data_5LR3 # _entry.id 5LR3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.284 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5LR3 WWPDB D_1200001229 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5LR3 _pdbx_database_status.recvd_initial_deposition_date 2016-08-18 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Huang, L.' 1 'Lilley, D.M.J.' 2 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'EMBO Rep.' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1469-3178 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 18 _citation.language ? _citation.page_first 1631 _citation.page_last 1645 _citation.title 'Control of box C/D snoRNP assembly by N(6)-methylation of adenine.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.15252/embr.201743967 _citation.pdbx_database_id_PubMed 28623187 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Huang, L.' 1 primary 'Ashraf, S.' 2 primary 'Wang, J.' 3 primary 'Lilley, D.M.' 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 5LR3 _cell.details ? _cell.formula_units_Z ? _cell.length_a 33.300 _cell.length_a_esd ? _cell.length_b 33.300 _cell.length_b_esd ? _cell.length_c 120.910 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 16 _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 5LR3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 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 (5'-R(*GP*(CBV)P*CP*GP*GP*AP*UP*GP*GP*C)-3') ; 3310.884 2 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 water nat water 18.015 33 ? ? ? ? # _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 'G(CBV)CGGAUGGC' _entity_poly.pdbx_seq_one_letter_code_can GCCGGAUGGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 CBV n 1 3 C n 1 4 G n 1 5 G n 1 6 A n 1 7 U n 1 8 G n 1 9 G n 1 10 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 10 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name HUMAN _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5LR3 _struct_ref.pdbx_db_accession 5LR3 _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 5LR3 A 1 ? 10 ? 5LR3 1 ? 10 ? 1 10 2 1 5LR3 B 1 ? 10 ? 5LR3 1 ? 10 ? 1 10 # 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 CBV 'RNA linking' n ;5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C9 H13 Br N3 O8 P' 402.093 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _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 5LR3 _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 2.53 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 51.40 _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 6.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;0.015 M Magnesium Acetate, 0.05 M Sodium Cacodylate pH 6.0, 1.7 M Ammonium Sulfate ; _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 2016-02-05 # _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 0.9796 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'DIAMOND BEAMLINE I02' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9796 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I02 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5LR3 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.65 _reflns.d_resolution_low 29.17 _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 8761 _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 1.0 _reflns.percent_possible_obs 98.5 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 9.9 _reflns.pdbx_Rmerge_I_obs 0.063 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 16.8 _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 ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1.0 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.65 _reflns_shell.d_res_low 1.69 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.0 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 95.2 _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 1.9 _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 10.2 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.6 _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 5LR3 _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 1.650 _refine.ls_d_res_low 29.168 _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 8701 _refine.ls_number_reflns_R_free 739 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.39 _refine.ls_percent_reflns_R_free 4.81 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2484 _refine.ls_R_factor_R_free 0.2656 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2474 _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 1.34 _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 SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _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 37.01 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.28 _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 432 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 33 _refine_hist.number_atoms_total 470 _refine_hist.d_res_high 1.650 _refine_hist.d_res_low 29.168 # 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' ? 0.001 ? 486 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 2.499 ? 760 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 9.510 ? 216 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.018 ? 96 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.003 ? 20 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 1.6501 1.7774 . . 129 2858 96.00 . . . 0.3714 . 0.4054 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.7774 1.9563 . . 153 2963 99.00 . . . 0.3675 . 0.3560 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.9563 2.2393 . . 171 2930 99.00 . . . 0.3008 . 0.3055 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.2393 2.8209 . . 154 2928 99.00 . . . 0.3394 . 0.2976 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.8209 29.1724 . . 132 2951 98.00 . . . 0.2043 . 0.1919 . . . . . . . . . . # _struct.entry_id 5LR3 _struct.title 'RNA duplex has central consecutive GA pairs flanked by G-U basepairs' _struct.pdbx_descriptor ;RNA (5'-R(*GP*(CBV)P*CP*GP*GP*AP*UP*GP*GP*C)-3') ; _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 5LR3 _struct_keywords.text 'N6-methyladenine, RNA folding, Watson-Crick basepairs, 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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale both ? A G 1 "O3'" ? ? ? 1_555 A CBV 2 P ? ? A G 1 A CBV 2 1_555 ? ? ? ? ? ? ? 1.610 ? covale2 covale one ? A CBV 2 "O3'" ? ? ? 1_555 A C 3 P ? ? A CBV 2 A C 3 1_555 ? ? ? ? ? ? ? 1.605 ? covale3 covale both ? B G 1 "O3'" ? ? ? 1_555 B CBV 2 P ? ? B G 1 B CBV 2 1_555 ? ? ? ? ? ? ? 1.609 ? covale4 covale one ? B CBV 2 "O3'" ? ? ? 1_555 B C 3 P ? ? B CBV 2 B C 3 1_555 ? ? ? ? ? ? ? 1.607 ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 1 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 1 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 1 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A CBV 2 N3 ? ? ? 1_555 B G 9 N1 ? ? A CBV 2 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A CBV 2 N4 ? ? ? 1_555 B G 9 O6 ? ? A CBV 2 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A CBV 2 O2 ? ? ? 1_555 B G 9 N2 ? ? A CBV 2 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 3 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 3 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 3 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B U 7 O4 ? ? A G 4 B U 7 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? hydrog11 hydrog ? ? A G 5 N2 ? ? ? 1_555 B A 6 N7 ? ? A G 5 B A 6 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? hydrog12 hydrog ? ? A G 5 N3 ? ? ? 1_555 B A 6 N6 ? ? A G 5 B A 6 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? hydrog13 hydrog ? ? A A 6 N6 ? ? ? 1_555 B G 5 N3 ? ? A A 6 B G 5 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? hydrog14 hydrog ? ? A A 6 N7 ? ? ? 1_555 B G 5 N2 ? ? A A 6 B G 5 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? hydrog15 hydrog ? ? A U 7 O4 ? ? ? 1_555 B G 4 N2 ? ? A U 7 B G 4 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? hydrog16 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 8 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 8 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A G 8 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 8 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A G 9 N1 ? ? ? 1_555 B CBV 2 N3 ? ? A G 9 B CBV 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A G 9 N2 ? ? ? 1_555 B CBV 2 O2 ? ? A G 9 B CBV 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A G 9 O6 ? ? ? 1_555 B CBV 2 N4 ? ? A G 9 B CBV 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 10 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 10 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 10 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B SO4 101 ? 4 'binding site for residue SO4 B 101' AC2 Software B G 1 ? 10 'binding site for Di-nucleotide G B 1 and CBV B 2' AC3 Software B CBV 2 ? 11 'binding site for Di-nucleotide CBV B 2 and C B 3' # 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 G B 1 ? G B 1 . ? 1_555 ? 2 AC1 4 CBV B 2 ? CBV B 2 . ? 1_555 ? 3 AC1 4 HOH E . ? HOH B 201 . ? 1_555 ? 4 AC1 4 HOH E . ? HOH B 207 . ? 1_555 ? 5 AC2 10 G A 1 ? G A 1 . ? 3_444 ? 6 AC2 10 G A 9 ? G A 9 . ? 1_555 ? 7 AC2 10 C A 10 ? C A 10 . ? 1_555 ? 8 AC2 10 C B 3 ? C B 3 . ? 1_555 ? 9 AC2 10 C B 10 ? C B 10 . ? 3_444 ? 10 AC2 10 SO4 C . ? SO4 B 101 . ? 1_555 ? 11 AC2 10 HOH E . ? HOH B 201 . ? 1_555 ? 12 AC2 10 HOH E . ? HOH B 207 . ? 1_555 ? 13 AC2 10 HOH E . ? HOH B 212 . ? 1_555 ? 14 AC2 10 HOH E . ? HOH B 214 . ? 1_555 ? 15 AC3 11 G A 8 ? G A 8 . ? 1_555 ? 16 AC3 11 G A 9 ? G A 9 . ? 1_555 ? 17 AC3 11 C A 10 ? C A 10 . ? 1_555 ? 18 AC3 11 C A 10 ? C A 10 . ? 7_555 ? 19 AC3 11 G B 1 ? G B 1 . ? 1_555 ? 20 AC3 11 G B 4 ? G B 4 . ? 1_555 ? 21 AC3 11 SO4 C . ? SO4 B 101 . ? 1_555 ? 22 AC3 11 HOH E . ? HOH B 207 . ? 1_555 ? 23 AC3 11 HOH E . ? HOH B 209 . ? 1_555 ? 24 AC3 11 HOH E . ? HOH B 212 . ? 1_555 ? 25 AC3 11 HOH E . ? HOH B 214 . ? 1_555 ? # _atom_sites.entry_id 5LR3 _atom_sites.fract_transf_matrix[1][1] 0.030030 _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] 0.030030 _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] 0.008271 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol BR C N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 CBV 2 2 2 CBV CBV A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 A 6 6 6 A A A . n A 1 7 U 7 7 7 U U A . n A 1 8 G 8 8 8 G G A . n A 1 9 G 9 9 9 G G A . n A 1 10 C 10 10 10 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 CBV 2 2 2 CBV CBV B . n B 1 3 C 3 3 3 C C B . n B 1 4 G 4 4 4 G G B . n B 1 5 G 5 5 5 G G B . n B 1 6 A 6 6 6 A A B . n B 1 7 U 7 7 7 U U B . n B 1 8 G 8 8 8 G G B . n B 1 9 G 9 9 9 G G B . n B 1 10 C 10 10 10 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 SO4 1 101 1 SO4 SO4 B . D 3 HOH 1 101 8 HOH HOH A . D 3 HOH 2 102 33 HOH HOH A . D 3 HOH 3 103 10 HOH HOH A . D 3 HOH 4 104 25 HOH HOH A . D 3 HOH 5 105 28 HOH HOH A . D 3 HOH 6 106 27 HOH HOH A . D 3 HOH 7 107 17 HOH HOH A . D 3 HOH 8 108 13 HOH HOH A . D 3 HOH 9 109 30 HOH HOH A . D 3 HOH 10 110 4 HOH HOH A . D 3 HOH 11 111 20 HOH HOH A . D 3 HOH 12 112 24 HOH HOH A . D 3 HOH 13 113 2 HOH HOH A . D 3 HOH 14 114 1 HOH HOH A . D 3 HOH 15 115 18 HOH HOH A . D 3 HOH 16 116 9 HOH HOH A . D 3 HOH 17 117 21 HOH HOH A . D 3 HOH 18 118 22 HOH HOH A . D 3 HOH 19 119 26 HOH HOH A . E 3 HOH 1 201 11 HOH HOH B . E 3 HOH 2 202 32 HOH HOH B . E 3 HOH 3 203 14 HOH HOH B . E 3 HOH 4 204 15 HOH HOH B . E 3 HOH 5 205 23 HOH HOH B . E 3 HOH 6 206 16 HOH HOH B . E 3 HOH 7 207 12 HOH HOH B . E 3 HOH 8 208 31 HOH HOH B . E 3 HOH 9 209 5 HOH HOH B . E 3 HOH 10 210 6 HOH HOH B . E 3 HOH 11 211 19 HOH HOH B . E 3 HOH 12 212 7 HOH HOH B . E 3 HOH 13 213 3 HOH HOH B . E 3 HOH 14 214 29 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2570 ? 1 MORE -7 ? 1 'SSA (A^2)' 3430 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2017-06-21 2 'Structure model' 1 1 2017-06-28 3 'Structure model' 1 2 2017-09-13 # _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 ? # 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' 'Database references' # 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' citation # 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.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.pdbx_database_id_DOI' 4 2 'Structure model' '_citation.pdbx_database_id_PubMed' 5 2 'Structure model' '_citation.title' 6 3 'Structure model' '_citation.journal_volume' 7 3 'Structure model' '_citation.page_first' 8 3 'Structure model' '_citation.page_last' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 9.4186 -18.2399 15.0204 0.9995 0.2801 0.3946 -0.0017 0.0152 0.0443 2.0382 0.4342 1.6172 0.1630 0.0223 0.8277 0.7857 0.0847 -0.0838 -1.0240 -0.2580 -0.1488 0.2197 -0.1246 -0.4835 'X-RAY DIFFRACTION' 2 ? refined -3.1101 -14.5796 0.5231 0.5471 0.3102 0.2989 -0.0299 -0.0014 -0.0032 2.7298 2.6603 2.8577 -0.1443 0.2258 -0.4158 0.2171 0.1307 -0.4820 0.0769 -0.0974 0.4692 1.4485 0.1220 -0.1938 'X-RAY DIFFRACTION' 3 ? refined 2.5467 -9.2098 1.6537 0.4902 0.3216 0.3464 0.0679 -0.0285 0.0105 0.7854 2.6164 3.0169 0.2001 1.4495 -0.4496 0.0345 -0.0755 0.0296 0.6547 -0.0934 0.0366 1.1169 1.0789 0.0393 'X-RAY DIFFRACTION' 4 ? refined 1.3140 -23.4444 14.8468 1.2218 0.3525 0.4390 -0.0665 -0.1096 0.0840 0.3622 0.0508 0.6843 -0.0513 -0.4922 0.0428 0.3426 0.1189 0.1528 -0.2958 -0.2566 0.0528 -0.2109 -0.0339 -0.2438 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? '(chain A and resid 1:4)' 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? '(chain A and resid 5:10)' 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? '(chain B and resid 1:5)' 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? '(chain B and resid 6:10)' # 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 ? ? ? '(dev_2481: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5LR3 'double helix' 5LR3 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B C 10 1_555 -0.653 -0.096 -0.205 -3.583 -0.402 3.020 1 A_G1:C10_B A 1 ? B 10 ? 19 1 1 A CBV 2 1_555 B G 9 1_555 0.016 -0.079 -0.277 1.644 -9.172 -0.189 2 A_CBV2:G9_B A 2 ? B 9 ? 19 1 1 A C 3 1_555 B G 8 1_555 0.314 0.219 0.147 -6.670 -6.173 -0.283 3 A_C3:G8_B A 3 ? B 8 ? 19 1 1 A G 4 1_555 B U 7 1_555 7.685 -2.938 -0.118 -6.675 -3.105 -7.324 4 A_G4:U7_B A 4 ? B 7 ? ? ? 1 A G 5 1_555 B A 6 1_555 6.645 -4.536 0.756 27.560 9.408 2.197 5 A_G5:A6_B A 5 ? B 6 ? 11 9 1 A A 6 1_555 B G 5 1_555 -6.601 -4.731 0.724 -29.101 13.757 -4.463 6 A_A6:G5_B A 6 ? B 5 ? 11 10 1 A U 7 1_555 B G 4 1_555 -7.467 -2.906 0.429 2.106 -3.680 2.758 7 A_U7:G4_B A 7 ? B 4 ? ? ? 1 A G 8 1_555 B C 3 1_555 -0.209 -0.038 0.087 7.985 -13.792 -1.799 8 A_G8:C3_B A 8 ? B 3 ? 19 1 1 A G 9 1_555 B CBV 2 1_555 -0.081 -0.121 0.054 0.807 -14.076 -0.061 9 A_G9:CBV2_B A 9 ? B 2 ? 19 1 1 A C 10 1_555 B G 1 1_555 0.458 -0.051 -0.009 5.453 -9.447 3.659 10 A_C10:G1_B A 10 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 10 1_555 A CBV 2 1_555 B G 9 1_555 -0.406 -1.833 3.182 -0.979 4.557 35.189 -3.634 0.531 2.939 7.497 1.611 35.487 1 AA_G1CBV2:G9C10_BB A 1 ? B 10 ? A 2 ? B 9 ? 1 A CBV 2 1_555 B G 9 1_555 A C 3 1_555 B G 8 1_555 0.501 -1.776 3.419 1.410 8.834 34.619 -4.151 -0.617 2.910 14.547 -2.322 35.722 2 AA_CBV2C3:G8G9_BB A 2 ? B 9 ? A 3 ? B 8 ? 1 A C 3 1_555 B G 8 1_555 A G 4 1_555 B U 7 1_555 -0.629 -1.009 3.516 7.168 7.739 57.042 -1.474 1.050 3.271 8.028 -7.436 57.928 3 AA_C3G4:U7G8_BB A 3 ? B 8 ? A 4 ? B 7 ? 1 A G 4 1_555 B U 7 1_555 A G 5 1_555 B A 6 1_555 1.296 -0.888 2.803 7.231 7.596 27.114 -3.229 -1.197 2.710 15.486 -14.742 29.036 4 AA_G4G5:A6U7_BB A 4 ? B 7 ? A 5 ? B 6 ? 1 A G 5 1_555 B A 6 1_555 A A 6 1_555 B G 5 1_555 -0.758 -1.424 4.815 -0.260 -12.051 -8.652 18.334 -3.212 1.646 54.442 -1.175 -14.828 5 AA_G5A6:G5A6_BB A 5 ? B 6 ? A 6 ? B 5 ? 1 A A 6 1_555 B G 5 1_555 A U 7 1_555 B G 4 1_555 -0.628 -1.275 2.977 -9.495 4.404 21.209 -4.457 -1.362 2.691 11.134 24.004 23.625 6 AA_A6U7:G4G5_BB A 6 ? B 5 ? A 7 ? B 4 ? 1 A U 7 1_555 B G 4 1_555 A G 8 1_555 B C 3 1_555 -0.252 -0.655 3.279 -2.888 7.183 56.785 -1.073 0.106 3.190 7.514 3.021 57.266 7 AA_U7G8:C3G4_BB A 7 ? B 4 ? A 8 ? B 3 ? 1 A G 8 1_555 B C 3 1_555 A G 9 1_555 B CBV 2 1_555 -0.171 -1.621 3.443 -2.218 5.885 33.611 -3.700 -0.063 3.128 10.067 3.794 34.178 8 AA_G8G9:CBV2C3_BB A 8 ? B 3 ? A 9 ? B 2 ? 1 A G 9 1_555 B CBV 2 1_555 A C 10 1_555 B G 1 1_555 0.629 -1.524 3.143 1.241 2.533 34.661 -2.917 -0.874 3.047 4.243 -2.078 34.772 9 AA_G9C10:G1CBV2_BB A 9 ? B 2 ? A 10 ? B 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 water HOH #