data_3NAO # _entry.id 3NAO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3NAO pdb_00003nao 10.2210/pdb3nao/pdb NDB NA0641 ? ? RCSB RCSB059591 ? ? WWPDB D_1000059591 ? ? # 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 2011-11-30 2 'Structure model' 1 1 2014-04-16 3 'Structure model' 1 2 2024-02-21 # _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' 'Experimental preparation' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # 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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_conn 5 3 'Structure model' struct_ref_seq # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_ref_seq.db_align_beg' 5 3 'Structure model' '_struct_ref_seq.db_align_end' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3NAO _pdbx_database_status.recvd_initial_deposition_date 2010-06-02 _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3GBI _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Wang, T.' 1 'Sha, R.' 2 'Birktoft, J.J.' 3 'Zheng, J.' 4 'Mao, M.' 5 'Seeman, N.C.' 6 # _citation.id primary _citation.title 'A DNA crystal designed to contain two molecules per asymmetric unit.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 132 _citation.page_first 15471 _citation.page_last 15473 _citation.year 2010 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20958065 _citation.pdbx_database_id_DOI 10.1021/ja104833t # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wang, T.' 1 ? primary 'Sha, R.' 2 ? primary 'Birktoft, J.' 3 ? primary 'Zheng, J.' 4 ? primary 'Mao, C.' 5 ? primary 'Seeman, N.C.' 6 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3') ; 6457.188 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3') ; 2082.400 1 ? ? 'SYMMETRICALLY- AND SEQUENTIALLY REPEATING UNIT OF CIRCULAR DNA MOLECULES, SEE REMARK 400 FOR DETAILS' ? 3 polymer syn ;DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3') ; 1825.216 1 ? ? 'LAST 6 RESIDUES OF A DNA MOLECULE USED IN EXPERIMENT, SEE REMARK 400 FOR DETAILS' ? 4 polymer syn ;DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*T)-3') ; 2432.614 1 ? ? 'FIRST 8 RESIDUES OF A DNA MOLECULE USED IN EXPERIMENT, SEE REMARK 400 FOR DETAILS' ? 5 polymer syn ;DNA (5'-D(*AP*GP*CP*CP*TP*AP*CP*CP*TP*GP*CP*GP*TP*GP*GP*AP*CP*AP*GP*AP*C)-3') ; 6433.163 1 ? ? ? ? 6 polymer syn ;DNA (5'-D(P*CP*CP*AP*CP*GP*CP*A)-3') ; 2067.389 1 ? ? 'SYMMETRICALLY- AND SEQUENTIALLY REPEATING UNIT OF A CIRCULAR DNA MOLECULES, SEE REMARK 400 FOR DETAILS' ? 7 polymer syn ;DNA (5'-D(P*GP*GP*TP*AP*GP*G)-3') ; 1889.265 1 ? ? 'LAST 6 RESIDUES OF A DNA MOLECULE USED IN EXPERIMENT, SEE REMARK 400 FOR DETAILS' ? 8 polymer syn ;DNA (5'-D(*TP*CP*GP*TP*CP*TP*GP*T)-3') ; 2408.589 1 ? ? 'FIRST 8 RESIDUES OF A DNA MOLECULE USED IN EXPERIMENT, SEE REMARK 400 FOR DETAILS' ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no ;(DG)(DA)(DG)(DC)(DA)(DG)(DC)(DC)(DT)(DG)(DT)(DA)(DC)(DG)(DG)(DA)(DC)(DA)(DT)(DC) (DA) ; GAGCAGCCTGTACGGACATCA A ? 2 polydeoxyribonucleotide no no '(DC)(DC)(DG)(DT)(DA)(DC)(DA)' CCGTACA B ? 3 polydeoxyribonucleotide no no '(DG)(DG)(DC)(DT)(DG)(DC)' GGCTGC C ? 4 polydeoxyribonucleotide no no '(DC)(DT)(DT)(DG)(DA)(DT)(DG)(DT)' CTTGATGT D ? 5 polydeoxyribonucleotide no no ;(DA)(DG)(DC)(DC)(DT)(DA)(DC)(DC)(DT)(DG)(DC)(DG)(DT)(DG)(DG)(DA)(DC)(DA)(DG)(DA) (DC) ; AGCCTACCTGCGTGGACAGAC E ? 6 polydeoxyribonucleotide no no '(DC)(DC)(DA)(DC)(DG)(DC)(DA)' CCACGCA F ? 7 polydeoxyribonucleotide no no '(DG)(DG)(DT)(DA)(DG)(DG)' GGTAGG G ? 8 polydeoxyribonucleotide no no '(DT)(DC)(DG)(DT)(DC)(DT)(DG)(DT)' TCGTCTGT H ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DA n 1 3 DG n 1 4 DC n 1 5 DA n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DT n 1 10 DG n 1 11 DT n 1 12 DA n 1 13 DC n 1 14 DG n 1 15 DG n 1 16 DA n 1 17 DC n 1 18 DA n 1 19 DT n 1 20 DC n 1 21 DA n 2 1 DC n 2 2 DC n 2 3 DG n 2 4 DT n 2 5 DA n 2 6 DC n 2 7 DA n 3 1 DG n 3 2 DG n 3 3 DC n 3 4 DT n 3 5 DG n 3 6 DC n 4 1 DC n 4 2 DT n 4 3 DT n 4 4 DG n 4 5 DA n 4 6 DT n 4 7 DG n 4 8 DT n 5 1 DA n 5 2 DG n 5 3 DC n 5 4 DC n 5 5 DT n 5 6 DA n 5 7 DC n 5 8 DC n 5 9 DT n 5 10 DG n 5 11 DC n 5 12 DG n 5 13 DT n 5 14 DG n 5 15 DG n 5 16 DA n 5 17 DC n 5 18 DA n 5 19 DG n 5 20 DA n 5 21 DC n 6 1 DC n 6 2 DC n 6 3 DA n 6 4 DC n 6 5 DG n 6 6 DC n 6 7 DA n 7 1 DG n 7 2 DG n 7 3 DT n 7 4 DA n 7 5 DG n 7 6 DG n 8 1 DT n 8 2 DC n 8 3 DG n 8 4 DT n 8 5 DC n 8 6 DT n 8 7 DG n 8 8 DT n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? ;DNA STRANDS WERE SYNTHESIZED BY STANDARD PHOSPHORAMIDITE TECHNIQUES ON AN APPLIED BIOSYSTEMS 394 DNA SYNTHESIZER USING TRITYL-ON MODE ; 2 1 sample ? ? ? ? ? ;DNA STRANDS WERE SYNTHESIZED BY STANDARD PHOSPHORAMIDITE TECHNIQUES ON AN APPLIED BIOSYSTEMS 394 DNA SYNTHESIZER USING TRITYL-ON MODE ; 3 1 sample ? ? ? ? ? ;DNA STRANDS WERE SYNTHESIZED BY STANDARD PHOSPHORAMIDITE TECHNIQUES ON AN APPLIED BIOSYSTEMS 394 DNA SYNTHESIZER USING TRITYL-ON MODE ; 4 1 sample ? ? ? ? ? ;DNA STRANDS WERE SYNTHESIZED BY STANDARD PHOSPHORAMIDITE TECHNIQUES ON AN APPLIED BIOSYSTEMS 394 DNA SYNTHESIZER USING TRITYL-ON MODE ; 5 1 sample ? ? ? ? ? ;DNA STRANDS WERE SYNTHESIZED BY STANDARD PHOSPHORAMIDITE TECHNIQUES ON AN APPLIED BIOSYSTEMS 394 DNA SYNTHESIZER USING TRITYL-ON MODE ; 6 1 sample ? ? ? ? ? ;DNA STRANDS WERE SYNTHESIZED BY STANDARD PHOSPHORAMIDITE TECHNIQUES ON AN APPLIED BIOSYSTEMS 394 DNA SYNTHESIZER USING TRITYL-ON MODE ; 7 1 sample ? ? ? ? ? ;DNA STRANDS WERE SYNTHESIZED BY STANDARD PHOSPHORAMIDITE TECHNIQUES ON AN APPLIED BIOSYSTEMS 394 DNA SYNTHESIZER USING TRITYL-ON MODE ; 8 1 sample ? ? ? ? ? ;DNA STRANDS WERE SYNTHESIZED BY STANDARD PHOSPHORAMIDITE TECHNIQUES ON AN APPLIED BIOSYSTEMS 394 DNA SYNTHESIZER USING TRITYL-ON MODE ; # 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 101 101 DG DG A . n A 1 2 DA 2 102 102 DA DA A . n A 1 3 DG 3 103 103 DG DG A . n A 1 4 DC 4 104 104 DC DC A . n A 1 5 DA 5 105 105 DA DA A . n A 1 6 DG 6 106 106 DG DG A . n A 1 7 DC 7 107 107 DC DC A . n A 1 8 DC 8 108 108 DC DC A . n A 1 9 DT 9 109 109 DT DT A . n A 1 10 DG 10 110 110 DG DG A . n A 1 11 DT 11 111 111 DT DT A . n A 1 12 DA 12 112 112 DA DA A . n A 1 13 DC 13 113 113 DC DC A . n A 1 14 DG 14 114 114 DG DG A . n A 1 15 DG 15 115 115 DG DG A . n A 1 16 DA 16 116 116 DA DA A . n A 1 17 DC 17 117 117 DC DC A . n A 1 18 DA 18 118 118 DA DA A . n A 1 19 DT 19 119 119 DT DT A . n A 1 20 DC 20 120 120 DC DC A . n A 1 21 DA 21 121 121 DA DA A . n B 2 1 DC 1 119 119 DC DC B . n B 2 2 DC 2 120 120 DC DC B . n B 2 3 DG 3 121 121 DG DG B . n B 2 4 DT 4 122 122 DT DT B . n B 2 5 DA 5 123 123 DA DA B . n B 2 6 DC 6 124 124 DC DC B . n B 2 7 DA 7 125 125 DA DA B . n C 3 1 DG 1 109 109 DG DG C . n C 3 2 DG 2 110 110 DG DG C . n C 3 3 DC 3 111 111 DC DC C . n C 3 4 DT 4 112 112 DT DT C . n C 3 5 DG 5 113 113 DG DG C . n C 3 6 DC 6 114 114 DC DC C . n D 4 1 DC 1 101 101 DC DC D . n D 4 2 DT 2 102 102 DT DT D . n D 4 3 DT 3 103 103 DT DT D . n D 4 4 DG 4 104 104 DG DG D . n D 4 5 DA 5 105 105 DA DA D . n D 4 6 DT 6 106 106 DT DT D . n D 4 7 DG 7 107 107 DG DG D . n D 4 8 DT 8 108 108 DT DT D . n E 5 1 DA 1 101 101 DA DA E . n E 5 2 DG 2 102 102 DG DG E . n E 5 3 DC 3 103 103 DC DC E . n E 5 4 DC 4 104 104 DC DC E . n E 5 5 DT 5 105 105 DT DT E . n E 5 6 DA 6 106 106 DA DA E . n E 5 7 DC 7 107 107 DC DC E . n E 5 8 DC 8 108 108 DC DC E . n E 5 9 DT 9 109 109 DT DT E . n E 5 10 DG 10 110 110 DG DG E . n E 5 11 DC 11 111 111 DC DC E . n E 5 12 DG 12 112 112 DG DG E . n E 5 13 DT 13 113 113 DT DT E . n E 5 14 DG 14 114 114 DG DG E . n E 5 15 DG 15 115 115 DG DG E . n E 5 16 DA 16 116 116 DA DA E . n E 5 17 DC 17 117 117 DC DC E . n E 5 18 DA 18 118 118 DA DA E . n E 5 19 DG 19 119 119 DG DG E . n E 5 20 DA 20 120 120 DA DA E . n E 5 21 DC 21 121 121 DC DC E . n F 6 1 DC 1 119 119 DC DC F . n F 6 2 DC 2 120 120 DC DC F . n F 6 3 DA 3 121 121 DA DA F . n F 6 4 DC 4 122 122 DC DC F . n F 6 5 DG 5 123 123 DG DG F . n F 6 6 DC 6 124 124 DC DC F . n F 6 7 DA 7 125 125 DA DA F . n G 7 1 DG 1 109 109 DG DG G . n G 7 2 DG 2 110 110 DG DG G . n G 7 3 DT 3 111 111 DT DT G . n G 7 4 DA 4 112 112 DA DA G . n G 7 5 DG 5 113 113 DG DG G . n G 7 6 DG 6 114 114 DG DG G . n H 8 1 DT 1 101 101 DT DT H . n H 8 2 DC 2 102 102 DC DC H . n H 8 3 DG 3 103 103 DG DG H . n H 8 4 DT 4 104 104 DT DT H . n H 8 5 DC 5 105 105 DC DC H . n H 8 6 DT 6 106 106 DT DT H . n H 8 7 DG 7 107 107 DG DG H . n H 8 8 DT 8 108 108 DT DT H . n # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 PHENIX 'model building' '(phenix.automr)' ? 2 PHENIX refinement '(phenix.refine)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 3NAO _cell.length_a 105.345 _cell.length_b 105.345 _cell.length_c 183.938 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 9 _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 3NAO _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 ? # _exptl.entry_id 3NAO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 7.67 _exptl_crystal.density_percent_sol 83.97 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'SLOW COOLING' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details 'slow colling from 90C to 20C' _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;125 mM magnesium acetate, 50 mM HEPES (pH 7.0) and 10% MPD in a 100 L sitting drop, equilibrated against a 0.5 ml reservoir of 1.4 M ammonium sulphate for two weeks. SLOW COOLING, temperature changed from 363K to 293K. ; # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 ? ? 1 # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M ? 'SINGLE WAVELENGTH' x-ray 2 1 ? ? ? x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.1 1.0 2 1.0 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'NSLS BEAMLINE X6A' NSLS X6A ? 1.1 2 SYNCHROTRON 'NSLS BEAMLINE X25' NSLS X25 ? 1.0 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 3NAO _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 34.12 _reflns.d_resolution_high 5.03 _reflns.number_obs 3129 _reflns.number_all 3237 _reflns.percent_possible_obs 85.1 _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 ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3NAO _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 2742 _refine.ls_number_reflns_all 3237 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.17 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 34.118 _refine.ls_d_res_high 5.030 _refine.ls_percent_reflns_obs 84.94 _refine.ls_R_factor_obs 0.1949 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1907 _refine.ls_R_factor_R_free 0.2288 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.58 _refine.ls_number_reflns_R_free 290 _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 ? _refine.aniso_B[1][1] 37.2900 _refine.aniso_B[2][2] 37.2900 _refine.aniso_B[3][3] 263.2329 _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 0.268 _refine.solvent_model_param_bsol 134.494 _refine.pdbx_solvent_vdw_probe_radii 1.10 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.83 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _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 ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.49 _refine.pdbx_overall_phase_error 39.12 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _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_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 1710 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1710 _refine_hist.d_res_high 5.030 _refine_hist.d_res_low 34.118 # 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 f_bond_d 0.005 ? ? 2116 'X-RAY DIFFRACTION' ? f_angle_d 1.260 ? ? 2934 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 33.054 ? ? 812 'X-RAY DIFFRACTION' ? f_chiral_restr 0.055 ? ? 332 'X-RAY DIFFRACTION' ? f_plane_restr 0.003 ? ? 84 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 5.0302 6.3309 1117 0.3143 78.00 0.3470 . . 130 . . . . 'X-RAY DIFFRACTION' . 6.3309 34.1190 1335 0.1596 92.00 0.2019 . . 160 . . . . # _database_PDB_matrix.entry_id 3NAO _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 # _struct.entry_id 3NAO _struct.title 'A DNA Crystal Designed to Contain Two Molecules per Asymmetric Unit Cell' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3NAO _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Nanotechnology, DNA Crossover, Designed Crystal Lattice, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 6 ? G N N 7 ? H N N 8 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 PDB 3NAO 3NAO 1 GAGCAGCCTGTACGGACATCA 1 ? 2 PDB 3NAO 3NAO 2 CCGTACA 1 ? 3 PDB 3NAO 3NAO 3 GGCTGC 1 ? 4 PDB 3NAO 3NAO 4 CTTGATGT 1 ? 5 PDB 3NAO 3NAO 5 AGCCTACCTGCGTGGACAGAC 1 ? 6 PDB 3NAO 3NAO 6 CCACGCA 1 ? 7 PDB 3NAO 3NAO 7 GGTAGG 1 ? 8 PDB 3NAO 3NAO 8 TCGTCTGT 1 ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3NAO A 1 ? 21 ? 3NAO 101 ? 121 ? 101 121 2 2 3NAO B 1 ? 7 ? 3NAO 119 ? 125 ? 119 125 3 3 3NAO C 1 ? 6 ? 3NAO 109 ? 114 ? 109 114 4 4 3NAO D 1 ? 8 ? 3NAO 101 ? 108 ? 101 108 5 5 3NAO E 1 ? 21 ? 3NAO 101 ? 121 ? 101 121 6 6 3NAO F 1 ? 7 ? 3NAO 119 ? 125 ? 119 125 7 7 3NAO G 1 ? 6 ? 3NAO 109 ? 114 ? 109 114 8 8 3NAO H 1 ? 8 ? 3NAO 101 ? 108 ? 101 108 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # 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 # _struct_biol.id 1 _struct_biol.details ;THE CRYSTAL IS AN INFINITE NETWORK MADE FROM SIX DNA STRANDS THAT SELF-ASSOCIATE. IN THIS ASSEMBLY THE ASYMMETRIC UNIT IS COMPRISED OF 8 CHAINS, 6 OF WHICH ARE FRAGMENTS OF LONGER DNA STRANDS. APPLYING THE SPACE GROUP H3 SYMMETRY OPERATORS (X, Y, Z,), (-Y, X-Y, Z), AND (-X+Y,-X,Z) TO CHAINS A, B, C AND D THE CONTENTS OF 1/2 THE ASYMMETRIC UNIT GENERATES ONE TRIMERIC UNIT OF THE SELF-ASSOCIATED DNA NETWORK APPLYING THE SPACE GROUP H3 SYMMETRY OPERATORS (X, Y, Z,), (-Y, X-Y, Z), AND (-X+Y,-X,Z) TO CHAINS E, F, G, AND H OF THE CONTENTS REMARK 300 OF 1/2 THE ASYMMETRIC UNIT GENERATES ONE TRIMERIC UNIT OF THE SELF-REMARK 300 ASSOCIATED NETWORK ADDITIONAL DETAILS ABOUT THE CHEMICAL COMPOSITION AND ASSOCIATION ARE INCLUDED IN A SPEARATE SECTION ; # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? B DC 1 P ? ? ? 1_555 B DA 7 "O3'" ? ? B DC 119 B DA 125 3_555 ? ? ? ? ? ? ? 1.611 ? ? covale2 covale both ? C DG 1 P ? ? ? 1_555 D DT 8 "O3'" ? ? C DG 109 D DT 108 2_555 ? ? ? ? ? ? ? 1.615 ? ? covale3 covale both ? F DC 1 P ? ? ? 1_555 F DA 7 "O3'" ? ? F DC 119 F DA 125 3_665 ? ? ? ? ? ? ? 1.614 ? ? covale4 covale both ? G DG 1 P ? ? ? 1_555 H DT 8 "O3'" ? ? G DG 109 H DT 108 2_655 ? ? ? ? ? ? ? 1.613 ? ? hydrog1 hydrog ? ? A DG 3 N1 ? ? ? 1_555 C DC 6 N3 ? ? A DG 103 C DC 114 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog2 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DG 5 O6 ? ? A DC 104 C DG 113 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog3 hydrog ? ? A DA 5 N1 ? ? ? 1_555 C DT 4 N3 ? ? A DA 105 C DT 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 5 N6 ? ? ? 1_555 C DT 4 O4 ? ? A DA 105 C DT 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 6 N1 ? ? ? 1_555 C DC 3 N3 ? ? A DG 106 C DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 6 N2 ? ? ? 1_555 C DC 3 O2 ? ? A DG 106 C DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 6 O6 ? ? ? 1_555 C DC 3 N4 ? ? A DG 106 C DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 7 N3 ? ? ? 1_555 C DG 2 N1 ? ? A DC 107 C DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 7 N4 ? ? ? 1_555 C DG 2 O6 ? ? A DC 107 C DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 7 O2 ? ? ? 1_555 C DG 2 N2 ? ? A DC 107 C DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 8 N3 ? ? ? 1_555 C DG 1 N1 ? ? A DC 108 C DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 8 N4 ? ? ? 1_555 C DG 1 O6 ? ? A DC 108 C DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 8 O2 ? ? ? 1_555 C DG 1 N2 ? ? A DC 108 C DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 O2 ? ? ? 1_555 C DG 2 N1 ? ? A DC 108 C DG 110 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog15 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 109 B DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 109 B DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 11 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 111 B DA 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 11 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 111 B DA 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 14 N1 ? ? ? 1_555 B DC 2 O2 ? ? A DG 114 B DC 120 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog28 hydrog ? ? A DG 15 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 15 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 15 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DA 16 N1 ? ? ? 1_555 D DT 8 N3 ? ? A DA 116 D DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DA 16 N6 ? ? ? 1_555 D DT 8 O4 ? ? A DA 116 D DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DC 17 N3 ? ? ? 1_555 D DG 7 N1 ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DC 17 N4 ? ? ? 1_555 D DG 7 O6 ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DC 17 O2 ? ? ? 1_555 D DG 7 N2 ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DA 18 N1 ? ? ? 1_555 D DT 6 N3 ? ? A DA 118 D DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DA 18 N6 ? ? ? 1_555 D DT 6 O4 ? ? A DA 118 D DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A DT 19 N3 ? ? ? 1_555 D DA 5 N1 ? ? A DT 119 D DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A DT 19 O4 ? ? ? 1_555 D DA 5 N6 ? ? A DT 119 D DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A DC 20 N4 ? ? ? 1_555 D DG 4 O6 ? ? A DC 120 D DG 104 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog41 hydrog ? ? A DA 21 N1 ? ? ? 1_555 D DT 3 N3 ? ? A DA 121 D DT 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A DA 21 N6 ? ? ? 1_555 D DT 3 O4 ? ? A DA 121 D DT 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? D DC 1 N3 ? ? ? 1_555 E DG 2 N1 ? ? D DC 101 E DG 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? D DC 1 N4 ? ? ? 1_555 E DG 2 O6 ? ? D DC 101 E DG 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? D DC 1 O2 ? ? ? 1_555 E DG 2 N2 ? ? D DC 101 E DG 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? D DT 2 N3 ? ? ? 1_555 E DA 1 N1 ? ? D DT 102 E DA 101 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? D DT 2 O4 ? ? ? 1_555 E DA 1 N6 ? ? D DT 102 E DA 101 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? E DC 3 N3 ? ? ? 1_555 G DG 6 N1 ? ? E DC 103 G DG 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? E DC 3 N4 ? ? ? 1_555 G DG 6 O6 ? ? E DC 103 G DG 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? E DC 3 O2 ? ? ? 1_555 G DG 6 N2 ? ? E DC 103 G DG 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? E DC 4 N3 ? ? ? 1_555 G DG 5 N1 ? ? E DC 104 G DG 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? E DC 4 N4 ? ? ? 1_555 G DG 5 O6 ? ? E DC 104 G DG 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? E DC 4 O2 ? ? ? 1_555 G DG 5 N2 ? ? E DC 104 G DG 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? E DT 5 N3 ? ? ? 1_555 G DA 4 N1 ? ? E DT 105 G DA 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? E DT 5 O4 ? ? ? 1_555 G DA 4 N6 ? ? E DT 105 G DA 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? E DA 6 N1 ? ? ? 1_555 G DT 3 N3 ? ? E DA 106 G DT 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? E DA 6 N6 ? ? ? 1_555 G DT 3 O4 ? ? E DA 106 G DT 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? E DC 7 N3 ? ? ? 1_555 G DG 2 N1 ? ? E DC 107 G DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? E DC 7 N4 ? ? ? 1_555 G DG 2 O6 ? ? E DC 107 G DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? E DC 7 O2 ? ? ? 1_555 G DG 2 N2 ? ? E DC 107 G DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? E DC 8 N3 ? ? ? 1_555 G DG 1 N1 ? ? E DC 108 G DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? E DC 8 N4 ? ? ? 1_555 G DG 1 O6 ? ? E DC 108 G DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? E DC 8 O2 ? ? ? 1_555 G DG 1 N2 ? ? E DC 108 G DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? E DC 8 O2 ? ? ? 1_555 G DG 2 N2 ? ? E DC 108 G DG 110 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog65 hydrog ? ? E DT 9 N3 ? ? ? 1_555 F DA 7 N1 ? ? E DT 109 F DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? E DT 9 O4 ? ? ? 1_555 F DA 7 N6 ? ? E DT 109 F DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? E DG 10 N1 ? ? ? 1_555 F DC 6 N3 ? ? E DG 110 F DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? E DG 10 N2 ? ? ? 1_555 F DC 6 O2 ? ? E DG 110 F DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? E DG 10 O6 ? ? ? 1_555 F DC 6 N4 ? ? E DG 110 F DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? E DC 11 N3 ? ? ? 1_555 F DG 5 N1 ? ? E DC 111 F DG 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? E DC 11 N4 ? ? ? 1_555 F DG 5 O6 ? ? E DC 111 F DG 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? E DC 11 O2 ? ? ? 1_555 F DG 5 N2 ? ? E DC 111 F DG 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? E DG 12 N1 ? ? ? 1_555 F DC 4 N3 ? ? E DG 112 F DC 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? E DG 12 N2 ? ? ? 1_555 F DC 4 O2 ? ? E DG 112 F DC 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? E DG 12 O6 ? ? ? 1_555 F DC 4 N4 ? ? E DG 112 F DC 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? E DT 13 N3 ? ? ? 1_555 F DA 3 N1 ? ? E DT 113 F DA 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? E DT 13 O4 ? ? ? 1_555 F DA 3 N6 ? ? E DT 113 F DA 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? E DG 14 N1 ? ? ? 1_555 F DC 2 O2 ? ? E DG 114 F DC 120 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog79 hydrog ? ? E DG 15 N1 ? ? ? 1_555 F DC 1 N3 ? ? E DG 115 F DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? E DG 15 N2 ? ? ? 1_555 F DC 1 O2 ? ? E DG 115 F DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? E DG 15 O6 ? ? ? 1_555 F DC 1 N4 ? ? E DG 115 F DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? E DA 16 N1 ? ? ? 1_555 H DT 8 N3 ? ? E DA 116 H DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? E DA 16 N6 ? ? ? 1_555 H DT 8 O4 ? ? E DA 116 H DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? E DC 17 N3 ? ? ? 1_555 H DG 7 N1 ? ? E DC 117 H DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? E DC 17 N4 ? ? ? 1_555 H DG 7 O6 ? ? E DC 117 H DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? E DC 17 O2 ? ? ? 1_555 H DG 7 N2 ? ? E DC 117 H DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? E DA 18 N1 ? ? ? 1_555 H DT 6 N3 ? ? E DA 118 H DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? E DA 18 N6 ? ? ? 1_555 H DT 6 O4 ? ? E DA 118 H DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? E DG 19 N1 ? ? ? 1_555 H DC 5 N3 ? ? E DG 119 H DC 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? E DG 19 N2 ? ? ? 1_555 H DC 5 O2 ? ? E DG 119 H DC 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? E DG 19 O6 ? ? ? 1_555 H DC 5 N4 ? ? E DG 119 H DC 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog92 hydrog ? ? E DA 20 N1 ? ? ? 1_555 H DT 4 N3 ? ? E DA 120 H DT 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog93 hydrog ? ? E DA 20 N6 ? ? ? 1_555 H DT 4 O4 ? ? E DA 120 H DT 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog94 hydrog ? ? E DC 21 N3 ? ? ? 1_555 H DG 3 N1 ? ? E DC 121 H DG 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog95 hydrog ? ? E DC 21 N4 ? ? ? 1_555 H DG 3 O6 ? ? E DC 121 H DG 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog96 hydrog ? ? E DC 21 O2 ? ? ? 1_555 H DG 3 N2 ? ? E DC 121 H DG 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 OP1 F DC 119 ? ? 1_555 "O3'" F DA 125 ? ? 3_665 1.84 2 1 OP2 G DG 109 ? ? 1_555 "O3'" H DT 108 ? ? 2_655 1.90 3 1 OP2 C DG 109 ? ? 1_555 "O3'" D DT 108 ? ? 2_555 1.92 4 1 OP1 B DC 119 ? ? 1_555 "O3'" B DA 125 ? ? 3_555 1.96 # 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 "C1'" A DA 102 ? ? "O4'" A DA 102 ? ? "C4'" A DA 102 ? ? 104.02 110.10 -6.08 1.00 N 2 1 "O4'" A DA 102 ? ? "C1'" A DA 102 ? ? N9 A DA 102 ? ? 116.03 108.30 7.73 0.30 N 3 1 "O4'" A DG 103 ? ? "C1'" A DG 103 ? ? N9 A DG 103 ? ? 111.95 108.30 3.65 0.30 N 4 1 "O4'" A DC 107 ? ? "C1'" A DC 107 ? ? N1 A DC 107 ? ? 111.09 108.30 2.79 0.30 N 5 1 "O4'" A DT 111 ? ? "C1'" A DT 111 ? ? N1 A DT 111 ? ? 110.16 108.30 1.86 0.30 N 6 1 "O4'" A DC 113 ? ? "C1'" A DC 113 ? ? N1 A DC 113 ? ? 111.08 108.30 2.78 0.30 N 7 1 "O4'" A DT 119 ? ? "C1'" A DT 119 ? ? N1 A DT 119 ? ? 110.94 108.30 2.64 0.30 N 8 1 "O4'" A DA 121 ? ? "C1'" A DA 121 ? ? N9 A DA 121 ? ? 111.11 108.30 2.81 0.30 N 9 1 "O4'" B DT 122 ? ? "C1'" B DT 122 ? ? N1 B DT 122 ? ? 110.18 108.30 1.88 0.30 N 10 1 "O4'" C DG 110 ? ? "C1'" C DG 110 ? ? N9 C DG 110 ? ? 112.23 108.30 3.93 0.30 N 11 1 "O4'" C DG 113 ? ? "C1'" C DG 113 ? ? N9 C DG 113 ? ? 110.20 108.30 1.90 0.30 N 12 1 "O4'" C DC 114 ? ? "C1'" C DC 114 ? ? N1 C DC 114 ? ? 110.87 108.30 2.57 0.30 N 13 1 "C1'" D DT 103 ? ? "O4'" D DT 103 ? ? "C4'" D DT 103 ? ? 103.84 110.10 -6.26 1.00 N 14 1 "O4'" D DT 103 ? ? "C1'" D DT 103 ? ? "C2'" D DT 103 ? ? 100.45 105.90 -5.45 0.80 N 15 1 "O4'" D DT 103 ? ? "C1'" D DT 103 ? ? N1 D DT 103 ? ? 116.29 108.30 7.99 0.30 N 16 1 "C3'" D DG 104 ? ? "C2'" D DG 104 ? ? "C1'" D DG 104 ? ? 97.47 102.40 -4.93 0.80 N 17 1 "O4'" D DG 104 ? ? "C1'" D DG 104 ? ? N9 D DG 104 ? ? 110.78 108.30 2.48 0.30 N 18 1 "C3'" D DA 105 ? ? "C2'" D DA 105 ? ? "C1'" D DA 105 ? ? 97.27 102.40 -5.13 0.80 N 19 1 "O4'" D DT 106 ? ? "C1'" D DT 106 ? ? N1 D DT 106 ? ? 111.01 108.30 2.71 0.30 N 20 1 "O4'" E DG 102 ? ? "C1'" E DG 102 ? ? N9 E DG 102 ? ? 111.54 108.30 3.24 0.30 N 21 1 "O4'" E DC 103 ? ? "C1'" E DC 103 ? ? N1 E DC 103 ? ? 113.87 108.30 5.57 0.30 N 22 1 "O4'" E DA 106 ? ? "C1'" E DA 106 ? ? N9 E DA 106 ? ? 111.50 108.30 3.20 0.30 N 23 1 "O4'" E DA 116 ? ? "C1'" E DA 116 ? ? N9 E DA 116 ? ? 111.41 108.30 3.11 0.30 N 24 1 "C3'" F DG 123 ? ? "C2'" F DG 123 ? ? "C1'" F DG 123 ? ? 96.96 102.40 -5.44 0.80 N 25 1 "O4'" F DG 123 ? ? "C1'" F DG 123 ? ? N9 F DG 123 ? ? 110.51 108.30 2.21 0.30 N 26 1 "O4'" F DC 124 ? ? "C1'" F DC 124 ? ? N1 F DC 124 ? ? 110.72 108.30 2.42 0.30 N 27 1 "O4'" G DG 110 ? ? "C1'" G DG 110 ? ? N9 G DG 110 ? ? 112.14 108.30 3.84 0.30 N 28 1 "O4'" G DG 113 ? ? "C1'" G DG 113 ? ? N9 G DG 113 ? ? 111.16 108.30 2.86 0.30 N 29 1 "O4'" H DG 103 ? ? "C1'" H DG 103 ? ? N9 H DG 103 ? ? 110.71 108.30 2.41 0.30 N 30 1 "C3'" H DT 106 ? ? "C2'" H DT 106 ? ? "C1'" H DT 106 ? ? 95.79 102.40 -6.61 0.80 N 31 1 "O4'" H DG 107 ? ? "C1'" H DG 107 ? ? N9 H DG 107 ? ? 110.13 108.30 1.83 0.30 N # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined -33.5134 0.1484 0.8518 2.3173 4.0984 5.2406 0.1236 0.3144 1.3984 1.8700 2.4350 0.5680 -2.0459 0.8307 -0.7051 -1.4370 -0.9839 -1.2255 0.5870 -0.6494 1.8118 0.4885 -1.0507 1.2761 'X-RAY DIFFRACTION' 2 ? refined -24.8524 11.8848 2.1269 2.2206 2.6550 4.0450 -0.3476 1.3613 1.4148 0.0594 0.9675 0.6846 0.2203 0.1154 0.2089 0.0326 0.0642 0.5311 1.0751 -0.3419 1.8538 0.2206 -0.6055 -1.4495 'X-RAY DIFFRACTION' 3 ? refined -7.8452 7.0314 0.4809 3.2200 3.1116 3.3692 0.3622 -0.7265 1.1586 9.6827 8.1572 0.0030 8.8795 0.1452 0.1312 -2.8732 -0.1524 -0.2043 -1.0659 -0.0466 -2.9908 -1.5862 -1.6026 0.9454 'X-RAY DIFFRACTION' 4 ? refined -1.2812 14.8429 -14.2893 3.0462 1.2746 2.8172 -0.5398 -0.8033 0.3046 3.2651 0.7152 0.2908 -1.2570 -0.8935 0.2263 -0.6715 0.1973 -0.3101 0.8773 0.5907 1.0044 2.6383 -0.0266 0.1544 'X-RAY DIFFRACTION' 5 ? refined 12.1344 25.0374 -16.8420 3.4852 1.6185 2.8685 -0.6653 -0.1457 -0.4760 0.1472 0.6371 3.1096 0.1906 -0.4773 0.0736 0.0522 0.6539 0.1202 0.3875 -0.1534 1.6631 -1.8708 -1.5263 -0.1067 'X-RAY DIFFRACTION' 6 ? refined -7.1436 12.1248 -6.8464 1.6073 1.8070 3.7795 0.0268 1.1246 0.4223 1.0807 1.2909 2.0081 -1.1977 3.6387 -3.9592 0.2411 -0.7620 -2.4101 -0.7114 3.4215 -0.5545 0.5087 -1.2256 3.5161 'X-RAY DIFFRACTION' 7 ? refined -25.2031 5.0025 5.8600 1.8014 1.8944 3.2094 0.3297 0.6236 -0.0269 0.5379 1.3781 2.5449 0.8599 1.1614 1.8641 -0.2463 0.6030 -0.6537 -2.2510 2.2683 -3.7080 -0.1111 0.7433 -1.4074 'X-RAY DIFFRACTION' 8 ? refined 9.8319 28.9862 -27.9010 2.4489 4.1921 2.3199 0.7843 0.4106 1.4187 5.0500 2.6485 1.1956 0.7234 0.2548 -0.0234 1.6748 0.1385 -0.1909 -0.8728 -0.3628 0.0189 0.5799 0.7079 -0.8255 'X-RAY DIFFRACTION' 9 ? refined 10.4050 17.1470 -17.7671 2.0005 2.5050 3.8811 -1.7765 0.4035 0.7635 0.3327 0.0121 1.4093 -0.0457 0.1078 -0.1528 -0.0069 0.2176 -0.3368 0.5886 -0.2406 0.2081 0.5584 -0.3009 -0.7392 'X-RAY DIFFRACTION' 10 ? refined 19.4729 30.0937 -29.7356 2.0817 1.9869 5.3080 0.4419 2.1358 -0.2356 0.0892 0.0728 1.3086 0.0832 0.3300 0.3143 1.2170 0.2721 1.7092 -1.0633 0.3733 -1.3286 -2.0884 -0.0420 -0.6301 'X-RAY DIFFRACTION' 11 ? refined 28.1044 42.4421 -28.1829 1.3277 2.9446 3.0169 -0.7315 1.3954 0.1667 1.0218 3.9856 0.4779 1.5086 -0.6973 -0.9651 0.1219 0.2782 0.1463 0.4816 -0.0314 2.1525 -0.3295 -0.4639 -0.3755 'X-RAY DIFFRACTION' 12 ? refined 45.0891 37.6194 -30.5112 2.5938 1.5445 1.5733 -1.8005 0.9360 -1.2346 0.1344 0.3251 0.5069 0.1993 0.0454 0.2086 -0.3094 0.2070 -0.2545 -0.1163 0.0199 -0.4477 -0.1647 -0.0488 -0.9428 'X-RAY DIFFRACTION' 13 ? refined 50.8731 43.3587 -44.9699 1.6094 2.3787 0.6903 -0.1420 0.2637 -0.2736 0.7594 0.2406 0.1122 0.3386 0.2636 0.0484 0.5143 0.5635 0.0727 0.6273 -0.5288 0.2089 0.9589 -0.6616 0.1030 'X-RAY DIFFRACTION' 14 ? refined 63.1796 54.5963 -46.5048 2.4587 3.1101 1.1962 -0.1223 1.9433 0.7931 1.3966 0.6883 0.1297 0.2080 0.4074 -0.0759 -0.4109 1.0609 -0.1376 -0.4425 0.0248 -0.2555 0.1606 1.1046 -0.1633 'X-RAY DIFFRACTION' 15 ? refined 45.6509 42.7508 -37.7734 1.2827 1.6676 0.6449 -0.0410 0.1956 0.7617 6.8265 5.5207 3.6943 -1.6633 0.7499 3.7828 1.9882 0.9209 0.7469 -1.6200 0.9839 -0.2437 0.3858 0.4223 7.1073 'X-RAY DIFFRACTION' 16 ? refined 27.5107 35.3372 -24.7720 1.1971 2.5507 3.5978 0.3408 1.1317 -0.7074 0.0041 0.6909 1.9327 0.0314 -0.0486 -1.1553 1.3990 1.6507 0.0607 0.6194 -0.1864 -0.4264 -0.0075 0.7138 1.7632 'X-RAY DIFFRACTION' 17 ? refined 63.3246 59.6197 -57.4135 2.2183 3.9350 2.9314 0.0697 1.7892 0.5793 0.0744 0.6743 1.4963 0.1846 -0.2593 -1.0078 0.4451 0.6277 1.0798 -0.1605 -0.2930 0.1340 -0.7774 -0.2424 -0.9499 'X-RAY DIFFRACTION' 18 ? refined 63.3304 47.1875 -47.7037 1.6506 2.5852 2.2101 0.4008 1.7941 -0.9678 0.9354 0.4593 2.2450 0.5280 -0.0342 0.5732 0.4524 0.9177 0.5013 -0.0002 -0.4502 -0.1356 0.9028 0.6774 -0.0136 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? '(chain A and resid 101:104)' 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? '(chain A and resid 105:108)' 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? '(chain A and resid 109:112)' 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? '(chain A and resid 113:117)' 'X-RAY DIFFRACTION' 5 5 ? ? ? ? ? ? ? ? ? '(chain A and resid 118:121)' 'X-RAY DIFFRACTION' 6 6 ? ? ? ? ? ? ? ? ? '(chain B and resid 119:125)' 'X-RAY DIFFRACTION' 7 7 ? ? ? ? ? ? ? ? ? '(chain C and resid 109:114)' 'X-RAY DIFFRACTION' 8 8 ? ? ? ? ? ? ? ? ? '(chain D and resid 101:104)' 'X-RAY DIFFRACTION' 9 9 ? ? ? ? ? ? ? ? ? '(chain D and resid 105:108)' 'X-RAY DIFFRACTION' 10 10 ? ? ? ? ? ? ? ? ? '(chain E and resid 101:104)' 'X-RAY DIFFRACTION' 11 11 ? ? ? ? ? ? ? ? ? '(chain E and resid 105:108)' 'X-RAY DIFFRACTION' 12 12 ? ? ? ? ? ? ? ? ? '(chain E and resid 109:112)' 'X-RAY DIFFRACTION' 13 13 ? ? ? ? ? ? ? ? ? '(chain E and resid 113:116)' 'X-RAY DIFFRACTION' 14 14 ? ? ? ? ? ? ? ? ? '(chain E and resid 117:121)' 'X-RAY DIFFRACTION' 15 15 ? ? ? ? ? ? ? ? ? '(chain F and resid 119:125)' 'X-RAY DIFFRACTION' 16 16 ? ? ? ? ? ? ? ? ? '(chain G and resid 109:114)' 'X-RAY DIFFRACTION' 17 17 ? ? ? ? ? ? ? ? ? '(chain H and resid 101:104)' 'X-RAY DIFFRACTION' 18 18 ? ? ? ? ? ? ? ? ? '(chain H and resid 105:108)' # _pdbx_entry_details.entry_id 3NAO _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ;THE STRUCTURE IS COMPRISED OF TWO TRIANGLES ARRANGED IN A TANDEM MANNER. EACH TRIANGLE IS GENERATED FROM THE STRUCTURE UNIT IS GENERATEDFROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH LOCAL INTERNAL 3-FOLD SYMMETRY. EXTENDING OF THE STRUCTURE UNIT IN 3-D SPACE RESULTS THE CRYSTAL AT R3 SPACE GROUP (REPRESENTED AS H3). (#1) 3 STRANDS 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A) -3'); (#2) 1 STRAND 5'-d(*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*A) -3' (#3) 3 STRANDS 5'-D(*CP*TP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C )-3' THE 1/2 OF THE ASYMMETRIC UNIT IS COMPRISED OF ONE FULL #1 STRAND (CHAIN A),7-RESIDUE REPEATING UNIT OF #2 STRAND (CHAIN B) AND TWO FRAGMENTS OF #3 STRAND (CHAINS C AND D). THE #2 STRAND SELF-ASSOICATES TO FORM A CIRCULAR DNA MOLECULE WITH INTERNAL 3-FOLD SYMMETRY. IT HAS 3 SYMMETRIC AND SEQUENTIAL REPEATING UNITS. CHAIN B IN THE ASYMMETRIC UNIT REPRESENTS ONE OF THESE REPEATING UNITS. CHAINS D (FIRST 8 RESIDUES OF STRAND #3) AND C (NEXT 6 RESIDUES OF STRAND #3) TOGETHER FORM THE THIRD DNA STRAND (#3) OF THE EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS - HENCE IT WAS DIVIDED INTO THE CURRENT CHAINS C AND D FOR CONVENIENT REPRESENTATION. CHAIN C (1_555) IS COVALENTLY LINKED TO CHAIN D OF ANOTHER ASYMMETRIC UNIT (3_555); AND CHAIN D (1_555) IS COVALENTLY LINKED TO CHAIN C OF ANOTHER ASYMMETRIC UNIT (2_555). THE SELECTION OF RESIDUES FROM THE DNA #2 AND #3 ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAIN A. THE DNA SEQUENCES OF THE 7 STRANDS COMPRISING THE SECOND 1/2 OF THE ASYMMETRIC UNIT (TRIANGLE B) ARE: (#4) 3 STRANDS (5'-D(*AP*GP*CP*CP*TP*AP*CP*CP*TP*GP*CP*GP*TP*GP*GP*AP*CP*AP*GP*AP* AP*C)-3' (#5) 1 STRAND 5'-D(*TP*CP*GP*TP*CP*TP*GP*TP*TP*CP*GP*TP*CP*TP*GP*TP*TP*CP*GP*TP* CP*TP*GP*T)-3' (#6) 3 STRANDS 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3' THE ASYMMETRIC UNIT IS COMPRISED OF ONE FULL #4 STRAND (CHAIN E), 7-RESIDUE REPEATING UNIT OF #5 STRAND (CHAIN F) AND TWO FRAGMENTS OF #6 STRAND (CHAINS G AND H). THE #5 STRAND SELF-ASSOICATES TO FORM A CIRCULAR DNA MOLECULE WITH INTERNAL 3-FOLD SYMMETRY. IT HAS 3 SYMMETRIC AND SEQUENTIAL REPEATING UNITS. CHAIN F IN THE ASYMMETRIC UNIT REPRESENTS ONE OF THESE REPEATING UNITS. CHAINS H(FIRST 8 RESIDUES OF STRAND #6) AND G (NEXT 6 RESIDUES OF STRAND #6) TOGETHER FORM THE THIRD DNA STRAND (#6) OF THE EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS - HENCE IT WAS DIVIDED INTO THE CURRENT CHAINS G AND H FOR CONVENIENT REPRESENTATION. CHAIN G (1_555) IS COVALENTLY LINKED TO CHAIN H OF ANOTHER ASYMMETRIC UNIT (3_665); AND CHAIN H (1_555) IS COVALENTLY LINKED TO CHAIN G OF ANOTHER ASYMMETRIC UNIT (2_655). THE SELECTION OF RESIDUES FROM THE DNA #5 AND #6 ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAIN E. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? # 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 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 # 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 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3NAO 'double helix' 3NAO 'b-form double helix' # _atom_sites.entry_id 3NAO _atom_sites.fract_transf_matrix[1][1] 0.009493 _atom_sites.fract_transf_matrix[1][2] 0.005481 _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] 0.010961 _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] 0.005437 _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_