data_5K8H # _entry.id 5K8H # _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 5K8H pdb_00005k8h 10.2210/pdb5k8h/pdb WWPDB D_1000221863 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5K8H _pdbx_database_status.recvd_initial_deposition_date 2016-05-30 _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 'Gleghorn, M.L.' 1 ? 'Maquat, L.E.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 44 _citation.language ? _citation.page_first 8417 _citation.page_last 8424 _citation.title ;Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation. ; _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkw526 _citation.pdbx_database_id_PubMed 27288442 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gleghorn, M.L.' 1 ? primary 'Zhao, J.' 2 ? primary 'Turner, D.H.' 3 ? primary 'Maquat, L.E.' 4 ? # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 5K8H _cell.details ? _cell.formula_units_Z ? _cell.length_a 21.253 _cell.length_a_esd ? _cell.length_b 21.253 _cell.length_b_esd ? _cell.length_c 14.946 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _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 5K8H _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' _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 7-mer' 2259.483 1 ? ? ? ? 2 non-polymer syn 'AMMONIUM ION' 18.038 1 ? ? ? ? 3 water nat water 18.015 8 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code AAAAAAA _entity_poly.pdbx_seq_one_letter_code_can AAAAAAA _entity_poly.pdbx_strand_id A _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 A n 1 2 A n 1 3 A n 1 4 A n 1 5 A n 1 6 A n 1 7 A 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 7 _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 5K8H _struct_ref.pdbx_db_accession 5K8H _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5K8H _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 7 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5K8H _struct_ref_seq.db_align_beg 0 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 0 _struct_ref_seq.pdbx_auth_seq_align_end 6 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 NH4 non-polymer . 'AMMONIUM ION' ? 'H4 N 1' 18.038 # _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 5K8H _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 1.33 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 8 _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 3.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;rA7 dissolved in water to 10 mM and was diluted 1/10 v/v in 0.75% PEG 1000. One uL of this was mixed with 1 uL of the following reservoir solution: (0.24 M ammonium sulfate and 0.06 M citric acid pH 3.5) to generate a hanging drop over 1 mL of this reservoir solution. ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-03-22 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.95530 _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 'SSRL BEAMLINE BL12-2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.95530 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL12-2 _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5K8H _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.069 _reflns.d_resolution_low 21.25 _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 1679 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 97.6 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 19.3 _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 15 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all 0.032 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.994 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.069 _reflns_shell.d_res_low 1.14 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 3.1 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all 247 _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 87.2 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 1.059 _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 8.9 _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 0.333 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.987 _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 5K8H _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 1.069 _refine.ls_d_res_low 15.028 _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 1619 _refine.ls_number_reflns_R_free 146 _refine.ls_number_reflns_R_work 1473 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 94.84 _refine.ls_percent_reflns_R_free 9.02 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1063 _refine.ls_R_factor_R_free 0.1080 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1061 _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 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'rA2 section of the 4JRD' _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 ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 44 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 8 _refine_hist.number_atoms_total 53 _refine_hist.d_res_high 1.069 _refine_hist.d_res_low 15.028 # _refine_ls_shell.R_factor_R_free 0.3975 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.3180 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs 0.318 _refine_ls_shell.d_res_high 1.069 _refine_ls_shell.d_res_low 1.107 _refine_ls_shell.number_reflns_R_free ? _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_fsc_free ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? # _struct.entry_id 5K8H _struct.title 'The X-ray crystal structure of a parallel poly(rA) double helix generated by rA7 at acidic pH' _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 5K8H _struct_keywords.text 'parallel double-helix poly(rA) acidic pH adenine N1 protonation, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details ;The asymmetric unit is rA2, however the input RNA polymer is rA7, and this forms a continual parallel poly(rA) double helix structure. This structure is referred to as a "staggered zipper" since the rA7 strands overlap in a many different registers relative to their opposite, paired strands, to form the helix. ; # 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 hydrog1 hydrog ? ? A A 2 N6 ? ? ? 1_555 A A 2 N7 ? ? A A 1 A A 1 2_835 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog2 hydrog ? ? A A 2 N7 ? ? ? 1_555 A A 2 N6 ? ? A A 1 A A 1 2_835 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog3 hydrog ? ? A A 3 N6 ? ? ? 1_555 A A 3 N7 ? ? A A 2 A A 2 2_835 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog4 hydrog ? ? A A 3 N7 ? ? ? 1_555 A A 3 N6 ? ? A A 2 A A 2 2_835 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id NH4 _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'binding site for residue NH4 A 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 A A 2 ? A A 1 . ? 7_736 ? 2 AC1 4 A A 2 ? A A 1 . ? 4_755 ? 3 AC1 4 A A 2 ? A A 1 . ? 1_555 ? 4 AC1 4 A A 3 ? A A 2 . ? 1_555 ? # _atom_sites.entry_id 5K8H _atom_sites.fract_transf_matrix[1][1] 0.047053 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.047053 _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] 0.066908 _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 H N O P # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 P P . A A 1 2 ? 28.742 -16.458 5.094 1.00 24.60 ? 1 A A P 1 ATOM 2 O OP1 . A A 1 2 ? 28.458 -15.384 6.081 1.00 29.35 ? 1 A A OP1 1 ATOM 3 O OP2 . A A 1 2 ? 30.221 -16.843 5.039 0.94 21.82 ? 1 A A OP2 1 ATOM 4 O "O5'" . A A 1 2 ? 27.850 -17.815 5.246 0.83 21.42 ? 1 A A "O5'" 1 ATOM 5 C "C5'" . A A 1 2 ? 26.513 -17.680 5.364 1.00 23.87 ? 1 A A "C5'" 1 ATOM 6 C "C4'" . A A 1 2 ? 25.784 -18.967 5.247 1.00 24.23 ? 1 A A "C4'" 1 ATOM 7 O "O4'" . A A 1 2 ? 26.211 -19.548 4.003 1.00 25.07 ? 1 A A "O4'" 1 ATOM 8 C "C3'" . A A 1 2 ? 26.203 -20.000 6.364 1.00 20.17 ? 1 A A "C3'" 1 ATOM 9 O "O3'" . A A 1 2 ? 25.475 -19.877 7.467 1.00 20.55 ? 1 A A "O3'" 1 ATOM 10 C "C2'" . A A 1 2 ? 25.941 -21.239 5.604 1.00 22.79 ? 1 A A "C2'" 1 ATOM 11 O "O2'" . A A 1 2 ? 24.472 -21.576 5.596 1.00 28.45 ? 1 A A "O2'" 1 ATOM 12 C "C1'" . A A 1 2 ? 26.328 -20.917 4.184 1.00 22.56 ? 1 A A "C1'" 1 ATOM 13 N N9 . A A 1 2 ? 27.811 -21.349 4.133 1.00 17.39 ? 1 A A N9 1 ATOM 14 C C8 . A A 1 2 ? 28.831 -20.502 4.030 1.00 16.65 ? 1 A A C8 1 ATOM 15 N N7 . A A 1 2 ? 30.020 -21.108 4.084 1.00 15.64 ? 1 A A N7 1 ATOM 16 C C5 . A A 1 2 ? 29.721 -22.471 4.185 1.00 14.96 ? 1 A A C5 1 ATOM 17 C C6 . A A 1 2 ? 30.620 -23.538 4.340 1.00 16.26 ? 1 A A C6 1 ATOM 18 N N6 . A A 1 2 ? 31.850 -23.565 4.370 1.00 16.19 ? 1 A A N6 1 ATOM 19 N N1 . A A 1 2 ? 29.855 -24.694 4.475 1.00 19.86 ? 1 A A N1 1 ATOM 20 C C2 . A A 1 2 ? 28.444 -24.785 4.436 1.00 22.78 ? 1 A A C2 1 ATOM 21 N N3 . A A 1 2 ? 27.680 -23.737 4.311 1.00 20.13 ? 1 A A N3 1 ATOM 22 C C4 . A A 1 2 ? 28.375 -22.634 4.203 1.00 17.28 ? 1 A A C4 1 ATOM 23 H "H5'" . A A 1 2 ? 26.198 -17.080 4.670 1.00 28.65 ? 1 A A "H5'" 1 ATOM 24 H "H5''" . A A 1 2 ? 26.315 -17.288 6.229 1.00 28.65 ? 1 A A "H5''" 1 ATOM 25 H "H4'" . A A 1 2 ? 24.825 -18.824 5.249 1.00 29.08 ? 1 A A "H4'" 1 ATOM 26 H "H3'" . A A 1 2 ? 27.148 -19.918 6.565 1.00 24.20 ? 1 A A "H3'" 1 ATOM 27 H "H2'" . A A 1 2 ? 26.467 -21.977 5.948 1.00 27.35 ? 1 A A "H2'" 1 ATOM 28 H "H1'" . A A 1 2 ? 25.789 -21.412 3.547 1.00 27.07 ? 1 A A "H1'" 1 ATOM 29 H H8 . A A 1 2 ? 28.728 -19.580 3.966 1.00 19.98 ? 1 A A H8 1 ATOM 30 H H61 . A A 1 2 ? 32.298 -22.836 4.284 1.00 19.43 ? 1 A A H61 1 ATOM 31 H H62 . A A 1 2 ? 32.261 -24.313 4.477 1.00 19.43 ? 1 A A H62 1 ATOM 32 H H2 . A A 1 2 ? 28.046 -25.621 4.527 1.00 27.34 ? 1 A A H2 1 ATOM 33 P P . A A 1 3 ? 26.177 -20.207 8.847 0.82 15.69 ? 2 A A P 1 ATOM 34 O OP1 . A A 1 3 ? 25.160 -19.887 9.892 0.99 19.66 ? 2 A A OP1 1 ATOM 35 O OP2 . A A 1 3 ? 27.462 -19.537 8.915 0.90 17.35 ? 2 A A OP2 1 ATOM 36 O "O5'" . A A 1 3 ? 26.554 -21.785 8.763 0.95 15.49 ? 2 A A "O5'" 1 ATOM 37 C "C5'" . A A 1 3 ? 25.522 -22.805 8.848 1.00 18.49 ? 2 A A "C5'" 1 ATOM 38 C "C4'" . A A 1 3 ? 26.087 -24.195 8.834 1.00 17.40 ? 2 A A "C4'" 1 ATOM 39 O "O4'" . A A 1 3 ? 26.885 -24.351 7.651 1.00 15.30 ? 2 A A "O4'" 1 ATOM 40 C "C3'" . A A 1 3 ? 27.086 -24.542 9.961 1.00 17.98 ? 2 A A "C3'" 1 ATOM 41 O "O3'" . A A 1 3 ? 26.418 -24.816 11.136 1.00 21.68 ? 2 A A "O3'" 1 ATOM 42 C "C2'" . A A 1 3 ? 27.913 -25.629 9.327 1.00 17.69 ? 2 A A "C2'" 1 ATOM 43 O "O2'" . A A 1 3 ? 27.187 -26.864 9.412 1.00 20.81 ? 2 A A "O2'" 1 ATOM 44 C "C1'" . A A 1 3 ? 28.022 -25.156 7.925 1.00 15.37 ? 2 A A "C1'" 1 ATOM 45 N N9 . A A 1 3 ? 29.259 -24.313 7.832 1.00 14.59 ? 2 A A N9 1 ATOM 46 C C8 . A A 1 3 ? 29.299 -22.932 7.728 1.00 14.12 ? 2 A A C8 1 ATOM 47 N N7 . A A 1 3 ? 30.524 -22.502 7.782 1.00 12.38 ? 2 A A N7 1 ATOM 48 C C5 . A A 1 3 ? 31.297 -23.657 7.901 1.00 11.91 ? 2 A A C5 1 ATOM 49 C C6 . A A 1 3 ? 32.653 -23.819 8.079 1.00 12.06 ? 2 A A C6 1 ATOM 50 N N6 . A A 1 3 ? 33.547 -22.889 8.117 1.00 13.45 ? 2 A A N6 1 ATOM 51 N N1 . A A 1 3 ? 33.088 -25.114 8.198 1.00 14.25 ? 2 A A N1 1 ATOM 52 C C2 . A A 1 3 ? 32.238 -26.088 8.206 1.00 16.50 ? 2 A A C2 1 ATOM 53 N N3 . A A 1 3 ? 30.968 -26.040 8.020 1.00 16.39 ? 2 A A N3 1 ATOM 54 C C4 . A A 1 3 ? 30.524 -24.794 7.923 1.00 13.65 ? 2 A A C4 1 ATOM 55 H "H5'" . A A 1 3 ? 24.919 -22.704 8.095 1.00 22.19 ? 2 A A "H5'" 1 ATOM 56 H "H5''" . A A 1 3 ? 25.022 -22.678 9.670 1.00 22.19 ? 2 A A "H5''" 1 ATOM 57 H "H4'" . A A 1 3 ? 25.364 -24.842 8.827 1.00 20.89 ? 2 A A "H4'" 1 ATOM 58 H "H3'" . A A 1 3 ? 27.658 -23.773 10.110 1.00 21.57 ? 2 A A "H3'" 1 ATOM 59 H "H2'" . A A 1 3 ? 28.785 -25.698 9.746 1.00 21.23 ? 2 A A "H2'" 1 ATOM 60 H "H1'" . A A 1 3 ? 28.069 -25.906 7.312 1.00 18.45 ? 2 A A "H1'" 1 ATOM 61 H H8 . A A 1 3 ? 28.550 -22.386 7.656 1.00 16.94 ? 2 A A H8 1 ATOM 62 H H61 . A A 1 3 ? 33.313 -22.065 8.046 1.00 16.15 ? 2 A A H61 1 ATOM 63 H H62 . A A 1 3 ? 34.377 -23.094 8.214 1.00 16.15 ? 2 A A H62 1 ATOM 64 H H2 . A A 1 3 ? 32.603 -26.941 8.276 1.00 19.80 ? 2 A A H2 1 HETATM 65 N N . NH4 B 2 . ? 28.160 -16.919 8.687 1.00 18.54 ? 101 NH4 A N 1 HETATM 66 O O . HOH C 3 . ? 22.257 -20.229 6.259 1.00 56.51 ? 201 HOH A O 1 HETATM 67 O O . HOH C 3 . ? 32.736 -15.465 4.861 1.00 30.00 ? 202 HOH A O 1 HETATM 68 O O . HOH C 3 . ? 29.662 -14.244 10.152 1.00 50.40 ? 203 HOH A O 1 HETATM 69 O O . HOH C 3 . ? 21.631 -19.785 4.553 0.31 30.00 ? 204 HOH A O 1 HETATM 70 O O . HOH C 3 . ? 31.276 -13.308 6.544 1.00 52.34 ? 205 HOH A O 1 HETATM 71 O O . HOH C 3 . ? 22.811 -22.674 11.547 1.00 61.79 ? 206 HOH A O 1 HETATM 72 O O . HOH C 3 . ? 31.109 -29.792 9.480 1.00 64.56 ? 207 HOH A O 1 HETATM 73 O O . HOH C 3 . ? 28.797 -28.959 6.149 1.00 33.52 ? 208 HOH A O 1 # loop_ _atom_site_anisotrop.id _atom_site_anisotrop.type_symbol _atom_site_anisotrop.pdbx_label_atom_id _atom_site_anisotrop.pdbx_label_alt_id _atom_site_anisotrop.pdbx_label_comp_id _atom_site_anisotrop.pdbx_label_asym_id _atom_site_anisotrop.pdbx_label_seq_id _atom_site_anisotrop.pdbx_PDB_ins_code _atom_site_anisotrop.U[1][1] _atom_site_anisotrop.U[2][2] _atom_site_anisotrop.U[3][3] _atom_site_anisotrop.U[1][2] _atom_site_anisotrop.U[1][3] _atom_site_anisotrop.U[2][3] _atom_site_anisotrop.pdbx_auth_seq_id _atom_site_anisotrop.pdbx_auth_comp_id _atom_site_anisotrop.pdbx_auth_asym_id _atom_site_anisotrop.pdbx_auth_atom_id 1 P P . A A 2 ? 0.4886 0.2944 0.1516 0.1750 0.0212 -0.0001 1 A A P 2 O OP1 . A A 2 ? 0.5904 0.3412 0.1834 0.1966 0.0413 0.0025 1 A A OP1 3 O OP2 . A A 2 ? 0.4600 0.2347 0.1342 0.1221 -0.0381 -0.0180 1 A A OP2 4 O "O5'" . A A 2 ? 0.3732 0.2644 0.1761 0.1453 0.0993 0.0624 1 A A "O5'" 5 C "C5'" . A A 2 ? 0.3684 0.3607 0.1779 0.1741 0.0887 0.0717 1 A A "C5'" 6 C "C4'" . A A 2 ? 0.2847 0.4071 0.2290 0.1347 0.0628 0.0539 1 A A "C4'" 7 O "O4'" . A A 2 ? 0.3085 0.4813 0.1629 0.1358 0.0284 0.0642 1 A A "O4'" 8 C "C3'" . A A 2 ? 0.2364 0.4166 0.1133 0.0706 0.0189 0.0104 1 A A "C3'" 9 O "O3'" . A A 2 ? 0.2277 0.3886 0.1645 0.0610 0.0312 0.0513 1 A A "O3'" 10 C "C2'" . A A 2 ? 0.1889 0.5194 0.1576 0.0841 0.0275 0.0754 1 A A "C2'" 11 O "O2'" . A A 2 ? 0.2991 0.6070 0.1749 0.0084 0.0189 0.0705 1 A A "O2'" 12 C "C1'" . A A 2 ? 0.2189 0.4634 0.1749 0.0521 0.0044 0.0303 1 A A "C1'" 13 N N9 . A A 2 ? 0.2563 0.2837 0.1206 0.0297 0.0336 0.0436 1 A A N9 14 C C8 . A A 2 ? 0.2813 0.2290 0.1223 0.0373 0.0358 0.0387 1 A A C8 15 N N7 . A A 2 ? 0.2411 0.2418 0.1113 0.0263 0.0053 0.0156 1 A A N7 16 C C5 . A A 2 ? 0.2230 0.2581 0.0873 -0.0312 0.0059 0.0116 1 A A C5 17 C C6 . A A 2 ? 0.3411 0.1870 0.0897 0.0104 0.0236 0.0055 1 A A C6 18 N N6 . A A 2 ? 0.2497 0.2424 0.1231 0.0394 0.0157 0.0049 1 A A N6 19 N N1 . A A 2 ? 0.3628 0.2629 0.1287 -0.0512 0.0183 0.0024 1 A A N1 20 C C2 . A A 2 ? 0.5039 0.2226 0.1391 -0.1145 0.0031 0.0112 1 A A C2 21 N N3 . A A 2 ? 0.3423 0.2754 0.1472 -0.0750 0.0046 0.0063 1 A A N3 22 C C4 . A A 2 ? 0.3097 0.2464 0.1005 -0.0414 -0.0055 0.0148 1 A A C4 33 P P . A A 3 ? 0.2030 0.2576 0.1357 0.0107 0.0238 0.0168 2 A A P 34 O OP1 . A A 3 ? 0.2498 0.3111 0.1860 0.0111 0.0483 0.0238 2 A A OP1 35 O OP2 . A A 3 ? 0.2342 0.2298 0.1953 0.0034 0.0311 0.0096 2 A A OP2 36 O "O5'" . A A 3 ? 0.1873 0.2382 0.1629 -0.0190 0.0205 -0.0075 2 A A "O5'" 37 C "C5'" . A A 3 ? 0.1942 0.3515 0.1568 -0.0303 0.0066 0.0010 2 A A "C5'" 38 C "C4'" . A A 3 ? 0.1936 0.2998 0.1679 -0.0728 -0.0012 0.0087 2 A A "C4'" 39 O "O4'" . A A 3 ? 0.2018 0.2412 0.1384 -0.0473 -0.0076 -0.0023 2 A A "O4'" 40 C "C3'" . A A 3 ? 0.2398 0.3352 0.1081 -0.1206 -0.0037 0.0236 2 A A "C3'" 41 O "O3'" . A A 3 ? 0.2575 0.4322 0.1340 -0.1388 -0.0050 0.0254 2 A A "O3'" 42 C "C2'" . A A 3 ? 0.2722 0.2791 0.1209 -0.1180 -0.0044 0.0298 2 A A "C2'" 43 O "O2'" . A A 3 ? 0.3300 0.2992 0.1614 -0.1403 -0.0512 0.0622 2 A A "O2'" 44 C "C1'" . A A 3 ? 0.2290 0.2042 0.1509 -0.0753 -0.0248 0.0147 2 A A "C1'" 45 N N9 . A A 3 ? 0.2261 0.2126 0.1158 -0.0409 -0.0049 -0.0091 2 A A N9 46 C C8 . A A 3 ? 0.2173 0.2067 0.1124 -0.0535 0.0008 0.0005 2 A A C8 47 N N7 . A A 3 ? 0.1729 0.1823 0.1153 -0.0122 0.0043 0.0020 2 A A N7 48 C C5 . A A 3 ? 0.1754 0.1866 0.0906 -0.0164 0.0137 -0.0008 2 A A C5 49 C C6 . A A 3 ? 0.1679 0.1926 0.0978 -0.0110 0.0211 0.0050 2 A A C6 50 N N6 . A A 3 ? 0.1834 0.2041 0.1237 0.0061 0.0089 0.0079 2 A A N6 51 N N1 . A A 3 ? 0.2026 0.2056 0.1332 0.0098 0.0058 0.0121 2 A A N1 52 C C2 . A A 3 ? 0.2554 0.2374 0.1341 -0.0173 0.0012 0.0012 2 A A C2 53 N N3 . A A 3 ? 0.2942 0.1784 0.1500 -0.0403 -0.0026 -0.0034 2 A A N3 54 C C4 . A A 3 ? 0.2115 0.1949 0.1122 -0.0373 -0.0038 -0.0031 2 A A C4 65 N N . NH4 B . ? 0.2121 0.2249 0.2673 0.0502 0.0390 -0.0021 101 NH4 A N 66 O O . HOH C . ? 0.5406 0.4594 1.1470 0.0792 -0.0530 0.0049 201 HOH A O 67 O O . HOH C . ? 0.3799 0.3799 0.3799 0.0000 0.0000 0.0000 202 HOH A O 68 O O . HOH C . ? 0.3361 0.4370 1.1417 0.0602 0.0412 -0.0435 203 HOH A O 69 O O . HOH C . ? 0.3799 0.3799 0.3799 0.0000 0.0000 0.0000 204 HOH A O 70 O O . HOH C . ? 0.7151 0.8003 0.4733 0.0129 0.0436 0.1014 205 HOH A O 71 O O . HOH C . ? 0.7653 0.7169 0.8654 -0.2297 0.0035 0.2180 206 HOH A O 72 O O . HOH C . ? 0.7917 0.6020 1.0593 0.2636 -0.4759 -0.2422 207 HOH A O 73 O O . HOH C . ? 0.2946 0.6175 0.3615 -0.0097 0.0461 -0.1078 208 HOH A O # 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 A 1 0 ? ? ? A . n A 1 2 A 2 1 1 A A A . n A 1 3 A 3 2 2 A A A . n A 1 4 A 4 3 ? ? ? A . n A 1 5 A 5 4 ? ? ? A . n A 1 6 A 6 5 ? ? ? A . n A 1 7 A 7 6 ? ? ? A . 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 B 2 NH4 1 101 1 NH4 NH4 A . C 3 HOH 1 201 7 HOH HOH A . C 3 HOH 2 202 10 HOH HOH A . C 3 HOH 3 203 4 HOH HOH A . C 3 HOH 4 204 11 HOH HOH A . C 3 HOH 5 205 9 HOH HOH A . C 3 HOH 6 206 5 HOH HOH A . C 3 HOH 7 207 1 HOH HOH A . C 3 HOH 8 208 2 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C 1 2 A,B,C # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_835 -x+3,-y-2,z -1.0000000000 0.0000000000 0.0000000000 63.7590000000 0.0000000000 -1.0000000000 0.0000000000 -42.5060000000 0.0000000000 0.0000000000 1.0000000000 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 2016-07-06 2 'Structure model' 1 1 2016-07-13 3 'Structure model' 1 2 2016-07-20 4 'Structure model' 1 3 2016-08-17 5 'Structure model' 1 4 2016-10-12 6 'Structure model' 1 5 2017-09-20 7 'Structure model' 1 6 2019-12-04 8 'Structure model' 1 7 2023-09-27 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 4 'Structure model' 'Structure summary' 4 5 'Structure model' 'Database references' 5 6 'Structure model' 'Author supporting evidence' 6 6 'Structure model' 'Database references' 7 6 'Structure model' 'Derived calculations' 8 7 'Structure model' 'Author supporting evidence' 9 8 'Structure model' 'Data collection' 10 8 'Structure model' 'Database references' 11 8 '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 6 'Structure model' citation 2 6 'Structure model' pdbx_audit_support 3 6 'Structure model' pdbx_struct_oper_list 4 7 'Structure model' pdbx_audit_support 5 8 'Structure model' chem_comp_atom 6 8 'Structure model' chem_comp_bond 7 8 'Structure model' database_2 8 8 'Structure model' diffrn_radiation_wavelength 9 8 '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 6 'Structure model' '_citation.journal_id_CSD' 2 6 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 3 7 'Structure model' '_pdbx_audit_support.funding_organization' 4 8 'Structure model' '_database_2.pdbx_DOI' 5 8 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.10.1_2155: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 P _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 A _pdbx_validate_symm_contact.auth_seq_id_1 1 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 "O3'" _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 A _pdbx_validate_symm_contact.auth_seq_id_2 2 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 4_754 _pdbx_validate_symm_contact.dist 1.63 # 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 "O5'" A A 1 ? ? "C5'" A A 1 ? ? 1.349 1.420 -0.071 0.009 N 2 1 "O3'" A A 1 ? ? "C3'" A A 1 ? ? 1.327 1.417 -0.090 0.014 N 3 1 "C2'" A A 1 ? ? "O2'" A A 1 ? ? 1.507 1.420 0.087 0.010 N 4 1 N1 A A 1 ? ? C2 A A 1 ? ? 1.414 1.339 0.075 0.009 N 5 1 C6 A A 1 ? ? N6 A A 1 ? ? 1.231 1.335 -0.104 0.008 N # 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 N9 A A 1 ? ? "C1'" A A 1 ? ? "C2'" A A 1 ? ? 102.58 112.00 -9.42 1.10 N 2 1 C6 A A 1 ? ? N1 A A 1 ? ? C2 A A 1 ? ? 126.77 118.60 8.17 0.60 N 3 1 N1 A A 1 ? ? C2 A A 1 ? ? N3 A A 1 ? ? 122.40 129.30 -6.90 0.50 N 4 1 C4 A A 1 ? ? C5 A A 1 ? ? C6 A A 1 ? ? 122.88 117.00 5.88 0.50 N 5 1 C5 A A 1 ? ? C6 A A 1 ? ? N1 A A 1 ? ? 106.85 117.70 -10.85 0.50 N 6 1 C6 A A 1 ? ? C5 A A 1 ? ? N7 A A 1 ? ? 127.70 132.30 -4.60 0.70 N 7 1 C5 A A 1 ? ? C6 A A 1 ? ? N6 A A 1 ? ? 131.26 123.70 7.56 0.80 N 8 1 N7 A A 2 ? ? C8 A A 2 ? ? N9 A A 2 ? ? 110.73 113.80 -3.07 0.50 N 9 1 C8 A A 2 ? ? N9 A A 2 ? ? C4 A A 2 ? ? 109.36 105.80 3.56 0.40 N 10 1 N9 A A 2 ? ? C4 A A 2 ? ? C5 A A 2 ? ? 103.30 105.80 -2.50 0.40 N # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A A 0 ? A A 1 2 1 Y 1 A A 3 ? A A 4 3 1 Y 1 A A 4 ? A A 5 4 1 Y 1 A A 5 ? A A 6 5 1 Y 1 A A 6 ? A A 7 # 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 HOH O O N N 38 HOH H1 H N N 39 HOH H2 H N N 40 NH4 N N N N 41 NH4 HN1 H N N 42 NH4 HN2 H N N 43 NH4 HN3 H N N 44 NH4 HN4 H N N 45 # 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 HOH O H1 sing N N 40 HOH O H2 sing N N 41 NH4 N HN1 sing N N 42 NH4 N HN2 sing N N 43 NH4 N HN3 sing N N 44 NH4 N HN4 sing N N 45 # _ndb_struct_conf_na.entry_id 5K8H _ndb_struct_conf_na.feature '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 A 2 1_555 A A 2 2_835 6.050 -5.029 0.000 -3.360 -10.764 180.000 1 A_A1:A1_A A 1 ? A 1 ? 2 8 1 A A 3 1_555 A A 3 2_835 6.078 -5.010 0.000 -3.420 -12.013 180.000 2 A_A2:A2_A A 2 ? A 2 ? 2 8 # _ndb_struct_na_base_pair_step.model_number 1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 A _ndb_struct_na_base_pair_step.i_label_comp_id_1 A _ndb_struct_na_base_pair_step.i_label_seq_id_1 2 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 A _ndb_struct_na_base_pair_step.j_label_comp_id_1 A _ndb_struct_na_base_pair_step.j_label_seq_id_1 2 _ndb_struct_na_base_pair_step.j_symmetry_1 2_835 _ndb_struct_na_base_pair_step.i_label_asym_id_2 A _ndb_struct_na_base_pair_step.i_label_comp_id_2 A _ndb_struct_na_base_pair_step.i_label_seq_id_2 3 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 A _ndb_struct_na_base_pair_step.j_label_comp_id_2 A _ndb_struct_na_base_pair_step.j_label_seq_id_2 3 _ndb_struct_na_base_pair_step.j_symmetry_2 2_835 _ndb_struct_na_base_pair_step.shift 0.000 _ndb_struct_na_base_pair_step.slide 0.000 _ndb_struct_na_base_pair_step.rise 3.748 _ndb_struct_na_base_pair_step.tilt 0.000 _ndb_struct_na_base_pair_step.roll 0.000 _ndb_struct_na_base_pair_step.twist 47.599 _ndb_struct_na_base_pair_step.x_displacement 0.000 _ndb_struct_na_base_pair_step.y_displacement 0.000 _ndb_struct_na_base_pair_step.helical_rise 3.748 _ndb_struct_na_base_pair_step.inclination 0.000 _ndb_struct_na_base_pair_step.tip 0.000 _ndb_struct_na_base_pair_step.helical_twist 47.599 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_A1A2:A2A1_AA _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 A _ndb_struct_na_base_pair_step.j_auth_seq_id_1 1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.i_auth_asym_id_2 A _ndb_struct_na_base_pair_step.i_auth_seq_id_2 2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 A _ndb_struct_na_base_pair_step.j_auth_seq_id_2 2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' 'R37 GM074593' 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' 'R01 GM22939' 2 'National Institutes of Health/National Cancer Institute (NIH/NCI)' 'United States' 'T32 CA09363' 3 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'AMMONIUM ION' NH4 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 4JRD _pdbx_initial_refinement_model.details 'rA2 section of the 4JRD' #