data_4U6M # _entry.id 4U6M # _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 4U6M pdb_00004u6m 10.2210/pdb4u6m/pdb WWPDB D_1000202903 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB . 4U6K unspecified PDB . 4U6L unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 4U6M _pdbx_database_status.recvd_initial_deposition_date 2014-07-29 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _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 'Nomura, Y.' 2 'Kitahara, Y.' 3 'Obika, S.' 4 'Torigoe, H.' 5 # _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 'Chem.Commun.(Camb.)' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1364-548X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 52 _citation.language ? _citation.page_first 2354 _citation.page_last 2357 _citation.title ;The crystal structure of a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer in complex with the target RNA. ; _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1039/c5cc08300a _citation.pdbx_database_id_PubMed 26731288 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Nomura, Y.' 2 ? primary 'Kitahara, Y.' 3 ? primary 'Obika, S.' 4 ? primary 'Torigoe, H.' 5 ? # _cell.length_a 49.090 _cell.length_b 49.090 _cell.length_c 45.990 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 4U6M _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U6M _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' _symmetry.pdbx_full_space_group_name_H-M ? # 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*AP*AP*GP*AP*AP*GP*AP*G)-3') ; 2981.895 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3') ; 2660.788 1 ? ? ? ? 3 water nat water 18.015 97 ? ? ? ? # 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 no GAAGAAGAG GAAGAAGAG A ? 2 polydeoxyribonucleotide no yes '(5CM)(DT)(DC)(DT)(DT)(DC)(DT)(DT)(5CM)' CTCTTCTTC B ? # 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 A n 1 3 A n 1 4 G n 1 5 A n 1 6 A n 1 7 G n 1 8 A n 1 9 G n 2 1 5CM n 2 2 DT n 2 3 DC n 2 4 DT n 2 5 DT n 2 6 DC n 2 7 DT n 2 8 DT n 2 9 5CM 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 9 'synthetic construct' ? 32630 ? 2 1 sample 1 9 'synthetic construct' ? 32630 ? # 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 4U6M 4U6M ? 1 ? 1 2 PDB 4U6M 4U6M ? 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 4U6M A 1 ? 9 ? 4U6M 1 ? 9 ? 1 9 2 2 4U6M B 1 ? 9 ? 4U6M 1 ? 9 ? 1 9 # 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 5CM 'DNA linking' n "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 # _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 4U6M _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 3.05 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 59.66 _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 'Na Cacodylate, Spermine tetrahydrochloride' _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 CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2013-10-27 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _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-5A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.0 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-5A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 4U6M _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.900 _reflns.d_resolution_low 42.520 _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 5022 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.800 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.170 _reflns.pdbx_Rmerge_I_obs 0.040 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 23.200 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.940 _reflns.pdbx_scaling_rejects 386 _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 51463 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _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 _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 _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 1.900 1.970 ? 5.700 5139 ? ? 500 ? 99.800 ? ? ? ? 0.358 ? ? ? ? ? ? ? ? 10.250 ? 1.370 ? ? ? ? 12 1 1 ? ? 1.970 2.050 ? 7.600 5348 ? ? 501 ? 100.000 ? ? ? ? 0.247 ? ? ? ? ? ? ? ? 10.650 ? 1.070 ? ? ? ? 11 2 1 ? ? 2.050 2.140 ? 8.000 4969 ? ? 488 ? 100.000 ? ? ? ? 0.240 ? ? ? ? ? ? ? ? 10.110 ? 1.190 ? ? ? ? 35 3 1 ? ? 2.140 2.250 ? 9.500 5323 ? ? 509 ? 100.000 ? ? ? ? 0.192 ? ? ? ? ? ? ? ? 10.420 ? 1.040 ? ? ? ? 21 4 1 ? ? 2.250 2.390 ? 10.400 5081 ? ? 492 ? 100.000 ? ? ? ? 0.144 ? ? ? ? ? ? ? ? 10.290 ? 0.880 ? ? ? ? 20 5 1 ? ? 2.390 2.580 ? 15.800 5314 ? ? 510 ? 100.000 ? ? ? ? 0.099 ? ? ? ? ? ? ? ? 10.390 ? 0.860 ? ? ? ? 13 6 1 ? ? 2.580 2.840 ? 18.500 5179 ? ? 504 ? 100.000 ? ? ? ? 0.082 ? ? ? ? ? ? ? ? 10.230 ? 0.770 ? ? ? ? 22 7 1 ? ? 2.840 3.250 ? 29.200 5001 ? ? 501 ? 100.000 ? ? ? ? 0.050 ? ? ? ? ? ? ? ? 9.900 ? 0.760 ? ? ? ? 43 8 1 ? ? 3.250 4.090 ? 46.700 4614 ? ? 503 ? 99.200 ? ? ? ? 0.030 ? ? ? ? ? ? ? ? 8.780 ? 0.780 ? ? ? ? 196 9 1 ? ? 4.090 42.520 ? 80.900 5495 ? ? 514 ? 98.800 ? ? ? ? 0.020 ? ? ? ? ? ? ? ? 10.670 ? 0.660 ? ? ? ? 13 10 1 ? ? # _refine.aniso_B[1][1] 0.8360 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][2] 0.8360 _refine.aniso_B[2][3] 0.0000 _refine.aniso_B[3][3] -1.6720 _refine.B_iso_max 82.750 _refine.B_iso_mean 35.5500 _refine.B_iso_min 21.350 _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 4U6M _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.9000 _refine.ls_d_res_low 42.520 _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 5020 _refine.ls_number_reflns_R_free 271 _refine.ls_number_reflns_R_work 4749 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.8000 _refine.ls_percent_reflns_R_free 5.4000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free 0.2334 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2065 _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 94.0510 _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 4U6L _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 ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set 0.8441 # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.9000 _refine_hist.d_res_low 42.520 _refine_hist.pdbx_number_atoms_ligand 20 _refine_hist.number_atoms_solvent 97 _refine_hist.number_atoms_total 491 _refine_hist.pdbx_number_residues_total 17 _refine_hist.pdbx_B_iso_mean_ligand 26.13 _refine_hist.pdbx_B_iso_mean_solvent 52.19 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 374 # 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' ? 0.006 ? ? ? c_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.163 ? ? ? c_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.000 1.500 ? ? c_mcbond_it ? ? 'X-RAY DIFFRACTION' ? 1.408 2.000 ? ? c_scbond_it ? ? 'X-RAY DIFFRACTION' ? 0.000 2.000 ? ? c_mcangle_it ? ? 'X-RAY DIFFRACTION' ? 2.039 2.500 ? ? c_scangle_it ? ? # 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_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error 'X-RAY DIFFRACTION' 1.9000 1.9700 . . 28 470 99.8000 . . . 0.3509 . 0.2823 . . . . . . . . 'X-RAY DIFFRACTION' 1.9700 2.0500 . . 32 469 100.0000 . . . 0.2663 . 0.2760 . . . . . . . . 'X-RAY DIFFRACTION' 2.0500 2.1400 . . 25 463 100.0000 . . . 0.2559 . 0.2685 . . . . . . . . 'X-RAY DIFFRACTION' 2.1400 2.2500 . . 27 482 100.0000 . . . 0.3020 . 0.2865 . . . . . . . . 'X-RAY DIFFRACTION' 2.2500 2.3900 . . 23 469 100.0000 . . . 0.3320 . 0.2802 . . . . . . . . 'X-RAY DIFFRACTION' 2.3900 2.5800 . . 29 481 100.0000 . . . 0.2421 . 0.2690 . . . . . . . . 'X-RAY DIFFRACTION' 2.5800 2.8400 . . 16 488 100.0000 . . . 0.2564 . 0.2413 . . . . . . . . 'X-RAY DIFFRACTION' 2.8400 3.2500 . . 39 462 100.0000 . . . 0.2299 . 0.2161 . . . . . . . . 'X-RAY DIFFRACTION' 3.2500 4.0900 . . 28 475 99.2000 . . . 0.1846 . 0.1615 . . . . . . . . 'X-RAY DIFFRACTION' 4.0900 42.520 . . 24 490 98.7000 . . . 0.2287 . 0.1697 . . . . . . . . # 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 nco_xplor.param ? 'X-RAY DIFFRACTION' 2 dna-rna_201312.param ? 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:water_rep.param ? 'X-RAY DIFFRACTION' 4 CNS_TOPPAR:ion.param ? # _struct.entry_id 4U6M _struct.title 'Crystal structure of DNA/RNA duplex obtained in the presence of Spermine' _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 4U6M _struct_keywords.text 'DNA/RNA hybrid duplex, antisense, DNA-RNA complex' _struct_keywords.pdbx_keywords DNA/RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 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 ? B 5CM 1 "O3'" ? ? ? 1_555 B DT 2 P ? ? B 5CM 1 B DT 2 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale both ? B DT 8 "O3'" ? ? ? 1_555 B 5CM 9 P ? ? B DT 8 B 5CM 9 1_555 ? ? ? ? ? ? ? 1.602 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B 5CM 9 N3 ? ? A G 1 B 5CM 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B 5CM 9 O2 ? ? A G 1 B 5CM 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B 5CM 9 N4 ? ? A G 1 B 5CM 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N1 ? ? ? 1_555 B DT 8 N3 ? ? A A 2 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 2 N6 ? ? ? 1_555 B DT 8 O4 ? ? A A 2 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A A 3 N1 ? ? ? 1_555 B DT 7 N3 ? ? A A 3 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N6 ? ? ? 1_555 B DT 7 O4 ? ? A A 3 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 B DC 6 N3 ? ? A G 4 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 B DC 6 O2 ? ? A G 4 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 B DC 6 N4 ? ? A G 4 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 B DT 5 N3 ? ? A A 5 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 B DT 5 O4 ? ? A A 5 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 6 N1 ? ? ? 1_555 B DT 4 N3 ? ? A A 6 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 6 N6 ? ? ? 1_555 B DT 4 O4 ? ? A A 6 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 B DC 3 N3 ? ? A G 7 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N2 ? ? ? 1_555 B DC 3 O2 ? ? A G 7 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 O6 ? ? ? 1_555 B DC 3 N4 ? ? A G 7 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N1 ? ? ? 1_555 B DT 2 N3 ? ? A A 8 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 8 N6 ? ? ? 1_555 B DT 2 O4 ? ? A A 8 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 N1 ? ? ? 1_555 B 5CM 1 N3 ? ? A G 9 B 5CM 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 9 N2 ? ? ? 1_555 B 5CM 1 O2 ? ? A G 9 B 5CM 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 O6 ? ? ? 1_555 B 5CM 1 N4 ? ? A G 9 B 5CM 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id 5CM _struct_site.pdbx_auth_seq_id 1 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 40 _struct_site.details 'binding site for B 1 to 9' # 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 40 G A 1 ? G A 1 . ? 6_555 ? 2 AC1 40 G A 1 ? G A 1 . ? 1_555 ? 3 AC1 40 A A 2 ? A A 2 . ? 1_555 ? 4 AC1 40 A A 3 ? A A 3 . ? 1_555 ? 5 AC1 40 G A 4 ? G A 4 . ? 1_555 ? 6 AC1 40 G A 4 ? G A 4 . ? 4_445 ? 7 AC1 40 A A 5 ? A A 5 . ? 4_445 ? 8 AC1 40 A A 5 ? A A 5 . ? 1_555 ? 9 AC1 40 A A 6 ? A A 6 . ? 1_555 ? 10 AC1 40 G A 7 ? G A 7 . ? 1_555 ? 11 AC1 40 A A 8 ? A A 8 . ? 1_555 ? 12 AC1 40 G A 9 ? G A 9 . ? 4_444 ? 13 AC1 40 G A 9 ? G A 9 . ? 1_555 ? 14 AC1 40 HOH D . ? HOH B 101 . ? 1_555 ? 15 AC1 40 HOH D . ? HOH B 102 . ? 1_555 ? 16 AC1 40 HOH D . ? HOH B 103 . ? 1_555 ? 17 AC1 40 HOH D . ? HOH B 104 . ? 1_555 ? 18 AC1 40 HOH D . ? HOH B 105 . ? 1_555 ? 19 AC1 40 HOH D . ? HOH B 106 . ? 1_555 ? 20 AC1 40 HOH D . ? HOH B 107 . ? 1_555 ? 21 AC1 40 HOH D . ? HOH B 108 . ? 1_555 ? 22 AC1 40 HOH D . ? HOH B 109 . ? 1_555 ? 23 AC1 40 HOH D . ? HOH B 110 . ? 1_555 ? 24 AC1 40 HOH D . ? HOH B 111 . ? 1_555 ? 25 AC1 40 HOH D . ? HOH B 112 . ? 1_555 ? 26 AC1 40 HOH D . ? HOH B 118 . ? 1_555 ? 27 AC1 40 HOH D . ? HOH B 119 . ? 1_555 ? 28 AC1 40 HOH D . ? HOH B 121 . ? 1_555 ? 29 AC1 40 HOH D . ? HOH B 122 . ? 1_555 ? 30 AC1 40 HOH D . ? HOH B 123 . ? 1_555 ? 31 AC1 40 HOH D . ? HOH B 124 . ? 1_555 ? 32 AC1 40 HOH D . ? HOH B 125 . ? 1_555 ? 33 AC1 40 HOH D . ? HOH B 126 . ? 1_555 ? 34 AC1 40 HOH D . ? HOH B 128 . ? 1_555 ? 35 AC1 40 HOH D . ? HOH B 129 . ? 1_555 ? 36 AC1 40 HOH D . ? HOH B 130 . ? 1_555 ? 37 AC1 40 HOH D . ? HOH B 132 . ? 1_555 ? 38 AC1 40 HOH D . ? HOH B 133 . ? 1_555 ? 39 AC1 40 HOH D . ? HOH B 140 . ? 1_555 ? 40 AC1 40 HOH D . ? HOH B 150 . ? 1_555 ? # _atom_sites.entry_id 4U6M _atom_sites.fract_transf_matrix[1][1] 0.020371 _atom_sites.fract_transf_matrix[1][2] 0.011761 _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] 0.023522 _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] 0.021744 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_ _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 A 2 2 2 A A A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 A 6 6 6 A A 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 G 9 9 9 G G A . n B 2 1 5CM 1 1 1 5CM ZZZ B . n B 2 2 DT 2 2 2 DT DT B . n B 2 3 DC 3 3 3 DC DC B . n B 2 4 DT 4 4 4 DT DT B . n B 2 5 DT 5 5 5 DT DT B . n B 2 6 DC 6 6 6 DC DC B . n B 2 7 DT 7 7 7 DT DT B . n B 2 8 DT 8 8 8 DT DT B . n B 2 9 5CM 9 9 9 5CM ZZZ 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 3 HOH 1 101 194 HOH HOH A . C 3 HOH 2 102 128 HOH HOH A . C 3 HOH 3 103 158 HOH HOH A . C 3 HOH 4 104 127 HOH HOH A . C 3 HOH 5 105 130 HOH HOH A . C 3 HOH 6 106 153 HOH HOH A . C 3 HOH 7 107 126 HOH HOH A . C 3 HOH 8 108 114 HOH HOH A . C 3 HOH 9 109 142 HOH HOH A . C 3 HOH 10 110 151 HOH HOH A . C 3 HOH 11 111 152 HOH HOH A . C 3 HOH 12 112 139 HOH HOH A . C 3 HOH 13 113 101 HOH HOH A . C 3 HOH 14 114 179 HOH HOH A . C 3 HOH 15 115 123 HOH HOH A . C 3 HOH 16 116 124 HOH HOH A . C 3 HOH 17 117 180 HOH HOH A . C 3 HOH 18 118 140 HOH HOH A . C 3 HOH 19 119 125 HOH HOH A . C 3 HOH 20 120 143 HOH HOH A . C 3 HOH 21 121 175 HOH HOH A . C 3 HOH 22 122 189 HOH HOH A . C 3 HOH 23 123 178 HOH HOH A . C 3 HOH 24 124 141 HOH HOH A . C 3 HOH 25 125 108 HOH HOH A . C 3 HOH 26 126 109 HOH HOH A . C 3 HOH 27 127 110 HOH HOH A . C 3 HOH 28 128 113 HOH HOH A . C 3 HOH 29 129 154 HOH HOH A . C 3 HOH 30 130 155 HOH HOH A . C 3 HOH 31 131 159 HOH HOH A . C 3 HOH 32 132 161 HOH HOH A . C 3 HOH 33 133 168 HOH HOH A . C 3 HOH 34 134 170 HOH HOH A . C 3 HOH 35 135 171 HOH HOH A . C 3 HOH 36 136 172 HOH HOH A . C 3 HOH 37 137 173 HOH HOH A . C 3 HOH 38 138 174 HOH HOH A . C 3 HOH 39 139 176 HOH HOH A . C 3 HOH 40 140 177 HOH HOH A . C 3 HOH 41 141 187 HOH HOH A . C 3 HOH 42 142 188 HOH HOH A . C 3 HOH 43 143 191 HOH HOH A . C 3 HOH 44 144 192 HOH HOH A . C 3 HOH 45 145 197 HOH HOH A . D 3 HOH 1 101 146 HOH HOH B . D 3 HOH 2 102 133 HOH HOH B . D 3 HOH 3 103 104 HOH HOH B . D 3 HOH 4 104 131 HOH HOH B . D 3 HOH 5 105 186 HOH HOH B . D 3 HOH 6 106 132 HOH HOH B . D 3 HOH 7 107 129 HOH HOH B . D 3 HOH 8 108 120 HOH HOH B . D 3 HOH 9 109 103 HOH HOH B . D 3 HOH 10 110 102 HOH HOH B . D 3 HOH 11 111 147 HOH HOH B . D 3 HOH 12 112 134 HOH HOH B . D 3 HOH 13 113 150 HOH HOH B . D 3 HOH 14 114 135 HOH HOH B . D 3 HOH 15 115 190 HOH HOH B . D 3 HOH 16 116 181 HOH HOH B . D 3 HOH 17 117 185 HOH HOH B . D 3 HOH 18 118 105 HOH HOH B . D 3 HOH 19 119 106 HOH HOH B . D 3 HOH 20 120 107 HOH HOH B . D 3 HOH 21 121 111 HOH HOH B . D 3 HOH 22 122 112 HOH HOH B . D 3 HOH 23 123 115 HOH HOH B . D 3 HOH 24 124 116 HOH HOH B . D 3 HOH 25 125 117 HOH HOH B . D 3 HOH 26 126 118 HOH HOH B . D 3 HOH 27 127 119 HOH HOH B . D 3 HOH 28 128 121 HOH HOH B . D 3 HOH 29 129 122 HOH HOH B . D 3 HOH 30 130 136 HOH HOH B . D 3 HOH 31 131 137 HOH HOH B . D 3 HOH 32 132 138 HOH HOH B . D 3 HOH 33 133 144 HOH HOH B . D 3 HOH 34 134 145 HOH HOH B . D 3 HOH 35 135 148 HOH HOH B . D 3 HOH 36 136 149 HOH HOH B . D 3 HOH 37 137 156 HOH HOH B . D 3 HOH 38 138 157 HOH HOH B . D 3 HOH 39 139 160 HOH HOH B . D 3 HOH 40 140 162 HOH HOH B . D 3 HOH 41 141 163 HOH HOH B . D 3 HOH 42 142 164 HOH HOH B . D 3 HOH 43 143 165 HOH HOH B . D 3 HOH 44 144 166 HOH HOH B . D 3 HOH 45 145 167 HOH HOH B . D 3 HOH 46 146 169 HOH HOH B . D 3 HOH 47 147 182 HOH HOH B . D 3 HOH 48 148 183 HOH HOH B . D 3 HOH 49 149 184 HOH HOH B . D 3 HOH 50 150 193 HOH HOH B . D 3 HOH 51 151 195 HOH HOH B . D 3 HOH 52 152 196 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 # 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)' 1400 ? 1 MORE 1 ? 1 'SSA (A^2)' 3360 ? # _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_ _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 2015-08-19 2 'Structure model' 1 1 2020-01-29 3 'Structure model' 1 2 2022-07-06 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' 'Data collection' 2 2 'Structure model' 'Derived calculations' 3 2 'Structure model' 'Refinement description' 4 3 'Structure model' 'Database references' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' computing 2 2 'Structure model' diffrn_source 3 2 'Structure model' pdbx_struct_oper_list 4 2 'Structure model' software 5 3 'Structure model' citation 6 3 'Structure model' database_2 7 4 'Structure model' chem_comp_atom 8 4 'Structure model' chem_comp_bond 9 4 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_computing.pdbx_data_reduction_ds' 2 2 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 3 2 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 4 2 'Structure model' '_software.name' 5 3 'Structure model' '_citation.country' 6 3 'Structure model' '_citation.journal_abbrev' 7 3 'Structure model' '_citation.journal_id_CSD' 8 3 'Structure model' '_citation.journal_id_ISSN' 9 3 'Structure model' '_citation.journal_volume' 10 3 'Structure model' '_citation.page_first' 11 3 'Structure model' '_citation.page_last' 12 3 'Structure model' '_citation.pdbx_database_id_DOI' 13 3 'Structure model' '_citation.pdbx_database_id_PubMed' 14 3 'Structure model' '_citation.title' 15 3 'Structure model' '_citation.year' 16 3 'Structure model' '_database_2.pdbx_DOI' 17 3 'Structure model' '_database_2.pdbx_database_accession' # _phasing.method MR # 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 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? CrystalClear ? ? ? . 1 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 2 ? refinement ? ? ? ? ? ? ? ? ? ? ? CNS ? ? ? . 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? . 4 ? 'model building' ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? d*TREK ? ? ? . 6 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 7 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 OP2 B DT 2 ? ? O B HOH 129 ? ? 1.85 2 1 O A HOH 109 ? ? O A HOH 120 ? ? 1.97 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 P A A 2 ? ? OP1 A A 2 ? ? 1.596 1.485 0.111 0.017 N 2 1 P A A 2 ? ? OP2 A A 2 ? ? 1.601 1.485 0.116 0.017 N 3 1 P A A 3 ? ? OP1 A A 3 ? ? 1.591 1.485 0.106 0.017 N 4 1 P A A 3 ? ? OP2 A A 3 ? ? 1.606 1.485 0.121 0.017 N 5 1 P A G 4 ? ? OP1 A G 4 ? ? 1.601 1.485 0.116 0.017 N 6 1 P A G 4 ? ? OP2 A G 4 ? ? 1.607 1.485 0.122 0.017 N 7 1 P A A 5 ? ? OP1 A A 5 ? ? 1.603 1.485 0.118 0.017 N 8 1 P A A 5 ? ? OP2 A A 5 ? ? 1.611 1.485 0.126 0.017 N 9 1 P A A 6 ? ? OP1 A A 6 ? ? 1.600 1.485 0.115 0.017 N 10 1 P A A 6 ? ? OP2 A A 6 ? ? 1.609 1.485 0.124 0.017 N 11 1 P A G 7 ? ? OP1 A G 7 ? ? 1.601 1.485 0.116 0.017 N 12 1 P A G 7 ? ? OP2 A G 7 ? ? 1.603 1.485 0.118 0.017 N 13 1 P A A 8 ? ? OP1 A A 8 ? ? 1.598 1.485 0.113 0.017 N 14 1 P A A 8 ? ? OP2 A A 8 ? ? 1.591 1.485 0.106 0.017 N 15 1 P A G 9 ? ? OP2 A G 9 ? ? 1.598 1.485 0.113 0.017 N 16 1 P B DT 2 ? ? OP1 B DT 2 ? ? 1.604 1.485 0.119 0.017 N 17 1 P B DT 2 ? ? OP2 B DT 2 ? ? 1.614 1.485 0.129 0.017 N 18 1 P B DC 3 ? ? OP1 B DC 3 ? ? 1.599 1.485 0.114 0.017 N 19 1 P B DC 3 ? ? OP2 B DC 3 ? ? 1.609 1.485 0.124 0.017 N 20 1 P B DT 4 ? ? OP1 B DT 4 ? ? 1.598 1.485 0.113 0.017 N 21 1 P B DT 4 ? ? OP2 B DT 4 ? ? 1.605 1.485 0.120 0.017 N 22 1 P B DT 5 ? ? OP1 B DT 5 ? ? 1.591 1.485 0.106 0.017 N 23 1 P B DT 5 ? ? OP2 B DT 5 ? ? 1.596 1.485 0.111 0.017 N 24 1 P B DC 6 ? ? OP1 B DC 6 ? ? 1.590 1.485 0.105 0.017 N 25 1 P B DC 6 ? ? OP2 B DC 6 ? ? 1.600 1.485 0.115 0.017 N 26 1 P B DT 7 ? ? OP1 B DT 7 ? ? 1.588 1.485 0.103 0.017 N 27 1 P B DT 7 ? ? OP2 B DT 7 ? ? 1.597 1.485 0.112 0.017 N 28 1 P B DT 8 ? ? OP2 B DT 8 ? ? 1.604 1.485 0.119 0.017 N # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O5'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 A _pdbx_validate_rmsd_angle.auth_seq_id_1 5 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 P _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 A _pdbx_validate_rmsd_angle.auth_seq_id_2 5 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 OP2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 A _pdbx_validate_rmsd_angle.auth_seq_id_3 5 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 99.79 _pdbx_validate_rmsd_angle.angle_target_value 105.70 _pdbx_validate_rmsd_angle.angle_deviation -5.91 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.90 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 141 ? 9.47 . 2 1 O ? A HOH 145 ? 11.29 . 3 1 O ? B HOH 141 ? 6.35 . 4 1 O ? B HOH 142 ? 7.68 . 5 1 O ? B HOH 143 ? 7.28 . 6 1 O ? B HOH 144 ? 5.96 . 7 1 O ? B HOH 145 ? 11.17 . 8 1 O ? B HOH 146 ? 7.57 . 9 1 O ? B HOH 147 ? 6.19 . 10 1 O ? B HOH 148 ? 6.58 . 11 1 O ? B HOH 151 ? 6.29 . 12 1 O ? B HOH 152 ? 6.71 . # 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 5CM N1 N N N 1 5CM C2 C N N 2 5CM N3 N N N 3 5CM C4 C N N 4 5CM C5 C N N 5 5CM C5A C N N 6 5CM C6 C N N 7 5CM O2 O N N 8 5CM N4 N N N 9 5CM "C1'" C N R 10 5CM "C2'" C N N 11 5CM "C3'" C N S 12 5CM "C4'" C N R 13 5CM "O4'" O N N 14 5CM "O3'" O N N 15 5CM "C5'" C N N 16 5CM "O5'" O N N 17 5CM P P N N 18 5CM OP1 O N N 19 5CM OP2 O N N 20 5CM OP3 O N N 21 5CM H5A1 H N N 22 5CM H5A2 H N N 23 5CM H5A3 H N N 24 5CM H6 H N N 25 5CM HN41 H N N 26 5CM HN42 H N N 27 5CM "H1'" H N N 28 5CM "H2'" H N N 29 5CM "H2''" H N N 30 5CM "H3'" H N N 31 5CM "H4'" H N N 32 5CM "HO3'" H N N 33 5CM "H5'" H N N 34 5CM "H5''" H N N 35 5CM HOP2 H N N 36 5CM HOP3 H N N 37 A OP3 O N N 38 A P P N N 39 A OP1 O N N 40 A OP2 O N N 41 A "O5'" O N N 42 A "C5'" C N N 43 A "C4'" C N R 44 A "O4'" O N N 45 A "C3'" C N S 46 A "O3'" O N N 47 A "C2'" C N R 48 A "O2'" O N N 49 A "C1'" C N R 50 A N9 N Y N 51 A C8 C Y N 52 A N7 N Y N 53 A C5 C Y N 54 A C6 C Y N 55 A N6 N N N 56 A N1 N Y N 57 A C2 C Y N 58 A N3 N Y N 59 A C4 C Y N 60 A HOP3 H N N 61 A HOP2 H N N 62 A "H5'" H N N 63 A "H5''" H N N 64 A "H4'" H N N 65 A "H3'" H N N 66 A "HO3'" H N N 67 A "H2'" H N N 68 A "HO2'" H N N 69 A "H1'" H N N 70 A H8 H N N 71 A H61 H N N 72 A H62 H N N 73 A H2 H N N 74 DC OP3 O N N 75 DC P P N N 76 DC OP1 O N N 77 DC OP2 O N N 78 DC "O5'" O N N 79 DC "C5'" C N N 80 DC "C4'" C N R 81 DC "O4'" O N N 82 DC "C3'" C N S 83 DC "O3'" O N N 84 DC "C2'" C N N 85 DC "C1'" C N R 86 DC N1 N N N 87 DC C2 C N N 88 DC O2 O N N 89 DC N3 N N N 90 DC C4 C N N 91 DC N4 N N N 92 DC C5 C N N 93 DC C6 C N N 94 DC HOP3 H N N 95 DC HOP2 H N N 96 DC "H5'" H N N 97 DC "H5''" H N N 98 DC "H4'" H N N 99 DC "H3'" H N N 100 DC "HO3'" H N N 101 DC "H2'" H N N 102 DC "H2''" H N N 103 DC "H1'" H N N 104 DC H41 H N N 105 DC H42 H N N 106 DC H5 H N N 107 DC H6 H N N 108 DT OP3 O N N 109 DT P P N N 110 DT OP1 O N N 111 DT OP2 O N N 112 DT "O5'" O N N 113 DT "C5'" C N N 114 DT "C4'" C N R 115 DT "O4'" O N N 116 DT "C3'" C N S 117 DT "O3'" O N N 118 DT "C2'" C N N 119 DT "C1'" C N R 120 DT N1 N N N 121 DT C2 C N N 122 DT O2 O N N 123 DT N3 N N N 124 DT C4 C N N 125 DT O4 O N N 126 DT C5 C N N 127 DT C7 C N N 128 DT C6 C N N 129 DT HOP3 H N N 130 DT HOP2 H N N 131 DT "H5'" H N N 132 DT "H5''" H N N 133 DT "H4'" H N N 134 DT "H3'" H N N 135 DT "HO3'" H N N 136 DT "H2'" H N N 137 DT "H2''" H N N 138 DT "H1'" H N N 139 DT H3 H N N 140 DT H71 H N N 141 DT H72 H N N 142 DT H73 H N N 143 DT H6 H N N 144 G OP3 O N N 145 G P P N N 146 G OP1 O N N 147 G OP2 O N N 148 G "O5'" O N N 149 G "C5'" C N N 150 G "C4'" C N R 151 G "O4'" O N N 152 G "C3'" C N S 153 G "O3'" O N N 154 G "C2'" C N R 155 G "O2'" O N N 156 G "C1'" C N R 157 G N9 N Y N 158 G C8 C Y N 159 G N7 N Y N 160 G C5 C Y N 161 G C6 C N N 162 G O6 O N N 163 G N1 N N N 164 G C2 C N N 165 G N2 N N N 166 G N3 N N N 167 G C4 C Y N 168 G HOP3 H N N 169 G HOP2 H N N 170 G "H5'" H N N 171 G "H5''" H N N 172 G "H4'" H N N 173 G "H3'" H N N 174 G "HO3'" H N N 175 G "H2'" H N N 176 G "HO2'" H N N 177 G "H1'" H N N 178 G H8 H N N 179 G H1 H N N 180 G H21 H N N 181 G H22 H N N 182 HOH O O N N 183 HOH H1 H N N 184 HOH H2 H N N 185 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 5CM N1 C2 sing N N 1 5CM N1 C6 sing N N 2 5CM N1 "C1'" sing N N 3 5CM C2 N3 sing N N 4 5CM C2 O2 doub N N 5 5CM N3 C4 doub N N 6 5CM C4 C5 sing N N 7 5CM C4 N4 sing N N 8 5CM C5 C5A sing N N 9 5CM C5 C6 doub N N 10 5CM C5A H5A1 sing N N 11 5CM C5A H5A2 sing N N 12 5CM C5A H5A3 sing N N 13 5CM C6 H6 sing N N 14 5CM N4 HN41 sing N N 15 5CM N4 HN42 sing N N 16 5CM "C1'" "C2'" sing N N 17 5CM "C1'" "O4'" sing N N 18 5CM "C1'" "H1'" sing N N 19 5CM "C2'" "C3'" sing N N 20 5CM "C2'" "H2'" sing N N 21 5CM "C2'" "H2''" sing N N 22 5CM "C3'" "C4'" sing N N 23 5CM "C3'" "O3'" sing N N 24 5CM "C3'" "H3'" sing N N 25 5CM "C4'" "O4'" sing N N 26 5CM "C4'" "C5'" sing N N 27 5CM "C4'" "H4'" sing N N 28 5CM "O3'" "HO3'" sing N N 29 5CM "C5'" "O5'" sing N N 30 5CM "C5'" "H5'" sing N N 31 5CM "C5'" "H5''" sing N N 32 5CM "O5'" P sing N N 33 5CM P OP1 doub N N 34 5CM P OP2 sing N N 35 5CM P OP3 sing N N 36 5CM OP2 HOP2 sing N N 37 5CM OP3 HOP3 sing N N 38 A OP3 P sing N N 39 A OP3 HOP3 sing N N 40 A P OP1 doub N N 41 A P OP2 sing N N 42 A P "O5'" sing N N 43 A OP2 HOP2 sing N N 44 A "O5'" "C5'" sing N N 45 A "C5'" "C4'" sing N N 46 A "C5'" "H5'" sing N N 47 A "C5'" "H5''" sing N N 48 A "C4'" "O4'" sing N N 49 A "C4'" "C3'" sing N N 50 A "C4'" "H4'" sing N N 51 A "O4'" "C1'" sing N N 52 A "C3'" "O3'" sing N N 53 A "C3'" "C2'" sing N N 54 A "C3'" "H3'" sing N N 55 A "O3'" "HO3'" sing N N 56 A "C2'" "O2'" sing N N 57 A "C2'" "C1'" sing N N 58 A "C2'" "H2'" sing N N 59 A "O2'" "HO2'" sing N N 60 A "C1'" N9 sing N N 61 A "C1'" "H1'" sing N N 62 A N9 C8 sing Y N 63 A N9 C4 sing Y N 64 A C8 N7 doub Y N 65 A C8 H8 sing N N 66 A N7 C5 sing Y N 67 A C5 C6 sing Y N 68 A C5 C4 doub Y N 69 A C6 N6 sing N N 70 A C6 N1 doub Y N 71 A N6 H61 sing N N 72 A N6 H62 sing N N 73 A N1 C2 sing Y N 74 A C2 N3 doub Y N 75 A C2 H2 sing N N 76 A N3 C4 sing Y N 77 DC OP3 P sing N N 78 DC OP3 HOP3 sing N N 79 DC P OP1 doub N N 80 DC P OP2 sing N N 81 DC P "O5'" sing N N 82 DC OP2 HOP2 sing N N 83 DC "O5'" "C5'" sing N N 84 DC "C5'" "C4'" sing N N 85 DC "C5'" "H5'" sing N N 86 DC "C5'" "H5''" sing N N 87 DC "C4'" "O4'" sing N N 88 DC "C4'" "C3'" sing N N 89 DC "C4'" "H4'" sing N N 90 DC "O4'" "C1'" sing N N 91 DC "C3'" "O3'" sing N N 92 DC "C3'" "C2'" sing N N 93 DC "C3'" "H3'" sing N N 94 DC "O3'" "HO3'" sing N N 95 DC "C2'" "C1'" sing N N 96 DC "C2'" "H2'" sing N N 97 DC "C2'" "H2''" sing N N 98 DC "C1'" N1 sing N N 99 DC "C1'" "H1'" sing N N 100 DC N1 C2 sing N N 101 DC N1 C6 sing N N 102 DC C2 O2 doub N N 103 DC C2 N3 sing N N 104 DC N3 C4 doub N N 105 DC C4 N4 sing N N 106 DC C4 C5 sing N N 107 DC N4 H41 sing N N 108 DC N4 H42 sing N N 109 DC C5 C6 doub N N 110 DC C5 H5 sing N N 111 DC C6 H6 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 G OP3 P sing N N 150 G OP3 HOP3 sing N N 151 G P OP1 doub N N 152 G P OP2 sing N N 153 G P "O5'" sing N N 154 G OP2 HOP2 sing N N 155 G "O5'" "C5'" sing N N 156 G "C5'" "C4'" sing N N 157 G "C5'" "H5'" sing N N 158 G "C5'" "H5''" sing N N 159 G "C4'" "O4'" sing N N 160 G "C4'" "C3'" sing N N 161 G "C4'" "H4'" sing N N 162 G "O4'" "C1'" sing N N 163 G "C3'" "O3'" sing N N 164 G "C3'" "C2'" sing N N 165 G "C3'" "H3'" sing N N 166 G "O3'" "HO3'" sing N N 167 G "C2'" "O2'" sing N N 168 G "C2'" "C1'" sing N N 169 G "C2'" "H2'" sing N N 170 G "O2'" "HO2'" sing N N 171 G "C1'" N9 sing N N 172 G "C1'" "H1'" sing N N 173 G N9 C8 sing Y N 174 G N9 C4 sing Y N 175 G C8 N7 doub Y N 176 G C8 H8 sing N N 177 G N7 C5 sing Y N 178 G C5 C6 sing N N 179 G C5 C4 doub Y N 180 G C6 O6 doub N N 181 G C6 N1 sing N N 182 G N1 C2 sing N N 183 G N1 H1 sing N N 184 G C2 N2 sing N N 185 G C2 N3 doub N N 186 G N2 H21 sing N N 187 G N2 H22 sing N N 188 G N3 C4 sing N N 189 HOH O H1 sing N N 190 HOH O H2 sing N N 191 # _ndb_struct_conf_na.entry_id 4U6M _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B 5CM 9 1_555 -0.315 -0.211 -0.149 -5.843 -14.803 0.847 1 A_G1:5CM9_B A 1 ? B 9 ? 19 1 1 A A 2 1_555 B DT 8 1_555 0.068 -0.135 -0.043 -5.349 -17.680 3.111 2 A_A2:DT8_B A 2 ? B 8 ? 20 1 1 A A 3 1_555 B DT 7 1_555 -0.041 -0.077 0.066 -4.968 -19.132 7.709 3 A_A3:DT7_B A 3 ? B 7 ? 20 1 1 A G 4 1_555 B DC 6 1_555 -0.238 -0.191 -0.157 -10.831 -8.549 -2.932 4 A_G4:DC6_B A 4 ? B 6 ? 19 1 1 A A 5 1_555 B DT 5 1_555 0.062 0.018 -0.400 -15.091 -9.595 -3.991 5 A_A5:DT5_B A 5 ? B 5 ? 20 1 1 A A 6 1_555 B DT 4 1_555 0.085 -0.223 0.206 0.180 -6.181 3.525 6 A_A6:DT4_B A 6 ? B 4 ? 20 1 1 A G 7 1_555 B DC 3 1_555 -0.065 -0.086 -0.209 -5.234 -10.724 2.965 7 A_G7:DC3_B A 7 ? B 3 ? 19 1 1 A A 8 1_555 B DT 2 1_555 -0.093 -0.121 -0.125 -1.241 -4.207 0.595 8 A_A8:DT2_B A 8 ? B 2 ? 20 1 1 A G 9 1_555 B 5CM 1 1_555 -0.071 -0.100 -0.050 6.846 -2.147 2.084 9 A_G9:5CM1_B A 9 ? 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 5CM 9 1_555 A A 2 1_555 B DT 8 1_555 0.493 -1.180 3.299 1.401 2.064 35.780 -2.213 -0.600 3.245 3.354 -2.277 35.864 1 AA_G1A2:DT85CM9_BB A 1 ? B 9 ? A 2 ? B 8 ? 1 A A 2 1_555 B DT 8 1_555 A A 3 1_555 B DT 7 1_555 0.457 -1.290 3.266 0.065 4.741 31.957 -3.134 -0.811 3.049 8.553 -0.116 32.298 2 AA_A2A3:DT7DT8_BB A 2 ? B 8 ? A 3 ? B 7 ? 1 A A 3 1_555 B DT 7 1_555 A G 4 1_555 B DC 6 1_555 -1.338 -1.407 3.378 -3.165 9.906 35.200 -3.588 1.695 2.992 15.954 5.097 36.658 3 AA_A3G4:DC6DT7_BB A 3 ? B 7 ? A 4 ? B 6 ? 1 A G 4 1_555 B DC 6 1_555 A A 5 1_555 B DT 5 1_555 0.898 -1.797 3.530 6.123 14.691 30.232 -5.375 -0.571 2.542 26.024 -10.846 34.079 4 AA_G4A5:DT5DC6_BB A 4 ? B 6 ? A 5 ? B 5 ? 1 A A 5 1_555 B DT 5 1_555 A A 6 1_555 B DT 4 1_555 0.724 -1.529 2.944 -2.545 2.582 27.207 -3.775 -2.072 2.712 5.457 5.381 27.442 5 AA_A5A6:DT4DT5_BB A 5 ? B 5 ? A 6 ? B 4 ? 1 A A 6 1_555 B DT 4 1_555 A G 7 1_555 B DC 3 1_555 0.100 -1.709 3.586 1.968 3.966 30.689 -4.011 0.217 3.344 7.445 -3.695 30.999 6 AA_A6G7:DC3DT4_BB A 6 ? B 4 ? A 7 ? B 3 ? 1 A G 7 1_555 B DC 3 1_555 A A 8 1_555 B DT 2 1_555 -0.809 -1.407 3.171 -1.481 7.043 33.664 -3.403 1.152 2.859 11.992 2.521 34.403 7 AA_G7A8:DT2DC3_BB A 7 ? B 3 ? A 8 ? B 2 ? 1 A A 8 1_555 B DT 2 1_555 A G 9 1_555 B 5CM 1 1_555 0.651 -1.888 3.126 0.740 1.845 28.148 -4.276 -1.174 3.014 3.788 -1.520 28.217 8 AA_A8G9:5CM1DT2_BB A 8 ? B 2 ? A 9 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 4U6L _pdbx_initial_refinement_model.details ? #