data_4E59 # _entry.id 4E59 # _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 4E59 pdb_00004e59 10.2210/pdb4e59/pdb NDB NA2423 ? ? RCSB RCSB071185 ? ? WWPDB D_1000071185 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 4E58 _pdbx_database_related.details 'Similar sequence but with an LNA nucleotide' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4E59 _pdbx_database_status.recvd_initial_deposition_date 2012-03-14 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _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 'Kiliszek, A.' 1 'Kierzek, R.' 2 'Krzyzosiak, W.J.' 3 'Rypniewski, W.' 4 # _citation.id primary _citation.title 'Crystallographic characterization of CCG repeats.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 40 _citation.page_first 8155 _citation.page_last 8162 _citation.year 2012 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22718980 _citation.pdbx_database_id_DOI 10.1093/nar/gks557 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kiliszek, A.' 1 ? primary 'Kierzek, R.' 2 ? primary 'Krzyzosiak, W.J.' 3 ? primary 'Rypniewski, W.' 4 ? # _cell.entry_id 4E59 _cell.length_a 40.580 _cell.length_b 40.580 _cell.length_c 56.144 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4E59 _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'RNA duplex containing CCG repeats' 2516.569 2 ? ? ? ? 2 water nat water 18.015 16 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GCCGCCGC _entity_poly.pdbx_seq_one_letter_code_can GCCGCCGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 C n 1 4 G n 1 5 C n 1 6 C n 1 7 G n 1 8 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details 'This sequence is a part of mRNA in humans' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4E59 _struct_ref.pdbx_db_accession 4E59 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code GCCGCCGC _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 4E59 A 1 ? 8 ? 4E59 1 ? 8 ? 1 8 2 1 4E59 B 1 ? 8 ? 4E59 1 ? 8 ? 1 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 # _exptl.entry_id 4E59 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.77 _exptl_crystal.density_percent_sol 30.41 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 303 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.pdbx_details 'magnesium acetate, MES and ammonium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2010-10-05 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator Si _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9184 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'BESSY BEAMLINE 14.2' _diffrn_source.pdbx_synchrotron_site BESSY _diffrn_source.pdbx_synchrotron_beamline 14.2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9184 # _reflns.entry_id 4E59 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 20.00 _reflns.d_resolution_high 1.54 _reflns.number_obs 5101 _reflns.number_all 5101 _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.040 _reflns.pdbx_netI_over_sigmaI 26.14 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.3 _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.54 _reflns_shell.d_res_low 1.57 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.711 _reflns_shell.meanI_over_sigI_obs 2.06 _reflns_shell.pdbx_redundancy 3.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 262 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4E59 _refine.ls_number_reflns_obs 5073 _refine.ls_number_reflns_all 5073 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.99 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 18.715 _refine.ls_d_res_high 1.540 _refine.ls_percent_reflns_obs 99.41 _refine.ls_R_factor_obs 0.2553 _refine.ls_R_factor_all 0.2570 _refine.ls_R_factor_R_work 0.2553 _refine.ls_R_factor_R_free 0.3035 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 100.00 _refine.ls_number_reflns_R_free 501 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 27.79 _refine.aniso_B[1][1] 4.8628 _refine.aniso_B[2][2] 4.8628 _refine.aniso_B[3][3] -9.7256 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] -0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.458 _refine.solvent_model_param_bsol 63.918 _refine.pdbx_solvent_vdw_probe_radii 0.50 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.16 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 4E58 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.25 _refine.pdbx_overall_phase_error 30.22 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 300 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 16 _refine_hist.number_atoms_total 316 _refine_hist.d_res_high 1.540 _refine_hist.d_res_low 18.715 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.010 ? ? 332 ? 'X-RAY DIFFRACTION' f_angle_d 1.290 ? ? 516 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 13.993 ? ? 164 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.076 ? ? 70 ? 'X-RAY DIFFRACTION' f_plane_restr 0.015 ? ? 14 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.540 _refine_ls_shell.d_res_low 1.6950 _refine_ls_shell.number_reflns_R_work 161 _refine_ls_shell.R_factor_R_work 0.3411 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.3627 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 130 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 1270 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 4E59 _struct.title 'Crystal structure of GCCGCCGC duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4E59 _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;3' slippery duplexes, X-linked mental retardation, Huntington's disease, myotonic dystrophy type 1, RNA, CCG repeats ; # 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 ? # 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 G 1 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 1 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 1 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 1 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 2 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 2 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 2 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 4 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 4 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 4 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 5 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 5 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 5 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 4E59 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 4E59 _atom_sites.fract_transf_matrix[1][1] 0.024643 _atom_sites.fract_transf_matrix[1][2] 0.014227 _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] 0.028455 _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] 0.017811 _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 G 1 1 1 G G A . n A 1 2 C 2 2 2 C C A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 C 5 5 5 C C A . n A 1 6 C 6 6 6 C C A . n A 1 7 G 7 7 7 G G A . n A 1 8 C 8 8 8 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 C 2 2 2 C C B . n B 1 3 C 3 3 3 C C B . n B 1 4 G 4 4 4 G G B . n B 1 5 C 5 5 5 C C B . n B 1 6 C 6 6 6 C C B . n B 1 7 G 7 7 7 G G B . n B 1 8 C 8 8 8 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 101 8 HOH HOH A . C 2 HOH 2 102 10 HOH HOH A . C 2 HOH 3 103 11 HOH HOH A . C 2 HOH 4 104 12 HOH HOH A . C 2 HOH 5 105 18 HOH HOH A . C 2 HOH 6 106 19 HOH HOH A . C 2 HOH 7 107 21 HOH HOH A . C 2 HOH 8 108 22 HOH HOH A . C 2 HOH 9 109 23 HOH HOH A . D 2 HOH 1 101 1 HOH HOH B . D 2 HOH 2 102 2 HOH HOH B . D 2 HOH 3 103 3 HOH HOH B . D 2 HOH 4 104 6 HOH HOH B . D 2 HOH 5 105 9 HOH HOH B . D 2 HOH 6 106 13 HOH HOH B . D 2 HOH 7 107 14 HOH HOH B . # 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 software_defined_assembly PISA hexameric 6 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D 2 1,2,3 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)' 570 ? 1 MORE -4 ? 1 'SSA (A^2)' 3060 ? 2 'ABSA (A^2)' 3640 ? 2 MORE -46 ? 2 'SSA (A^2)' 7280 ? # 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_555 -y,x-y,z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 105 ? C HOH . 2 1 A HOH 106 ? C HOH . 3 1 B HOH 105 ? D HOH . 4 1 B HOH 106 ? D HOH . # 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 2012-12-12 2 'Structure model' 1 1 2017-11-15 3 'Structure model' 1 2 2023-09-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _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' 'Refinement description' 2 2 'Structure model' 'Source and taxonomy' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 3 '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' pdbx_entity_src_syn 2 2 'Structure model' software 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' database_2 6 3 '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' '_pdbx_entity_src_syn.ncbi_taxonomy_id' 2 2 'Structure model' '_pdbx_entity_src_syn.organism_scientific' 3 2 'Structure model' '_software.name' 4 3 'Structure model' '_database_2.pdbx_DOI' 5 3 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345 'data collection' . ? 1 PHASER phasing . ? 2 PHENIX refinement '(phenix.refine: 1.7_650)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 C6 A C 6 ? ? N1 A C 6 ? ? C2 A C 6 ? ? 116.59 120.30 -3.71 0.40 N 2 1 N3 A C 6 ? ? C2 A C 6 ? ? O2 A C 6 ? ? 117.61 121.90 -4.29 0.70 N # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A C 8 ? "C5'" ? A C 8 "C5'" 2 1 Y 1 A C 8 ? "C4'" ? A C 8 "C4'" 3 1 Y 1 A C 8 ? "O4'" ? A C 8 "O4'" 4 1 Y 1 A C 8 ? "C3'" ? A C 8 "C3'" 5 1 Y 1 A C 8 ? "O3'" ? A C 8 "O3'" 6 1 Y 1 A C 8 ? "C2'" ? A C 8 "C2'" 7 1 Y 1 A C 8 ? "O2'" ? A C 8 "O2'" 8 1 Y 1 A C 8 ? "C1'" ? A C 8 "C1'" 9 1 Y 1 A C 8 ? N1 ? A C 8 N1 10 1 Y 1 A C 8 ? C2 ? A C 8 C2 11 1 Y 1 A C 8 ? O2 ? A C 8 O2 12 1 Y 1 A C 8 ? N3 ? A C 8 N3 13 1 Y 1 A C 8 ? C4 ? A C 8 C4 14 1 Y 1 A C 8 ? N4 ? A C 8 N4 15 1 Y 1 A C 8 ? C5 ? A C 8 C5 16 1 Y 1 A C 8 ? C6 ? A C 8 C6 17 1 Y 1 B C 8 ? "C5'" ? B C 8 "C5'" 18 1 Y 1 B C 8 ? "C4'" ? B C 8 "C4'" 19 1 Y 1 B C 8 ? "O4'" ? B C 8 "O4'" 20 1 Y 1 B C 8 ? "C3'" ? B C 8 "C3'" 21 1 Y 1 B C 8 ? "O3'" ? B C 8 "O3'" 22 1 Y 1 B C 8 ? "C2'" ? B C 8 "C2'" 23 1 Y 1 B C 8 ? "O2'" ? B C 8 "O2'" 24 1 Y 1 B C 8 ? "C1'" ? B C 8 "C1'" 25 1 Y 1 B C 8 ? N1 ? B C 8 N1 26 1 Y 1 B C 8 ? C2 ? B C 8 C2 27 1 Y 1 B C 8 ? O2 ? B C 8 O2 28 1 Y 1 B C 8 ? N3 ? B C 8 N3 29 1 Y 1 B C 8 ? C4 ? B C 8 C4 30 1 Y 1 B C 8 ? N4 ? B C 8 N4 31 1 Y 1 B C 8 ? C5 ? B C 8 C5 32 1 Y 1 B C 8 ? C6 ? B C 8 C6 # 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 G OP3 O N N 36 G P P N N 37 G OP1 O N N 38 G OP2 O N N 39 G "O5'" O N N 40 G "C5'" C N N 41 G "C4'" C N R 42 G "O4'" O N N 43 G "C3'" C N S 44 G "O3'" O N N 45 G "C2'" C N R 46 G "O2'" O N N 47 G "C1'" C N R 48 G N9 N Y N 49 G C8 C Y N 50 G N7 N Y N 51 G C5 C Y N 52 G C6 C N N 53 G O6 O N N 54 G N1 N N N 55 G C2 C N N 56 G N2 N N N 57 G N3 N N N 58 G C4 C Y N 59 G HOP3 H N N 60 G HOP2 H N N 61 G "H5'" H N N 62 G "H5''" H N N 63 G "H4'" H N N 64 G "H3'" H N N 65 G "HO3'" H N N 66 G "H2'" H N N 67 G "HO2'" H N N 68 G "H1'" H N N 69 G H8 H N N 70 G H1 H N N 71 G H21 H N N 72 G H22 H N N 73 HOH O O N N 74 HOH H1 H N N 75 HOH H2 H N N 76 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 G OP3 P sing N N 37 G OP3 HOP3 sing N N 38 G P OP1 doub N N 39 G P OP2 sing N N 40 G P "O5'" sing N N 41 G OP2 HOP2 sing N N 42 G "O5'" "C5'" sing N N 43 G "C5'" "C4'" sing N N 44 G "C5'" "H5'" sing N N 45 G "C5'" "H5''" sing N N 46 G "C4'" "O4'" sing N N 47 G "C4'" "C3'" sing N N 48 G "C4'" "H4'" sing N N 49 G "O4'" "C1'" sing N N 50 G "C3'" "O3'" sing N N 51 G "C3'" "C2'" sing N N 52 G "C3'" "H3'" sing N N 53 G "O3'" "HO3'" sing N N 54 G "C2'" "O2'" sing N N 55 G "C2'" "C1'" sing N N 56 G "C2'" "H2'" sing N N 57 G "O2'" "HO2'" sing N N 58 G "C1'" N9 sing N N 59 G "C1'" "H1'" sing N N 60 G N9 C8 sing Y N 61 G N9 C4 sing Y N 62 G C8 N7 doub Y N 63 G C8 H8 sing N N 64 G N7 C5 sing Y N 65 G C5 C6 sing N N 66 G C5 C4 doub Y N 67 G C6 O6 doub N N 68 G C6 N1 sing N N 69 G N1 C2 sing N N 70 G N1 H1 sing N N 71 G C2 N2 sing N N 72 G C2 N3 doub N N 73 G N2 H21 sing N N 74 G N2 H22 sing N N 75 G N3 C4 sing N N 76 HOH O H1 sing N N 77 HOH O H2 sing N N 78 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4E59 'double helix' 4E59 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B C 5 1_555 -0.420 -0.453 0.172 -3.491 -14.140 -2.878 1 A_G1:C5_B A 1 ? B 5 ? 19 1 1 A C 2 1_555 B G 4 1_555 0.051 -0.338 -0.093 -2.460 -11.623 -3.431 2 A_C2:G4_B A 2 ? B 4 ? 19 1 1 A G 4 1_555 B C 2 1_555 -0.433 -0.129 0.137 2.220 -9.655 3.313 3 A_G4:C2_B A 4 ? B 2 ? 19 1 1 A C 5 1_555 B G 1 1_555 0.270 -0.268 -0.076 3.252 -14.000 -0.697 4 A_C5:G1_B A 5 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 5 1_555 A C 2 1_555 B G 4 1_555 -0.155 -1.685 3.249 1.778 3.697 37.656 -3.056 0.460 3.066 5.707 -2.745 37.871 1 AA_G1C2:G4C5_BB A 1 ? B 5 ? A 2 ? B 4 ? 1 A C 2 1_555 B G 4 1_555 A G 4 1_555 B C 2 1_555 -0.300 -3.425 6.047 -1.528 20.444 61.748 -4.673 0.170 4.828 19.359 1.447 64.742 2 AA_C2G4:C2G4_BB A 2 ? B 4 ? A 4 ? B 2 ? 1 A G 4 1_555 B C 2 1_555 A C 5 1_555 B G 1 1_555 0.217 -1.445 3.244 2.344 7.619 34.457 -3.447 -0.029 2.877 12.653 -3.892 35.340 3 AA_G4C5:G1C2_BB A 4 ? B 2 ? A 5 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 4E58 _pdbx_initial_refinement_model.details ? #