data_6C8I # _entry.id 6C8I # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 6C8I pdb_00006c8i 10.2210/pdb6c8i/pdb WWPDB D_1000232279 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6C8I _pdbx_database_status.recvd_initial_deposition_date 2018-01-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Zhang, W.' 1 ? 'Szostak, J.W.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Elife _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2050-084X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 7 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Crystallographic observation of nonenzymatic RNA primer extension.' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.7554/eLife.36422 _citation.pdbx_database_id_PubMed 29851379 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhang, W.' 1 0000-0003-4811-4384 primary 'Walton, T.' 2 0000-0001-6812-1579 primary 'Li, L.' 3 0000-0003-4766-5782 primary 'Szostak, J.W.' 4 0000-0003-4131-1203 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 6C8I _cell.details ? _cell.formula_units_Z ? _cell.length_a 43.843 _cell.length_a_esd ? _cell.length_b 43.843 _cell.length_b_esd ? _cell.length_c 85.219 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C8I _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' _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(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') ; 4512.804 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 non-polymer syn "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine" 428.297 4 ? ? ? ? 4 water nat water 18.015 19 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(LCC)(LCC)(LCC)(LCG)ACUUAAGUCG' _entity_poly.pdbx_seq_one_letter_code_can NNNGACUUAAGUCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LCC n 1 2 LCC n 1 3 LCC n 1 4 LCG n 1 5 A n 1 6 C n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 G n 1 12 U n 1 13 C n 1 14 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 14 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6C8I _struct_ref.pdbx_db_accession 6C8I _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 6C8I A 1 ? 14 ? 6C8I 1 ? 14 ? 1 14 2 1 6C8I B 1 ? 14 ? 6C8I 1 ? 14 ? 1 14 # 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 EQ4 'RNA linking' n "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine" ? 'C13 H17 N8 O7 P' 428.297 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 LCC 'RNA linking' . '[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' ? 'C11 H16 N3 O8 P' 349.234 LCG 'RNA linking' n '[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' ? 'C11 H14 N5 O8 P' 375.231 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 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 6C8I _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 2.44 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 49.64 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate pH 7.0, 0.012 M Spermine tetrahydrochloride, 0.080 M Sodium chloride, 0.020 M Magnesium chloride hexahydrate ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 99 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MAR CCD 130 mm' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-10-25 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6C8I _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.77 _reflns.d_resolution_low 50 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 9699 _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 99.1 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 7.6 _reflns.pdbx_Rmerge_I_obs 0.127 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 14.19 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.952 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.137 _reflns.pdbx_Rpim_I_all 0.051 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.947 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.77 _reflns_shell.d_res_low 1.83 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.95 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 965 _reflns_shell.percent_possible_all 99.8 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.680 _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 7.2 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 0.484 _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all 0.732 _reflns_shell.pdbx_Rpim_I_all 0.265 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.836 _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] -0.00 _refine.aniso_B[1][2] -0.00 _refine.aniso_B[1][3] -0.00 _refine.aniso_B[2][2] -0.00 _refine.aniso_B[2][3] 0.00 _refine.aniso_B[3][3] 0.01 _refine.B_iso_max ? _refine.B_iso_mean 31.614 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.953 _refine.correlation_coeff_Fo_to_Fc_free 0.937 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _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 6C8I _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 1.77 _refine.ls_d_res_low 50 _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 9234 _refine.ls_number_reflns_R_free 463 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.69 _refine.ls_percent_reflns_R_free 4.8 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.23272 _refine.ls_R_factor_R_free 0.28295 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.23037 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 5DHC _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.142 _refine.pdbx_overall_ESU_R_Free 0.144 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B 2.966 _refine.overall_SU_ML 0.094 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id 1 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 598 _refine_hist.pdbx_number_atoms_ligand 118 _refine_hist.number_atoms_solvent 19 _refine_hist.number_atoms_total 735 _refine_hist.d_res_high 1.77 _refine_hist.d_res_low 50 # 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' ? 0.025 0.017 792 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.074 0.024 356 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 3.585 2.014 1224 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 3.785 3.279 848 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_2_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_4_deg ? ? 'X-RAY DIFFRACTION' ? 0.348 0.200 138 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.018 0.021 424 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.003 0.022 160 ? r_gen_planes_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_other ? ? 'X-RAY DIFFRACTION' ? 3.098 3.321 792 ? r_scbond_it ? ? 'X-RAY DIFFRACTION' ? 3.096 3.328 793 ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? 4.630 4.964 1225 ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? 5.382 33.100 1159 ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? 5.387 33.149 1158 ? r_long_range_B_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.767 _refine_ls_shell.d_res_low 1.812 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 27 _refine_ls_shell.number_reflns_R_work 681 _refine_ls_shell.percent_reflns_obs 97.79 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.231 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.229 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 6C8I _struct.title 'RNA-activated 2-AIpG monomer complex, 5 min soaking' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6C8I _struct_keywords.text 'RNA, activated monomer' _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 ? F N N 2 ? G N N 3 ? H N N 3 ? I N N 4 ? J N N 4 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A LCC 1 "O3'" ? ? ? 1_555 A LCC 2 P ? ? A LCC 1 A LCC 2 1_555 ? ? ? ? ? ? ? 1.673 ? ? covale2 covale both ? A LCC 2 "O3'" ? ? ? 1_555 A LCC 3 P ? ? A LCC 2 A LCC 3 1_555 ? ? ? ? ? ? ? 1.696 ? ? covale3 covale both ? A LCC 3 "O3'" ? ? ? 1_555 A LCG 4 P ? ? A LCC 3 A LCG 4 1_555 ? ? ? ? ? ? ? 1.681 ? ? covale4 covale both ? A LCG 4 "O3'" ? ? ? 1_555 A A 5 P ? ? A LCG 4 A A 5 1_555 ? ? ? ? ? ? ? 1.682 ? ? covale5 covale both ? B LCC 1 "O3'" ? ? ? 1_555 B LCC 2 P ? ? B LCC 1 B LCC 2 1_555 ? ? ? ? ? ? ? 1.649 ? ? covale6 covale both ? B LCC 2 "O3'" ? ? ? 1_555 B LCC 3 P ? ? B LCC 2 B LCC 3 1_555 ? ? ? ? ? ? ? 1.678 ? ? covale7 covale both ? B LCC 3 "O3'" ? ? ? 1_555 B LCG 4 P ? ? B LCC 3 B LCG 4 1_555 ? ? ? ? ? ? ? 1.701 ? ? covale8 covale both ? B LCG 4 "O3'" ? ? ? 1_555 B A 5 P ? ? B LCG 4 B A 5 1_555 ? ? ? ? ? ? ? 1.660 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 G EQ4 . O6 ? ? A MG 101 B EQ4 102 1_555 ? ? ? ? ? ? ? 2.325 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 G EQ4 . O5 ? ? A MG 101 B EQ4 102 1_555 ? ? ? ? ? ? ? 2.573 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 G EQ4 . O6 ? ? A MG 101 B EQ4 102 3_665 ? ? ? ? ? ? ? 2.329 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 G EQ4 . O5 ? ? A MG 101 B EQ4 102 3_665 ? ? ? ? ? ? ? 2.573 ? ? metalc5 metalc ? ? D EQ4 . O5 ? ? ? 1_555 F MG . MG ? ? A EQ4 102 B MG 101 1_555 ? ? ? ? ? ? ? 2.379 ? ? metalc6 metalc ? ? D EQ4 . O6 ? ? ? 1_555 F MG . MG ? ? A EQ4 102 B MG 101 1_555 ? ? ? ? ? ? ? 2.558 ? ? metalc7 metalc ? ? D EQ4 . O5 ? ? ? 1_555 F MG . MG ? ? A EQ4 102 B MG 101 3_665 ? ? ? ? ? ? ? 2.340 ? ? metalc8 metalc ? ? D EQ4 . O6 ? ? ? 1_555 F MG . MG ? ? A EQ4 102 B MG 101 3_665 ? ? ? ? ? ? ? 2.524 ? ? hydrog1 hydrog ? ? A LCG 4 N1 ? ? ? 1_555 B C 13 N3 ? ? A LCG 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A LCG 4 N2 ? ? ? 1_555 B C 13 O2 ? ? A LCG 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A LCG 4 O6 ? ? ? 1_555 B C 13 N4 ? ? A LCG 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 12 N3 ? ? A A 5 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 12 O4 ? ? A A 5 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 6 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 6 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 6 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 7 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 7 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 8 B A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 8 O4 ? ? ? 1_555 B A 9 N6 ? ? A U 8 B A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 9 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 9 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 10 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 10 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 11 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 11 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 11 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 12 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 12 B A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 13 N3 ? ? ? 1_555 B LCG 4 N1 ? ? A C 13 B LCG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 13 N4 ? ? ? 1_555 B LCG 4 O6 ? ? A C 13 B LCG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 13 O2 ? ? ? 1_555 B LCG 4 N2 ? ? A C 13 B LCG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 A MG 101 ? 3 'binding site for residue MG A 101' AC2 Software A EQ4 102 ? 12 'binding site for residue EQ4 A 102' AC3 Software A EQ4 103 ? 6 'binding site for residue EQ4 A 103' AC4 Software B MG 101 ? 3 'binding site for residue MG B 101' AC5 Software B EQ4 102 ? 10 'binding site for residue EQ4 B 102' AC6 Software B EQ4 103 ? 5 'binding site for residue EQ4 B 103' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 3 EQ4 G . ? EQ4 B 102 . ? 1_555 ? 2 AC1 3 EQ4 G . ? EQ4 B 102 . ? 3_665 ? 3 AC1 3 EQ4 G . ? EQ4 B 102 . ? 2_655 ? 4 AC2 12 LCC A 1 ? LCC A 1 . ? 6_765 ? 5 AC2 12 LCC A 2 ? LCC A 2 . ? 1_555 ? 6 AC2 12 LCC A 3 ? LCC A 3 . ? 1_555 ? 7 AC2 12 EQ4 E . ? EQ4 A 103 . ? 1_555 ? 8 AC2 12 EQ4 E . ? EQ4 A 103 . ? 3_665 ? 9 AC2 12 HOH I . ? HOH A 201 . ? 1_555 ? 10 AC2 12 HOH I . ? HOH A 207 . ? 1_555 ? 11 AC2 12 G B 14 ? G B 14 . ? 1_555 ? 12 AC2 12 G B 14 ? G B 14 . ? 2_655 ? 13 AC2 12 MG F . ? MG B 101 . ? 1_555 ? 14 AC2 12 MG F . ? MG B 101 . ? 3_665 ? 15 AC2 12 MG F . ? MG B 101 . ? 2_655 ? 16 AC3 6 LCC A 1 ? LCC A 1 . ? 6_765 ? 17 AC3 6 LCC A 1 ? LCC A 1 . ? 1_555 ? 18 AC3 6 LCC A 2 ? LCC A 2 . ? 1_555 ? 19 AC3 6 EQ4 D . ? EQ4 A 102 . ? 2_655 ? 20 AC3 6 EQ4 D . ? EQ4 A 102 . ? 1_555 ? 21 AC3 6 G B 14 ? G B 14 . ? 2_655 ? 22 AC4 3 EQ4 D . ? EQ4 A 102 . ? 3_665 ? 23 AC4 3 EQ4 D . ? EQ4 A 102 . ? 1_555 ? 24 AC4 3 EQ4 D . ? EQ4 A 102 . ? 2_655 ? 25 AC5 10 G A 14 ? G A 14 . ? 1_555 ? 26 AC5 10 G A 14 ? G A 14 . ? 3_665 ? 27 AC5 10 MG C . ? MG A 101 . ? 1_555 ? 28 AC5 10 MG C . ? MG A 101 . ? 2_655 ? 29 AC5 10 MG C . ? MG A 101 . ? 3_665 ? 30 AC5 10 LCC B 2 ? LCC B 2 . ? 1_555 ? 31 AC5 10 LCC B 3 ? LCC B 3 . ? 1_555 ? 32 AC5 10 EQ4 H . ? EQ4 B 103 . ? 1_555 ? 33 AC5 10 HOH J . ? HOH B 202 . ? 1_555 ? 34 AC5 10 HOH J . ? HOH B 206 . ? 1_555 ? 35 AC6 5 C A 13 ? C A 13 . ? 6_766 ? 36 AC6 5 LCC B 1 ? LCC B 1 . ? 5_556 ? 37 AC6 5 LCC B 1 ? LCC B 1 . ? 1_555 ? 38 AC6 5 LCC B 2 ? LCC B 2 . ? 1_555 ? 39 AC6 5 EQ4 G . ? EQ4 B 102 . ? 1_555 ? # _atom_sites.entry_id 6C8I _atom_sites.fract_transf_matrix[1][1] 0.022809 _atom_sites.fract_transf_matrix[1][2] 0.013169 _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] 0.026337 _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] 0.011734 _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 MG 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 LCC 1 1 1 LCC LCC A . n A 1 2 LCC 2 2 2 LCC LCC A . n A 1 3 LCC 3 3 3 LCC LCC A . n A 1 4 LCG 4 4 4 LCG LCG A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n B 1 1 LCC 1 1 1 LCC LCC B . n B 1 2 LCC 2 2 2 LCC LCC B . n B 1 3 LCC 3 3 3 LCC LCC B . n B 1 4 LCG 4 4 4 LCG LCG B . n B 1 5 A 5 5 5 A A B . n B 1 6 C 6 6 6 C C B . n B 1 7 U 7 7 7 U U B . n B 1 8 U 8 8 8 U U B . n B 1 9 A 9 9 9 A A B . n B 1 10 A 10 10 10 A A B . n B 1 11 G 11 11 11 G G B . n B 1 12 U 12 12 12 U U B . n B 1 13 C 13 13 13 C C B . n B 1 14 G 14 14 14 G G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 MG 1 101 2 MG MG A . D 3 EQ4 1 102 1 EQ4 NG A . E 3 EQ4 1 103 2 EQ4 NG A . F 2 MG 1 101 1 MG MG B . G 3 EQ4 1 102 3 EQ4 NG B . H 3 EQ4 1 103 4 EQ4 NG B . I 4 HOH 1 201 17 HOH HOH A . I 4 HOH 2 202 8 HOH HOH A . I 4 HOH 3 203 15 HOH HOH A . I 4 HOH 4 204 16 HOH HOH A . I 4 HOH 5 205 4 HOH HOH A . I 4 HOH 6 206 13 HOH HOH A . I 4 HOH 7 207 1 HOH HOH A . I 4 HOH 8 208 9 HOH HOH A . I 4 HOH 9 209 5 HOH HOH A . J 4 HOH 1 201 3 HOH HOH B . J 4 HOH 2 202 19 HOH HOH B . J 4 HOH 3 203 10 HOH HOH B . J 4 HOH 4 204 2 HOH HOH B . J 4 HOH 5 205 14 HOH HOH B . J 4 HOH 6 206 7 HOH HOH B . J 4 HOH 7 207 6 HOH HOH B . J 4 HOH 8 208 18 HOH HOH B . J 4 HOH 9 209 12 HOH HOH B . J 4 HOH 10 210 11 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,F,G,H,I,J # 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)' 2690 ? 1 MORE 8 ? 1 'SSA (A^2)' 5930 ? # _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_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A MG 101 ? C MG . 2 1 B MG 101 ? F MG . 3 1 A HOH 203 ? I HOH . 4 1 A HOH 209 ? I HOH . 5 1 B HOH 205 ? J HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O6 ? G EQ4 . ? B EQ4 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O5 ? G EQ4 . ? B EQ4 102 ? 1_555 70.2 ? 2 O6 ? G EQ4 . ? B EQ4 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O6 ? G EQ4 . ? B EQ4 102 ? 3_665 89.4 ? 3 O5 ? G EQ4 . ? B EQ4 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O6 ? G EQ4 . ? B EQ4 102 ? 3_665 153.8 ? 4 O6 ? G EQ4 . ? B EQ4 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O5 ? G EQ4 . ? B EQ4 102 ? 3_665 106.4 ? 5 O5 ? G EQ4 . ? B EQ4 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O5 ? G EQ4 . ? B EQ4 102 ? 3_665 99.3 ? 6 O6 ? G EQ4 . ? B EQ4 102 ? 3_665 MG ? C MG . ? A MG 101 ? 1_555 O5 ? G EQ4 . ? B EQ4 102 ? 3_665 70.2 ? 7 O5 ? D EQ4 . ? A EQ4 102 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O6 ? D EQ4 . ? A EQ4 102 ? 1_555 65.0 ? 8 O5 ? D EQ4 . ? A EQ4 102 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O5 ? D EQ4 . ? A EQ4 102 ? 1_555 0.0 ? 9 O6 ? D EQ4 . ? A EQ4 102 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O5 ? D EQ4 . ? A EQ4 102 ? 1_555 65.0 ? 10 O5 ? D EQ4 . ? A EQ4 102 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O6 ? D EQ4 . ? A EQ4 102 ? 1_555 65.0 ? 11 O6 ? D EQ4 . ? A EQ4 102 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O6 ? D EQ4 . ? A EQ4 102 ? 1_555 0.0 ? 12 O5 ? D EQ4 . ? A EQ4 102 ? 1_555 MG ? F MG . ? B MG 101 ? 1_555 O6 ? D EQ4 . ? A EQ4 102 ? 1_555 65.0 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2018-05-30 2 'Structure model' 1 1 2018-10-31 3 'Structure model' 1 2 2019-11-20 4 'Structure model' 1 3 2023-10-04 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Database references' 3 3 'Structure model' 'Author supporting evidence' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' pdbx_audit_support 4 4 'Structure model' chem_comp_atom 5 4 'Structure model' chem_comp_bond 6 4 'Structure model' database_2 7 4 'Structure model' pdbx_initial_refinement_model 8 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 2 'Structure model' '_citation.page_first' 2 2 'Structure model' '_citation.pdbx_database_id_PubMed' 3 2 'Structure model' '_citation.title' 4 2 'Structure model' '_citation_author.identifier_ORCID' 5 3 'Structure model' '_pdbx_audit_support.funding_organization' 6 4 'Structure model' '_database_2.pdbx_DOI' 7 4 'Structure model' '_database_2.pdbx_database_accession' 8 4 'Structure model' '_struct_conn.pdbx_dist_value' 9 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 10 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 12 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 13 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 14 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 18 4 'Structure model' '_struct_conn.ptnr2_label_comp_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 ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0135 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A LCC 2 ? ? P A LCC 3 ? ? 1.696 1.607 0.089 0.012 Y 2 1 "O3'" A LCC 3 ? ? P A LCG 4 ? ? 1.681 1.607 0.074 0.012 Y 3 1 "O3'" A LCG 4 ? ? P A A 5 ? ? 1.682 1.607 0.075 0.012 Y 4 1 "O3'" B LCC 3 ? ? P B LCG 4 ? ? 1.701 1.607 0.094 0.012 Y # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O3'" A LCC 3 ? ? P A LCG 4 ? ? OP2 A LCG 4 ? ? 118.35 110.50 7.85 1.10 Y 2 1 "C3'" A LCG 4 ? ? "O3'" A LCG 4 ? ? P A A 5 ? ? 109.64 119.70 -10.06 1.20 Y # 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 EQ4 P1 P N N 73 EQ4 O1 O N N 74 EQ4 O2 O N N 75 EQ4 C1 C N N 76 EQ4 O3 O N N 77 EQ4 C2 C N R 78 EQ4 O4 O N N 79 EQ4 C3 C N S 80 EQ4 O5 O N N 81 EQ4 C4 C N R 82 EQ4 O6 O N N 83 EQ4 C5 C N R 84 EQ4 N1 N N N 85 EQ4 C6 C N N 86 EQ4 N2 N N N 87 EQ4 N3 N N N 88 EQ4 C7 C Y N 89 EQ4 C8 C Y N 90 EQ4 C9 C N N 91 EQ4 O7 O N N 92 EQ4 N4 N Y N 93 EQ4 C10 C Y N 94 EQ4 N5 N Y N 95 EQ4 N6 N Y N 96 EQ4 C11 C Y N 97 EQ4 C12 C Y N 98 EQ4 N7 N Y N 99 EQ4 C13 C Y N 100 EQ4 N8 N N N 101 EQ4 H1 H N N 102 EQ4 H2 H N N 103 EQ4 H3 H N N 104 EQ4 H4 H N N 105 EQ4 H5 H N N 106 EQ4 H6 H N N 107 EQ4 H7 H N N 108 EQ4 H8 H N N 109 EQ4 H9 H N N 110 EQ4 H10 H N N 111 EQ4 H11 H N N 112 EQ4 H12 H N N 113 EQ4 H13 H N N 114 EQ4 H14 H N N 115 EQ4 H15 H N N 116 EQ4 H16 H N N 117 EQ4 H17 H N N 118 G OP3 O N N 119 G P P N N 120 G OP1 O N N 121 G OP2 O N N 122 G "O5'" O N N 123 G "C5'" C N N 124 G "C4'" C N R 125 G "O4'" O N N 126 G "C3'" C N S 127 G "O3'" O N N 128 G "C2'" C N R 129 G "O2'" O N N 130 G "C1'" C N R 131 G N9 N Y N 132 G C8 C Y N 133 G N7 N Y N 134 G C5 C Y N 135 G C6 C N N 136 G O6 O N N 137 G N1 N N N 138 G C2 C N N 139 G N2 N N N 140 G N3 N N N 141 G C4 C Y N 142 G HOP3 H N N 143 G HOP2 H N N 144 G "H5'" H N N 145 G "H5''" H N N 146 G "H4'" H N N 147 G "H3'" H N N 148 G "HO3'" H N N 149 G "H2'" H N N 150 G "HO2'" H N N 151 G "H1'" H N N 152 G H8 H N N 153 G H1 H N N 154 G H21 H N N 155 G H22 H N N 156 HOH O O N N 157 HOH H1 H N N 158 HOH H2 H N N 159 LCC "O5'" O N N 160 LCC "C5'" C N N 161 LCC "C4'" C N R 162 LCC "O4'" O N N 163 LCC "C1'" C N R 164 LCC N1 N N N 165 LCC C6 C N N 166 LCC C5 C N N 167 LCC C5M C N N 168 LCC C4 C N N 169 LCC N4 N N N 170 LCC N3 N N N 171 LCC C2 C N N 172 LCC O2 O N N 173 LCC "C3'" C N S 174 LCC "C2'" C N R 175 LCC "O2'" O N N 176 LCC "O3'" O N N 177 LCC "C6'" C N N 178 LCC P P N N 179 LCC O1P O N N 180 LCC O2P O N N 181 LCC OXT O N N 182 LCC "H5'1" H N N 183 LCC "H5'2" H N N 184 LCC "H1'" H N N 185 LCC H6 H N N 186 LCC H5M1 H N N 187 LCC H5M2 H N N 188 LCC H5M3 H N N 189 LCC H41 H N N 190 LCC H42 H N N 191 LCC "H3'" H N N 192 LCC "H2'1" H N N 193 LCC H3T H N N 194 LCC "H6'1" H N N 195 LCC "H6'2" H N N 196 LCC H1P H N N 197 LCC HXT H N N 198 LCG P P N N 199 LCG OP1 O N N 200 LCG "O5'" O N N 201 LCG "C5'" C N N 202 LCG "C3'" C N S 203 LCG "C6'" C N N 204 LCG N9 N Y N 205 LCG C8 C Y N 206 LCG C4 C Y N 207 LCG N7 N Y N 208 LCG C5 C Y N 209 LCG C6 C N N 210 LCG "C2'" C N R 211 LCG O6 O N N 212 LCG "C4'" C N R 213 LCG "C1'" C N R 214 LCG C2 C N N 215 LCG N1 N N N 216 LCG "O4'" O N N 217 LCG OP2 O N N 218 LCG N2 N N N 219 LCG N3 N N N 220 LCG "O2'" O N N 221 LCG "O3'" O N N 222 LCG OP3 O N N 223 LCG "H5'" H N N 224 LCG "H5''" H N N 225 LCG "H3'" H N N 226 LCG "H6'1" H N N 227 LCG "H6'2" H N N 228 LCG H8 H N N 229 LCG "H2'" H N N 230 LCG "H1'" H N N 231 LCG H1 H N N 232 LCG HOP2 H N N 233 LCG H21 H N N 234 LCG H22 H N N 235 LCG "HO3'" H N N 236 LCG HOP3 H N N 237 MG MG MG N N 238 U OP3 O N N 239 U P P N N 240 U OP1 O N N 241 U OP2 O N N 242 U "O5'" O N N 243 U "C5'" C N N 244 U "C4'" C N R 245 U "O4'" O N N 246 U "C3'" C N S 247 U "O3'" O N N 248 U "C2'" C N R 249 U "O2'" O N N 250 U "C1'" C N R 251 U N1 N N N 252 U C2 C N N 253 U O2 O N N 254 U N3 N N N 255 U C4 C N N 256 U O4 O N N 257 U C5 C N N 258 U C6 C N N 259 U HOP3 H N N 260 U HOP2 H N N 261 U "H5'" H N N 262 U "H5''" H N N 263 U "H4'" H N N 264 U "H3'" H N N 265 U "HO3'" H N N 266 U "H2'" H N N 267 U "HO2'" H N N 268 U "H1'" H N N 269 U H3 H N N 270 U H5 H N N 271 U H6 H N N 272 # 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 EQ4 C12 N7 sing Y N 76 EQ4 C12 C11 doub Y N 77 EQ4 N7 C13 doub Y N 78 EQ4 C11 N6 sing Y N 79 EQ4 C13 N8 sing N N 80 EQ4 C13 N6 sing Y N 81 EQ4 N6 P1 sing N N 82 EQ4 O2 P1 doub N N 83 EQ4 O5 C3 sing N N 84 EQ4 P1 O3 sing N N 85 EQ4 P1 O1 sing N N 86 EQ4 O3 C1 sing N N 87 EQ4 C3 C2 sing N N 88 EQ4 C3 C4 sing N N 89 EQ4 O6 C4 sing N N 90 EQ4 C2 C1 sing N N 91 EQ4 C2 O4 sing N N 92 EQ4 C4 C5 sing N N 93 EQ4 O4 C5 sing N N 94 EQ4 C5 N5 sing N N 95 EQ4 C10 N5 sing Y N 96 EQ4 C10 N4 doub Y N 97 EQ4 N5 C7 sing Y N 98 EQ4 N4 C8 sing Y N 99 EQ4 C7 C8 doub Y N 100 EQ4 C7 N3 sing N N 101 EQ4 C8 C9 sing N N 102 EQ4 N3 C6 doub N N 103 EQ4 C9 O7 doub N N 104 EQ4 C9 N1 sing N N 105 EQ4 C6 N1 sing N N 106 EQ4 C6 N2 sing N N 107 EQ4 O1 H1 sing N N 108 EQ4 C1 H2 sing N N 109 EQ4 C1 H3 sing N N 110 EQ4 C2 H4 sing N N 111 EQ4 C3 H5 sing N N 112 EQ4 O5 H6 sing N N 113 EQ4 C4 H7 sing N N 114 EQ4 O6 H8 sing N N 115 EQ4 C5 H9 sing N N 116 EQ4 N1 H10 sing N N 117 EQ4 N2 H11 sing N N 118 EQ4 N2 H12 sing N N 119 EQ4 C10 H13 sing N N 120 EQ4 C11 H14 sing N N 121 EQ4 C12 H15 sing N N 122 EQ4 N8 H16 sing N N 123 EQ4 N8 H17 sing N N 124 G OP3 P sing N N 125 G OP3 HOP3 sing N N 126 G P OP1 doub N N 127 G P OP2 sing N N 128 G P "O5'" sing N N 129 G OP2 HOP2 sing N N 130 G "O5'" "C5'" sing N N 131 G "C5'" "C4'" sing N N 132 G "C5'" "H5'" sing N N 133 G "C5'" "H5''" sing N N 134 G "C4'" "O4'" sing N N 135 G "C4'" "C3'" sing N N 136 G "C4'" "H4'" sing N N 137 G "O4'" "C1'" sing N N 138 G "C3'" "O3'" sing N N 139 G "C3'" "C2'" sing N N 140 G "C3'" "H3'" sing N N 141 G "O3'" "HO3'" sing N N 142 G "C2'" "O2'" sing N N 143 G "C2'" "C1'" sing N N 144 G "C2'" "H2'" sing N N 145 G "O2'" "HO2'" sing N N 146 G "C1'" N9 sing N N 147 G "C1'" "H1'" sing N N 148 G N9 C8 sing Y N 149 G N9 C4 sing Y N 150 G C8 N7 doub Y N 151 G C8 H8 sing N N 152 G N7 C5 sing Y N 153 G C5 C6 sing N N 154 G C5 C4 doub Y N 155 G C6 O6 doub N N 156 G C6 N1 sing N N 157 G N1 C2 sing N N 158 G N1 H1 sing N N 159 G C2 N2 sing N N 160 G C2 N3 doub N N 161 G N2 H21 sing N N 162 G N2 H22 sing N N 163 G N3 C4 sing N N 164 HOH O H1 sing N N 165 HOH O H2 sing N N 166 LCC "O5'" "C5'" sing N N 167 LCC "O5'" P sing N N 168 LCC "C5'" "C4'" sing N N 169 LCC "C5'" "H5'1" sing N N 170 LCC "C5'" "H5'2" sing N N 171 LCC "C4'" "O4'" sing N N 172 LCC "C4'" "C3'" sing N N 173 LCC "C4'" "C6'" sing N N 174 LCC "O4'" "C1'" sing N N 175 LCC "C1'" N1 sing N N 176 LCC "C1'" "C2'" sing N N 177 LCC "C1'" "H1'" sing N N 178 LCC N1 C6 sing N N 179 LCC N1 C2 sing N N 180 LCC C6 C5 doub N N 181 LCC C6 H6 sing N N 182 LCC C5 C5M sing N N 183 LCC C5 C4 sing N N 184 LCC C5M H5M1 sing N N 185 LCC C5M H5M2 sing N N 186 LCC C5M H5M3 sing N N 187 LCC C4 N4 sing N N 188 LCC C4 N3 doub N N 189 LCC N4 H41 sing N N 190 LCC N4 H42 sing N N 191 LCC N3 C2 sing N N 192 LCC C2 O2 doub N N 193 LCC "C3'" "C2'" sing N N 194 LCC "C3'" "O3'" sing N N 195 LCC "C3'" "H3'" sing N N 196 LCC "C2'" "O2'" sing N N 197 LCC "C2'" "H2'1" sing N N 198 LCC "O2'" "C6'" sing N N 199 LCC "O3'" H3T sing N N 200 LCC "C6'" "H6'1" sing N N 201 LCC "C6'" "H6'2" sing N N 202 LCC P O1P sing N N 203 LCC P O2P doub N N 204 LCC P OXT sing N N 205 LCC O1P H1P sing N N 206 LCC OXT HXT sing N N 207 LCG P OP1 doub N N 208 LCG P "O5'" sing N N 209 LCG P OP2 sing N N 210 LCG P OP3 sing N N 211 LCG "O5'" "C5'" sing N N 212 LCG "C5'" "C4'" sing N N 213 LCG "C5'" "H5'" sing N N 214 LCG "C5'" "H5''" sing N N 215 LCG "C3'" "C2'" sing N N 216 LCG "C3'" "C4'" sing N N 217 LCG "C3'" "O3'" sing N N 218 LCG "C3'" "H3'" sing N N 219 LCG "C6'" "C4'" sing N N 220 LCG "C6'" "O2'" sing N N 221 LCG "C6'" "H6'1" sing N N 222 LCG "C6'" "H6'2" sing N N 223 LCG N9 C8 sing Y N 224 LCG N9 C4 sing Y N 225 LCG N9 "C1'" sing N N 226 LCG C8 N7 doub Y N 227 LCG C8 H8 sing N N 228 LCG C4 C5 doub Y N 229 LCG C4 N3 sing N N 230 LCG N7 C5 sing Y N 231 LCG C5 C6 sing N N 232 LCG C6 O6 doub N N 233 LCG C6 N1 sing N N 234 LCG "C2'" "C1'" sing N N 235 LCG "C2'" "O2'" sing N N 236 LCG "C2'" "H2'" sing N N 237 LCG "C4'" "O4'" sing N N 238 LCG "C1'" "O4'" sing N N 239 LCG "C1'" "H1'" sing N N 240 LCG C2 N1 sing N N 241 LCG C2 N2 sing N N 242 LCG C2 N3 doub N N 243 LCG N1 H1 sing N N 244 LCG OP2 HOP2 sing N N 245 LCG N2 H21 sing N N 246 LCG N2 H22 sing N N 247 LCG "O3'" "HO3'" sing N N 248 LCG OP3 HOP3 sing N N 249 U OP3 P sing N N 250 U OP3 HOP3 sing N N 251 U P OP1 doub N N 252 U P OP2 sing N N 253 U P "O5'" sing N N 254 U OP2 HOP2 sing N N 255 U "O5'" "C5'" sing N N 256 U "C5'" "C4'" sing N N 257 U "C5'" "H5'" sing N N 258 U "C5'" "H5''" sing N N 259 U "C4'" "O4'" sing N N 260 U "C4'" "C3'" sing N N 261 U "C4'" "H4'" sing N N 262 U "O4'" "C1'" sing N N 263 U "C3'" "O3'" sing N N 264 U "C3'" "C2'" sing N N 265 U "C3'" "H3'" sing N N 266 U "O3'" "HO3'" sing N N 267 U "C2'" "O2'" sing N N 268 U "C2'" "C1'" sing N N 269 U "C2'" "H2'" sing N N 270 U "O2'" "HO2'" sing N N 271 U "C1'" N1 sing N N 272 U "C1'" "H1'" sing N N 273 U N1 C2 sing N N 274 U N1 C6 sing N N 275 U C2 O2 doub N N 276 U C2 N3 sing N N 277 U N3 C4 sing N N 278 U N3 H3 sing N N 279 U C4 O4 doub N N 280 U C4 C5 sing N N 281 U C5 C6 doub N N 282 U C5 H5 sing N N 283 U C6 H6 sing N N 284 # _ndb_struct_conf_na.entry_id 6C8I _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A LCG 4 1_555 B C 13 1_555 -0.270 -0.239 0.083 -2.798 -16.628 -1.689 1 A_LCG4:C13_B A 4 ? B 13 ? 19 1 1 A A 5 1_555 B U 12 1_555 0.052 -0.083 0.159 6.719 -12.248 -2.687 2 A_A5:U12_B A 5 ? B 12 ? 20 1 1 A C 6 1_555 B G 11 1_555 0.132 -0.145 -0.057 8.509 -19.086 -0.271 3 A_C6:G11_B A 6 ? B 11 ? 19 1 1 A U 7 1_555 B A 10 1_555 -0.136 -0.105 -0.047 2.875 -15.544 1.746 4 A_U7:A10_B A 7 ? B 10 ? 20 1 1 A U 8 1_555 B A 9 1_555 -0.012 -0.061 -0.212 3.572 -12.060 0.421 5 A_U8:A9_B A 8 ? B 9 ? 20 1 1 A A 9 1_555 B U 8 1_555 0.055 -0.109 0.121 -3.488 -18.032 4.007 6 A_A9:U8_B A 9 ? B 8 ? 20 1 1 A A 10 1_555 B U 7 1_555 0.114 -0.131 -0.107 -5.386 -12.705 0.449 7 A_A10:U7_B A 10 ? B 7 ? 20 1 1 A G 11 1_555 B C 6 1_555 -0.190 -0.161 -0.081 -7.378 -16.592 -0.024 8 A_G11:C6_B A 11 ? B 6 ? 19 1 1 A U 12 1_555 B A 5 1_555 0.012 -0.061 0.000 -0.811 -10.433 -3.955 9 A_U12:A5_B A 12 ? B 5 ? 20 1 1 A C 13 1_555 B LCG 4 1_555 0.170 -0.221 0.056 2.313 -12.196 -0.992 10 A_C13:LCG4_B A 13 ? B 4 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A LCG 4 1_555 B C 13 1_555 A A 5 1_555 B U 12 1_555 -0.093 -1.181 3.066 -0.544 3.419 32.391 -2.654 0.079 2.930 6.108 0.971 32.571 1 AA_LCG4A5:U12C13_BB A 4 ? B 13 ? A 5 ? B 12 ? 1 A A 5 1_555 B U 12 1_555 A C 6 1_555 B G 11 1_555 0.441 -1.554 3.255 2.704 3.344 32.196 -3.351 -0.326 3.108 5.997 -4.849 32.475 2 AA_A5C6:G11U12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A C 6 1_555 B G 11 1_555 A U 7 1_555 B A 10 1_555 -0.391 -1.684 3.336 -2.289 12.095 29.641 -5.075 0.325 2.498 22.461 4.250 32.043 3 AA_C6U7:A10G11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A U 7 1_555 B A 10 1_555 A U 8 1_555 B A 9 1_555 -0.170 -1.058 3.232 -0.918 11.344 32.178 -3.496 0.154 2.718 19.712 1.594 34.081 4 AA_U7U8:A9A10_BB A 7 ? B 10 ? A 8 ? B 9 ? 1 A U 8 1_555 B A 9 1_555 A A 9 1_555 B U 8 1_555 0.533 -1.497 3.288 -0.494 19.702 31.554 -4.690 -0.897 2.030 32.563 0.817 37.070 5 AA_U8A9:U8A9_BB A 8 ? B 9 ? A 9 ? B 8 ? 1 A A 9 1_555 B U 8 1_555 A A 10 1_555 B U 7 1_555 -0.576 -1.343 3.304 1.332 5.973 32.824 -3.301 1.218 2.995 10.456 -2.332 33.374 6 AA_A9A10:U7U8_BB A 9 ? B 8 ? A 10 ? B 7 ? 1 A A 10 1_555 B U 7 1_555 A G 11 1_555 B C 6 1_555 0.284 -1.644 3.309 1.648 8.586 28.841 -4.821 -0.228 2.728 16.758 -3.216 30.110 7 AA_A10G11:C6U7_BB A 10 ? B 7 ? A 11 ? B 6 ? 1 A G 11 1_555 B C 6 1_555 A U 12 1_555 B A 5 1_555 -0.417 -1.431 3.131 -1.966 4.468 31.948 -3.308 0.424 2.929 8.058 3.546 32.309 8 AA_G11U12:A5C6_BB A 11 ? B 6 ? A 12 ? B 5 ? 1 A U 12 1_555 B A 5 1_555 A C 13 1_555 B LCG 4 1_555 0.412 -1.251 3.206 0.339 5.111 32.467 -3.044 -0.673 2.984 9.071 -0.601 32.857 9 AA_U12C13:LCG4A5_BB A 12 ? B 5 ? A 13 ? B 4 ? # _pdbx_audit_support.funding_organization 'Howard Hughes Medical Institute (HHMI)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine" EQ4 4 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 5DHC _pdbx_initial_refinement_model.details ? # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #