data_1O56 # _entry.id 1O56 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.286 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1O56 NDB UD0039 RCSB rcsb001816 WWPDB D_1000001816 # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.pdb_id 1O56 _pdbx_database_PDB_obs_spr.replace_pdb_id 416d _pdbx_database_PDB_obs_spr.date 2003-08-26 _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1O56 _pdbx_database_status.recvd_initial_deposition_date 2003-08-20 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gao, Y.G.' 1 'Robinson, H.' 2 'Guan, Y.' 3 'Liaw, Y.C.' 4 'van Boom, J.H.' 5 'van der Marel, G.A.' 6 'Wang, A.H.' 7 # _citation.id primary _citation.title 'Molecular structure of two crystal forms of cyclic triadenylic acid at 1A resolution.' _citation.journal_abbrev J.Biomol.Struct.Dyn. _citation.journal_volume 16 _citation.page_first 69 _citation.page_last 76 _citation.year 1998 _citation.journal_id_ASTM JBSDD6 _citation.country US _citation.journal_id_ISSN 0739-1102 _citation.journal_id_CSD 0646 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9745896 _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Gao, Y.G.' 1 primary 'Robinson, H.' 2 primary 'Guan, Y.' 3 primary 'Liaw, Y.C.' 4 primary 'van Boom, J.H.' 5 primary 'van der Marel, G.A.' 6 primary 'Wang, A.H.' 7 # _cell.entry_id 1O56 _cell.length_a 23.328 _cell.length_b 23.328 _cell.length_c 9.680 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 1O56 _symmetry.space_group_name_H-M 'P 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _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 ;DNA (5'-CD(*AP*AP*AP*)-3') ; 894.663 2 ? ? ? ? 2 water nat water 18.015 13 ? ? ? ? # _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)(DA)(DA)' _entity_poly.pdbx_seq_one_letter_code_can AAA _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 DA n 1 2 DA n 1 3 DA 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 ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details Synthetic # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1O56 _struct_ref.pdbx_db_accession 1O56 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1O56 A 1 ? 3 ? 1O56 1 ? 3 ? 1 3 2 1 1O56 B 1 ? 3 ? 1O56 2 ? 4 ? 2 4 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 # _exptl.entry_id 1O56 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.41 _exptl_crystal.density_percent_sol 42.0000 _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 298.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.50 _exptl_crystal_grow.pdbx_details 'pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 GLYCINE ? ? ? 1 3 1 MGCL2 ? ? ? 1 4 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 298.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type RIGAKU _diffrn_detector.pdbx_collection_date 1997-12-29 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1O56 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 3.000 _reflns.d_resolution_low 10.000 _reflns.d_resolution_high 0.900 _reflns.number_obs 3059 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1O56 _refine.ls_number_reflns_obs 3059 _refine.ls_number_reflns_all 3059 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 3.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 0.900 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all 0.109 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 42 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 13 _refine_hist.number_atoms_total 55 _refine_hist.d_res_high 0.900 _refine_hist.d_res_low 10.000 # 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_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.032 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1O56 _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff 0.109 _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? _pdbx_refine.number_reflns_obs_no_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _struct.entry_id 1O56 _struct.title 'MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION' _struct.pdbx_descriptor "5'-CD(*AP*AP*AP)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1O56 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'CYCLIC TRINUCLEOTIDE, 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 ? # loop_ _struct_biol.id _struct_biol.pdbx_parent_biol_id _struct_biol.details 1 ? ? 2 ? ? # _database_PDB_matrix.entry_id 1O56 _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 1O56 _atom_sites.fract_transf_matrix[1][1] 0.042867 _atom_sites.fract_transf_matrix[1][2] 0.024749 _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] 0.049498 _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] 0.103306 _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_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 P P . DA A 1 1 ? 0.421 4.039 -2.933 1.00 0.10 ? 1 DA A P 1 ATOM 2 O OP1 . DA A 1 1 ? 0.818 5.069 -3.901 1.00 0.16 ? 1 DA A OP1 1 ATOM 3 O OP2 . DA A 1 1 ? 0.311 4.338 -1.509 1.00 0.12 ? 1 DA A OP2 1 ATOM 4 O "O5'" . DA A 1 1 ? 1.400 2.800 -2.997 1.00 0.11 ? 1 DA A "O5'" 1 ATOM 5 C "C5'" . DA A 1 1 ? 1.801 2.311 -4.251 1.00 0.13 ? 1 DA A "C5'" 1 ATOM 6 C "C4'" . DA A 1 1 ? 2.995 1.329 -4.062 1.00 0.08 ? 1 DA A "C4'" 1 ATOM 7 O "O4'" . DA A 1 1 ? 4.119 2.107 -3.636 1.00 0.08 ? 1 DA A "O4'" 1 ATOM 8 C "C3'" . DA A 1 1 ? 2.825 0.234 -2.994 1.00 0.07 ? 1 DA A "C3'" 1 ATOM 9 O "O3'" . DA A 1 1 ? 3.486 -0.903 -3.541 1.00 0.09 ? 1 DA A "O3'" 1 ATOM 10 C "C2'" . DA A 1 1 ? 3.512 0.802 -1.757 1.00 0.09 ? 1 DA A "C2'" 1 ATOM 11 C "C1'" . DA A 1 1 ? 4.621 1.636 -2.392 1.00 0.09 ? 1 DA A "C1'" 1 ATOM 12 N N9 . DA A 1 1 ? 5.017 2.794 -1.636 1.00 0.08 ? 1 DA A N9 1 ATOM 13 C C8 . DA A 1 1 ? 4.355 3.964 -1.571 1.00 0.10 ? 1 DA A C8 1 ATOM 14 N N7 . DA A 1 1 ? 4.943 4.873 -0.817 1.00 0.10 ? 1 DA A N7 1 ATOM 15 C C5 . DA A 1 1 ? 6.031 4.196 -0.300 1.00 0.08 ? 1 DA A C5 1 ATOM 16 C C6 . DA A 1 1 ? 7.094 4.570 0.542 1.00 0.07 ? 1 DA A C6 1 ATOM 17 N N6 . DA A 1 1 ? 7.194 5.794 1.058 1.00 0.08 ? 1 DA A N6 1 ATOM 18 N N1 . DA A 1 1 ? 8.004 3.701 0.819 1.00 0.09 ? 1 DA A N1 1 ATOM 19 C C2 . DA A 1 1 ? 7.926 2.564 0.285 1.00 0.10 ? 1 DA A C2 1 ATOM 20 N N3 . DA A 1 1 ? 6.983 2.026 -0.522 1.00 0.10 ? 1 DA A N3 1 ATOM 21 C C4 . DA A 1 1 ? 6.068 2.946 -0.788 1.00 0.07 ? 1 DA A C4 1 ATOM 22 P P . DA B 1 1 ? 14.944 9.099 5.933 1.00 0.09 ? 2 DA B P 1 ATOM 23 O OP1 . DA B 1 1 ? 15.269 9.154 4.483 1.00 0.15 ? 2 DA B OP1 1 ATOM 24 O OP2 . DA B 1 1 ? 15.672 9.976 6.862 1.00 0.13 ? 2 DA B OP2 1 ATOM 25 O "O5'" . DA B 1 1 ? 13.348 9.362 5.980 1.00 0.10 ? 2 DA B "O5'" 1 ATOM 26 C "C5'" . DA B 1 1 ? 12.696 9.433 7.234 1.00 0.12 ? 2 DA B "C5'" 1 ATOM 27 C "C4'" . DA B 1 1 ? 11.318 9.990 7.024 1.00 0.10 ? 2 DA B "C4'" 1 ATOM 28 O "O4'" . DA B 1 1 ? 11.421 11.354 6.614 1.00 0.11 ? 2 DA B "O4'" 1 ATOM 29 C "C3'" . DA B 1 1 ? 10.430 9.273 5.987 1.00 0.10 ? 2 DA B "C3'" 1 ATOM 30 O "O3'" . DA B 1 1 ? 9.132 9.324 6.513 1.00 0.08 ? 2 DA B "O3'" 1 ATOM 31 C "C2'" . DA B 1 1 ? 10.633 10.186 4.785 1.00 0.09 ? 2 DA B "C2'" 1 ATOM 32 C "C1'" . DA B 1 1 ? 10.804 11.562 5.401 1.00 0.09 ? 2 DA B "C1'" 1 ATOM 33 N N9 . DA B 1 1 ? 11.568 12.473 4.612 1.00 0.09 ? 2 DA B N9 1 ATOM 34 C C8 . DA B 1 1 ? 12.900 12.477 4.536 1.00 0.15 ? 2 DA B C8 1 ATOM 35 N N7 . DA B 1 1 ? 13.380 13.505 3.788 1.00 0.12 ? 2 DA B N7 1 ATOM 36 C C5 . DA B 1 1 ? 12.238 14.069 3.280 1.00 0.10 ? 2 DA B C5 1 ATOM 37 C C6 . DA B 1 1 ? 12.104 15.166 2.454 1.00 0.12 ? 2 DA B C6 1 ATOM 38 N N6 . DA B 1 1 ? 13.096 15.851 1.925 1.00 0.14 ? 2 DA B N6 1 ATOM 39 N N1 . DA B 1 1 ? 10.788 15.546 2.175 1.00 0.11 ? 2 DA B N1 1 ATOM 40 C C2 . DA B 1 1 ? 9.927 14.827 2.742 1.00 0.13 ? 2 DA B C2 1 ATOM 41 N N3 . DA B 1 1 ? 9.928 13.794 3.511 1.00 0.11 ? 2 DA B N3 1 ATOM 42 C C4 . DA B 1 1 ? 11.185 13.473 3.789 1.00 0.10 ? 2 DA B C4 1 HETATM 43 O O . HOH C 2 . ? 0.000 0.000 -0.975 0.33 0.17 ? 4 HOH A O 1 HETATM 44 O O . HOH C 2 . ? 11.665 6.734 3.904 0.33 0.18 ? 5 HOH A O 1 HETATM 45 O O . HOH C 2 . ? 0.000 0.000 3.307 0.33 0.19 ? 6 HOH A O 1 HETATM 46 O O . HOH C 2 . ? 0.890 2.325 0.214 1.00 0.11 ? 7 HOH A O 1 HETATM 47 O O . HOH C 2 . ? 9.230 7.154 2.752 1.00 0.10 ? 8 HOH A O 1 HETATM 48 O O . HOH C 2 . ? 0.020 5.012 3.134 1.00 0.22 ? 9 HOH A O 1 HETATM 49 O O . HOH C 2 . ? 10.807 4.273 0.669 1.00 0.13 ? 10 HOH A O 1 HETATM 50 O O . HOH C 2 . ? -0.877 2.489 2.321 1.00 0.14 ? 11 HOH A O 1 HETATM 51 O O . HOH C 2 . ? 11.664 6.735 -0.303 0.33 0.21 ? 12 HOH A O 1 HETATM 52 O O . HOH C 2 . ? 0.146 6.831 1.878 1.00 0.17 ? 13 HOH A O 1 HETATM 53 O O . HOH C 2 . ? 1.701 5.931 0.657 1.00 0.24 ? 14 HOH A O 1 HETATM 54 O O . HOH C 2 . ? -1.182 6.653 9.847 1.00 0.28 ? 15 HOH A O 1 HETATM 55 O O . HOH D 2 . ? 11.619 1.752 9.559 1.00 0.29 ? 9 HOH B O 1 # 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 A A . n A 1 2 DA 2 2 ? ? ? A . n A 1 3 DA 3 3 ? ? ? A . n B 1 1 DA 1 2 2 DA A B . n B 1 2 DA 2 3 ? ? ? B . n B 1 3 DA 3 4 ? ? ? 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 4 3 HOH HOH A . C 2 HOH 2 5 4 HOH HOH A . C 2 HOH 3 6 5 HOH HOH A . C 2 HOH 4 7 6 HOH HOH A . C 2 HOH 5 8 7 HOH HOH A . C 2 HOH 6 9 8 HOH HOH A . C 2 HOH 7 10 10 HOH HOH A . C 2 HOH 8 11 11 HOH HOH A . C 2 HOH 9 12 12 HOH HOH A . C 2 HOH 10 13 13 HOH HOH A . C 2 HOH 11 14 14 HOH HOH A . C 2 HOH 12 15 15 HOH HOH A . D 2 HOH 1 9 9 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_defined_assembly ? trimeric 3 2 author_defined_assembly ? trimeric 3 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2,3 A,C 2 1,4,5 B,D # 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 4 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5000000000 -0.8660254038 0.0000000000 23.3280000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 5 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5000000000 0.8660254038 0.0000000000 11.6640000000 -0.8660254038 -0.5000000000 0.0000000000 20.2026406195 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 4 ? C HOH . 2 1 A HOH 5 ? C HOH . 3 1 A HOH 6 ? C HOH . 4 1 A HOH 12 ? C 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 2003-08-26 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-11-16 5 'Structure model' 1 4 2017-10-04 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 5 'Structure model' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 5 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXS phasing . ? 1 SHELXL-97 refinement . ? 2 # _pdbx_database_remark.id 999 _pdbx_database_remark.text ;SEQUENCE The crystallized entity is 5'-CD(*AP*AP*AP)-3', however, each of the two independent molecules sits on the crystallographic 3-fold axis. Remark 350 provides the way to create cyclic D(*Ap*Ap*Ap) molecule. ; # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 13 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 14 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.17 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 P B DA 2 ? ? 1_555 "O3'" B DA 2 ? ? 3_665 1.59 2 1 P A DA 1 ? ? 1_555 "O3'" A DA 1 ? ? 2_555 1.61 3 1 O A HOH 13 ? ? 1_555 O A HOH 15 ? ? 1_554 2.17 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C5'" A DA 1 ? ? "C4'" A DA 1 ? ? 1.557 1.512 0.045 0.007 N 2 1 N1 A DA 1 ? ? C2 A DA 1 ? ? 1.259 1.339 -0.080 0.009 N 3 1 C6 A DA 1 ? ? N1 A DA 1 ? ? 1.288 1.351 -0.063 0.007 N 4 1 N1 B DA 2 ? ? C2 B DA 2 ? ? 1.257 1.339 -0.082 0.009 N 5 1 C4 B DA 2 ? ? C5 B DA 2 ? ? 1.313 1.383 -0.070 0.007 N 6 1 C6 B DA 2 ? ? N1 B DA 2 ? ? 1.398 1.351 0.047 0.007 N 7 1 N7 B DA 2 ? ? C8 B DA 2 ? ? 1.359 1.311 0.048 0.007 N # 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 "O4'" B DA 2 ? ? "C1'" B DA 2 ? ? N9 B DA 2 ? ? 110.10 108.30 1.80 0.30 N 2 1 C6 B DA 2 ? ? N1 B DA 2 ? ? C2 B DA 2 ? ? 113.54 118.60 -5.06 0.60 N 3 1 N1 B DA 2 ? ? C2 B DA 2 ? ? N3 B DA 2 ? ? 136.69 129.30 7.39 0.50 N 4 1 C4 B DA 2 ? ? C5 B DA 2 ? ? C6 B DA 2 ? ? 121.01 117.00 4.01 0.50 N 5 1 N9 B DA 2 ? ? C4 B DA 2 ? ? C5 B DA 2 ? ? 110.18 105.80 4.38 0.40 N # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A DA 2 ? A DA 2 2 1 Y 1 A DA 3 ? A DA 3 3 1 Y 1 B DA 3 ? B DA 2 4 1 Y 1 B DA 4 ? B DA 3 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #