 28 U U A . n A 1 23 G 23 29 29 G G A . n A 1 24 A 24 30 30 A A A . n A 1 25 C 25 31 31 C C A . n A 1 26 C 26 32 32 C C A . n B 2 1 A 1 43 43 A A B . n B 2 2 U 2 44 44 U U B . n B 2 3 U 3 45 45 U U B . n B 2 4 G 4 46 46 G G B . n B 2 5 G 5 47 47 G G B . n B 2 6 A 6 48 48 A A B . n B 2 7 G 7 49 49 G G B . n B 2 8 C 8 50 50 C C B . n B 2 9 A 9 51 51 A A B . n C 1 1 G 1 7 7 G G C . n C 1 2 G 2 8 8 G G C . n C 1 3 U 3 9 9 U U C . n C 1 4 CBV 4 10 10 CBV CBV C . n C 1 5 A 5 11 11 A A C . n C 1 6 C 6 12 12 C C C . n C 1 7 A 7 13 13 A A C . n C 1 8 A 8 14 14 A A C . n C 1 9 C 9 15 15 C C C . n C 1 10 G 10 16 16 G G C . n C 1 11 G 11 17 17 G G C . n C 1 12 C 12 18 18 C C C . n C 1 13 U 13 19 19 U U C . n C 1 14 U 14 20 20 U U C . n C 1 15 C 15 21 21 C C C . n C 1 16 C 16 22 22 C C C . n C 1 17 U 17 23 23 U U C . n C 1 18 G 18 24 24 G G C . n C 1 19 G 19 25 25 G G C . n C 1 20 C 20 26 26 C C C . n C 1 21 G 21 27 27 G G C . n C 1 22 U 22 28 28 U U C . n C 1 23 G 23 29 29 G G C . n C 1 24 A 24 30 30 A A C . n C 1 25 C 25 31 31 C C C . n C 1 26 C 26 32 32 C C C . n D 2 1 A 1 43 43 A A D . n D 2 2 U 2 44 44 U U D . n D 2 3 U 3 45 45 U U D . n D 2 4 G 4 46 46 G G D . n D 2 5 G 5 47 47 G G D . n D 2 6 A 6 48 48 A A D . n D 2 7 G 7 49 49 G G D . n D 2 8 C 8 50 50 C C D . n D 2 9 A 9 51 51 A A D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 3 AMP 1 101 1 AMP AMP A . F 4 DSH 1 102 1 DSH SAH A . G 5 SO4 1 103 1 SO4 SO4 A . H 4 DSH 1 101 2 DSH SAH C . I 6 HOH 1 201 4 HOH HOH A . I 6 HOH 2 202 1 HOH HOH A . J 6 HOH 1 201 2 HOH HOH C . J 6 HOH 2 202 5 HOH HOH C . K 6 HOH 1 101 3 HOH HOH D . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 N 1 A AMP 101 ? P ? E AMP 1 P 2 1 N 1 A AMP 101 ? O1P ? E AMP 1 O1P 3 1 N 1 A AMP 101 ? O2P ? E AMP 1 O2P 4 1 N 1 A AMP 101 ? O3P ? E AMP 1 O3P # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1_3660 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1_3660 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 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 6YML _cell.details ? _cell.formula_units_Z ? _cell.length_a 86.218 _cell.length_a_esd ? _cell.length_b 86.218 _cell.length_b_esd ? _cell.length_c 75.395 _cell.length_c_esd ? _cell.volume 485365.682 _cell.volume_esd ? _cell.Z_PDB 12 _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 6YML _symmetry.cell_setting ? _symmetry.Int_Tables_number 149 _symmetry.space_group_name_Hall 'P 3 2' _symmetry.space_group_name_H-M 'P 3 1 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 6YML _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 3.72 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 66.9 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.01 M Magnesium Sulfate, 0.05 M Sodium Cacodylate pH 6.0, 1.8 M Lithium Sulfate monohydrate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-09-15 _diffrn_detector.pdbx_frequency ? # _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 0.9188 _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 'DIAMOND BEAMLINE I24' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9188 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I24 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate 69.42 _reflns.entry_id 6YML _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.17 _reflns.d_resolution_low 75.4 _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 17121 _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 0.6 _reflns.percent_possible_obs 100 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 9.7 _reflns.pdbx_Rmerge_I_obs 0.095 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 9.4 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all 0.033 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.997 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.17 _reflns_shell.d_res_low 2.20 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 0.6 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 867 _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 1.5 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all 1.0 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.355 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 74.95 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 6YML _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 2.17 _refine.ls_d_res_low 53.05 _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 17121 _refine.ls_number_reflns_R_free 725 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.23 _refine.ls_percent_reflns_R_free 4.23 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1998 _refine.ls_R_factor_R_free 0.2332 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1983 _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.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.35 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 6YL5 _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 32.1866 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.3452 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 2.17 _refine_hist.d_res_low 53.05 _refine_hist.number_atoms_solvent 5 _refine_hist.number_atoms_total 1559 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1484 _refine_hist.pdbx_number_atoms_ligand 70 _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' ? 0.0066 ? 1731 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.4885 ? 2683 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.1262 ? 356 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0106 ? 73 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 17.5480 ? 857 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.17 2.33 . . 126 3156 96.13 . . . 0.3536 . 0.2990 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.33 2.57 . . 172 3230 100.00 . . . 0.3989 . 0.3192 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.57 2.94 . . 141 3318 100.00 . . . 0.3678 . 0.3347 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.94 3.70 . . 130 3317 100.00 . . . 0.2864 . 0.2243 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.70 53.05 . . 156 3375 99.97 . . . 0.1730 . 0.1475 . . . . . . . . . . . # _struct.entry_id 6YML _struct.title 'Crystal structure of the SAM-SAH riboswitch with decarboxylated SAH' _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 6YML _struct_keywords.text 'Pseudoknot; SAM; Riboswitch, 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 1 ? D N N 2 ? E N N 3 ? F N N 4 ? G N N 5 ? H N N 4 ? I N N 6 ? J N N 6 ? K N N 6 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 6YML 6YML ? 1 ? 1 2 PDB 6YML 6YML ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 6YML A 1 ? 26 ? 6YML 7 ? 32 ? 7 32 2 2 6YML B 1 ? 9 ? 6YML 43 ? 51 ? 43 51 3 1 6YML C 1 ? 26 ? 6YML 7 ? 32 ? 7 32 4 2 6YML D 1 ? 9 ? 6YML 43 ? 51 ? 43 51 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,G,I 2 1 C,D,H,J,K # _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 U 3 "O3'" ? ? ? 1_555 A CBV 4 P ? ? A U 9 A CBV 10 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale2 covale one ? A CBV 4 "O3'" ? ? ? 1_555 A A 5 P ? ? A CBV 10 A A 11 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale3 covale both ? C U 3 "O3'" ? ? ? 1_555 C CBV 4 P ? ? C U 9 C CBV 10 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale4 covale one ? C CBV 4 "O3'" ? ? ? 1_555 C A 5 P ? ? C CBV 10 C A 11 1_555 ? ? ? ? ? ? ? 1.620 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 7 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 7 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 7 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 25 N3 ? ? A G 8 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 25 O2 ? ? A G 8 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 25 N4 ? ? A G 8 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 24 N1 ? ? A U 9 A A 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 24 N6 ? ? A U 9 A A 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A CBV 4 N3 ? ? ? 1_555 A G 23 N1 ? ? A CBV 10 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A CBV 4 N4 ? ? ? 1_555 A G 23 O6 ? ? A CBV 10 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A CBV 4 O2 ? ? ? 1_555 A G 23 N2 ? ? A CBV 10 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 22 N3 ? ? A A 11 A U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 22 O4 ? ? A A 11 A U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 12 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 12 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 12 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 7 N3 ? ? ? 1_555 A C 20 N4 ? ? A A 13 A C 26 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog18 hydrog ? ? A A 8 N6 ? ? ? 1_555 A G 19 N3 ? ? A A 14 A G 25 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog19 hydrog ? ? A A 8 N7 ? ? ? 1_555 A G 19 N2 ? ? A A 14 A G 25 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog20 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 18 N1 ? ? A C 15 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 18 O6 ? ? A C 15 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 18 N2 ? ? A C 15 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 16 A C 21 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog24 hydrog ? ? A G 10 N1 ? ? ? 1_555 B G 5 O6 ? ? A G 16 B G 47 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog25 hydrog ? ? A G 10 N2 ? ? ? 1_555 B G 5 N7 ? ? A G 16 B G 47 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog26 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 17 B C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 17 B C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 17 B C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 18 B G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 18 B G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 18 B G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 13 N3 ? ? ? 1_555 B A 6 N1 ? ? A U 19 B A 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A U 13 O4 ? ? ? 1_555 B A 6 N6 ? ? A U 19 B A 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 21 B G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 21 B G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 21 B G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 16 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 22 B G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 16 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 22 B G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 16 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 22 B G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 18 N2 ? ? ? 1_555 B U 2 O2 ? ? A G 24 B U 44 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog41 hydrog ? ? C G 1 N1 ? ? ? 1_555 C C 26 N3 ? ? C G 7 C C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C G 1 N2 ? ? ? 1_555 C C 26 O2 ? ? C G 7 C C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C G 1 O6 ? ? ? 1_555 C C 26 N4 ? ? C G 7 C C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C G 2 N1 ? ? ? 1_555 C C 25 N3 ? ? C G 8 C C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C G 2 N2 ? ? ? 1_555 C C 25 O2 ? ? C G 8 C C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C G 2 O6 ? ? ? 1_555 C C 25 N4 ? ? C G 8 C C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C U 3 N3 ? ? ? 1_555 C A 24 N1 ? ? C U 9 C A 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C U 3 O4 ? ? ? 1_555 C A 24 N6 ? ? C U 9 C A 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C CBV 4 N3 ? ? ? 1_555 C G 23 N1 ? ? C CBV 10 C G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C CBV 4 N4 ? ? ? 1_555 C G 23 O6 ? ? C CBV 10 C G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C CBV 4 O2 ? ? ? 1_555 C G 23 N2 ? ? C CBV 10 C G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C A 5 N1 ? ? ? 1_555 C U 22 N3 ? ? C A 11 C U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C A 5 N6 ? ? ? 1_555 C U 22 O4 ? ? C A 11 C U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C C 6 N3 ? ? ? 1_555 C G 21 N1 ? ? C C 12 C G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C C 6 N4 ? ? ? 1_555 C G 21 O6 ? ? C C 12 C G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C C 6 O2 ? ? ? 1_555 C G 21 N2 ? ? C C 12 C G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C A 7 N3 ? ? ? 1_555 C C 20 N4 ? ? C A 13 C C 26 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog58 hydrog ? ? C A 8 N6 ? ? ? 1_555 C G 19 N3 ? ? C A 14 C G 25 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog59 hydrog ? ? C A 8 N7 ? ? ? 1_555 C G 19 N2 ? ? C A 14 C G 25 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog60 hydrog ? ? C A 8 N1 ? ? ? 1_555 D A 1 N6 ? ? C A 14 D A 43 1_555 ? ? ? ? ? ? TYPE_1_PAIR ? ? ? hydrog61 hydrog ? ? C A 8 N6 ? ? ? 1_555 D A 1 N1 ? ? C A 14 D A 43 1_555 ? ? ? ? ? ? TYPE_1_PAIR ? ? ? hydrog62 hydrog ? ? C C 9 N3 ? ? ? 1_555 C G 18 N1 ? ? C C 15 C G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C C 9 N4 ? ? ? 1_555 C G 18 O6 ? ? C C 15 C G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? C C 9 O2 ? ? ? 1_555 C G 18 N2 ? ? C C 15 C G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? C G 10 O6 ? ? ? 1_555 C C 15 N4 ? ? C G 16 C C 21 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog66 hydrog ? ? C G 10 N1 ? ? ? 1_555 D G 5 O6 ? ? C G 16 D G 47 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog67 hydrog ? ? C G 10 N2 ? ? ? 1_555 D G 5 N7 ? ? C G 16 D G 47 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog68 hydrog ? ? C G 11 N1 ? ? ? 1_555 D C 8 N3 ? ? C G 17 D C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? C G 11 N2 ? ? ? 1_555 D C 8 O2 ? ? C G 17 D C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? C G 11 O6 ? ? ? 1_555 D C 8 N4 ? ? C G 17 D C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? C C 12 N3 ? ? ? 1_555 D G 7 N1 ? ? C C 18 D G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? C C 12 N4 ? ? ? 1_555 D G 7 O6 ? ? C C 18 D G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? C C 12 O2 ? ? ? 1_555 D G 7 N2 ? ? C C 18 D G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? C U 13 N3 ? ? ? 1_555 D A 6 N1 ? ? C U 19 D A 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? C U 13 O4 ? ? ? 1_555 D A 6 N6 ? ? C U 19 D A 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? C C 15 N3 ? ? ? 1_555 D G 5 N1 ? ? C C 21 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? C C 15 N4 ? ? ? 1_555 D G 5 O6 ? ? C C 21 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? C C 15 O2 ? ? ? 1_555 D G 5 N2 ? ? C C 21 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? C C 16 N3 ? ? ? 1_555 D G 4 N1 ? ? C C 22 D G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? C C 16 N4 ? ? ? 1_555 D G 4 O6 ? ? C C 22 D G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? C C 16 O2 ? ? ? 1_555 D G 4 N2 ? ? C C 22 D G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? C G 18 N2 ? ? ? 1_555 D A 1 N1 ? ? C G 24 D A 43 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog83 hydrog ? ? C G 18 N2 ? ? ? 1_555 D U 2 O2 ? ? C G 24 D U 44 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? # 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 AMP 101 ? 7 'binding site for residue AMP A 101' AC2 Software A DSH 102 ? 8 'binding site for residue DSH A 102' AC3 Software A SO4 103 ? 2 'binding site for residue SO4 A 103' AC4 Software C DSH 101 ? 8 'binding site for residue DSH C 101' AC5 Software C CBV 10 ? 6 'binding site for Di-nucleotide CBV C 10 and A C 11' # 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 7 A A 8 ? A A 14 . ? 1_555 ? 2 AC1 7 G A 18 ? G A 24 . ? 1_555 ? 3 AC1 7 G A 19 ? G A 25 . ? 1_555 ? 4 AC1 7 C A 20 ? C A 26 . ? 1_555 ? 5 AC1 7 U B 2 ? U B 44 . ? 1_555 ? 6 AC1 7 C C 16 ? C C 22 . ? 2_545 ? 7 AC1 7 U C 17 ? U C 23 . ? 2_545 ? 8 AC2 8 C A 9 ? C A 15 . ? 1_555 ? 9 AC2 8 G A 10 ? G A 16 . ? 1_555 ? 10 AC2 8 U A 17 ? U A 23 . ? 1_555 ? 11 AC2 8 G A 18 ? G A 24 . ? 1_555 ? 12 AC2 8 G A 19 ? G A 25 . ? 1_555 ? 13 AC2 8 U B 2 ? U B 44 . ? 1_555 ? 14 AC2 8 U B 3 ? U B 45 . ? 1_555 ? 15 AC2 8 G B 4 ? G B 46 . ? 1_555 ? 16 AC3 2 C A 25 ? C A 31 . ? 1_555 ? 17 AC3 2 C A 26 ? C A 32 . ? 1_555 ? 18 AC4 8 A B 1 ? A B 43 . ? 3_655 ? 19 AC4 8 C C 9 ? C C 15 . ? 1_555 ? 20 AC4 8 G C 10 ? G C 16 . ? 1_555 ? 21 AC4 8 U C 17 ? U C 23 . ? 1_555 ? 22 AC4 8 G C 18 ? G C 24 . ? 1_555 ? 23 AC4 8 U D 2 ? U D 44 . ? 1_555 ? 24 AC4 8 U D 3 ? U D 45 . ? 1_555 ? 25 AC4 8 G D 4 ? G D 46 . ? 1_555 ? 26 AC5 6 U C 3 ? U C 9 . ? 1_555 ? 27 AC5 6 C C 6 ? C C 12 . ? 1_555 ? 28 AC5 6 U C 22 ? U C 28 . ? 1_555 ? 29 AC5 6 G C 23 ? G C 29 . ? 1_555 ? 30 AC5 6 A C 24 ? A C 30 . ? 1_555 ? 31 AC5 6 HOH J . ? HOH C 201 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 "O2'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 C _pdbx_validate_close_contact.auth_seq_id_1 22 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 201 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.17 # 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 C2 A G 24 ? ? N3 A G 24 ? ? C4 A G 24 ? ? 115.71 111.90 3.81 0.50 N 2 1 C5 A G 24 ? ? C6 A G 24 ? ? N1 A G 24 ? ? 115.02 111.50 3.52 0.50 N 3 1 "O3'" C CBV 10 ? ? P C A 11 ? ? OP2 C A 11 ? ? 88.32 105.20 -16.88 2.20 Y 4 1 "O3'" C CBV 10 ? ? P C A 11 ? ? OP1 C A 11 ? ? 79.92 105.20 -25.28 2.20 Y 5 1 OP1 C A 11 ? ? P C A 11 ? ? OP2 C A 11 ? ? 129.81 119.60 10.21 1.50 N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x-y,z 3 -x+y,-x,z 4 -y,-x,-z 5 -x+y,y,-z 6 x,x-y,-z # _pdbx_refine_tls.id 1 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 20.5268773692 _pdbx_refine_tls.origin_y -28.5433780996 _pdbx_refine_tls.origin_z 17.9665400538 _pdbx_refine_tls.T[1][1] 0.792646920848 _pdbx_refine_tls.T[1][1]_esd ? _pdbx_refine_tls.T[1][2] -0.0282211245561 _pdbx_refine_tls.T[1][2]_esd ? _pdbx_refine_tls.T[1][3] -0.00305360737992 _pdbx_refine_tls.T[1][3]_esd ? _pdbx_refine_tls.T[2][2] 0.611988832929 _pdbx_refine_tls.T[2][2]_esd ? _pdbx_refine_tls.T[2][3] 0.0299842351869 _pdbx_refine_tls.T[2][3]_esd ? _pdbx_refine_tls.T[3][3] 0.75943010969 _pdbx_refine_tls.T[3][3]_esd ? _pdbx_refine_tls.L[1][1] -0.602024258174 _pdbx_refine_tls.L[1][1]_esd ? _pdbx_refine_tls.L[1][2] 0.181644062808 _pdbx_refine_tls.L[1][2]_esd ? _pdbx_refine_tls.L[1][3] 0.15970629244 _pdbx_refine_tls.L[1][3]_esd ? _pdbx_refine_tls.L[2][2] 0.264042713503 _pdbx_refine_tls.L[2][2]_esd ? _pdbx_refine_tls.L[2][3] 0.0681717530977 _pdbx_refine_tls.L[2][3]_esd ? _pdbx_refine_tls.L[3][3] -0.233417418023 _pdbx_refine_tls.L[3][3]_esd ? _pdbx_refine_tls.S[1][1] 0.0258798603246 _pdbx_refine_tls.S[1][1]_esd ? _pdbx_refine_tls.S[1][2] -0.031269661099 _pdbx_refine_tls.S[1][2]_esd ? _pdbx_refine_tls.S[1][3] 0.00601602852387 _pdbx_refine_tls.S[1][3]_esd ? _pdbx_refine_tls.S[2][1] -0.111139223502 _pdbx_refine_tls.S[2][1]_esd ? _pdbx_refine_tls.S[2][2] -0.160528492185 _pdbx_refine_tls.S[2][2]_esd ? _pdbx_refine_tls.S[2][3] 0.082266351334 _pdbx_refine_tls.S[2][3]_esd ? _pdbx_refine_tls.S[3][1] -0.0299861146124 _pdbx_refine_tls.S[3][1]_esd ? _pdbx_refine_tls.S[3][2] 0.0429710393775 _pdbx_refine_tls.S[3][2]_esd ? _pdbx_refine_tls.S[3][3] -0.0022242663072 _pdbx_refine_tls.S[3][3]_esd ? # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.beg_auth_asym_id ? _pdbx_refine_tls_group.beg_auth_seq_id ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id ? _pdbx_refine_tls_group.end_auth_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details all # _pdbx_entry_details.entry_id 6YML _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # 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 AMP P P N N 38 AMP O1P O N N 39 AMP O2P O N N 40 AMP O3P O N N 41 AMP "O5'" O N N 42 AMP "C5'" C N N 43 AMP "C4'" C N R 44 AMP "O4'" O N N 45 AMP "C3'" C N S 46 AMP "O3'" O N N 47 AMP "C2'" C N R 48 AMP "O2'" O N N 49 AMP "C1'" C N R 50 AMP N9 N Y N 51 AMP C8 C Y N 52 AMP N7 N Y N 53 AMP C5 C Y N 54 AMP C6 C Y N 55 AMP N6 N N N 56 AMP N1 N Y N 57 AMP C2 C Y N 58 AMP N3 N Y N 59 AMP C4 C Y N 60 AMP HOP2 H N N 61 AMP HOP3 H N N 62 AMP "H5'1" H N N 63 AMP "H5'2" H N N 64 AMP "H4'" H N N 65 AMP "H3'" H N N 66 AMP "HO3'" H N N 67 AMP "H2'" H N N 68 AMP "HO2'" H N N 69 AMP "H1'" H N N 70 AMP H8 H N N 71 AMP HN61 H N N 72 AMP HN62 H N N 73 AMP H2 H N N 74 C OP3 O N N 75 C P P N N 76 C OP1 O N N 77 C OP2 O N N 78 C "O5'" O N N 79 C "C5'" C N N 80 C "C4'" C N R 81 C "O4'" O N N 82 C "C3'" C N S 83 C "O3'" O N N 84 C "C2'" C N R 85 C "O2'" O N N 86 C "C1'" C N R 87 C N1 N N N 88 C C2 C N N 89 C O2 O N N 90 C N3 N N N 91 C C4 C N N 92 C N4 N N N 93 C C5 C N N 94 C C6 C N N 95 C HOP3 H N N 96 C HOP2 H N N 97 C "H5'" H N N 98 C "H5''" H N N 99 C "H4'" H N N 100 C "H3'" H N N 101 C "HO3'" H N N 102 C "H2'" H N N 103 C "HO2'" H N N 104 C "H1'" H N N 105 C H41 H N N 106 C H42 H N N 107 C H5 H N N 108 C H6 H N N 109 CBV O3P O N N 110 CBV P P N N 111 CBV O1P O N N 112 CBV O2P O N N 113 CBV "O5'" O N N 114 CBV "C5'" C N N 115 CBV "C4'" C N R 116 CBV "O4'" O N N 117 CBV "C3'" C N S 118 CBV "O3'" O N N 119 CBV "C2'" C N R 120 CBV "O2'" O N N 121 CBV "C1'" C N R 122 CBV N1 N N N 123 CBV C2 C N N 124 CBV O2 O N N 125 CBV N3 N N N 126 CBV C4 C N N 127 CBV N4 N N N 128 CBV C5 C N N 129 CBV C6 C N N 130 CBV BR BR N N 131 CBV HO3P H N N 132 CBV HO1P H N N 133 CBV "H5'1" H N N 134 CBV "H5'2" H N N 135 CBV "H4'" H N N 136 CBV "H3'" H N N 137 CBV "HO3'" H N N 138 CBV "H2'" H N N 139 CBV "HO2'" H N N 140 CBV "H1'" H N N 141 CBV HN41 H N N 142 CBV HN42 H N N 143 CBV H6 H N N 144 DSH N N N N 145 DSH N1 N Y N 146 DSH C2 C Y N 147 DSH N3 N Y N 148 DSH C4 C Y N 149 DSH C5 C Y N 150 DSH C6 C Y N 151 DSH N6 N N N 152 DSH N7 N Y N 153 DSH C8 C Y N 154 DSH N9 N Y N 155 DSH CA C N N 156 DSH CB C N N 157 DSH SD S N N 158 DSH CG C N N 159 DSH "C1'" C N R 160 DSH "C2'" C N R 161 DSH "O2'" O N N 162 DSH "C3'" C N S 163 DSH "O3'" O N N 164 DSH "C4'" C N S 165 DSH "O4'" O N N 166 DSH "C5'" C N N 167 DSH HN H N N 168 DSH HNA H N N 169 DSH H2 H N N 170 DSH HN6 H N N 171 DSH HN6A H N N 172 DSH H8 H N N 173 DSH HA H N N 174 DSH HB H N N 175 DSH HG H N N 176 DSH HGA H N N 177 DSH "H1'" H N N 178 DSH "H2'" H N N 179 DSH "HO2'" H N N 180 DSH "H3'" H N N 181 DSH "HO3'" H N N 182 DSH "H4'" H N N 183 DSH "H5'" H N N 184 DSH "H5'A" H N N 185 DSH HAA H N N 186 DSH HBA H N N 187 G OP3 O N N 188 G P P N N 189 G OP1 O N N 190 G OP2 O N N 191 G "O5'" O N N 192 G "C5'" C N N 193 G "C4'" C N R 194 G "O4'" O N N 195 G "C3'" C N S 196 G "O3'" O N N 197 G "C2'" C N R 198 G "O2'" O N N 199 G "C1'" C N R 200 G N9 N Y N 201 G C8 C Y N 202 G N7 N Y N 203 G C5 C Y N 204 G C6 C N N 205 G O6 O N N 206 G N1 N N N 207 G C2 C N N 208 G N2 N N N 209 G N3 N N N 210 G C4 C Y N 211 G HOP3 H N N 212 G HOP2 H N N 213 G "H5'" H N N 214 G "H5''" H N N 215 G "H4'" H N N 216 G "H3'" H N N 217 G "HO3'" H N N 218 G "H2'" H N N 219 G "HO2'" H N N 220 G "H1'" H N N 221 G H8 H N N 222 G H1 H N N 223 G H21 H N N 224 G H22 H N N 225 HOH O O N N 226 HOH H1 H N N 227 HOH H2 H N N 228 SO4 S S N N 229 SO4 O1 O N N 230 SO4 O2 O N N 231 SO4 O3 O N N 232 SO4 O4 O N N 233 U OP3 O N N 234 U P P N N 235 U OP1 O N N 236 U OP2 O N N 237 U "O5'" O N N 238 U "C5'" C N N 239 U "C4'" C N R 240 U "O4'" O N N 241 U "C3'" C N S 242 U "O3'" O N N 243 U "C2'" C N R 244 U "O2'" O N N 245 U "C1'" C N R 246 U N1 N N N 247 U C2 C N N 248 U O2 O N N 249 U N3 N N N 250 U C4 C N N 251 U O4 O N N 252 U C5 C N N 253 U C6 C N N 254 U HOP3 H N N 255 U HOP2 H N N 256 U "H5'" H N N 257 U "H5''" H N N 258 U "H4'" H N N 259 U "H3'" H N N 260 U "HO3'" H N N 261 U "H2'" H N N 262 U "HO2'" H N N 263 U "H1'" H N N 264 U H3 H N N 265 U H5 H N N 266 U H6 H N N 267 # 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 AMP P O1P doub N N 40 AMP P O2P sing N N 41 AMP P O3P sing N N 42 AMP P "O5'" sing N N 43 AMP O2P HOP2 sing N N 44 AMP O3P HOP3 sing N N 45 AMP "O5'" "C5'" sing N N 46 AMP "C5'" "C4'" sing N N 47 AMP "C5'" "H5'1" sing N N 48 AMP "C5'" "H5'2" sing N N 49 AMP "C4'" "O4'" sing N N 50 AMP "C4'" "C3'" sing N N 51 AMP "C4'" "H4'" sing N N 52 AMP "O4'" "C1'" sing N N 53 AMP "C3'" "O3'" sing N N 54 AMP "C3'" "C2'" sing N N 55 AMP "C3'" "H3'" sing N N 56 AMP "O3'" "HO3'" sing N N 57 AMP "C2'" "O2'" sing N N 58 AMP "C2'" "C1'" sing N N 59 AMP "C2'" "H2'" sing N N 60 AMP "O2'" "HO2'" sing N N 61 AMP "C1'" N9 sing N N 62 AMP "C1'" "H1'" sing N N 63 AMP N9 C8 sing Y N 64 AMP N9 C4 sing Y N 65 AMP C8 N7 doub Y N 66 AMP C8 H8 sing N N 67 AMP N7 C5 sing Y N 68 AMP C5 C6 sing Y N 69 AMP C5 C4 doub Y N 70 AMP C6 N6 sing N N 71 AMP C6 N1 doub Y N 72 AMP N6 HN61 sing N N 73 AMP N6 HN62 sing N N 74 AMP N1 C2 sing Y N 75 AMP C2 N3 doub Y N 76 AMP C2 H2 sing N N 77 AMP N3 C4 sing Y N 78 C OP3 P sing N N 79 C OP3 HOP3 sing N N 80 C P OP1 doub N N 81 C P OP2 sing N N 82 C P "O5'" sing N N 83 C OP2 HOP2 sing N N 84 C "O5'" "C5'" sing N N 85 C "C5'" "C4'" sing N N 86 C "C5'" "H5'" sing N N 87 C "C5'" "H5''" sing N N 88 C "C4'" "O4'" sing N N 89 C "C4'" "C3'" sing N N 90 C "C4'" "H4'" sing N N 91 C "O4'" "C1'" sing N N 92 C "C3'" "O3'" sing N N 93 C "C3'" "C2'" sing N N 94 C "C3'" "H3'" sing N N 95 C "O3'" "HO3'" sing N N 96 C "C2'" "O2'" sing N N 97 C "C2'" "C1'" sing N N 98 C "C2'" "H2'" sing N N 99 C "O2'" "HO2'" sing N N 100 C "C1'" N1 sing N N 101 C "C1'" "H1'" sing N N 102 C N1 C2 sing N N 103 C N1 C6 sing N N 104 C C2 O2 doub N N 105 C C2 N3 sing N N 106 C N3 C4 doub N N 107 C C4 N4 sing N N 108 C C4 C5 sing N N 109 C N4 H41 sing N N 110 C N4 H42 sing N N 111 C C5 C6 doub N N 112 C C5 H5 sing N N 113 C C6 H6 sing N N 114 CBV O3P P sing N N 115 CBV O3P HO3P sing N N 116 CBV P O1P sing N N 117 CBV P O2P doub N N 118 CBV P "O5'" sing N N 119 CBV O1P HO1P sing N N 120 CBV "O5'" "C5'" sing N N 121 CBV "C5'" "C4'" sing N N 122 CBV "C5'" "H5'1" sing N N 123 CBV "C5'" "H5'2" sing N N 124 CBV "C4'" "O4'" sing N N 125 CBV "C4'" "C3'" sing N N 126 CBV "C4'" "H4'" sing N N 127 CBV "O4'" "C1'" sing N N 128 CBV "C3'" "O3'" sing N N 129 CBV "C3'" "C2'" sing N N 130 CBV "C3'" "H3'" sing N N 131 CBV "O3'" "HO3'" sing N N 132 CBV "C2'" "O2'" sing N N 133 CBV "C2'" "C1'" sing N N 134 CBV "C2'" "H2'" sing N N 135 CBV "O2'" "HO2'" sing N N 136 CBV "C1'" N1 sing N N 137 CBV "C1'" "H1'" sing N N 138 CBV N1 C2 sing N N 139 CBV N1 C6 sing N N 140 CBV C2 O2 doub N N 141 CBV C2 N3 sing N N 142 CBV N3 C4 doub N N 143 CBV C4 N4 sing N N 144 CBV C4 C5 sing N N 145 CBV N4 HN41 sing N N 146 CBV N4 HN42 sing N N 147 CBV C5 C6 doub N N 148 CBV C5 BR sing N N 149 CBV C6 H6 sing N N 150 DSH N CA sing N N 151 DSH N1 C2 doub Y N 152 DSH N1 C6 sing Y N 153 DSH C2 N3 sing Y N 154 DSH N3 C4 doub Y N 155 DSH C4 C5 sing Y N 156 DSH C4 N9 sing Y N 157 DSH C5 C6 doub Y N 158 DSH C5 N7 sing Y N 159 DSH C6 N6 sing N N 160 DSH N7 C8 doub Y N 161 DSH C8 N9 sing Y N 162 DSH N9 "C1'" sing N N 163 DSH CA CB sing N N 164 DSH CB CG sing N N 165 DSH SD CG sing N N 166 DSH SD "C5'" sing N N 167 DSH "C1'" "C2'" sing N N 168 DSH "C1'" "O4'" sing N N 169 DSH "C2'" "O2'" sing N N 170 DSH "C2'" "C3'" sing N N 171 DSH "C3'" "O3'" sing N N 172 DSH "C3'" "C4'" sing N N 173 DSH "C4'" "O4'" sing N N 174 DSH "C4'" "C5'" sing N N 175 DSH N HN sing N N 176 DSH N HNA sing N N 177 DSH C2 H2 sing N N 178 DSH N6 HN6 sing N N 179 DSH N6 HN6A sing N N 180 DSH C8 H8 sing N N 181 DSH CA HA sing N N 182 DSH CB HB sing N N 183 DSH CG HG sing N N 184 DSH CG HGA sing N N 185 DSH "C1'" "H1'" sing N N 186 DSH "C2'" "H2'" sing N N 187 DSH "O2'" "HO2'" sing N N 188 DSH "C3'" "H3'" sing N N 189 DSH "O3'" "HO3'" sing N N 190 DSH "C4'" "H4'" sing N N 191 DSH "C5'" "H5'" sing N N 192 DSH "C5'" "H5'A" sing N N 193 DSH CA HAA sing N N 194 DSH CB HBA sing N N 195 G OP3 P sing N N 196 G OP3 HOP3 sing N N 197 G P OP1 doub N N 198 G P OP2 sing N N 199 G P "O5'" sing N N 200 G OP2 HOP2 sing N N 201 G "O5'" "C5'" sing N N 202 G "C5'" "C4'" sing N N 203 G "C5'" "H5'" sing N N 204 G "C5'" "H5''" sing N N 205 G "C4'" "O4'" sing N N 206 G "C4'" "C3'" sing N N 207 G "C4'" "H4'" sing N N 208 G "O4'" "C1'" sing N N 209 G "C3'" "O3'" sing N N 210 G "C3'" "C2'" sing N N 211 G "C3'" "H3'" sing N N 212 G "O3'" "HO3'" sing N N 213 G "C2'" "O2'" sing N N 214 G "C2'" "C1'" sing N N 215 G "C2'" "H2'" sing N N 216 G "O2'" "HO2'" sing N N 217 G "C1'" N9 sing N N 218 G "C1'" "H1'" sing N N 219 G N9 C8 sing Y N 220 G N9 C4 sing Y N 221 G C8 N7 doub Y N 222 G C8 H8 sing N N 223 G N7 C5 sing Y N 224 G C5 C6 sing N N 225 G C5 C4 doub Y N 226 G C6 O6 doub N N 227 G C6 N1 sing N N 228 G N1 C2 sing N N 229 G N1 H1 sing N N 230 G C2 N2 sing N N 231 G C2 N3 doub N N 232 G N2 H21 sing N N 233 G N2 H22 sing N N 234 G N3 C4 sing N N 235 HOH O H1 sing N N 236 HOH O H2 sing N N 237 SO4 S O1 doub N N 238 SO4 S O2 doub N N 239 SO4 S O3 sing N N 240 SO4 S O4 sing N N 241 U OP3 P sing N N 242 U OP3 HOP3 sing N N 243 U P OP1 doub N N 244 U P OP2 sing N N 245 U P "O5'" sing N N 246 U OP2 HOP2 sing N N 247 U "O5'" "C5'" sing N N 248 U "C5'" "C4'" sing N N 249 U "C5'" "H5'" sing N N 250 U "C5'" "H5''" sing N N 251 U "C4'" "O4'" sing N N 252 U "C4'" "C3'" sing N N 253 U "C4'" "H4'" sing N N 254 U "O4'" "C1'" sing N N 255 U "C3'" "O3'" sing N N 256 U "C3'" "C2'" sing N N 257 U "C3'" "H3'" sing N N 258 U "O3'" "HO3'" sing N N 259 U "C2'" "O2'" sing N N 260 U "C2'" "C1'" sing N N 261 U "C2'" "H2'" sing N N 262 U "O2'" "HO2'" sing N N 263 U "C1'" N1 sing N N 264 U "C1'" "H1'" sing N N 265 U N1 C2 sing N N 266 U N1 C6 sing N N 267 U C2 O2 doub N N 268 U C2 N3 sing N N 269 U N3 C4 sing N N 270 U N3 H3 sing N N 271 U C4 O4 doub N N 272 U C4 C5 sing N N 273 U C5 C6 doub N N 274 U C5 H5 sing N N 275 U C6 H6 sing N N 276 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6YML 'double helix' 6YML 'a-form double helix' 6YML 'hairpin loop' 6YML '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 11 1_555 B C 8 1_555 -0.219 -0.191 0.506 7.660 -1.413 -1.437 1 A_G17:C50_B A 17 ? B 50 ? 19 1 1 A C 12 1_555 B G 7 1_555 0.270 -0.274 0.233 -1.630 -17.315 4.542 2 A_C18:G49_B A 18 ? B 49 ? 19 1 1 A U 13 1_555 B A 6 1_555 0.011 -0.084 -0.040 0.850 -2.230 1.299 3 A_U19:A48_B A 19 ? B 48 ? 20 1 1 A C 15 1_555 B G 5 1_555 0.182 -0.142 -0.309 7.129 -3.528 0.346 4 A_C21:G47_B A 21 ? B 47 ? 19 1 1 A C 16 1_555 B G 4 1_555 0.156 -0.176 -0.227 -2.380 -3.926 1.890 5 A_C22:G46_B A 22 ? B 46 ? 19 1 1 A G 18 1_555 A C 9 1_555 -0.193 -0.099 -0.439 -1.972 7.179 1.657 6 A_G24:C15_A A 24 ? A 15 ? 19 1 1 A G 19 1_555 A A 8 1_555 6.415 -4.514 1.059 26.148 17.292 -0.470 7 A_G25:A14_A A 25 ? A 14 ? 11 9 1 A C 20 1_555 A A 7 1_555 -7.034 -4.795 -0.347 -4.966 -21.272 2.629 8 A_C26:A13_A A 26 ? A 13 ? ? 6 1 A G 21 1_555 A C 6 1_555 -0.389 -0.176 0.068 -10.120 -17.361 -1.598 9 A_G27:C12_A A 27 ? A 12 ? 19 1 1 A U 22 1_555 A A 5 1_555 0.051 -0.265 0.463 -6.338 -10.789 4.368 10 A_U28:A11_A A 28 ? A 11 ? 20 1 1 A G 23 1_555 A CBV 4 1_555 -0.243 -0.291 0.191 -2.294 -8.101 0.348 11 A_G29:CBV10_A A 29 ? A 10 ? 19 1 1 A A 24 1_555 A U 3 1_555 -0.135 -0.174 -0.057 1.723 -6.430 4.271 12 A_A30:U9_A A 30 ? A 9 ? 20 1 1 A C 25 1_555 A G 2 1_555 0.209 -0.294 0.138 5.627 -6.861 -1.044 13 A_C31:G8_A A 31 ? A 8 ? 19 1 1 A C 26 1_555 A G 1 1_555 0.214 -0.210 0.036 5.071 -7.845 0.260 14 A_C32:G7_A A 32 ? A 7 ? 19 1 1 C G 1 1_555 C C 26 1_555 -0.268 -0.096 0.254 2.524 -2.792 3.361 15 C_G7:C32_C C 7 ? C 32 ? 19 1 1 C G 2 1_555 C C 25 1_555 -0.263 -0.152 0.373 0.847 -10.782 0.720 16 C_G8:C31_C C 8 ? C 31 ? 19 1 1 C U 3 1_555 C A 24 1_555 0.185 -0.100 0.346 -4.431 -8.353 4.923 17 C_U9:A30_C C 9 ? C 30 ? 20 1 1 C CBV 4 1_555 C G 23 1_555 -0.125 -0.113 0.043 3.418 -6.006 -0.953 18 C_CBV10:G29_C C 10 ? C 29 ? 19 1 1 C A 5 1_555 C U 22 1_555 0.028 -0.098 -0.040 1.664 1.292 3.904 19 C_A11:U28_C C 11 ? C 28 ? 20 1 1 C C 6 1_555 C G 21 1_555 0.269 -0.234 0.157 4.853 -5.142 2.768 20 C_C12:G27_C C 12 ? C 27 ? 19 1 1 C A 7 1_555 C C 20 1_555 6.720 -5.022 -0.009 2.074 -19.790 3.022 21 C_A13:C26_C C 13 ? C 26 ? ? 10 1 C A 8 1_555 D A 1 1_555 1.211 1.803 -0.343 33.376 40.088 -160.302 22 C_A14:A43_D C 14 ? D 43 ? 1 2 1 C C 9 1_555 C G 18 1_555 0.176 -0.185 -0.413 2.527 9.099 -0.729 23 C_C15:G24_C C 15 ? C 24 ? 19 1 1 D G 4 1_555 C C 16 1_555 -0.287 -0.176 0.049 4.001 -2.642 1.396 24 D_G46:C22_C D 46 ? C 22 ? 19 1 1 D G 5 1_555 C C 15 1_555 -0.187 -0.189 -0.152 -8.660 -5.047 1.376 25 D_G47:C21_C D 47 ? C 21 ? 19 1 1 D A 6 1_555 C U 13 1_555 0.035 -0.055 -0.234 -11.085 -1.811 -3.623 26 D_A48:U19_C D 48 ? C 19 ? 20 1 1 D G 7 1_555 C C 12 1_555 -0.285 -0.215 0.270 -0.318 -11.746 2.008 27 D_G49:C18_C D 49 ? C 18 ? 19 1 1 D C 8 1_555 C G 11 1_555 0.139 -0.233 0.260 -0.510 -18.718 -0.052 28 D_C50:G17_C D 50 ? C 17 ? 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 G 11 1_555 B C 8 1_555 A C 12 1_555 B G 7 1_555 0.543 -1.560 3.503 -0.168 15.940 33.960 -4.472 -0.868 2.542 25.614 0.269 37.415 1 AA_G17C18:G49C50_BB A 17 ? B 50 ? A 18 ? B 49 ? 1 A C 12 1_555 B G 7 1_555 A U 13 1_555 B A 6 1_555 -1.153 -1.175 3.033 0.912 19.612 31.525 -4.041 1.918 1.961 32.460 -1.510 37.006 2 AA_C18U19:A48G49_BB A 18 ? B 49 ? A 19 ? B 48 ? 1 A U 13 1_555 B A 6 1_555 A C 15 1_555 B G 5 1_555 -1.983 -0.520 2.994 1.141 7.827 53.908 -0.996 2.230 2.860 8.581 -1.251 54.443 3 AA_U19C21:G47A48_BB A 19 ? B 48 ? A 21 ? B 47 ? 1 A C 15 1_555 B G 5 1_555 A C 16 1_555 B G 4 1_555 0.152 -2.469 3.400 1.106 6.689 34.239 -5.102 -0.091 2.885 11.225 -1.855 34.884 4 AA_C21C22:G46G47_BB A 21 ? B 47 ? A 22 ? B 46 ? 1 A C 16 1_555 B G 4 1_555 A G 18 1_555 A C 9 1_555 1.557 -2.855 6.471 4.584 8.529 61.862 -3.501 -1.096 6.160 8.243 -4.430 62.541 5 AA_C22G24:C15G46_AB A 22 ? B 46 ? A 24 ? A 15 ? 1 A G 18 1_555 A C 9 1_555 A G 19 1_555 A A 8 1_555 -0.418 -0.752 2.614 -3.074 16.221 56.285 -1.428 0.303 2.353 16.798 3.184 58.466 6 AA_G24G25:A14C15_AA A 24 ? A 15 ? A 25 ? A 14 ? 1 A G 19 1_555 A A 8 1_555 A C 20 1_555 A A 7 1_555 -0.285 -1.847 3.879 1.923 -0.931 -12.237 9.859 1.416 3.728 4.324 8.930 -12.421 7 AA_G25C26:A13A14_AA A 25 ? A 14 ? A 26 ? A 13 ? 1 A C 20 1_555 A A 7 1_555 A G 21 1_555 A C 6 1_555 0.391 -0.457 3.841 -2.209 1.415 63.484 -0.507 -0.485 3.817 1.345 2.098 63.533 8 AA_C26G27:C12A13_AA A 26 ? A 13 ? A 27 ? A 12 ? 1 A G 21 1_555 A C 6 1_555 A U 22 1_555 A A 5 1_555 0.349 -1.145 3.208 -0.545 1.638 33.930 -2.215 -0.681 3.145 2.805 0.934 33.973 9 AA_G27U28:A11C12_AA A 27 ? A 12 ? A 28 ? A 11 ? 1 A U 22 1_555 A A 5 1_555 A G 23 1_555 A CBV 4 1_555 0.142 -2.048 2.971 3.089 4.525 25.605 -5.574 0.406 2.576 10.063 -6.871 26.175 10 AA_U28G29:CBV10A11_AA A 28 ? A 11 ? A 29 ? A 10 ? 1 A G 23 1_555 A CBV 4 1_555 A A 24 1_555 A U 3 1_555 -0.284 -1.786 3.176 -0.584 -0.452 31.480 -3.208 0.417 3.206 -0.833 1.076 31.489 11 AA_G29A30:U9CBV10_AA A 29 ? A 10 ? A 30 ? A 9 ? 1 A A 24 1_555 A U 3 1_555 A C 25 1_555 A G 2 1_555 -0.741 -1.419 3.146 -4.179 2.627 32.057 -2.985 0.621 3.092 4.721 7.512 32.424 12 AA_A30C31:G8U9_AA A 30 ? A 9 ? A 31 ? A 8 ? 1 A C 25 1_555 A G 2 1_555 A C 26 1_555 A G 1 1_555 0.032 -1.960 3.223 -0.748 2.131 31.808 -3.943 -0.190 3.087 3.883 1.363 31.886 13 AA_C31C32:G7G8_AA A 31 ? A 8 ? A 32 ? A 7 ? 1 A C 26 1_555 A G 1 1_555 C G 1 1_555 C C 26 1_555 0.231 -3.928 3.188 -4.319 3.959 -8.797 13.124 -7.696 4.218 -22.780 -24.853 -10.566 14 AC_C32G7:C32G7_CA A 32 ? A 7 ? C 7 ? C 32 ? 1 C G 1 1_555 C C 26 1_555 C G 2 1_555 C C 25 1_555 0.007 -2.207 3.172 -2.283 3.642 32.048 -4.564 -0.390 2.903 6.559 4.112 32.327 15 CC_G7G8:C31C32_CC C 7 ? C 32 ? C 8 ? C 31 ? 1 C G 2 1_555 C C 25 1_555 C U 3 1_555 C A 24 1_555 0.074 -1.575 3.354 -0.023 4.331 33.731 -3.382 -0.130 3.133 7.426 0.040 34.000 16 CC_G8U9:A30C31_CC C 8 ? C 31 ? C 9 ? C 30 ? 1 C U 3 1_555 C A 24 1_555 C CBV 4 1_555 C G 23 1_555 -0.253 -1.809 2.996 3.661 4.160 30.214 -4.131 1.107 2.680 7.897 -6.949 30.706 17 CC_U9CBV10:G29A30_CC C 9 ? C 30 ? C 10 ? C 29 ? 1 C CBV 4 1_555 C G 23 1_555 C A 5 1_555 C U 22 1_555 0.536 -1.743 3.207 2.180 8.256 27.916 -5.103 -0.630 2.628 16.627 -4.391 29.168 18 CC_CBV10A11:U28G29_CC C 10 ? C 29 ? C 11 ? C 28 ? 1 C A 5 1_555 C U 22 1_555 C C 6 1_555 C G 21 1_555 1.043 -2.408 3.030 0.175 6.155 28.031 -6.038 -2.072 2.462 12.516 -0.356 28.686 19 CC_A11C12:G27U28_CC C 11 ? C 28 ? C 12 ? C 27 ? 1 C C 6 1_555 C G 21 1_555 C A 7 1_555 C C 20 1_555 -0.717 -0.495 3.547 4.535 4.472 61.462 -0.705 0.924 3.452 4.363 -4.424 61.759 20 CC_C12A13:C26G27_CC C 12 ? C 27 ? C 13 ? C 26 ? 1 C A 7 1_555 C C 20 1_555 C A 8 1_555 D A 1 1_555 -5.010 -1.918 5.046 -6.371 -14.743 67.631 -0.792 4.019 5.705 -13.058 5.643 69.291 21 CC_A13A14:A43C26_DC C 13 ? C 26 ? C 14 ? D 43 ? 1 C A 8 1_555 D A 1 1_555 C C 9 1_555 C G 18 1_555 4.106 -2.043 1.859 21.391 19.561 -26.685 2.207 7.037 0.080 -32.555 35.601 -39.205 22 CC_A14C15:G24A43_CD C 14 ? D 43 ? C 15 ? C 24 ? 1 C C 9 1_555 C G 18 1_555 D G 4 1_555 C C 16 1_555 -0.756 -2.723 6.429 -5.136 6.963 62.250 -3.218 0.279 6.164 6.701 4.943 62.789 23 CD_C15G46:C22G24_CC C 15 ? C 24 ? D 46 ? C 22 ? 1 D G 4 1_555 C C 16 1_555 D G 5 1_555 C C 15 1_555 -0.021 -2.535 3.429 0.619 4.791 36.295 -4.695 0.118 3.080 7.649 -0.988 36.604 24 DD_G46G47:C21C22_CC D 46 ? C 22 ? D 47 ? C 21 ? 1 D G 5 1_555 C C 15 1_555 D A 6 1_555 C U 13 1_555 1.912 -0.600 3.191 3.700 9.997 52.805 -1.273 -1.888 3.155 11.112 -4.113 53.794 25 DD_G47A48:U19C21_CC D 47 ? C 21 ? D 48 ? C 19 ? 1 D A 6 1_555 C U 13 1_555 D G 7 1_555 C C 12 1_555 0.815 -1.591 3.022 -2.063 11.370 28.803 -4.793 -1.854 2.189 21.782 3.953 30.989 26 DD_A48G49:C18U19_CC D 48 ? C 19 ? D 49 ? C 18 ? 1 D G 7 1_555 C C 12 1_555 D C 8 1_555 C G 11 1_555 0.746 -1.474 3.117 7.392 1.438 38.130 -2.386 -0.251 3.146 2.175 -11.182 38.840 27 DD_G49C50:G17C18_CC D 49 ? C 18 ? D 50 ? C 17 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Cancer Research UK' 'United Kingdom' A18604 1 'Ministry of Education (MoE, China)' China ? 2 # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 DSH ? ? DSH ? ? 'SUBJECT OF INVESTIGATION' ? 2 AMP ? ? AMP ? ? 'SUBJECT OF INVESTIGATION' ? # _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 6YL5 _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'P 3 1 2' _space_group.name_Hall 'P 3 2' _space_group.IT_number 149 _space_group.crystal_system trigonal _space_group.id 1 # _atom_sites.entry_id 6YML _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] 0.011599 _atom_sites.fract_transf_matrix[1][2] 0.006696 _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] 0.013393 _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] 0.013263 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source BR ? ? 25.79822 9.11301 ? ? 1.35700 25.34896 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? H ? ? 0.51345 0.48472 ? ? 24.73122 6.32584 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? S ? ? 9.55732 6.39887 ? ? 1.23737 29.19336 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_