data_5MVU # _entry.id 5MVU # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 5MVU pdb_00005mvu 10.2210/pdb5mvu/pdb WWPDB D_1200003091 ? ? # 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 2017-05-10 2 'Structure model' 1 1 2017-05-17 3 'Structure model' 1 2 2017-05-24 4 'Structure model' 1 3 2017-06-14 5 'Structure model' 1 4 2017-08-30 6 'Structure model' 1 5 2019-10-16 7 'Structure model' 1 6 2024-01-17 # _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' 'Database references' 3 4 'Structure model' 'Database references' 4 5 'Structure model' 'Author supporting evidence' 5 6 'Structure model' 'Data collection' 6 7 'Structure model' 'Data collection' 7 7 'Structure model' 'Database references' 8 7 '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 4 'Structure model' citation 2 5 'Structure model' pdbx_audit_support 3 6 'Structure model' reflns_shell 4 7 'Structure model' chem_comp_atom 5 7 'Structure model' chem_comp_bond 6 7 'Structure model' database_2 7 7 '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 4 'Structure model' '_citation.country' 2 4 'Structure model' '_citation.journal_volume' 3 4 'Structure model' '_citation.page_first' 4 4 'Structure model' '_citation.page_last' 5 5 'Structure model' '_pdbx_audit_support.funding_organization' 6 7 'Structure model' '_database_2.pdbx_DOI' 7 7 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5MVU _pdbx_database_status.recvd_initial_deposition_date 2017-01-17 _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 _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Hardwick, J.S.' 1 0000-0002-3117-1035 'Ptchelkine, D.' 2 ? 'Phillips, S.E.V.' 3 0000-0001-8922-0250 'Brown, T.' 4 0000-0002-6538-3036 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat. Struct. Mol. Biol.' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1545-9985 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 24 _citation.language ? _citation.page_first 544 _citation.page_last 552 _citation.title '5-Formylcytosine does not change the global structure of DNA.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/nsmb.3411 _citation.pdbx_database_id_PubMed 28504696 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hardwick, J.S.' 1 ? primary 'Ptchelkine, D.' 2 ? primary 'El-Sagheer, A.H.' 3 ? primary 'Tear, I.' 4 ? primary 'Singleton, D.' 5 ? primary 'Phillips, S.E.V.' 6 ? primary 'Lane, A.N.' 7 ? primary 'Brown, T.' 8 ? # 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 3747.422 2 ? ? ? ? 2 water nat water 18.015 3 ? ? ? ? # _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 '(DC)(DT)(DA)(5FC)(DG)(5FC)(DG)(5FC)(DG)(DT)(DA)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CTACGCGCGTAG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DT n 1 3 DA n 1 4 5FC n 1 5 DG n 1 6 5FC n 1 7 DG n 1 8 5FC n 1 9 DG n 1 10 DT n 1 11 DA n 1 12 DG 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 12 _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 ? # 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 5FC 'DNA linking' n "5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" "2'-DEOXY-5-FORMYLCYTIDINE-5'-MONOPHOSPHATE" 'C10 H14 N3 O8 P' 335.207 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 DC 1 1 1 DC DC A . n A 1 2 DT 2 2 2 DT DT A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 5FC 4 4 4 5FC 5FC A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 5FC 6 6 6 5FC 5FC A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 5FC 8 8 8 5FC 5FC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DA 11 11 11 DA DA A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DT 2 2 2 DT DT B . n B 1 3 DA 3 3 3 DA DA B . n B 1 4 5FC 4 4 4 5FC 5FC B . n B 1 5 DG 5 5 5 DG DG B . n B 1 6 5FC 6 6 6 5FC 5FC B . n B 1 7 DG 7 7 7 DG DG B . n B 1 8 5FC 8 8 8 5FC 5FC B . n B 1 9 DG 9 9 9 DG DG B . n B 1 10 DT 10 10 10 DT DT B . n B 1 11 DA 11 11 11 DA DA B . n B 1 12 DG 12 12 12 DG DG 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 HOH 1 101 2 HOH HOH A . D 2 HOH 1 101 7 HOH HOH B . D 2 HOH 2 102 3 HOH HOH B . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0135 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 5MVU _cell.details ? _cell.formula_units_Z ? _cell.length_a 44.200 _cell.length_a_esd ? _cell.length_b 44.200 _cell.length_b_esd ? _cell.length_c 61.683 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MVU _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # _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 5MVU _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 2.32 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 47.00 _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 ? _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 ;Magnesium chloride (18 mM) Spermine tetrahydrochloride (3 mM) Sodium cacodylate (50 mM) 2-Propanol (10% v/v) ; _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 PILATUS3 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 2016-09-10 # _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 0.976 _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 I03' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.976 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I03 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5MVU _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.30 _reflns.d_resolution_low 38.28 _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 3349 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.91 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 8.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 15.4 _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 ? _reflns.pdbx_R_split ? # _refine.aniso_B[1][1] -3.75 _refine.aniso_B[1][2] -0.00 _refine.aniso_B[1][3] -0.00 _refine.aniso_B[2][2] -3.75 _refine.aniso_B[2][3] -0.00 _refine.aniso_B[3][3] 7.51 _refine.B_iso_max ? _refine.B_iso_mean 63.078 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.984 _refine.correlation_coeff_Fo_to_Fc_free 0.982 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 5MVU _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 2.30 _refine.ls_d_res_low 32.52 _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 3170 _refine.ls_number_reflns_R_free 161 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.91 _refine.ls_percent_reflns_R_free 4.8 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.14921 _refine.ls_R_factor_R_free 0.15756 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.14881 _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 5MVL _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.048 _refine.pdbx_overall_ESU_R_Free 0.031 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B 6.313 _refine.overall_SU_ML 0.133 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id 1 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 498 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 501 _refine_hist.d_res_high 2.30 _refine_hist.d_res_low 32.52 # 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' ? 0.008 0.013 556 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.005 0.020 270 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.510 1.551 854 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 1.533 3.000 638 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_2_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_4_deg ? ? 'X-RAY DIFFRACTION' ? 0.085 0.200 72 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.010 0.020 300 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.002 0.020 112 ? r_gen_planes_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_other ? ? 'X-RAY DIFFRACTION' ? 5.328 6.419 556 ? r_scbond_it ? ? 'X-RAY DIFFRACTION' ? 5.329 6.421 555 ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? 8.382 9.697 855 ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? 9.477 60.447 810 ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? 9.472 60.439 811 ? r_long_range_B_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 2.301 _refine_ls_shell.d_res_low 2.361 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 14 _refine_ls_shell.number_reflns_R_work 217 _refine_ls_shell.percent_reflns_obs 99.57 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.170 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.240 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 5MVU _struct.title 'Crystal structure of an A-DNA dodecamer containing 5-formylcytosine in 3 consecutive CpG steps' _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 5MVU _struct_keywords.text 'A-DNA, DNA, 5-formylcytosine, CpG' _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 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5MVU _struct_ref.pdbx_db_accession 5MVU _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 5MVU A 1 ? 12 ? 5MVU 1 ? 12 ? 1 12 2 1 5MVU B 1 ? 12 ? 5MVU 1 ? 12 ? 1 12 # _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 # 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)' 4770 ? 1 MORE 27 ? 1 'SSA (A^2)' 3710 ? # _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 # _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_ _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 DA 3 "O3'" ? ? ? 1_555 A 5FC 4 P ? ? A DA 3 A 5FC 4 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A 5FC 4 "O3'" ? ? ? 1_555 A DG 5 P ? ? A 5FC 4 A DG 5 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale3 covale both ? A DG 5 "O3'" ? ? ? 1_555 A 5FC 6 P ? ? A DG 5 A 5FC 6 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale4 covale both ? A 5FC 6 "O3'" ? ? ? 1_555 A DG 7 P ? ? A 5FC 6 A DG 7 1_555 ? ? ? ? ? ? ? 1.581 ? ? covale5 covale both ? A DG 7 "O3'" ? ? ? 1_555 A 5FC 8 P ? ? A DG 7 A 5FC 8 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale6 covale both ? A 5FC 8 "O3'" ? ? ? 1_555 A DG 9 P ? ? A 5FC 8 A DG 9 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale7 covale both ? B DA 3 "O3'" ? ? ? 1_555 B 5FC 4 P ? ? B DA 3 B 5FC 4 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale8 covale both ? B 5FC 4 "O3'" ? ? ? 1_555 B DG 5 P ? ? B 5FC 4 B DG 5 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale9 covale both ? B DG 5 "O3'" ? ? ? 1_555 B 5FC 6 P ? ? B DG 5 B 5FC 6 1_555 ? ? ? ? ? ? ? 1.593 ? ? covale10 covale both ? B 5FC 6 "O3'" ? ? ? 1_555 B DG 7 P ? ? B 5FC 6 B DG 7 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale11 covale both ? B DG 7 "O3'" ? ? ? 1_555 B 5FC 8 P ? ? B DG 7 B 5FC 8 1_555 ? ? ? ? ? ? ? 1.575 ? ? covale12 covale both ? B 5FC 8 "O3'" ? ? ? 1_555 B DG 9 P ? ? B 5FC 8 B DG 9 1_555 ? ? ? ? ? ? ? 1.599 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B DA 11 N1 ? ? A DT 2 B DA 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B DA 11 N6 ? ? A DT 2 B DA 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 10 N3 ? ? A DA 3 B DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 10 O4 ? ? A DA 3 B DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A 5FC 4 N3 ? ? ? 1_555 B DG 9 N1 ? ? A 5FC 4 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A 5FC 4 N4 ? ? ? 1_555 B DG 9 O6 ? ? A 5FC 4 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 5FC 4 O2 ? ? ? 1_555 B DG 9 N2 ? ? A 5FC 4 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B 5FC 8 N3 ? ? A DG 5 B 5FC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B 5FC 8 O2 ? ? A DG 5 B 5FC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B 5FC 8 N4 ? ? A DG 5 B 5FC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 5FC 6 N3 ? ? ? 1_555 B DG 7 N1 ? ? A 5FC 6 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 5FC 6 N4 ? ? ? 1_555 B DG 7 O6 ? ? A 5FC 6 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A 5FC 6 O2 ? ? ? 1_555 B DG 7 N2 ? ? A 5FC 6 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B 5FC 6 N3 ? ? A DG 7 B 5FC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B 5FC 6 O2 ? ? A DG 7 B 5FC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B 5FC 6 N4 ? ? A DG 7 B 5FC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A 5FC 8 N3 ? ? ? 1_555 B DG 5 N1 ? ? A 5FC 8 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A 5FC 8 N4 ? ? ? 1_555 B DG 5 O6 ? ? A 5FC 8 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A 5FC 8 O2 ? ? ? 1_555 B DG 5 N2 ? ? A 5FC 8 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B 5FC 4 N3 ? ? A DG 9 B 5FC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B 5FC 4 O2 ? ? A DG 9 B 5FC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B 5FC 4 N4 ? ? A DG 9 B 5FC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 10 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 10 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DA 11 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 11 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DA 11 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 11 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 5FC P P N N 1 5FC OP2 O N N 2 5FC OP1 O N N 3 5FC "O5'" O N N 4 5FC N1 N N N 5 5FC C6 C N N 6 5FC C2 C N N 7 5FC O2 O N N 8 5FC N3 N N N 9 5FC C4 C N N 10 5FC N4 N N N 11 5FC C5 C N N 12 5FC "C2'" C N N 13 5FC "C5'" C N N 14 5FC "C4'" C N R 15 5FC "O4'" O N N 16 5FC "C1'" C N R 17 5FC "C3'" C N S 18 5FC "O3'" O N N 19 5FC C5A C N N 20 5FC O5A O N N 21 5FC OP3 O N N 22 5FC HOP2 H N N 23 5FC H6 H N N 24 5FC HN41 H N N 25 5FC HN42 H N N 26 5FC "H2'" H N N 27 5FC "H2''" H N N 28 5FC "H5'" H N N 29 5FC "H5''" H N N 30 5FC "H4'" H N N 31 5FC "H1'" H N N 32 5FC "H3'" H N N 33 5FC "HO3'" H N N 34 5FC H5A H N N 35 5FC HOP3 H N N 36 DA OP3 O N N 37 DA P P N N 38 DA OP1 O N N 39 DA OP2 O N N 40 DA "O5'" O N N 41 DA "C5'" C N N 42 DA "C4'" C N R 43 DA "O4'" O N N 44 DA "C3'" C N S 45 DA "O3'" O N N 46 DA "C2'" C N N 47 DA "C1'" C N R 48 DA N9 N Y N 49 DA C8 C Y N 50 DA N7 N Y N 51 DA C5 C Y N 52 DA C6 C Y N 53 DA N6 N N N 54 DA N1 N Y N 55 DA C2 C Y N 56 DA N3 N Y N 57 DA C4 C Y N 58 DA HOP3 H N N 59 DA HOP2 H N N 60 DA "H5'" H N N 61 DA "H5''" H N N 62 DA "H4'" H N N 63 DA "H3'" H N N 64 DA "HO3'" H N N 65 DA "H2'" H N N 66 DA "H2''" H N N 67 DA "H1'" H N N 68 DA H8 H N N 69 DA H61 H N N 70 DA H62 H N N 71 DA H2 H N N 72 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 DG OP3 O N N 107 DG P P N N 108 DG OP1 O N N 109 DG OP2 O N N 110 DG "O5'" O N N 111 DG "C5'" C N N 112 DG "C4'" C N R 113 DG "O4'" O N N 114 DG "C3'" C N S 115 DG "O3'" O N N 116 DG "C2'" C N N 117 DG "C1'" C N R 118 DG N9 N Y N 119 DG C8 C Y N 120 DG N7 N Y N 121 DG C5 C Y N 122 DG C6 C N N 123 DG O6 O N N 124 DG N1 N N N 125 DG C2 C N N 126 DG N2 N N N 127 DG N3 N N N 128 DG C4 C Y N 129 DG HOP3 H N N 130 DG HOP2 H N N 131 DG "H5'" H N N 132 DG "H5''" H N N 133 DG "H4'" H N N 134 DG "H3'" H N N 135 DG "HO3'" H N N 136 DG "H2'" H N N 137 DG "H2''" H N N 138 DG "H1'" H N N 139 DG H8 H N N 140 DG H1 H N N 141 DG H21 H N N 142 DG H22 H N N 143 DT OP3 O N N 144 DT P P N N 145 DT OP1 O N N 146 DT OP2 O N N 147 DT "O5'" O N N 148 DT "C5'" C N N 149 DT "C4'" C N R 150 DT "O4'" O N N 151 DT "C3'" C N S 152 DT "O3'" O N N 153 DT "C2'" C N N 154 DT "C1'" C N R 155 DT N1 N N N 156 DT C2 C N N 157 DT O2 O N N 158 DT N3 N N N 159 DT C4 C N N 160 DT O4 O N N 161 DT C5 C N N 162 DT C7 C N N 163 DT C6 C N N 164 DT HOP3 H N N 165 DT HOP2 H N N 166 DT "H5'" H N N 167 DT "H5''" H N N 168 DT "H4'" H N N 169 DT "H3'" H N N 170 DT "HO3'" H N N 171 DT "H2'" H N N 172 DT "H2''" H N N 173 DT "H1'" H N N 174 DT H3 H N N 175 DT H71 H N N 176 DT H72 H N N 177 DT H73 H N N 178 DT H6 H N N 179 HOH O O N N 180 HOH H1 H N N 181 HOH H2 H N N 182 # 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 5FC P OP2 sing N N 1 5FC P OP1 doub N N 2 5FC P "O5'" sing N N 3 5FC P OP3 sing N N 4 5FC OP2 HOP2 sing N N 5 5FC "O5'" "C5'" sing N N 6 5FC N1 C6 sing N N 7 5FC N1 C2 sing N N 8 5FC N1 "C1'" sing N N 9 5FC C6 C5 doub N N 10 5FC C6 H6 sing N N 11 5FC C2 O2 doub N N 12 5FC C2 N3 sing N N 13 5FC N3 C4 doub N N 14 5FC C4 N4 sing N N 15 5FC C4 C5 sing N N 16 5FC N4 HN41 sing N N 17 5FC N4 HN42 sing N N 18 5FC C5 C5A sing N N 19 5FC "C2'" "C1'" sing N N 20 5FC "C2'" "C3'" sing N N 21 5FC "C2'" "H2'" sing N N 22 5FC "C2'" "H2''" sing N N 23 5FC "C5'" "C4'" sing N N 24 5FC "C5'" "H5'" sing N N 25 5FC "C5'" "H5''" sing N N 26 5FC "C4'" "O4'" sing N N 27 5FC "C4'" "C3'" sing N N 28 5FC "C4'" "H4'" sing N N 29 5FC "O4'" "C1'" sing N N 30 5FC "C1'" "H1'" sing N N 31 5FC "C3'" "O3'" sing N N 32 5FC "C3'" "H3'" sing N N 33 5FC "O3'" "HO3'" sing N N 34 5FC C5A O5A doub N N 35 5FC C5A H5A sing N N 36 5FC OP3 HOP3 sing N N 37 DA OP3 P sing N N 38 DA OP3 HOP3 sing N N 39 DA P OP1 doub N N 40 DA P OP2 sing N N 41 DA P "O5'" sing N N 42 DA OP2 HOP2 sing N N 43 DA "O5'" "C5'" sing N N 44 DA "C5'" "C4'" sing N N 45 DA "C5'" "H5'" sing N N 46 DA "C5'" "H5''" sing N N 47 DA "C4'" "O4'" sing N N 48 DA "C4'" "C3'" sing N N 49 DA "C4'" "H4'" sing N N 50 DA "O4'" "C1'" sing N N 51 DA "C3'" "O3'" sing N N 52 DA "C3'" "C2'" sing N N 53 DA "C3'" "H3'" sing N N 54 DA "O3'" "HO3'" sing N N 55 DA "C2'" "C1'" sing N N 56 DA "C2'" "H2'" sing N N 57 DA "C2'" "H2''" sing N N 58 DA "C1'" N9 sing N N 59 DA "C1'" "H1'" sing N N 60 DA N9 C8 sing Y N 61 DA N9 C4 sing Y N 62 DA C8 N7 doub Y N 63 DA C8 H8 sing N N 64 DA N7 C5 sing Y N 65 DA C5 C6 sing Y N 66 DA C5 C4 doub Y N 67 DA C6 N6 sing N N 68 DA C6 N1 doub Y N 69 DA N6 H61 sing N N 70 DA N6 H62 sing N N 71 DA N1 C2 sing Y N 72 DA C2 N3 doub Y N 73 DA C2 H2 sing N N 74 DA N3 C4 sing Y N 75 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 DG OP3 P sing N N 111 DG OP3 HOP3 sing N N 112 DG P OP1 doub N N 113 DG P OP2 sing N N 114 DG P "O5'" sing N N 115 DG OP2 HOP2 sing N N 116 DG "O5'" "C5'" sing N N 117 DG "C5'" "C4'" sing N N 118 DG "C5'" "H5'" sing N N 119 DG "C5'" "H5''" sing N N 120 DG "C4'" "O4'" sing N N 121 DG "C4'" "C3'" sing N N 122 DG "C4'" "H4'" sing N N 123 DG "O4'" "C1'" sing N N 124 DG "C3'" "O3'" sing N N 125 DG "C3'" "C2'" sing N N 126 DG "C3'" "H3'" sing N N 127 DG "O3'" "HO3'" sing N N 128 DG "C2'" "C1'" sing N N 129 DG "C2'" "H2'" sing N N 130 DG "C2'" "H2''" sing N N 131 DG "C1'" N9 sing N N 132 DG "C1'" "H1'" sing N N 133 DG N9 C8 sing Y N 134 DG N9 C4 sing Y N 135 DG C8 N7 doub Y N 136 DG C8 H8 sing N N 137 DG N7 C5 sing Y N 138 DG C5 C6 sing N N 139 DG C5 C4 doub Y N 140 DG C6 O6 doub N N 141 DG C6 N1 sing N N 142 DG N1 C2 sing N N 143 DG N1 H1 sing N N 144 DG C2 N2 sing N N 145 DG C2 N3 doub N N 146 DG N2 H21 sing N N 147 DG N2 H22 sing N N 148 DG N3 C4 sing N N 149 DT OP3 P sing N N 150 DT OP3 HOP3 sing N N 151 DT P OP1 doub N N 152 DT P OP2 sing N N 153 DT P "O5'" sing N N 154 DT OP2 HOP2 sing N N 155 DT "O5'" "C5'" sing N N 156 DT "C5'" "C4'" sing N N 157 DT "C5'" "H5'" sing N N 158 DT "C5'" "H5''" sing N N 159 DT "C4'" "O4'" sing N N 160 DT "C4'" "C3'" sing N N 161 DT "C4'" "H4'" sing N N 162 DT "O4'" "C1'" sing N N 163 DT "C3'" "O3'" sing N N 164 DT "C3'" "C2'" sing N N 165 DT "C3'" "H3'" sing N N 166 DT "O3'" "HO3'" sing N N 167 DT "C2'" "C1'" sing N N 168 DT "C2'" "H2'" sing N N 169 DT "C2'" "H2''" sing N N 170 DT "C1'" N1 sing N N 171 DT "C1'" "H1'" sing N N 172 DT N1 C2 sing N N 173 DT N1 C6 sing N N 174 DT C2 O2 doub N N 175 DT C2 N3 sing N N 176 DT N3 C4 sing N N 177 DT N3 H3 sing N N 178 DT C4 O4 doub N N 179 DT C4 C5 sing N N 180 DT C5 C7 sing N N 181 DT C5 C6 doub N N 182 DT C7 H71 sing N N 183 DT C7 H72 sing N N 184 DT C7 H73 sing N N 185 DT C6 H6 sing N N 186 HOH O H1 sing N N 187 HOH O H2 sing N N 188 # _ndb_struct_conf_na.entry_id 5MVU _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.107 -0.046 0.387 -7.701 -2.713 1.551 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DT 2 1_555 B DA 11 1_555 0.254 -0.034 0.488 3.427 -13.010 1.359 2 A_DT2:DA11_B A 2 ? B 11 ? 20 1 1 A DA 3 1_555 B DT 10 1_555 -0.274 -0.044 0.199 7.536 -14.085 5.004 3 A_DA3:DT10_B A 3 ? B 10 ? 20 1 1 A 5FC 4 1_555 B DG 9 1_555 -0.089 0.056 -0.129 9.119 -18.575 2.051 4 A_5FC4:DG9_B A 4 ? B 9 ? 19 1 1 A DG 5 1_555 B 5FC 8 1_555 -0.595 -0.118 0.106 -6.075 -8.760 3.143 5 A_DG5:5FC8_B A 5 ? B 8 ? 19 1 1 A 5FC 6 1_555 B DG 7 1_555 -0.135 -0.016 0.123 -2.338 -13.757 -0.364 6 A_5FC6:DG7_B A 6 ? B 7 ? 19 1 1 A DG 7 1_555 B 5FC 6 1_555 -0.163 -0.038 0.068 -2.567 -12.981 -3.502 7 A_DG7:5FC6_B A 7 ? B 6 ? 19 1 1 A 5FC 8 1_555 B DG 5 1_555 0.047 -0.037 0.003 8.650 -9.514 -1.477 8 A_5FC8:DG5_B A 8 ? B 5 ? 19 1 1 A DG 9 1_555 B 5FC 4 1_555 -0.382 -0.117 0.085 -4.910 -14.139 1.104 9 A_DG9:5FC4_B A 9 ? B 4 ? 19 1 1 A DT 10 1_555 B DA 3 1_555 -0.656 -0.184 0.098 -2.766 -18.041 -6.393 10 A_DT10:DA3_B A 10 ? B 3 ? 20 1 1 A DA 11 1_555 B DT 2 1_555 0.419 -0.004 0.603 -3.569 -4.075 -3.731 11 A_DA11:DT2_B A 11 ? B 2 ? 20 1 1 A DG 12 1_555 B DC 1 1_555 0.347 0.163 0.529 11.580 -0.506 1.607 12 A_DG12:DC1_B A 12 ? 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 DC 1 1_555 B DG 12 1_555 A DT 2 1_555 B DA 11 1_555 -0.652 -2.127 2.987 -3.771 1.593 29.533 -4.437 0.554 2.930 3.106 7.352 29.809 1 AA_DC1DT2:DA11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DT 2 1_555 B DA 11 1_555 A DA 3 1_555 B DT 10 1_555 -0.596 -1.399 3.004 -0.216 8.881 23.116 -5.538 1.335 2.319 21.186 0.516 24.742 2 AA_DT2DA3:DT10DA11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DA 3 1_555 B DT 10 1_555 A 5FC 4 1_555 B DG 9 1_555 0.227 -1.304 3.279 0.864 2.514 37.179 -2.371 -0.241 3.192 3.936 -1.353 37.271 3 AA_DA35FC4:DG9DT10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A 5FC 4 1_555 B DG 9 1_555 A DG 5 1_555 B 5FC 8 1_555 -0.061 -1.998 3.487 -4.936 12.838 26.547 -6.379 -0.843 2.275 25.867 9.946 29.842 4 AA_5FC4DG5:5FC8DG9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DG 5 1_555 B 5FC 8 1_555 A 5FC 6 1_555 B DG 7 1_555 -0.803 -1.388 3.203 -1.305 5.172 35.428 -2.966 1.127 3.004 8.439 2.130 35.814 5 AA_DG55FC6:DG75FC8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A 5FC 6 1_555 B DG 7 1_555 A DG 7 1_555 B 5FC 6 1_555 0.815 -2.126 3.227 1.613 17.762 25.142 -6.783 -1.285 1.483 35.642 -3.236 30.743 6 AA_5FC6DG7:5FC6DG7_BB A 6 ? B 7 ? A 7 ? B 6 ? 1 A DG 7 1_555 B 5FC 6 1_555 A 5FC 8 1_555 B DG 5 1_555 -0.902 -2.132 3.049 -2.513 4.335 24.301 -6.130 1.425 2.711 10.161 5.890 24.805 7 AA_DG75FC8:DG55FC6_BB A 7 ? B 6 ? A 8 ? B 5 ? 1 A 5FC 8 1_555 B DG 5 1_555 A DG 9 1_555 B 5FC 4 1_555 0.911 -2.019 3.360 2.236 16.497 30.416 -5.662 -1.225 2.083 28.886 -3.916 34.579 8 AA_5FC8DG9:5FC4DG5_BB A 8 ? B 5 ? A 9 ? B 4 ? 1 A DG 9 1_555 B 5FC 4 1_555 A DT 10 1_555 B DA 3 1_555 -0.869 -1.376 3.188 -0.918 4.170 35.048 -2.858 1.304 3.031 6.892 1.518 35.299 9 AA_DG9DT10:DA35FC4_BB A 9 ? B 4 ? A 10 ? B 3 ? 1 A DT 10 1_555 B DA 3 1_555 A DA 11 1_555 B DT 2 1_555 0.618 -1.481 3.212 -1.797 8.638 33.559 -3.710 -1.292 2.723 14.648 3.046 34.667 10 AA_DT10DA11:DT2DA3_BB A 10 ? B 3 ? A 11 ? B 2 ? 1 A DA 11 1_555 B DT 2 1_555 A DG 12 1_555 B DC 1 1_555 0.682 -2.209 2.870 4.498 -1.052 28.333 -4.242 -0.458 3.018 -2.132 -9.113 28.699 11 AA_DA11DG12:DC1DT2_BB A 11 ? B 2 ? A 12 ? B 1 ? # _pdbx_audit_support.country ? _pdbx_audit_support.funding_organization 'Biotechnology and Biological Sciences Research Council' _pdbx_audit_support.grant_number BB/J001694/2 _pdbx_audit_support.ordinal 1 # _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 5MVL _pdbx_initial_refinement_model.details ? # loop_ _pdbx_reflns_twin.domain_id _pdbx_reflns_twin.crystal_id _pdbx_reflns_twin.diffrn_id _pdbx_reflns_twin.type _pdbx_reflns_twin.operator _pdbx_reflns_twin.fraction 1 1 1 ? 'H, K, L' 0.633 2 1 1 ? -h,-k,l 0.367 # _atom_sites.entry_id 5MVU _atom_sites.fract_transf_matrix[1][1] 0.022624 _atom_sites.fract_transf_matrix[1][2] 0.013062 _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] 0.026124 _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] 0.016212 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_