data_5AY4 # _entry.id 5AY4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 5AY4 pdb_00005ay4 10.2210/pdb5ay4/pdb WWPDB D_1300000160 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 5AY2 PDB . unspecified 5AY3 PDB . # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5AY4 _pdbx_database_status.recvd_initial_deposition_date 2015-08-06 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 'Kondo, J.' 1 'Tada, Y.' 2 'Dairaku, T.' 3 'Saneyoshi, H.' 4 'Okamoto, I.' 5 'Tanaka, Y.' 6 'Ono, A.' 7 # _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 GE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_id_ASTM ACIEAY _citation.journal_id_CSD 0179 _citation.journal_id_ISSN 1521-3773 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 54 _citation.language ? _citation.page_first 13323 _citation.page_last 13326 _citation.title 'High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs' _citation.year 2015 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/anie.201507894 _citation.pdbx_database_id_PubMed 26448329 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Tada, Y.' 2 ? primary 'Dairaku, T.' 3 ? primary 'Saneyoshi, H.' 4 ? primary 'Okamoto, I.' 5 ? primary 'Tanaka, Y.' 6 ? primary 'Ono, A.' 7 ? # _cell.length_a 27.000 _cell.length_b 44.540 _cell.length_c 27.550 _cell.angle_alpha 90.000 _cell.angle_beta 109.100 _cell.angle_gamma 90.000 _cell.entry_id 5AY4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.entry_id 5AY4 _symmetry.Int_Tables_number 4 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? # 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(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3') ; 3850.208 2 ? ? ? ? 2 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 3 water nat water 18.015 158 ? ? ? ? # _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 'GGACU(CBR)GACUCC' _entity_poly.pdbx_seq_one_letter_code_can GGACUCGACUCC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 A n 1 4 C n 1 5 U n 1 6 CBR n 1 7 G n 1 8 A n 1 9 C n 1 10 U n 1 11 C n 1 12 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 12 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5AY4 _struct_ref.pdbx_db_accession 5AY4 _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 5AY4 A 1 ? 12 ? 5AY4 1 ? 12 ? 1 12 2 1 5AY4 B 1 ? 12 ? 5AY4 1 ? 12 ? 1 12 # 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 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _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 5AY4 _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 2.08 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 40.73 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'MPD, Spermine, Sodium Nitrate, MOPS' _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_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-12-09 # _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 0.98 _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 'PHOTON FACTORY BEAMLINE BL-17A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.98 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.d_resolution_high 1.700 _reflns.pdbx_number_measured_all 45309 _reflns.number_obs 6831 _reflns.pdbx_Rmerge_I_obs 0.088 _reflns.pdbx_netI_over_sigmaI 13.380 _reflns.pdbx_chi_squared 0.939 _reflns.percent_possible_obs 99.500 _reflns.Rmerge_F_obs 0.997 _reflns.observed_criterion_sigma_I -3.000 _reflns.pdbx_Rrim_I_all 0.096 _reflns.B_iso_Wilson_estimate 23.161 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 5AY4 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 26.000 _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy ? _reflns.pdbx_CC_half ? _reflns.pdbx_Rpim_I_all ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_CC_half 1 1 1.700 1.750 3067 ? 490 0 0.323 5.580 ? ? ? ? ? 507 ? ? 0.955 ? ? 96.600 0.353 ? ? 1 2 1.750 1.790 3142 ? 478 0 0.317 5.910 ? ? ? ? ? 481 ? ? 0.957 ? ? 99.400 0.345 ? ? 1 3 1.790 1.850 3245 ? 486 0 0.290 6.340 ? ? ? ? ? 482 ? ? 0.959 ? ? 100.000 0.314 ? ? 1 4 1.850 1.900 2870 ? 451 0 0.232 7.390 ? ? ? ? ? 454 ? ? 0.974 ? ? 99.300 0.253 ? ? 1 5 1.900 1.960 3101 ? 457 0 0.212 8.240 ? ? ? ? ? 457 ? ? 0.981 ? ? 100.000 0.230 ? ? 1 6 1.960 2.030 2923 ? 435 0 0.181 9.800 ? ? ? ? ? 438 ? ? 0.981 ? ? 99.300 0.196 ? ? 1 7 2.030 2.110 2825 ? 429 0 0.169 10.460 ? ? ? ? ? 430 ? ? 0.984 ? ? 99.800 0.184 ? ? 1 8 2.110 2.200 2643 ? 391 0 0.142 11.440 ? ? ? ? ? 391 ? ? 0.990 ? ? 100.000 0.154 ? ? 1 9 2.200 2.290 2706 ? 400 0 0.131 12.480 ? ? ? ? ? 404 ? ? 0.990 ? ? 99.000 0.142 ? ? 1 10 2.290 2.410 2325 ? 353 0 0.109 14.480 ? ? ? ? ? 352 ? ? 0.991 ? ? 100.000 0.119 ? ? 1 11 2.410 2.540 2529 ? 360 0 0.102 15.700 ? ? ? ? ? 360 ? ? 0.992 ? ? 100.000 0.110 ? ? 1 12 2.540 2.690 2342 ? 337 0 0.092 17.110 ? ? ? ? ? 339 ? ? 0.996 ? ? 99.400 0.100 ? ? 1 13 2.690 2.880 2034 ? 319 0 0.086 18.390 ? ? ? ? ? 316 ? ? 0.993 ? ? 100.000 0.095 ? ? 1 14 2.880 3.110 2007 ? 294 0 0.064 21.770 ? ? ? ? ? 300 ? ? 0.998 ? ? 98.000 0.070 ? ? 1 15 3.110 3.400 1804 ? 274 0 0.062 23.290 ? ? ? ? ? 275 ? ? 0.999 ? ? 99.600 0.067 ? ? 1 16 3.400 3.800 1638 ? 240 0 0.061 24.680 ? ? ? ? ? 240 ? ? 0.997 ? ? 100.000 0.066 ? ? 1 17 3.800 4.390 1407 ? 218 0 0.058 25.870 ? ? ? ? ? 219 ? ? 0.998 ? ? 99.500 0.063 ? ? 1 18 4.390 5.380 1252 ? 187 0 0.066 26.160 ? ? ? ? ? 189 ? ? 0.996 ? ? 98.900 0.072 ? ? 1 19 5.380 7.610 966 ? 149 0 0.064 24.530 ? ? ? ? ? 150 ? ? 0.996 ? ? 99.300 0.069 ? ? 1 20 7.610 ? 483 ? 81 0 0.052 26.040 ? ? ? ? ? 82 ? ? 0.995 ? ? 98.800 0.056 ? ? # _refine.entry_id 5AY4 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 1.7000 _refine.ls_d_res_low 26.000 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.6000 _refine.ls_number_reflns_obs 6831 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.1601 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.1956 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 10.9000 _refine.ls_number_reflns_R_free 745 _refine.ls_number_reflns_R_work 6086 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 18.9720 _refine.solvent_model_param_bsol 36.2882 _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.2080 _refine.aniso_B[2][2] -1.8310 _refine.aniso_B[3][3] 0.6220 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -2.4850 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _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.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.solvent_model_details ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 5AY3 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.8766 _refine.B_iso_max 58.960 _refine.B_iso_min 9.200 _refine.pdbx_overall_phase_error ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_R_factor_R_free_error_details ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.7000 _refine_hist.d_res_low 26.000 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 158 _refine_hist.number_atoms_total 659 _refine_hist.pdbx_number_residues_total 24 _refine_hist.pdbx_B_iso_mean_ligand 22.38 _refine_hist.pdbx_B_iso_mean_solvent 31.88 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 500 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' c_bond_d ? 0.003 ? ? ? 'X-RAY DIFFRACTION' c_angle_d ? 0.839 ? ? ? 'X-RAY DIFFRACTION' c_mcbond_it ? 0.000 1.500 ? ? 'X-RAY DIFFRACTION' c_scbond_it ? 1.393 2.000 ? ? 'X-RAY DIFFRACTION' c_mcangle_it ? 0.000 2.000 ? ? 'X-RAY DIFFRACTION' c_scangle_it ? 1.838 2.500 ? ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.R_factor_obs 1.7000 1.7600 10 96.3000 584 . 0.1950 0.2062 . 70 . 654 . 'X-RAY DIFFRACTION' . 1.7600 1.8300 10 100.0000 607 . 0.2094 0.2388 . 61 . 668 . 'X-RAY DIFFRACTION' . 1.8300 1.9100 10 100.0000 601 . 0.2036 0.2662 . 85 . 686 . 'X-RAY DIFFRACTION' . 1.9100 2.0200 10 100.0000 609 . 0.2041 0.2653 . 77 . 686 . 'X-RAY DIFFRACTION' . 2.0200 2.1400 10 100.0000 594 . 0.1843 0.1992 . 81 . 675 . 'X-RAY DIFFRACTION' . 2.1400 2.3100 10 100.0000 615 . 0.1766 0.2374 . 71 . 686 . 'X-RAY DIFFRACTION' . 2.3100 2.5400 10 100.0000 612 . 0.1678 0.2001 . 73 . 685 . 'X-RAY DIFFRACTION' . 2.5400 2.9100 10 100.0000 620 . 0.1532 0.1889 . 74 . 694 . 'X-RAY DIFFRACTION' . 2.9100 3.6600 10 99.9000 607 . 0.1389 0.1732 . 78 . 685 . 'X-RAY DIFFRACTION' . 3.6600 26.000 10 99.9000 637 . 0.1263 0.1464 . 75 . 712 . 'X-RAY DIFFRACTION' . # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 bru.param ? 'X-RAY DIFFRACTION' 2 dna-rna_free.param ? 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:water_rep.param ? 'X-RAY DIFFRACTION' 4 CNS_TOPPAR:ion.param ? # _struct.entry_id 5AY4 _struct.title 'Crystal structure of RNA duplex containing C-C base pairs obtained in the presence of Hg(II)' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5AY4 _struct_keywords.text 'RNA, X-Ray analysis, metallo base pair, Ag(I), Hg(II)' _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 3 ? E N N 3 ? # 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 5 "O3'" ? ? ? 1_555 A CBR 6 P ? ? A U 5 A CBR 6 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale2 covale both ? A CBR 6 "O3'" ? ? ? 1_555 A G 7 P ? ? A CBR 6 A G 7 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale3 covale both ? B U 5 "O3'" ? ? ? 1_555 B CBR 6 P ? ? B U 5 B CBR 6 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale4 covale both ? B CBR 6 "O3'" ? ? ? 1_555 B G 7 P ? ? B CBR 6 B G 7 1_555 ? ? ? ? ? ? ? 1.601 ? ? metalc1 metalc ? ? B C 4 O2 ? ? ? 1_555 C NA . NA ? ? B C 4 B NA 101 2_556 ? ? ? ? ? ? ? 2.605 ? ? metalc2 metalc ? ? B C 12 "O3'" ? ? ? 1_555 C NA . NA ? ? B C 12 B NA 101 1_555 ? ? ? ? ? ? ? 2.620 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 2 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 2 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 2 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 10 N3 ? ? A A 3 B U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 10 O4 ? ? A A 3 B U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 B C 9 N4 ? ? A C 4 B C 9 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog10 hydrog ? ? A U 5 N3 ? ? ? 1_555 B A 8 N1 ? ? A U 5 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 5 O4 ? ? ? 1_555 B A 8 N6 ? ? A U 5 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A CBR 6 N3 ? ? ? 1_555 B G 7 N1 ? ? A CBR 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A CBR 6 N4 ? ? ? 1_555 B G 7 O6 ? ? A CBR 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A CBR 6 O2 ? ? ? 1_555 B G 7 N2 ? ? A CBR 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 B CBR 6 N3 ? ? A G 7 B CBR 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N2 ? ? ? 1_555 B CBR 6 O2 ? ? A G 7 B CBR 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 O6 ? ? ? 1_555 B CBR 6 N4 ? ? A G 7 B CBR 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N1 ? ? ? 1_555 B U 5 N3 ? ? A A 8 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 8 N6 ? ? ? 1_555 B U 5 O4 ? ? A A 8 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 N4 ? ? ? 1_555 B C 4 N3 ? ? A C 9 B C 4 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog21 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 10 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 10 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? 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 B NA 101 ? 1 'binding site for residue NA B 101' AC2 Software B CBR 6 ? 19 'binding site for Di-nucleotide CBR B 6 and G B 7' # 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 1 C B 12 ? C B 12 . ? 1_555 ? 2 AC2 19 CBR A 6 ? CBR A 6 . ? 1_555 ? 3 AC2 19 G A 7 ? G A 7 . ? 1_555 ? 4 AC2 19 A A 8 ? A A 8 . ? 1_555 ? 5 AC2 19 C A 12 ? C A 12 . ? 1_554 ? 6 AC2 19 HOH D . ? HOH A 149 . ? 1_554 ? 7 AC2 19 U B 5 ? U B 5 . ? 1_555 ? 8 AC2 19 A B 8 ? A B 8 . ? 1_555 ? 9 AC2 19 HOH E . ? HOH B 203 . ? 1_555 ? 10 AC2 19 HOH E . ? HOH B 208 . ? 1_555 ? 11 AC2 19 HOH E . ? HOH B 212 . ? 1_555 ? 12 AC2 19 HOH E . ? HOH B 220 . ? 1_555 ? 13 AC2 19 HOH E . ? HOH B 226 . ? 1_555 ? 14 AC2 19 HOH E . ? HOH B 227 . ? 1_555 ? 15 AC2 19 HOH E . ? HOH B 228 . ? 1_555 ? 16 AC2 19 HOH E . ? HOH B 233 . ? 1_555 ? 17 AC2 19 HOH E . ? HOH B 238 . ? 1_555 ? 18 AC2 19 HOH E . ? HOH B 243 . ? 1_555 ? 19 AC2 19 HOH E . ? HOH B 257 . ? 1_555 ? 20 AC2 19 HOH E . ? HOH B 261 . ? 1_555 ? # _atom_sites.entry_id 5AY4 _atom_sites.fract_transf_matrix[1][1] 0.037037 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.012825 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022452 _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] 0.038412 _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 BR C N NA O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 U 5 5 5 U U A . n A 1 6 CBR 6 6 6 CBR CBR A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 C 9 9 9 C C A . n A 1 10 U 10 10 10 U U A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 G 2 2 2 G G B . n B 1 3 A 3 3 3 A A B . n B 1 4 C 4 4 4 C C B . n B 1 5 U 5 5 5 U U B . n B 1 6 CBR 6 6 6 CBR CBR B . n B 1 7 G 7 7 7 G G B . n B 1 8 A 8 8 8 A A B . n B 1 9 C 9 9 9 C C B . n B 1 10 U 10 10 10 U U B . n B 1 11 C 11 11 11 C C B . n B 1 12 C 12 12 12 C C 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 NA 1 101 101 NA NA B . D 3 HOH 1 101 196 HOH HOH A . D 3 HOH 2 102 191 HOH HOH A . D 3 HOH 3 103 107 HOH HOH A . D 3 HOH 4 104 219 HOH HOH A . D 3 HOH 5 105 241 HOH HOH A . D 3 HOH 6 106 237 HOH HOH A . D 3 HOH 7 107 180 HOH HOH A . D 3 HOH 8 108 142 HOH HOH A . D 3 HOH 9 109 204 HOH HOH A . D 3 HOH 10 110 157 HOH HOH A . D 3 HOH 11 111 114 HOH HOH A . D 3 HOH 12 112 176 HOH HOH A . D 3 HOH 13 113 233 HOH HOH A . D 3 HOH 14 114 154 HOH HOH A . D 3 HOH 15 115 125 HOH HOH A . D 3 HOH 16 116 126 HOH HOH A . D 3 HOH 17 117 257 HOH HOH A . D 3 HOH 18 118 251 HOH HOH A . D 3 HOH 19 119 103 HOH HOH A . D 3 HOH 20 120 217 HOH HOH A . D 3 HOH 21 121 236 HOH HOH A . D 3 HOH 22 122 129 HOH HOH A . D 3 HOH 23 123 117 HOH HOH A . D 3 HOH 24 124 194 HOH HOH A . D 3 HOH 25 125 153 HOH HOH A . D 3 HOH 26 126 141 HOH HOH A . D 3 HOH 27 127 148 HOH HOH A . D 3 HOH 28 128 189 HOH HOH A . D 3 HOH 29 129 128 HOH HOH A . D 3 HOH 30 130 122 HOH HOH A . D 3 HOH 31 131 256 HOH HOH A . D 3 HOH 32 132 112 HOH HOH A . D 3 HOH 33 133 116 HOH HOH A . D 3 HOH 34 134 160 HOH HOH A . D 3 HOH 35 135 118 HOH HOH A . D 3 HOH 36 136 171 HOH HOH A . D 3 HOH 37 137 179 HOH HOH A . D 3 HOH 38 138 138 HOH HOH A . D 3 HOH 39 139 199 HOH HOH A . D 3 HOH 40 140 174 HOH HOH A . D 3 HOH 41 141 115 HOH HOH A . D 3 HOH 42 142 259 HOH HOH A . D 3 HOH 43 143 109 HOH HOH A . D 3 HOH 44 144 152 HOH HOH A . D 3 HOH 45 145 136 HOH HOH A . D 3 HOH 46 146 149 HOH HOH A . D 3 HOH 47 147 175 HOH HOH A . D 3 HOH 48 148 159 HOH HOH A . D 3 HOH 49 149 161 HOH HOH A . D 3 HOH 50 150 167 HOH HOH A . D 3 HOH 51 151 187 HOH HOH A . D 3 HOH 52 152 144 HOH HOH A . D 3 HOH 53 153 132 HOH HOH A . D 3 HOH 54 154 108 HOH HOH A . D 3 HOH 55 155 183 HOH HOH A . D 3 HOH 56 156 216 HOH HOH A . D 3 HOH 57 157 188 HOH HOH A . D 3 HOH 58 158 124 HOH HOH A . D 3 HOH 59 159 235 HOH HOH A . D 3 HOH 60 160 208 HOH HOH A . D 3 HOH 61 161 177 HOH HOH A . D 3 HOH 62 162 223 HOH HOH A . D 3 HOH 63 163 145 HOH HOH A . D 3 HOH 64 164 252 HOH HOH A . D 3 HOH 65 165 210 HOH HOH A . D 3 HOH 66 166 231 HOH HOH A . D 3 HOH 67 167 212 HOH HOH A . D 3 HOH 68 168 203 HOH HOH A . D 3 HOH 69 169 222 HOH HOH A . D 3 HOH 70 170 248 HOH HOH A . D 3 HOH 71 171 186 HOH HOH A . D 3 HOH 72 172 173 HOH HOH A . D 3 HOH 73 173 249 HOH HOH A . D 3 HOH 74 174 250 HOH HOH A . D 3 HOH 75 175 207 HOH HOH A . D 3 HOH 76 176 240 HOH HOH A . D 3 HOH 77 177 205 HOH HOH A . D 3 HOH 78 178 242 HOH HOH A . D 3 HOH 79 179 220 HOH HOH A . D 3 HOH 80 180 209 HOH HOH A . D 3 HOH 81 181 234 HOH HOH A . E 3 HOH 1 201 130 HOH HOH B . E 3 HOH 2 202 206 HOH HOH B . E 3 HOH 3 203 163 HOH HOH B . E 3 HOH 4 204 226 HOH HOH B . E 3 HOH 5 205 192 HOH HOH B . E 3 HOH 6 206 131 HOH HOH B . E 3 HOH 7 207 243 HOH HOH B . E 3 HOH 8 208 258 HOH HOH B . E 3 HOH 9 209 164 HOH HOH B . E 3 HOH 10 210 168 HOH HOH B . E 3 HOH 11 211 147 HOH HOH B . E 3 HOH 12 212 113 HOH HOH B . E 3 HOH 13 213 211 HOH HOH B . E 3 HOH 14 214 155 HOH HOH B . E 3 HOH 15 215 127 HOH HOH B . E 3 HOH 16 216 184 HOH HOH B . E 3 HOH 17 217 111 HOH HOH B . E 3 HOH 18 218 182 HOH HOH B . E 3 HOH 19 219 165 HOH HOH B . E 3 HOH 20 220 104 HOH HOH B . E 3 HOH 21 221 135 HOH HOH B . E 3 HOH 22 222 181 HOH HOH B . E 3 HOH 23 223 140 HOH HOH B . E 3 HOH 24 224 230 HOH HOH B . E 3 HOH 25 225 150 HOH HOH B . E 3 HOH 26 226 238 HOH HOH B . E 3 HOH 27 227 102 HOH HOH B . E 3 HOH 28 228 162 HOH HOH B . E 3 HOH 29 229 214 HOH HOH B . E 3 HOH 30 230 246 HOH HOH B . E 3 HOH 31 231 228 HOH HOH B . E 3 HOH 32 232 134 HOH HOH B . E 3 HOH 33 233 133 HOH HOH B . E 3 HOH 34 234 146 HOH HOH B . E 3 HOH 35 235 195 HOH HOH B . E 3 HOH 36 236 200 HOH HOH B . E 3 HOH 37 237 106 HOH HOH B . E 3 HOH 38 238 121 HOH HOH B . E 3 HOH 39 239 166 HOH HOH B . E 3 HOH 40 240 120 HOH HOH B . E 3 HOH 41 241 253 HOH HOH B . E 3 HOH 42 242 119 HOH HOH B . E 3 HOH 43 243 178 HOH HOH B . E 3 HOH 44 244 139 HOH HOH B . E 3 HOH 45 245 123 HOH HOH B . E 3 HOH 46 246 156 HOH HOH B . E 3 HOH 47 247 143 HOH HOH B . E 3 HOH 48 248 110 HOH HOH B . E 3 HOH 49 249 151 HOH HOH B . E 3 HOH 50 250 227 HOH HOH B . E 3 HOH 51 251 137 HOH HOH B . E 3 HOH 52 252 198 HOH HOH B . E 3 HOH 53 253 105 HOH HOH B . E 3 HOH 54 254 170 HOH HOH B . E 3 HOH 55 255 232 HOH HOH B . E 3 HOH 56 256 213 HOH HOH B . E 3 HOH 57 257 172 HOH HOH B . E 3 HOH 58 258 202 HOH HOH B . E 3 HOH 59 259 158 HOH HOH B . E 3 HOH 60 260 244 HOH HOH B . E 3 HOH 61 261 169 HOH HOH B . E 3 HOH 62 262 190 HOH HOH B . E 3 HOH 63 263 229 HOH HOH B . E 3 HOH 64 264 197 HOH HOH B . E 3 HOH 65 265 225 HOH HOH B . E 3 HOH 66 266 193 HOH HOH B . E 3 HOH 67 267 239 HOH HOH B . E 3 HOH 68 268 201 HOH HOH B . E 3 HOH 69 269 215 HOH HOH B . E 3 HOH 70 270 224 HOH HOH B . E 3 HOH 71 271 245 HOH HOH B . E 3 HOH 72 272 247 HOH HOH B . E 3 HOH 73 273 221 HOH HOH B . E 3 HOH 74 274 255 HOH HOH B . E 3 HOH 75 275 218 HOH HOH B . E 3 HOH 76 276 185 HOH HOH B . E 3 HOH 77 277 254 HOH HOH B . # _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 # _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 # 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)' 2420 ? 1 MORE -10 ? 1 'SSA (A^2)' 4200 ? # _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 # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id O2 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id B _pdbx_struct_conn_angle.ptnr1_label_comp_id C _pdbx_struct_conn_angle.ptnr1_label_seq_id 4 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id B _pdbx_struct_conn_angle.ptnr1_auth_comp_id C _pdbx_struct_conn_angle.ptnr1_auth_seq_id 4 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id NA _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id C _pdbx_struct_conn_angle.ptnr2_label_comp_id NA _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id B _pdbx_struct_conn_angle.ptnr2_auth_comp_id NA _pdbx_struct_conn_angle.ptnr2_auth_seq_id 101 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 2_556 _pdbx_struct_conn_angle.ptnr3_label_atom_id "O3'" _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id B _pdbx_struct_conn_angle.ptnr3_label_comp_id C _pdbx_struct_conn_angle.ptnr3_label_seq_id 12 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id B _pdbx_struct_conn_angle.ptnr3_auth_comp_id C _pdbx_struct_conn_angle.ptnr3_auth_seq_id 12 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 56.0 _pdbx_struct_conn_angle.value_esd ? # 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 2015-10-21 2 'Structure model' 1 1 2015-11-11 3 'Structure model' 1 2 2017-10-11 4 'Structure model' 1 3 2023-11-08 # _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' 'Derived calculations' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 'Structure model' 'Derived calculations' 8 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' citation 2 3 'Structure model' diffrn_source 3 3 'Structure model' pdbx_struct_oper_list 4 3 'Structure model' reflns_shell 5 4 'Structure model' chem_comp_atom 6 4 'Structure model' chem_comp_bond 7 4 'Structure model' database_2 8 4 'Structure model' pdbx_initial_refinement_model 9 4 'Structure model' pdbx_struct_conn_angle 10 4 'Structure model' struct_conn # 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 3 'Structure model' '_citation.journal_id_CSD' 2 3 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 3 3 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 4 3 'Structure model' '_reflns_shell.percent_possible_all' 5 4 'Structure model' '_database_2.pdbx_DOI' 6 4 'Structure model' '_database_2.pdbx_database_accession' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_symmetry' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.value' 15 4 'Structure model' '_struct_conn.pdbx_dist_value' 16 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 17 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 18 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 19 4 'Structure model' '_struct_conn.ptnr2_symmetry' # 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 ? ? ? ? ? ? ? ? ? ? ? CNS ? ? ? 1.3 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.15 3 # _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 B _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 277 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.35 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # 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 CBR BR BR N N 73 CBR P P N N 74 CBR OP1 O N N 75 CBR OP2 O N N 76 CBR "O5'" O N N 77 CBR N1 N N N 78 CBR C6 C N N 79 CBR C2 C N N 80 CBR O2 O N N 81 CBR N3 N N N 82 CBR C4 C N N 83 CBR N4 N N N 84 CBR C5 C N N 85 CBR "C2'" C N N 86 CBR "C5'" C N N 87 CBR "C4'" C N R 88 CBR "O4'" O N N 89 CBR "C1'" C N R 90 CBR "C3'" C N S 91 CBR "O3'" O N N 92 CBR OP3 O N N 93 CBR HOP2 H N N 94 CBR H6 H N N 95 CBR H41 H N N 96 CBR H42 H N N 97 CBR "H2'" H N N 98 CBR "H2''" H N N 99 CBR "H5'" H N N 100 CBR "H5''" H N N 101 CBR "H4'" H N N 102 CBR "H1'" H N N 103 CBR "H3'" H N N 104 CBR "HO3'" H N N 105 CBR HOP3 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 NA NA NA N N 148 U OP3 O N N 149 U P P N N 150 U OP1 O N N 151 U OP2 O N N 152 U "O5'" O N N 153 U "C5'" C N N 154 U "C4'" C N R 155 U "O4'" O N N 156 U "C3'" C N S 157 U "O3'" O N N 158 U "C2'" C N R 159 U "O2'" O N N 160 U "C1'" C N R 161 U N1 N N N 162 U C2 C N N 163 U O2 O N N 164 U N3 N N N 165 U C4 C N N 166 U O4 O N N 167 U C5 C N N 168 U C6 C N N 169 U HOP3 H N N 170 U HOP2 H N N 171 U "H5'" H N N 172 U "H5''" H N N 173 U "H4'" H N N 174 U "H3'" H N N 175 U "HO3'" H N N 176 U "H2'" H N N 177 U "HO2'" H N N 178 U "H1'" H N N 179 U H3 H N N 180 U H5 H N N 181 U H6 H N N 182 # 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 CBR BR C5 sing N N 76 CBR P OP1 doub N N 77 CBR P OP2 sing N N 78 CBR P "O5'" sing N N 79 CBR P OP3 sing N N 80 CBR OP2 HOP2 sing N N 81 CBR "O5'" "C5'" sing N N 82 CBR N1 C6 sing N N 83 CBR N1 C2 sing N N 84 CBR N1 "C1'" sing N N 85 CBR C6 C5 doub N N 86 CBR C6 H6 sing N N 87 CBR C2 O2 doub N N 88 CBR C2 N3 sing N N 89 CBR N3 C4 doub N N 90 CBR C4 N4 sing N N 91 CBR C4 C5 sing N N 92 CBR N4 H41 sing N N 93 CBR N4 H42 sing N N 94 CBR "C2'" "C1'" sing N N 95 CBR "C2'" "C3'" sing N N 96 CBR "C2'" "H2'" sing N N 97 CBR "C2'" "H2''" sing N N 98 CBR "C5'" "C4'" sing N N 99 CBR "C5'" "H5'" sing N N 100 CBR "C5'" "H5''" sing N N 101 CBR "C4'" "O4'" sing N N 102 CBR "C4'" "C3'" sing N N 103 CBR "C4'" "H4'" sing N N 104 CBR "O4'" "C1'" sing N N 105 CBR "C1'" "H1'" sing N N 106 CBR "C3'" "O3'" sing N N 107 CBR "C3'" "H3'" sing N N 108 CBR "O3'" "HO3'" sing N N 109 CBR OP3 HOP3 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 U OP3 P sing N N 153 U OP3 HOP3 sing N N 154 U P OP1 doub N N 155 U P OP2 sing N N 156 U P "O5'" sing N N 157 U OP2 HOP2 sing N N 158 U "O5'" "C5'" sing N N 159 U "C5'" "C4'" sing N N 160 U "C5'" "H5'" sing N N 161 U "C5'" "H5''" sing N N 162 U "C4'" "O4'" sing N N 163 U "C4'" "C3'" sing N N 164 U "C4'" "H4'" sing N N 165 U "O4'" "C1'" sing N N 166 U "C3'" "O3'" sing N N 167 U "C3'" "C2'" sing N N 168 U "C3'" "H3'" sing N N 169 U "O3'" "HO3'" sing N N 170 U "C2'" "O2'" sing N N 171 U "C2'" "C1'" sing N N 172 U "C2'" "H2'" sing N N 173 U "O2'" "HO2'" sing N N 174 U "C1'" N1 sing N N 175 U "C1'" "H1'" sing N N 176 U N1 C2 sing N N 177 U N1 C6 sing N N 178 U C2 O2 doub N N 179 U C2 N3 sing N N 180 U N3 C4 sing N N 181 U N3 H3 sing N N 182 U C4 O4 doub N N 183 U C4 C5 sing N N 184 U C5 C6 doub N N 185 U C5 H5 sing N N 186 U C6 H6 sing N N 187 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5AY4 'double helix' 5AY4 '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 G 1 1_555 B C 12 1_555 -0.210 -0.114 0.036 -3.924 -4.905 -1.882 1 A_G1:C12_B A 1 ? B 12 ? 19 1 1 A G 2 1_555 B C 11 1_555 -0.174 -0.096 0.055 -4.781 -16.019 5.210 2 A_G2:C11_B A 2 ? B 11 ? 19 1 1 A A 3 1_555 B U 10 1_555 -0.005 -0.049 0.012 0.430 -11.013 -2.968 3 A_A3:U10_B A 3 ? B 10 ? 20 1 1 A C 4 1_555 B C 9 1_555 2.684 -0.957 -0.399 -2.934 -12.947 -13.498 4 A_C4:C9_B A 4 ? B 9 ? ? ? 1 A U 5 1_555 B A 8 1_555 -0.053 -0.091 0.029 8.230 -5.684 3.828 5 A_U5:A8_B A 5 ? B 8 ? 20 1 1 A CBR 6 1_555 B G 7 1_555 0.147 -0.146 -0.144 9.111 -17.430 1.809 6 A_CBR6:G7_B A 6 ? B 7 ? 19 1 1 A G 7 1_555 B CBR 6 1_555 -0.154 -0.160 -0.082 -4.194 -11.302 -0.003 7 A_G7:CBR6_B A 7 ? B 6 ? 19 1 1 A A 8 1_555 B U 5 1_555 0.074 -0.095 0.196 2.685 -11.751 7.744 8 A_A8:U5_B A 8 ? B 5 ? 20 1 1 A C 9 1_555 B C 4 1_555 -2.591 -1.051 -0.186 -2.581 -11.364 -15.953 9 A_C9:C4_B A 9 ? B 4 ? ? ? 1 A U 10 1_555 B A 3 1_555 -0.030 -0.072 -0.090 0.758 -7.667 -3.655 10 A_U10:A3_B A 10 ? B 3 ? 20 1 1 A C 11 1_555 B G 2 1_555 0.180 -0.150 -0.036 3.087 -13.006 3.087 11 A_C11:G2_B A 11 ? B 2 ? 19 1 1 A C 12 1_555 B G 1 1_555 0.214 -0.143 0.062 1.031 -6.718 -1.107 12 A_C12:G1_B A 12 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 12 1_555 A G 2 1_555 B C 11 1_555 0.852 -1.982 3.186 1.199 9.739 32.233 -4.842 -1.296 2.526 17.054 -2.100 33.655 1 AA_G1G2:C11C12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A G 2 1_555 B C 11 1_555 A A 3 1_555 B U 10 1_555 -1.118 -1.360 3.092 -0.737 4.488 34.120 -2.944 1.784 2.918 7.607 1.249 34.413 2 AA_G2A3:U10C11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A A 3 1_555 B U 10 1_555 A C 4 1_555 B C 9 1_555 -0.334 -1.323 3.432 3.659 7.815 42.872 -2.535 0.803 3.118 10.564 -4.946 43.692 3 AA_A3C4:C9U10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A C 4 1_555 B C 9 1_555 A U 5 1_555 B A 8 1_555 0.155 -2.515 2.900 -4.368 10.318 13.354 -12.278 -2.194 0.705 36.973 15.652 17.415 4 AA_C4U5:A8C9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A U 5 1_555 B A 8 1_555 A CBR 6 1_555 B G 7 1_555 -0.488 -1.997 3.193 -1.034 8.095 31.727 -4.807 0.705 2.632 14.508 1.854 32.734 5 AA_U5CBR6:G7A8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A CBR 6 1_555 B G 7 1_555 A G 7 1_555 B CBR 6 1_555 -0.599 -1.635 3.425 -1.732 14.192 31.253 -4.891 0.758 2.500 24.784 3.024 34.294 6 AA_CBR6G7:CBR6G7_BB A 6 ? B 7 ? A 7 ? B 6 ? 1 A G 7 1_555 B CBR 6 1_555 A A 8 1_555 B U 5 1_555 0.863 -1.367 2.990 -0.413 6.223 31.710 -3.420 -1.615 2.669 11.252 0.746 32.302 7 AA_G7A8:U5CBR6_BB A 7 ? B 6 ? A 8 ? B 5 ? 1 A A 8 1_555 B U 5 1_555 A C 9 1_555 B C 4 1_555 -1.522 -2.089 3.231 -2.853 10.097 23.246 -7.302 2.726 2.304 23.579 6.662 25.474 8 AA_A8C9:C4U5_BB A 8 ? B 5 ? A 9 ? B 4 ? 1 A C 9 1_555 B C 4 1_555 A U 10 1_555 B A 3 1_555 0.587 -1.298 3.244 -0.816 2.349 43.006 -1.995 -0.878 3.161 3.201 1.112 43.074 9 AA_C9U10:A3C4_BB A 9 ? B 4 ? A 10 ? B 3 ? 1 A U 10 1_555 B A 3 1_555 A C 11 1_555 B G 2 1_555 0.925 -1.495 3.151 1.230 6.903 33.183 -3.589 -1.404 2.823 11.921 -2.125 33.896 10 AA_U10C11:G2A3_BB A 10 ? B 3 ? A 11 ? B 2 ? 1 A C 11 1_555 B G 2 1_555 A C 12 1_555 B G 1 1_555 -0.374 -1.900 3.288 -0.775 7.198 33.737 -4.264 0.518 2.843 12.227 1.316 34.482 11 AA_C11C12:G1G2_BB A 11 ? B 2 ? A 12 ? B 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SODIUM ION' NA 3 water HOH # _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 5AY3 _pdbx_initial_refinement_model.details ? #