data_4U9M # _entry.id 4U9M # _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 4U9M pdb_00004u9m 10.2210/pdb4u9m/pdb WWPDB D_1000203001 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 4U9M _pdbx_database_status.recvd_initial_deposition_date 2014-08-06 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _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 'Acosta-Reyes, F.J.' 1 'Alechaga, E.' 2 'Subirana, J.A.' 3 'Campos, J.L.' 4 # _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 'Plos One' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1932-6203 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 10 _citation.language ? _citation.page_first e0120241 _citation.page_last e0120241 _citation.title 'Structure of the DNA Duplex d(ATTAAT)2 with Hoogsteen Hydrogen Bonds.' _citation.year 2015 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1371/journal.pone.0120241 _citation.pdbx_database_id_PubMed 25781995 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Acosta-Reyes, F.J.' 1 ? primary 'Alechaga, E.' 2 ? primary 'Subirana, J.A.' 3 ? primary 'Campos, J.L.' 4 ? # _cell.entry_id 4U9M _cell.length_a 24.756 _cell.length_b 42.898 _cell.length_c 99.422 _cell.angle_alpha 90.00 _cell.angle_beta 90.04 _cell.angle_gamma 90.00 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U9M _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*AP*TP*TP*AP*AP*T)-3') ; _entity.formula_weight 1807.241 _entity.pdbx_number_of_molecules 5 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DA)(DT)(DT)(DA)(DA)(DT)' _entity_poly.pdbx_seq_one_letter_code_can ATTAAT _entity_poly.pdbx_strand_id A,B,C,D,E _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 DA n 1 2 DT n 1 3 DT n 1 4 DA n 1 5 DA n 1 6 DT 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 6 _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 4U9M _struct_ref.pdbx_db_accession 4U9M _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # 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 4U9M A 1 ? 6 ? 4U9M 1 ? 6 ? 1 6 2 1 4U9M B 1 ? 6 ? 4U9M 7 ? 12 ? 7 12 3 1 4U9M C 1 ? 6 ? 4U9M 1 ? 6 ? 1 6 4 1 4U9M D 1 ? 6 ? 4U9M 7 ? 12 ? 7 12 5 1 4U9M E 1 ? 6 ? 4U9M 1 ? 6 ? 1 6 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # _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 4U9M _exptl.crystals_number ? _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.92 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 57.89 _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' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 286 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;0.8mM of the oligonucleotide, 20mM sodium cacodylate buffer (pH = 6.5), 3mM spermine, 100mM N-ethylaniline hydrochloride and 5% MPD, equilibrated against a reservoir with 30% MPD. ; _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 CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2005-03-18 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Double crystal monochromator Si(111)' _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 0.9762 _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 'ESRF BEAMLINE BM16' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9762 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BM16 _diffrn_source.pdbx_synchrotron_site ESRF # _reflns.B_iso_Wilson_estimate 144 _reflns.entry_id 4U9M _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 3.13 _reflns.d_resolution_low 33.14 _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 1888 _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 99.6 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.7 _reflns.pdbx_Rmerge_I_obs 0.107 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 7.48 _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 ? # _reflns_shell.d_res_high 3.13 _reflns_shell.d_res_low 3.241 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.88 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 99.35 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.585 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 3.8 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] -9.92 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 93.61 _refine.aniso_B[2][2] 41.24 _refine.aniso_B[2][3] 0.00 _refine.aniso_B[3][3] -31.32 _refine.B_iso_max ? _refine.B_iso_mean 138.561 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.991 _refine.correlation_coeff_Fo_to_Fc_free 0.973 _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 4U9M _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 3.13 _refine.ls_d_res_low 33.14 _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 1773 _refine.ls_number_reflns_R_free 107 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.26 _refine.ls_percent_reflns_R_free 5.7 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.14810 _refine.ls_R_factor_R_free 0.19979 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.14582 _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 MASK _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'helical parameters taken from 2qs6, 1rsb' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 0.079 _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 24.326 _refine.overall_SU_ML 0.327 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _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 600 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 600 _refine_hist.d_res_high 3.13 _refine_hist.d_res_low 33.14 # 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' ? 0.007 0.011 670 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.023 0.020 350 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 0.939 1.178 1025 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 6.678 3.000 830 ? 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' ? 0.068 0.200 90 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.003 0.020 335 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.001 0.020 110 ? 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' ? 16.550 14.236 668 ? r_scbond_it ? ? 'X-RAY DIFFRACTION' ? 16.542 14.241 667 ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? 24.345 21.352 1024 ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? 26.712 ? 2892 ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? 26.717 ? 2891 ? 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 3.129 _refine_ls_shell.d_res_low 3.210 _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 116 _refine_ls_shell.percent_reflns_obs 96.83 _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 ? # _struct.entry_id 4U9M _struct.title 'Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 4U9M _struct_keywords.text DNA _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 1 ? D N N 1 ? E N N 1 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 1 B DT 12 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog2 hydrog ? ? A DA 1 N7 ? ? ? 1_555 B DT 6 N3 ? ? A DA 1 B DT 12 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog3 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B DA 5 N7 ? ? A DT 2 B DA 11 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog4 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 2 B DA 11 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog5 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 4 N7 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog6 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog7 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog8 hydrog ? ? A DA 4 N7 ? ? ? 1_555 B DT 3 N3 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog9 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog10 hydrog ? ? A DA 5 N7 ? ? ? 1_555 B DT 2 N3 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog11 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 1 N7 ? ? A DT 6 B DA 7 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog12 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 6 B DA 7 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog13 hydrog ? ? C DA 1 N6 ? ? ? 1_555 D DT 6 O4 ? ? C DA 1 D DT 12 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog14 hydrog ? ? C DA 1 N7 ? ? ? 1_555 D DT 6 N3 ? ? C DA 1 D DT 12 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog15 hydrog ? ? C DT 2 N3 ? ? ? 1_555 D DA 5 N7 ? ? C DT 2 D DA 11 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog16 hydrog ? ? C DT 2 O4 ? ? ? 1_555 D DA 5 N6 ? ? C DT 2 D DA 11 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog17 hydrog ? ? C DT 3 N3 ? ? ? 1_555 D DA 4 N7 ? ? C DT 3 D DA 10 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog18 hydrog ? ? C DT 3 O4 ? ? ? 1_555 D DA 4 N6 ? ? C DT 3 D DA 10 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog19 hydrog ? ? C DA 4 N6 ? ? ? 1_555 D DT 2 O4 ? ? C DA 4 D DT 8 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog20 hydrog ? ? C DA 4 N6 ? ? ? 1_555 D DT 3 O4 ? ? C DA 4 D DT 9 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog21 hydrog ? ? C DA 4 N7 ? ? ? 1_555 D DT 3 N3 ? ? C DA 4 D DT 9 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog22 hydrog ? ? C DA 5 N6 ? ? ? 1_555 D DT 2 O4 ? ? C DA 5 D DT 8 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog23 hydrog ? ? C DA 5 N7 ? ? ? 1_555 D DT 2 N3 ? ? C DA 5 D DT 8 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog24 hydrog ? ? C DT 6 N3 ? ? ? 1_555 D DA 1 N7 ? ? C DT 6 D DA 7 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog25 hydrog ? ? C DT 6 O4 ? ? ? 1_555 D DA 1 N6 ? ? C DT 6 D DA 7 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog26 hydrog ? ? E DA 1 N6 ? ? ? 1_555 E DT 6 O4 ? ? E DA 1 E DT 6 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog27 hydrog ? ? E DA 1 N7 ? ? ? 1_555 E DT 6 N3 ? ? E DA 1 E DT 6 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog28 hydrog ? ? E DT 2 N3 ? ? ? 1_555 E DA 5 N7 ? ? E DT 2 E DA 5 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog29 hydrog ? ? E DT 2 O4 ? ? ? 1_555 E DA 5 N6 ? ? E DT 2 E DA 5 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog30 hydrog ? ? E DT 3 N3 ? ? ? 1_555 E DA 4 N7 ? ? E DT 3 E DA 4 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog31 hydrog ? ? E DT 3 O4 ? ? ? 1_555 E DA 4 N6 ? ? E DT 3 E DA 4 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog32 hydrog ? ? E DA 4 N6 ? ? ? 1_555 E DT 3 O4 ? ? E DA 4 E DT 3 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog33 hydrog ? ? E DA 4 N7 ? ? ? 1_555 E DT 3 N3 ? ? E DA 4 E DT 3 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog34 hydrog ? ? E DA 5 N6 ? ? ? 1_555 E DT 2 O4 ? ? E DA 5 E DT 2 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog35 hydrog ? ? E DA 5 N7 ? ? ? 1_555 E DT 2 N3 ? ? E DA 5 E DT 2 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog36 hydrog ? ? E DT 6 N3 ? ? ? 1_555 E DA 1 N7 ? ? E DT 6 E DA 1 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog37 hydrog ? ? E DT 6 O4 ? ? ? 1_555 E DA 1 N6 ? ? E DT 6 E DA 1 2_756 ? ? ? ? ? ? HOOGSTEEN ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 4U9M _atom_sites.fract_transf_matrix[1][1] 0.040394 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000029 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.023311 _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] 0.010058 _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_ _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 DA 1 1 1 DA DA A . n A 1 2 DT 2 2 2 DT DT A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DT 6 6 6 DT DT A . n B 1 1 DA 1 7 7 DA DA B . n B 1 2 DT 2 8 8 DT DT B . n B 1 3 DT 3 9 9 DT DT B . n B 1 4 DA 4 10 10 DA DA B . n B 1 5 DA 5 11 11 DA DA B . n B 1 6 DT 6 12 12 DT DT B . n C 1 1 DA 1 1 1 DA DA C . n C 1 2 DT 2 2 2 DT DT C . n C 1 3 DT 3 3 3 DT DT C . n C 1 4 DA 4 4 4 DA DA C . n C 1 5 DA 5 5 5 DA DA C . n C 1 6 DT 6 6 6 DT DT C . n D 1 1 DA 1 7 7 DA DA D . n D 1 2 DT 2 8 8 DT DT D . n D 1 3 DT 3 9 9 DT DT D . n D 1 4 DA 4 10 10 DA DA D . n D 1 5 DA 5 11 11 DA DA D . n D 1 6 DT 6 12 12 DT DT D . n E 1 1 DA 1 1 1 DA DA E . n E 1 2 DT 2 2 2 DT DT E . n E 1 3 DT 3 3 3 DT DT E . n E 1 4 DA 4 4 4 DA DA E . n E 1 5 DA 5 5 5 DA DA E . n E 1 6 DT 6 6 6 DT DT E . n # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA Dimeric 2 2 author_and_software_defined_assembly PISA Dimeric 2 3 author_and_software_defined_assembly PISA Dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B 2 1 C,D 3 1,2 E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 570 ? 1 MORE -6 ? 1 'SSA (A^2)' 2370 ? 2 'ABSA (A^2)' 550 ? 2 MORE -6 ? 2 'SSA (A^2)' 2370 ? 3 'ABSA (A^2)' 540 ? 3 MORE -6 ? 3 'SSA (A^2)' 2430 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_756 -x+2,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 49.4425903557 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 99.4219757715 # 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 2015-04-01 2 'Structure model' 1 1 2023-12-20 # _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 2 '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' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 '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' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0071 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 3 # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DT OP3 O N N 37 DT P P N N 38 DT OP1 O N N 39 DT OP2 O N N 40 DT "O5'" O N N 41 DT "C5'" C N N 42 DT "C4'" C N R 43 DT "O4'" O N N 44 DT "C3'" C N S 45 DT "O3'" O N N 46 DT "C2'" C N N 47 DT "C1'" C N R 48 DT N1 N N N 49 DT C2 C N N 50 DT O2 O N N 51 DT N3 N N N 52 DT C4 C N N 53 DT O4 O N N 54 DT C5 C N N 55 DT C7 C N N 56 DT C6 C N N 57 DT HOP3 H N N 58 DT HOP2 H N N 59 DT "H5'" H N N 60 DT "H5''" H N N 61 DT "H4'" H N N 62 DT "H3'" H N N 63 DT "HO3'" H N N 64 DT "H2'" H N N 65 DT "H2''" H N N 66 DT "H1'" H N N 67 DT H3 H N N 68 DT H71 H N N 69 DT H72 H N N 70 DT H73 H N N 71 DT H6 H N N 72 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DT OP3 P sing N N 39 DT OP3 HOP3 sing N N 40 DT P OP1 doub N N 41 DT P OP2 sing N N 42 DT P "O5'" sing N N 43 DT OP2 HOP2 sing N N 44 DT "O5'" "C5'" sing N N 45 DT "C5'" "C4'" sing N N 46 DT "C5'" "H5'" sing N N 47 DT "C5'" "H5''" sing N N 48 DT "C4'" "O4'" sing N N 49 DT "C4'" "C3'" sing N N 50 DT "C4'" "H4'" sing N N 51 DT "O4'" "C1'" sing N N 52 DT "C3'" "O3'" sing N N 53 DT "C3'" "C2'" sing N N 54 DT "C3'" "H3'" sing N N 55 DT "O3'" "HO3'" sing N N 56 DT "C2'" "C1'" sing N N 57 DT "C2'" "H2'" sing N N 58 DT "C2'" "H2''" sing N N 59 DT "C1'" N1 sing N N 60 DT "C1'" "H1'" sing N N 61 DT N1 C2 sing N N 62 DT N1 C6 sing N N 63 DT C2 O2 doub N N 64 DT C2 N3 sing N N 65 DT N3 C4 sing N N 66 DT N3 H3 sing N N 67 DT C4 O4 doub N N 68 DT C4 C5 sing N N 69 DT C5 C7 sing N N 70 DT C5 C6 doub N N 71 DT C7 H71 sing N N 72 DT C7 H72 sing N N 73 DT C7 H73 sing N N 74 DT C6 H6 sing N N 75 # _ndb_struct_conf_na.entry_id 4U9M _ndb_struct_conf_na.feature 'double helix' _ndb_struct_conf_na.feature_count ? # 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 B DA 1 1_555 A DT 6 1_555 0.103 -3.071 0.440 -6.845 -1.197 68.878 1 B_DA7:DT6_A B 7 ? A 6 ? 23 3 1 B DT 2 1_555 A DA 5 1_555 -0.417 3.429 0.144 -5.613 -8.540 -70.536 2 B_DT8:DA5_A B 8 ? A 5 ? 23 3 1 B DT 3 1_555 A DA 4 1_555 -0.983 3.803 0.429 -10.304 -2.819 -74.356 3 B_DT9:DA4_A B 9 ? A 4 ? 23 3 1 B DA 4 1_555 A DT 3 1_555 1.021 -3.822 -0.216 6.351 9.411 74.473 4 B_DA10:DT3_A B 10 ? A 3 ? 23 3 1 B DA 5 1_555 A DT 2 1_555 0.235 -3.220 -0.046 0.150 10.379 69.135 5 B_DA11:DT2_A B 11 ? A 2 ? 23 3 1 B DT 6 1_555 A DA 1 1_555 -0.289 3.470 -0.127 1.023 -7.545 -66.227 6 B_DT12:DA1_A B 12 ? A 1 ? 23 3 1 C DA 1 1_555 D DT 6 1_555 0.324 -3.332 0.334 -5.576 13.632 69.210 7 C_DA1:DT12_D C 1 ? D 12 ? 23 3 1 C DT 2 1_555 D DA 5 1_555 -1.188 3.895 -0.044 -1.555 -15.867 -75.248 8 C_DT2:DA11_D C 2 ? D 11 ? 23 3 1 C DT 3 1_555 D DA 4 1_555 -0.984 3.651 1.001 -23.200 -12.872 -76.268 9 C_DT3:DA10_D C 3 ? D 10 ? 23 3 1 C DA 4 1_555 D DT 3 1_555 1.376 -3.969 -0.276 8.133 12.516 77.151 10 C_DA4:DT9_D C 4 ? D 9 ? 23 3 1 C DA 5 1_555 D DT 2 1_555 0.338 -3.206 -0.882 14.358 7.425 71.807 11 C_DA5:DT8_D C 5 ? D 8 ? 23 3 1 C DT 6 1_555 D DA 1 1_555 -0.425 3.474 -0.133 3.077 -10.155 -66.903 12 C_DT6:DA7_D C 6 ? D 7 ? 23 3 1 E DA 1 1_555 E DT 6 2_756 0.117 -3.187 0.258 -5.484 6.910 67.833 13 E_DA1:DT6_E E 1 ? E 6 ? 23 3 1 E DT 2 1_555 E DA 5 2_756 -0.301 3.321 0.152 -3.144 -4.857 -69.407 14 E_DT2:DA5_E E 2 ? E 5 ? 23 3 1 E DT 3 1_555 E DA 4 2_756 -1.559 4.020 0.437 -5.749 -7.105 -78.099 15 E_DT3:DA4_E E 3 ? E 4 ? 23 3 1 E DA 4 1_555 E DT 3 2_756 1.559 -4.020 -0.437 5.749 7.105 78.099 16 E_DA4:DT3_E E 4 ? E 3 ? 23 3 1 E DA 5 1_555 E DT 2 2_756 0.301 -3.321 -0.152 3.144 4.857 69.407 17 E_DA5:DT2_E E 5 ? E 2 ? 23 3 1 E DT 6 1_555 E DA 1 2_756 -0.117 3.187 -0.258 5.484 -6.910 -67.833 18 E_DT6:DA1_E E 6 ? E 1 ? 23 3 # 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 B DA 1 1_555 A DT 6 1_555 B DT 2 1_555 A DA 5 1_555 4.355 -0.423 2.975 -91.660 149.077 93.605 -0.774 -2.525 0.363 75.115 46.185 176.579 1 BB_DA7DT8:DA5DT6_AA B 7 ? A 6 ? B 8 ? A 5 ? 1 B DT 2 1_555 A DA 5 1_555 B DT 3 1_555 A DA 4 1_555 0.302 -0.285 3.457 1.695 -1.239 30.623 -0.280 -0.218 3.477 -2.342 -3.205 30.693 2 BB_DT8DT9:DA4DA5_AA B 8 ? A 5 ? B 9 ? A 4 ? 1 B DT 3 1_555 A DA 4 1_555 B DA 4 1_555 A DT 3 1_555 2.185 -4.636 1.473 -164.293 67.180 141.457 -2.370 -1.219 0.144 33.617 82.212 179.174 3 BB_DT9DA10:DT3DA4_AA B 9 ? A 4 ? B 10 ? A 3 ? 1 B DA 4 1_555 A DT 3 1_555 B DA 5 1_555 A DT 2 1_555 -0.620 0.142 -3.292 -1.702 0.097 -36.571 -0.213 -0.751 -3.317 -0.154 -2.710 -36.610 4 BB_DA10DA11:DT2DT3_AA B 10 ? A 3 ? B 11 ? A 2 ? 1 B DA 5 1_555 A DT 2 1_555 B DT 6 1_555 A DA 1 1_555 0.781 4.344 -0.031 -92.668 152.147 -172.381 -2.168 0.393 -0.250 -76.075 -46.335 -179.877 5 BB_DA11DT12:DA1DT2_AA B 11 ? A 2 ? B 12 ? A 1 ? 1 B DT 6 1_555 A DA 1 1_555 C DA 1 1_555 D DT 6 1_555 -3.202 -2.868 0.360 -165.411 65.276 -170.223 1.429 -1.612 0.194 -32.640 -82.709 -179.815 6 BC_DT12DA1:DT12DA1_DA B 12 ? A 1 ? C 1 ? D 12 ? 1 C DA 1 1_555 D DT 6 1_555 C DT 2 1_555 D DA 5 1_555 0.214 4.115 0.750 -100.588 144.682 -149.036 -2.091 0.084 -0.146 -72.397 -50.333 -178.989 7 CC_DA1DT2:DA11DT12_DD C 1 ? D 12 ? C 2 ? D 11 ? 1 C DT 2 1_555 D DA 5 1_555 C DT 3 1_555 D DA 4 1_555 0.770 -0.156 3.337 3.874 2.201 37.549 -0.533 -0.674 3.383 3.405 -5.992 37.803 8 CC_DT2DT3:DA10DA11_DD C 2 ? D 11 ? C 3 ? D 10 ? 1 C DT 3 1_555 D DA 4 1_555 C DA 4 1_555 D DT 3 1_555 2.191 3.141 -4.431 166.160 -62.207 14.092 0.946 -2.765 0.400 -31.500 -84.139 177.442 9 CC_DT3DA4:DT9DA10_DD C 3 ? D 10 ? C 4 ? D 9 ? 1 C DA 4 1_555 D DT 3 1_555 C DA 5 1_555 D DT 2 1_555 -0.325 0.349 -2.822 -4.120 -0.297 -29.709 -0.728 0.109 -2.837 0.576 -7.987 -29.989 10 CC_DA4DA5:DT8DT9_DD C 4 ? D 9 ? C 5 ? D 8 ? 1 C DA 5 1_555 D DT 2 1_555 C DT 6 1_555 D DA 1 1_555 0.698 4.473 1.532 -93.839 151.002 -130.078 -2.375 0.263 -0.059 -75.589 -46.974 -179.065 11 CC_DA5DT6:DA7DT8_DD C 5 ? D 8 ? C 6 ? D 7 ? 1 E DA 1 1_555 E DT 6 2_756 E DT 2 1_555 E DA 5 2_756 -0.621 -4.667 -0.350 94.273 -150.281 172.521 -2.340 0.306 -0.113 -75.143 -47.138 179.831 12 EE_DA1DT2:DA5DT6_EE E 1 ? E 6 ? E 2 ? E 5 ? 1 E DT 2 1_555 E DA 5 2_756 E DT 3 1_555 E DA 4 2_756 0.159 0.255 3.307 1.910 0.535 32.461 0.360 0.055 3.314 0.956 -3.413 32.520 13 EE_DT2DT3:DA4DA5_EE E 2 ? E 5 ? E 3 ? E 4 ? 1 E DT 3 1_555 E DA 4 2_756 E DA 4 1_555 E DT 3 2_756 -2.864 4.715 0.000 169.145 -55.452 -180.000 -2.358 -1.432 0.000 27.726 84.573 -180.000 14 EE_DT3DA4:DT3DA4_EE E 3 ? E 4 ? E 4 ? E 3 ? 1 E DA 4 1_555 E DT 3 2_756 E DA 5 1_555 E DT 2 2_756 -0.159 -0.255 -3.307 -1.910 -0.535 -32.461 0.360 0.055 -3.314 0.956 -3.413 -32.520 15 EE_DA4DA5:DT2DT3_EE E 4 ? E 3 ? E 5 ? E 2 ? 1 E DA 5 1_555 E DT 2 2_756 E DT 6 1_555 E DA 1 2_756 0.621 4.667 0.350 -94.273 150.281 -172.521 -2.340 0.306 0.113 -75.143 -47.138 -179.831 16 EE_DA5DT6:DA1DT2_EE E 5 ? E 2 ? E 6 ? E 1 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Feder funds and the Ministerio de Ciencia e Inovacion' Spain BFU-2009-10380 1 'Generalitat de Catalunya' Spain SRG2009-1208 2 CONACYT Mexico 'Reg. 212993' 3 # loop_ _pdbx_initial_refinement_model.id _pdbx_initial_refinement_model.entity_id_list _pdbx_initial_refinement_model.type _pdbx_initial_refinement_model.source_name _pdbx_initial_refinement_model.accession_code _pdbx_initial_refinement_model.details 1 ? 'experimental model' PDB 2QS6 'helical parameters taken from 2qs6, 1rsb' 2 ? 'experimental model' PDB 1RSB 'helical parameters taken from 2qs6, 1rsb' # 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' 0.184 2 1 1 ? '1/2H+1/2K, -3/2H+1/2K, L' 0.156 3 1 1 ? '1/2H-1/2K, 3/2H+1/2K, L' 0.147 4 1 1 ? -h,-k,l 0.168 5 1 1 ? '-1/2H+1/2K, -3/2H-1/2K, L' 0.185 6 1 1 ? '-1/2H-1/2K, 3/2H-1/2K, L' 0.159 #