data_6D54 # _entry.id 6D54 # _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 6D54 pdb_00006d54 10.2210/pdb6d54/pdb WWPDB D_1000234003 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.details . _pdbx_database_related.db_id 6D4L _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6D54 _pdbx_database_status.recvd_initial_deposition_date 2018-04-19 _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 'Kovalevsky, A.' 1 ? 'Huang, Z.' 2 ? 'Vandavasi, V.G.' 3 ? # loop_ _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 _citation.database_id_Medline _citation.details _citation.id _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.unpublished_flag ? ? ? ? ? ? ? UK ? ? primary Structure STRUE6 2005 1878-4186 ? ? 26 ? 1645 ? 'Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA.' 2018 ? 10.1016/j.str.2018.08.001 30244969 ? ? ? ? ? ? ? ? US ? ? 1 'Acta Crystallogr. D Biol. Crystallogr.' ABCRE6 ? 1399-0047 ? ? 65 ? 567 573 'Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.' 2009 ? 10.1107/S0907444909011548 19465771 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Vandavasi, V.G.' 1 ? primary 'Blakeley, M.P.' 2 ? primary 'Keen, D.A.' 3 ? primary 'Hu, L.R.' 4 ? primary 'Huang, Z.' 5 ? primary 'Kovalevsky, A.' 6 ? 1 'Adams, P.D.' 7 ? 1 'Mustyakimov, M.' 8 ? 1 'Afonine, P.V.' 9 ? 1 'Langan, P.' 10 ? # _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 6D54 _cell.details ? _cell.formula_units_Z ? _cell.length_a 41.884 _cell.length_a_esd ? _cell.length_b 41.884 _cell.length_b_esd ? _cell.length_c 24.307 _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 6D54 _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 ;DNA (5'-D(*GP*TP*GP*GP*(CSL)P*CP*AP*C)-3') ; 2520.592 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 water nat water 18.015 39 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DT)(DG)(DG)(CSL)(DC)(DA)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GTGGCCAC _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 DG n 1 2 DT n 1 3 DG n 1 4 DG n 1 5 CSL n 1 6 DC n 1 7 DA n 1 8 DC 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 8 _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 6D54 _struct_ref.pdbx_db_accession 6D54 _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 6D54 _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 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6D54 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 8 # 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 CSL 'DNA linking' n "(D)-2'-METHYLSELENYL-2'-DEOXYCYTIDINE-5'-PHOSPHATE" "(D)-2'-DEOXY-2'-SE-METHYLCYTIDINE-5'-PHOSPHATE" 'C10 H16 N3 O7 P Se' 400.184 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DOD non-polymer . 'DEUTERATED WATER' ? 'D2 O' 20.028 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # loop_ _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 _exptl.crystals_number _exptl.details _exptl.method _exptl.method_details ? ? ? ? ? 6D54 1 ? 'X-RAY DIFFRACTION' ? ? ? ? ? ? 6D54 1 ? 'NEUTRON DIFFRACTION' ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.06 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 40.38 _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, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 303 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.1 M magnesium acetate, 30% MPD, 0.1 M MES' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _diffrn.ambient_environment _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.ambient_temp_esd _diffrn.crystal_id _diffrn.crystal_support _diffrn.crystal_treatment _diffrn.details _diffrn.id _diffrn.ambient_pressure _diffrn.ambient_pressure_esd _diffrn.ambient_pressure_gt _diffrn.ambient_pressure_lt _diffrn.ambient_temp_gt _diffrn.ambient_temp_lt ? 100 ? ? 1 ? ? ? 1 ? ? ? ? ? ? ? 100 ? ? 1 ? ? ? 2 ? ? ? ? ? ? # loop_ _diffrn_detector.details _diffrn_detector.detector _diffrn_detector.diffrn_id _diffrn_detector.type _diffrn_detector.area_resol_mean _diffrn_detector.dtime _diffrn_detector.pdbx_frames_total _diffrn_detector.pdbx_collection_time_total _diffrn_detector.pdbx_collection_date 'osmic varimax' 'IMAGE PLATE' 1 'RIGAKU RAXIS IV++' ? ? ? ? 2017-12-12 collimators 'IMAGE PLATE' 2 'LADI III' ? ? ? ? 2017-11-20 # loop_ _diffrn_radiation.collimation _diffrn_radiation.diffrn_id _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 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.pdbx_wavelength_list _diffrn_radiation.pdbx_wavelength _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_analyzer _diffrn_radiation.pdbx_scattering_type ? 1 ? ? ? ? ? ? ? ? 1 M ? ? 'SINGLE WAVELENGTH' ? x-ray ? 2 ? ? ? ? ? ? ? ? 2 L ? ? LAUE ? neutron # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.54 1.0 2 2.8 1.0 3 4.0 1.0 # loop_ _diffrn_source.current _diffrn_source.details _diffrn_source.diffrn_id _diffrn_source.power _diffrn_source.size _diffrn_source.source _diffrn_source.target _diffrn_source.type _diffrn_source.voltage _diffrn_source.take-off_angle _diffrn_source.pdbx_wavelength_list _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_synchrotron_site ? ? 1 ? ? 'ROTATING ANODE' ? 'RIGAKU MICROMAX-007 HF' ? ? 1.54 ? ? ? ? ? 2 ? ? 'NUCLEAR REACTOR' ? 'ILL BEAMLINE LADI III' ? ? 2.8-4.0 ? 'LADI III' ILL # loop_ _reflns.entry_id _reflns.d_resolution_high _reflns.d_resolution_low _reflns.number_obs _reflns.percent_possible_obs _reflns.pdbx_redundancy _reflns.pdbx_Rmerge_I_obs _reflns.pdbx_netI_over_sigmaI _reflns.pdbx_diffrn_id _reflns.pdbx_ordinal _reflns.number_all _reflns.observed_criterion_sigma_F _reflns.observed_criterion_sigma_I _reflns.pdbx_Rsym_value _reflns.pdbx_CC_half _reflns.pdbx_Rpim_I_all _reflns.pdbx_Rrim_I_all _reflns.B_iso_Wilson_estimate 6D54 1.65 40 2866 100.0 10.4 0.056 16.6 1 1 ? ? ? ? ? ? ? ? 6D54 1.90 21.3 1629 84.6 7.0 0.179 9.10 2 2 ? ? ? ? ? ? ? ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.number_measured_obs _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.meanI_over_sigI_obs 1.65 1.71 100.0 0.149 10.2 16.6 1 1 ? ? ? ? ? ? ? ? 1.90 2.00 66.0 0.226 3.4 5.30 2 2 ? ? ? ? ? ? ? ? # loop_ _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 _refine.pdbx_refine_id _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 _refine.ls_d_res_low _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 _refine.ls_number_reflns_R_free _refine.ls_number_reflns_R_work _refine.ls_number_restraints _refine.ls_percent_reflns_obs _refine.ls_percent_reflns_R_free _refine.ls_R_factor_all _refine.ls_R_factor_obs _refine.ls_R_factor_R_free _refine.ls_R_factor_R_free_error _refine.ls_R_factor_R_free_error_details _refine.ls_R_factor_R_work _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 _refine.pdbx_method_to_determine_struct _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 _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 _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 ? ? ? ? ? ? 61.45 24.54 5.01 ? ? ? ? ? ? ? ? ? 6D54 'X-RAY DIFFRACTION' ? ? ? ? ? 1.65 40.00 ? ? ? ? ? ? ? ? ? ? ? ? 2843 2800 136 ? ? 98.2 5.0 ? ? 0.246 ? ? 0.230 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 92.2058 0.546925 ? ? ? ? ? ? ? ? 2.5 ? ? ? ? ? 'FREE R-VALUE' 'MOLECULAR REPLACEMENT' 'PDB entry 4FP6' 'joint X-ray/neutron ML' random ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 61.45 24.54 5.01 ? ? ? ? ? ? ? ? ? 6D54 'NEUTRON DIFFRACTION' ? ? ? ? ? 1.90 21.30 ? ? ? ? ? ? ? ? ? ? ? ? 1909 1572 65 ? ? 82.3 5.0 ? ? 0.260 ? ? 0.234 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 92.2058 0.546925 ? ? ? ? ? ? ? ? 2.5 ? ? ? ? ? 'FREE R-VALUE' 'MOLECULAR REPLACEMENT' ? 'joint X-ray/neutron ML' random ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # loop_ _refine_analyze.entry_id _refine_analyze.pdbx_refine_id _refine_analyze.Luzzati_coordinate_error_free _refine_analyze.Luzzati_coordinate_error_obs _refine_analyze.Luzzati_d_res_low_free _refine_analyze.Luzzati_d_res_low_obs _refine_analyze.Luzzati_sigma_a_free _refine_analyze.Luzzati_sigma_a_free_details _refine_analyze.Luzzati_sigma_a_obs _refine_analyze.Luzzati_sigma_a_obs_details _refine_analyze.number_disordered_residues _refine_analyze.occupancy_sum_hydrogen _refine_analyze.occupancy_sum_non_hydrogen _refine_analyze.RG_d_res_high _refine_analyze.RG_d_res_low _refine_analyze.RG_free _refine_analyze.RG_work _refine_analyze.RG_free_work_ratio _refine_analyze.pdbx_Luzzati_d_res_high_obs 6D54 'X-RAY DIFFRACTION' 0.21 0.19 ? 5.00 0.18 ? 0.07 ? ? ? ? ? ? ? ? ? 1.65 6D54 'NEUTRON DIFFRACTION' ? 0.23 ? 5.00 ? ? 0.19 ? ? ? ? ? ? ? ? ? 1.90 # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 163 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 39 _refine_hist.number_atoms_total 204 _refine_hist.d_res_high 1.65 _refine_hist.d_res_low 40.00 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.006 ? ? ? x_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.9 ? ? ? x_angle_deg ? ? 'X-RAY DIFFRACTION' ? 0.7 ? ? ? x_torsion_deg ? ? 'X-RAY DIFFRACTION' ? 0.95 ? ? ? x_torsion_impr_deg ? ? 'NEUTRON DIFFRACTION' ? 0.006 ? ? ? x_bond_d ? ? 'NEUTRON DIFFRACTION' ? 0.9 ? ? ? x_angle_deg ? ? 'NEUTRON DIFFRACTION' ? 0.7 ? ? ? x_torsion_deg ? ? 'NEUTRON DIFFRACTION' ? 0.95 ? ? ? x_torsion_impr_deg ? ? # 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' 1.65 1.73 355 335 18 317 94.1 5.0 . . 0.510 0.120 0.235 . . . . . . 8 . . . 'X-RAY DIFFRACTION' 1.73 1.82 339 324 18 306 95.6 5.6 . . 0.310 0.073 0.219 . . . . . . 8 . . . 'X-RAY DIFFRACTION' 1.82 1.93 338 331 16 315 97.6 4.8 . . 0.268 0.067 0.225 . . . . . . 8 . . . 'X-RAY DIFFRACTION' 1.93 2.08 347 338 11 327 97.4 3.3 . . 0.231 0.070 0.228 . . . . . . 8 . . . 'X-RAY DIFFRACTION' 2.08 2.29 357 352 26 326 98.6 7.4 . . 0.211 0.041 0.204 . . . . . . 8 . . . 'X-RAY DIFFRACTION' 2.29 2.62 348 347 11 336 99.4 3.2 . . 0.272 0.082 0.222 . . . . . . 8 . . . 'X-RAY DIFFRACTION' 2.62 3.30 361 360 15 345 99.7 4.2 . . 0.174 0.045 0.233 . . . . . . 8 . . . 'X-RAY DIFFRACTION' 3.30 21.02 401 398 21 377 99.3 5.3 . . 0.197 0.043 0.244 . . . . . . 8 . . . 'NEUTRON DIFFRACTION' 1.90 1.99 236 155 6 149 65.7 5.0 . . 0.270 0.110 0.250 . . . . . . 8 . . . 'NEUTRON DIFFRACTION' 1.99 2.09 224 168 7 161 74.7 4.2 . . 0.249 0.094 0.266 . . . . . . 8 . . . 'NEUTRON DIFFRACTION' 2.09 2.22 234 180 14 166 76.6 7.8 . . 0.201 0.054 0.252 . . . . . . 8 . . . 'NEUTRON DIFFRACTION' 2.22 2.39 229 185 6 179 80.8 3.2 . . 0.256 0.104 0.229 . . . . . . 8 . . . 'NEUTRON DIFFRACTION' 2.39 2.63 235 193 7 186 82.1 3.6 . . 0.243 0.092 0.214 . . . . . . 8 . . . 'NEUTRON DIFFRACTION' 2.63 3.01 242 212 8 204 87.6 3.8 . . 0.181 0.064 0.233 . . . . . . 8 . . . 'NEUTRON DIFFRACTION' 3.01 3.79 243 226 18 208 93.0 8.0 . . 0.218 0.051 0.207 . . . . . . 8 . . . 'NEUTRON DIFFRACTION' 3.79 21.02 269 253 8 245 94.1 3.2 . . 0.526 0.186 0.252 . . . . . . 8 . . . # _struct.entry_id 6D54 _struct.title ;Low Temperature joint X-ray/neutron structure of DNA oligonucleotide d(GTGGCCAC)2 with 2'-SeCH3 modification on Cyt5 ; _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 6D54 _struct_keywords.text 'DNA, oligonucleotide, selenium modification' _struct_keywords.pdbx_keywords DNA # 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 2 ? D N N 3 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DG 4 "O3'" ? ? ? 1_555 A CSL 5 P ? ? A DG 4 A CSL 5 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale2 covale both ? A CSL 5 "O3'" ? ? ? 1_555 A DC 6 P ? ? A CSL 5 A DC 6 1_555 ? ? ? ? ? ? ? 1.605 ? ? metalc1 metalc ? ? A DA 7 OP2 ? ? ? 1_555 C MG . MG ? ? A DA 7 A MG 102 1_555 ? ? ? ? ? ? ? 1.978 ? ? metalc2 metalc ? ? B MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 101 A DOD 208 1_555 ? ? ? ? ? ? ? 2.087 ? ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 101 A DOD 209 1_555 ? ? ? ? ? ? ? 2.220 ? ? metalc4 metalc ? ? B MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 101 A DOD 210 1_555 ? ? ? ? ? ? ? 1.874 ? ? metalc5 metalc ? ? B MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 101 A DOD 235 1_555 ? ? ? ? ? ? ? 2.241 ? ? metalc6 metalc ? ? B MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 101 A DOD 237 1_555 ? ? ? ? ? ? ? 2.011 ? ? metalc7 metalc ? ? B MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 101 A DOD 238 1_555 ? ? ? ? ? ? ? 2.095 ? ? metalc8 metalc ? ? C MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 102 A DOD 218 1_555 ? ? ? ? ? ? ? 2.051 ? ? metalc9 metalc ? ? C MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 102 A DOD 224 1_555 ? ? ? ? ? ? ? 2.097 ? ? metalc10 metalc ? ? C MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 102 A DOD 226 1_555 ? ? ? ? ? ? ? 2.202 ? ? metalc11 metalc ? ? C MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 102 A DOD 229 1_555 ? ? ? ? ? ? ? 2.299 ? ? metalc12 metalc ? ? C MG . MG ? ? ? 1_555 D DOD . O ? ? A MG 102 A DOD 236 4_555 ? ? ? ? ? ? ? 2.141 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # 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 ? 6 'binding site for residue MG A 101' AC2 Software A MG 102 ? 5 'binding site for residue MG A 102' # 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 6 DOD D . ? DOD A 208 . ? 1_555 ? 2 AC1 6 DOD D . ? DOD A 209 . ? 1_555 ? 3 AC1 6 DOD D . ? DOD A 210 . ? 1_555 ? 4 AC1 6 DOD D . ? DOD A 235 . ? 1_555 ? 5 AC1 6 DOD D . ? DOD A 237 . ? 1_555 ? 6 AC1 6 DOD D . ? DOD A 238 . ? 1_555 ? 7 AC2 5 DA A 7 ? DA A 7 . ? 1_555 ? 8 AC2 5 DOD D . ? DOD A 218 . ? 1_555 ? 9 AC2 5 DOD D . ? DOD A 224 . ? 1_555 ? 10 AC2 5 DOD D . ? DOD A 226 . ? 1_555 ? 11 AC2 5 DOD D . ? DOD A 229 . ? 1_555 ? # _atom_sites.entry_id 6D54 _atom_sites.fract_transf_matrix[1][1] 0.023875 _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] 0.023875 _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] 0.041140 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C D H MG N O P SE # 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 DG 1 1 1 DG GUA A . n A 1 2 DT 2 2 2 DT THY A . n A 1 3 DG 3 3 3 DG GUA A . n A 1 4 DG 4 4 4 DG GUA A . n A 1 5 CSL 5 5 5 CSL SEC A . n A 1 6 DC 6 6 6 DC CYT A . n A 1 7 DA 7 7 7 DA ADE A . n A 1 8 DC 8 8 8 DC CYT 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 MG 1 101 11 MG MG A . C 2 MG 1 102 12 MG MG A . D 3 DOD 1 201 1008 DOD DOD A . D 3 DOD 2 202 1033 DOD DOD A . D 3 DOD 3 203 1029 DOD DOD A . D 3 DOD 4 204 1021 DOD DOD A . D 3 DOD 5 205 1020 DOD DOD A . D 3 DOD 6 206 1034 DOD DOD A . D 3 DOD 7 207 1026 DOD DOD A . D 3 DOD 8 208 1001 DOD DOD A . D 3 DOD 9 209 1005 DOD DOD A . D 3 DOD 10 210 1004 DOD DOD A . D 3 DOD 11 211 1036 DOD DOD A . D 3 DOD 12 212 1028 DOD DOD A . D 3 DOD 13 213 1009 DOD DOD A . D 3 DOD 14 214 1017 DOD DOD A . D 3 DOD 15 215 1025 DOD DOD A . D 3 DOD 16 216 1007 DOD DOD A . D 3 DOD 17 217 1015 DOD DOD A . D 3 DOD 18 218 1010 DOD DOD A . D 3 DOD 19 219 1039 DOD DOD A . D 3 DOD 20 220 1016 DOD DOD A . D 3 DOD 21 221 1006 DOD DOD A . D 3 DOD 22 222 1037 DOD DOD A . D 3 DOD 23 223 1022 DOD DOD A . D 3 DOD 24 224 1011 DOD DOD A . D 3 DOD 25 225 1024 DOD DOD A . D 3 DOD 26 226 1014 DOD DOD A . D 3 DOD 27 227 1038 DOD DOD A . D 3 DOD 28 228 1027 DOD DOD A . D 3 DOD 29 229 1013 DOD DOD A . D 3 DOD 30 230 1018 DOD DOD A . D 3 DOD 31 231 1035 DOD DOD A . D 3 DOD 32 232 1030 DOD DOD A . D 3 DOD 33 233 1031 DOD DOD A . D 3 DOD 34 234 1019 DOD DOD A . D 3 DOD 35 235 1023 DOD DOD A . D 3 DOD 36 236 1012 DOD DOD A . D 3 DOD 37 237 1002 DOD DOD A . D 3 DOD 38 238 1003 DOD DOD A . D 3 DOD 39 239 1032 DOD DOD A . # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 9340 ? 1 MORE -16 ? 1 'SSA (A^2)' 4680 ? # 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' 8_554 -y,-x,-z-1/2 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 -12.1535000000 # 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 OP2 ? A DA 7 ? A DA 7 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 218 ? 1_555 89.3 ? 2 OP2 ? A DA 7 ? A DA 7 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 224 ? 1_555 92.0 ? 3 O ? D DOD . ? A DOD 218 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 224 ? 1_555 96.2 ? 4 OP2 ? A DA 7 ? A DA 7 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 226 ? 1_555 91.2 ? 5 O ? D DOD . ? A DOD 218 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 226 ? 1_555 174.5 ? 6 O ? D DOD . ? A DOD 224 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 226 ? 1_555 89.2 ? 7 OP2 ? A DA 7 ? A DA 7 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 229 ? 1_555 92.0 ? 8 O ? D DOD . ? A DOD 218 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 229 ? 1_555 94.0 ? 9 O ? D DOD . ? A DOD 224 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 229 ? 1_555 169.0 ? 10 O ? D DOD . ? A DOD 226 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 229 ? 1_555 80.4 ? 11 OP2 ? A DA 7 ? A DA 7 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 236 ? 4_555 171.7 ? 12 O ? D DOD . ? A DOD 218 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 236 ? 4_555 95.0 ? 13 O ? D DOD . ? A DOD 224 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 236 ? 4_555 94.6 ? 14 O ? D DOD . ? A DOD 226 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 236 ? 4_555 83.8 ? 15 O ? D DOD . ? A DOD 229 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D DOD . ? A DOD 236 ? 4_555 80.6 ? 16 O ? D DOD . ? A DOD 208 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 209 ? 1_555 100.1 ? 17 O ? D DOD . ? A DOD 208 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 210 ? 1_555 98.9 ? 18 O ? D DOD . ? A DOD 209 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 210 ? 1_555 83.3 ? 19 O ? D DOD . ? A DOD 208 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 235 ? 1_555 90.2 ? 20 O ? D DOD . ? A DOD 209 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 235 ? 1_555 88.9 ? 21 O ? D DOD . ? A DOD 210 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 235 ? 1_555 169.0 ? 22 O ? D DOD . ? A DOD 208 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 237 ? 1_555 99.1 ? 23 O ? D DOD . ? A DOD 209 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 237 ? 1_555 160.8 ? 24 O ? D DOD . ? A DOD 210 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 237 ? 1_555 94.3 ? 25 O ? D DOD . ? A DOD 235 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 237 ? 1_555 90.5 ? 26 O ? D DOD . ? A DOD 208 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 238 ? 1_555 174.5 ? 27 O ? D DOD . ? A DOD 209 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 238 ? 1_555 76.1 ? 28 O ? D DOD . ? A DOD 210 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 238 ? 1_555 84.6 ? 29 O ? D DOD . ? A DOD 235 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 238 ? 1_555 85.9 ? 30 O ? D DOD . ? A DOD 237 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D DOD . ? A DOD 238 ? 1_555 84.8 ? # 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 2018-10-17 2 'Structure model' 1 1 2018-12-19 3 'Structure model' 2 0 2022-03-02 4 'Structure model' 2 1 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' Advisory 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' 6 3 'Structure model' 'Derived calculations' 7 3 'Structure model' 'Polymer sequence' 8 3 'Structure model' 'Refinement description' 9 3 'Structure model' 'Structure summary' 10 4 'Structure model' 'Data collection' 11 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 3 'Structure model' database_2 3 3 'Structure model' diffrn_radiation_wavelength 4 3 'Structure model' diffrn_source 5 3 'Structure model' entity 6 3 'Structure model' entity_poly 7 3 'Structure model' pdbx_struct_conn_angle 8 3 'Structure model' pdbx_unobs_or_zero_occ_atoms 9 3 'Structure model' refine_hist 10 3 'Structure model' struct_conn 11 4 'Structure model' chem_comp_atom 12 4 'Structure model' chem_comp_bond 13 4 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 3 'Structure model' '_database_2.pdbx_DOI' 4 3 'Structure model' '_database_2.pdbx_database_accession' 5 3 'Structure model' '_diffrn_source.pdbx_synchrotron_beamline' 6 3 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 7 3 'Structure model' '_entity.formula_weight' 8 3 'Structure model' '_entity_poly.type' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.value' 12 3 'Structure model' '_refine_hist.d_res_low' 13 3 'Structure model' '_struct_conn.pdbx_dist_value' 14 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' # 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 ? ? ? ? ? ? ? ? ? ? ? nCNS ? ? ? 1.0.0 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? LAUEGEN ? ? ? . 5 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? LSCALE ? ? ? . 6 ? phasing ? ? ? ? ? ? ? ? ? ? ? CNS ? ? ? . 7 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O1P A CSL 5 ? ? D2 A DOD 201 ? ? 1.51 2 1 O2P A CSL 5 ? ? D2 A DOD 202 ? ? 1.60 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 D1 A DOD 214 ? ? 1_555 O A DOD 230 ? ? 4_555 1.54 2 1 O A DOD 203 ? ? 1_555 D1 A DOD 231 ? ? 8_554 1.57 # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id DOD _pdbx_distant_solvent_atoms.auth_seq_id 239 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.09 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal CSL P P N N 1 CSL O2P O N N 2 CSL O1P O N N 3 CSL "O5'" O N N 4 CSL "C5'" C N N 5 CSL "C4'" C N R 6 CSL "O4'" O N N 7 CSL "C1'" C N R 8 CSL N1 N N N 9 CSL C2 C N N 10 CSL O2 O N N 11 CSL N3 N N N 12 CSL C4 C N N 13 CSL N4 N N N 14 CSL C5 C N N 15 CSL C6 C N N 16 CSL "C2'" C N R 17 CSL "SE2'" SE N N 18 CSL "CA'" C N N 19 CSL "C3'" C N R 20 CSL "O3'" O N N 21 CSL O3P O N N 22 CSL HOP2 H N N 23 CSL "H5'1" H N N 24 CSL "H5'2" H N N 25 CSL "H4'" H N N 26 CSL "H1'" H N N 27 CSL HN41 H N N 28 CSL HN42 H N N 29 CSL H5 H N N 30 CSL H6 H N N 31 CSL "H2'" H N N 32 CSL "HA'1" H N N 33 CSL "HA'2" H N N 34 CSL "HA'3" H N N 35 CSL "H3'" H N N 36 CSL H3T H N N 37 CSL HOP3 H N N 38 DA OP3 O N N 39 DA P P N N 40 DA OP1 O N N 41 DA OP2 O N N 42 DA "O5'" O N N 43 DA "C5'" C N N 44 DA "C4'" C N R 45 DA "O4'" O N N 46 DA "C3'" C N S 47 DA "O3'" O N N 48 DA "C2'" C N N 49 DA "C1'" C N R 50 DA N9 N Y N 51 DA C8 C Y N 52 DA N7 N Y N 53 DA C5 C Y N 54 DA C6 C Y N 55 DA N6 N N N 56 DA N1 N Y N 57 DA C2 C Y N 58 DA N3 N Y N 59 DA C4 C Y N 60 DA HOP3 H N N 61 DA HOP2 H N N 62 DA "H5'" H N N 63 DA "H5''" H N N 64 DA "H4'" H N N 65 DA "H3'" H N N 66 DA "HO3'" H N N 67 DA "H2'" H N N 68 DA "H2''" H N N 69 DA "H1'" H N N 70 DA H8 H N N 71 DA H61 H N N 72 DA H62 H N N 73 DA H2 H N N 74 DC OP3 O N N 75 DC P P N N 76 DC OP1 O N N 77 DC OP2 O N N 78 DC "O5'" O N N 79 DC "C5'" C N N 80 DC "C4'" C N R 81 DC "O4'" O N N 82 DC "C3'" C N S 83 DC "O3'" O N N 84 DC "C2'" C N N 85 DC "C1'" C N R 86 DC N1 N N N 87 DC C2 C N N 88 DC O2 O N N 89 DC N3 N N N 90 DC C4 C N N 91 DC N4 N N N 92 DC C5 C N N 93 DC C6 C N N 94 DC HOP3 H N N 95 DC HOP2 H N N 96 DC "H5'" H N N 97 DC "H5''" H N N 98 DC "H4'" H N N 99 DC "H3'" H N N 100 DC "HO3'" H N N 101 DC "H2'" H N N 102 DC "H2''" H N N 103 DC "H1'" H N N 104 DC H41 H N N 105 DC H42 H N N 106 DC H5 H N N 107 DC H6 H N N 108 DG OP3 O N N 109 DG P P N N 110 DG OP1 O N N 111 DG OP2 O N N 112 DG "O5'" O N N 113 DG "C5'" C N N 114 DG "C4'" C N R 115 DG "O4'" O N N 116 DG "C3'" C N S 117 DG "O3'" O N N 118 DG "C2'" C N N 119 DG "C1'" C N R 120 DG N9 N Y N 121 DG C8 C Y N 122 DG N7 N Y N 123 DG C5 C Y N 124 DG C6 C N N 125 DG O6 O N N 126 DG N1 N N N 127 DG C2 C N N 128 DG N2 N N N 129 DG N3 N N N 130 DG C4 C Y N 131 DG HOP3 H N N 132 DG HOP2 H N N 133 DG "H5'" H N N 134 DG "H5''" H N N 135 DG "H4'" H N N 136 DG "H3'" H N N 137 DG "HO3'" H N N 138 DG "H2'" H N N 139 DG "H2''" H N N 140 DG "H1'" H N N 141 DG H8 H N N 142 DG H1 H N N 143 DG H21 H N N 144 DG H22 H N N 145 DOD O O N N 146 DOD D1 D N N 147 DOD D2 D N N 148 DT OP3 O N N 149 DT P P N N 150 DT OP1 O N N 151 DT OP2 O N N 152 DT "O5'" O N N 153 DT "C5'" C N N 154 DT "C4'" C N R 155 DT "O4'" O N N 156 DT "C3'" C N S 157 DT "O3'" O N N 158 DT "C2'" C N N 159 DT "C1'" C N R 160 DT N1 N N N 161 DT C2 C N N 162 DT O2 O N N 163 DT N3 N N N 164 DT C4 C N N 165 DT O4 O N N 166 DT C5 C N N 167 DT C7 C N N 168 DT C6 C N N 169 DT HOP3 H N N 170 DT HOP2 H N N 171 DT "H5'" H N N 172 DT "H5''" H N N 173 DT "H4'" H N N 174 DT "H3'" H N N 175 DT "HO3'" H N N 176 DT "H2'" H N N 177 DT "H2''" H N N 178 DT "H1'" H N N 179 DT H3 H N N 180 DT H71 H N N 181 DT H72 H N N 182 DT H73 H N N 183 DT H6 H N N 184 MG MG MG N N 185 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal CSL P O2P sing N N 1 CSL P O1P doub N N 2 CSL P "O5'" sing N N 3 CSL P O3P sing N N 4 CSL O2P HOP2 sing N N 5 CSL "O5'" "C5'" sing N N 6 CSL "C5'" "C4'" sing N N 7 CSL "C5'" "H5'1" sing N N 8 CSL "C5'" "H5'2" sing N N 9 CSL "C4'" "O4'" sing N N 10 CSL "C4'" "C3'" sing N N 11 CSL "C4'" "H4'" sing N N 12 CSL "O4'" "C1'" sing N N 13 CSL "C1'" N1 sing N N 14 CSL "C1'" "C2'" sing N N 15 CSL "C1'" "H1'" sing N N 16 CSL N1 C2 sing N N 17 CSL N1 C6 sing N N 18 CSL C2 O2 doub N N 19 CSL C2 N3 sing N N 20 CSL N3 C4 doub N N 21 CSL C4 N4 sing N N 22 CSL C4 C5 sing N N 23 CSL N4 HN41 sing N N 24 CSL N4 HN42 sing N N 25 CSL C5 C6 doub N N 26 CSL C5 H5 sing N N 27 CSL C6 H6 sing N N 28 CSL "C2'" "SE2'" sing N N 29 CSL "C2'" "C3'" sing N N 30 CSL "C2'" "H2'" sing N N 31 CSL "SE2'" "CA'" sing N N 32 CSL "CA'" "HA'1" sing N N 33 CSL "CA'" "HA'2" sing N N 34 CSL "CA'" "HA'3" sing N N 35 CSL "C3'" "O3'" sing N N 36 CSL "C3'" "H3'" sing N N 37 CSL "O3'" H3T sing N N 38 CSL O3P HOP3 sing N N 39 DA OP3 P sing N N 40 DA OP3 HOP3 sing N N 41 DA P OP1 doub N N 42 DA P OP2 sing N N 43 DA P "O5'" sing N N 44 DA OP2 HOP2 sing N N 45 DA "O5'" "C5'" sing N N 46 DA "C5'" "C4'" sing N N 47 DA "C5'" "H5'" sing N N 48 DA "C5'" "H5''" sing N N 49 DA "C4'" "O4'" sing N N 50 DA "C4'" "C3'" sing N N 51 DA "C4'" "H4'" sing N N 52 DA "O4'" "C1'" sing N N 53 DA "C3'" "O3'" sing N N 54 DA "C3'" "C2'" sing N N 55 DA "C3'" "H3'" sing N N 56 DA "O3'" "HO3'" sing N N 57 DA "C2'" "C1'" sing N N 58 DA "C2'" "H2'" sing N N 59 DA "C2'" "H2''" sing N N 60 DA "C1'" N9 sing N N 61 DA "C1'" "H1'" sing N N 62 DA N9 C8 sing Y N 63 DA N9 C4 sing Y N 64 DA C8 N7 doub Y N 65 DA C8 H8 sing N N 66 DA N7 C5 sing Y N 67 DA C5 C6 sing Y N 68 DA C5 C4 doub Y N 69 DA C6 N6 sing N N 70 DA C6 N1 doub Y N 71 DA N6 H61 sing N N 72 DA N6 H62 sing N N 73 DA N1 C2 sing Y N 74 DA C2 N3 doub Y N 75 DA C2 H2 sing N N 76 DA N3 C4 sing Y N 77 DC OP3 P sing N N 78 DC OP3 HOP3 sing N N 79 DC P OP1 doub N N 80 DC P OP2 sing N N 81 DC P "O5'" sing N N 82 DC OP2 HOP2 sing N N 83 DC "O5'" "C5'" sing N N 84 DC "C5'" "C4'" sing N N 85 DC "C5'" "H5'" sing N N 86 DC "C5'" "H5''" sing N N 87 DC "C4'" "O4'" sing N N 88 DC "C4'" "C3'" sing N N 89 DC "C4'" "H4'" sing N N 90 DC "O4'" "C1'" sing N N 91 DC "C3'" "O3'" sing N N 92 DC "C3'" "C2'" sing N N 93 DC "C3'" "H3'" sing N N 94 DC "O3'" "HO3'" sing N N 95 DC "C2'" "C1'" sing N N 96 DC "C2'" "H2'" sing N N 97 DC "C2'" "H2''" sing N N 98 DC "C1'" N1 sing N N 99 DC "C1'" "H1'" sing N N 100 DC N1 C2 sing N N 101 DC N1 C6 sing N N 102 DC C2 O2 doub N N 103 DC C2 N3 sing N N 104 DC N3 C4 doub N N 105 DC C4 N4 sing N N 106 DC C4 C5 sing N N 107 DC N4 H41 sing N N 108 DC N4 H42 sing N N 109 DC C5 C6 doub N N 110 DC C5 H5 sing N N 111 DC C6 H6 sing N N 112 DG OP3 P sing N N 113 DG OP3 HOP3 sing N N 114 DG P OP1 doub N N 115 DG P OP2 sing N N 116 DG P "O5'" sing N N 117 DG OP2 HOP2 sing N N 118 DG "O5'" "C5'" sing N N 119 DG "C5'" "C4'" sing N N 120 DG "C5'" "H5'" sing N N 121 DG "C5'" "H5''" sing N N 122 DG "C4'" "O4'" sing N N 123 DG "C4'" "C3'" sing N N 124 DG "C4'" "H4'" sing N N 125 DG "O4'" "C1'" sing N N 126 DG "C3'" "O3'" sing N N 127 DG "C3'" "C2'" sing N N 128 DG "C3'" "H3'" sing N N 129 DG "O3'" "HO3'" sing N N 130 DG "C2'" "C1'" sing N N 131 DG "C2'" "H2'" sing N N 132 DG "C2'" "H2''" sing N N 133 DG "C1'" N9 sing N N 134 DG "C1'" "H1'" sing N N 135 DG N9 C8 sing Y N 136 DG N9 C4 sing Y N 137 DG C8 N7 doub Y N 138 DG C8 H8 sing N N 139 DG N7 C5 sing Y N 140 DG C5 C6 sing N N 141 DG C5 C4 doub Y N 142 DG C6 O6 doub N N 143 DG C6 N1 sing N N 144 DG N1 C2 sing N N 145 DG N1 H1 sing N N 146 DG C2 N2 sing N N 147 DG C2 N3 doub N N 148 DG N2 H21 sing N N 149 DG N2 H22 sing N N 150 DG N3 C4 sing N N 151 DOD O D1 sing N N 152 DOD O D2 sing N N 153 DT OP3 P sing N N 154 DT OP3 HOP3 sing N N 155 DT P OP1 doub N N 156 DT P OP2 sing N N 157 DT P "O5'" sing N N 158 DT OP2 HOP2 sing N N 159 DT "O5'" "C5'" sing N N 160 DT "C5'" "C4'" sing N N 161 DT "C5'" "H5'" sing N N 162 DT "C5'" "H5''" sing N N 163 DT "C4'" "O4'" sing N N 164 DT "C4'" "C3'" sing N N 165 DT "C4'" "H4'" sing N N 166 DT "O4'" "C1'" sing N N 167 DT "C3'" "O3'" sing N N 168 DT "C3'" "C2'" sing N N 169 DT "C3'" "H3'" sing N N 170 DT "O3'" "HO3'" sing N N 171 DT "C2'" "C1'" sing N N 172 DT "C2'" "H2'" sing N N 173 DT "C2'" "H2''" sing N N 174 DT "C1'" N1 sing N N 175 DT "C1'" "H1'" sing N N 176 DT N1 C2 sing N N 177 DT N1 C6 sing N N 178 DT C2 O2 doub N N 179 DT C2 N3 sing N N 180 DT N3 C4 sing N N 181 DT N3 H3 sing N N 182 DT C4 O4 doub N N 183 DT C4 C5 sing N N 184 DT C5 C7 sing N N 185 DT C5 C6 doub N N 186 DT C7 H71 sing N N 187 DT C7 H72 sing N N 188 DT C7 H73 sing N N 189 DT C6 H6 sing N N 190 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water DOD # _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 4FP6 _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 ? # loop_ _refine_funct_minimized.pdbx_refine_id _refine_funct_minimized.type 'X-RAY DIFFRACTION' 'Joint X-ray/neutron ML' 'NEUTRON DIFFRACTION' 'Joint X-ray/neutron ML' #