data_3GBI # _entry.id 3GBI # _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 3GBI pdb_00003gbi 10.2210/pdb3gbi/pdb NDB BD0116 ? ? RCSB RCSB051659 ? ? WWPDB D_1000051659 ? ? # 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 2009-09-01 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-01 4 'Structure model' 1 3 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' 'Version format compliance' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' struct_conn 6 4 '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' '_software.name' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 6 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 7 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 12 4 'Structure model' '_struct_conn.ptnr1_symmetry' 13 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 18 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 19 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 20 4 'Structure model' '_struct_conn.ptnr2_symmetry' 21 4 'Structure model' '_struct_ref_seq.db_align_beg' 22 4 'Structure model' '_struct_ref_seq.db_align_end' # _pdbx_database_status.entry_id 3GBI _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-02-19 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _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 ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Birktoft, J.J.' 1 'Zheng, J.' 2 'Seeman, N.C.' 3 # _citation.id primary _citation.title 'From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.' _citation.journal_abbrev Nature _citation.journal_volume 461 _citation.page_first 74 _citation.page_last 77 _citation.year 2009 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19727196 _citation.pdbx_database_id_DOI 10.1038/nature08274 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zheng, J.' 1 ? primary 'Birktoft, J.J.' 2 ? primary 'Chen, Y.' 3 ? primary 'Wang, T.' 4 ? primary 'Sha, R.' 5 ? primary 'Constantinou, P.E.' 6 ? primary 'Ginell, S.L.' 7 ? primary 'Mao, C.' 8 ? primary 'Seeman, N.C.' 9 ? # 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 a 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(*TP*CP*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.' ? # 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 '(DT)(DC)(DT)(DG)(DA)(DT)(DG)(DT)' TCTGATGT D ? # 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 DT n 4 2 DC 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 # 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' 3 1 sample ? ? ? ? ? 'DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on' 4 1 sample ? ? ? ? ? 'DNA strands were synthesized by standard phosphoramidite techniques on an Applied Biosystems 394 DNA synthesizer using trityl-on' # 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 1 209 209 DG DG C . n C 3 2 DG 2 210 210 DG DG C . n C 3 3 DC 3 211 211 DC DC C . n C 3 4 DT 4 212 212 DT DT C . n C 3 5 DG 5 213 213 DG DG C . n C 3 6 DC 6 214 214 DC DC C . n D 4 1 DT 1 101 101 DT DT D . n D 4 2 DC 2 102 102 DC DC 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 # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal PHENIX . ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 1 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 2 HKL-3000 . ? ? ? ? 'data collection' ? ? ? 3 HKL-3000 . ? ? ? ? 'data reduction' ? ? ? 4 HKL-3000 . ? ? ? ? 'data scaling' ? ? ? 5 HKL2Map . ? ? ? ? phasing ? ? ? 6 # _cell.entry_id 3GBI _cell.length_a 107.161 _cell.length_b 107.161 _cell.length_c 93.144 _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 3GBI _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 3GBI _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;Grown by vapor diffusion while treated with a controlled temperature gradient from 333 degs to 293 degs., pH 8.5, VAPOR DIFFUSION, SITTING DROP ; # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2008-06-17 _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 Graphite _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 3GBI _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 17.3 _reflns.d_resolution_high 4.01 _reflns.number_obs 3211 _reflns.number_all 3341 _reflns.percent_possible_obs 96.1 _reflns.pdbx_Rmerge_I_obs 0.067 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 10.9 _reflns.B_iso_Wilson_estimate 199.880 _reflns.pdbx_redundancy 7.3 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 4.00 _reflns_shell.d_res_low 4.07 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3GBI _refine.ls_number_reflns_obs 2022 _refine.ls_number_reflns_all 3211 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.14 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 17.288 _refine.ls_d_res_high 4.018 _refine.ls_percent_reflns_obs 61.140 _refine.ls_R_factor_obs 0.246 _refine.ls_R_factor_all 0.246 _refine.ls_R_factor_R_work 0.240 _refine.ls_R_factor_R_free 0.309 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.040 _refine.ls_number_reflns_R_free 203 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min 1.00 _refine.occupancy_max 1.00 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 80.000 _refine.aniso_B[1][1] 63.252 _refine.aniso_B[2][2] 63.252 _refine.aniso_B[3][3] 227.851 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.090 _refine.solvent_model_param_bsol 20.001 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ;In reality all 3211 measured reflections were used in the refinement (using PHENIX). Of these only 2022 had FOBS/SIGMA_FOBS >/= 0.140. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _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 0.830 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _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_diffrn_id 1 _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 855 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 855 _refine_hist.d_res_high 4.018 _refine_hist.d_res_low 17.288 # 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 0.016 ? ? 1052 'X-RAY DIFFRACTION' ? f_angle_d 1.364 ? ? 1465 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 31.823 ? ? 406 'X-RAY DIFFRACTION' ? f_chiral_restr 0.058 ? ? 166 'X-RAY DIFFRACTION' ? f_plane_restr 0.002 ? ? 42 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 1 _refine_ls_shell.d_res_high 4.018 _refine_ls_shell.d_res_low ? _refine_ls_shell.number_reflns_R_work 1819 _refine_ls_shell.R_factor_R_work 0.240 _refine_ls_shell.percent_reflns_obs 61.000 _refine_ls_shell.R_factor_R_free 0.309 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 203 _refine_ls_shell.number_reflns_all 2022 _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 3GBI _struct.title 'The Rational Design and Structural Analysis of a Self-Assembled Three-Dimensional DNA Crystal' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3GBI _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'nanotechnology, DNA crystals, 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 ? # loop_ _struct_ref.entity_id _struct_ref.pdbx_db_accession _struct_ref.db_code _struct_ref.db_name _struct_ref.id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 3GBI 3GBI PDB 1 1 GAGCAGCCTGTACGGACATCA ? 2 3GBI 3GBI PDB 2 1 CCGTACA ? 3 3GBI 3GBI PDB 3 1 GGCTGC ? 4 3GBI 3GBI PDB 4 1 TCTGATGT ? # 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 3GBI A 1 ? 21 ? 3GBI 101 ? 121 ? 101 121 2 2 3GBI B 1 ? 7 ? 3GBI 119 ? 125 ? 119 125 3 3 3GBI C 1 ? 6 ? 3GBI 209 ? 214 ? 209 214 4 4 3GBI D 1 ? 8 ? 3GBI 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 heptameric _pdbx_struct_assembly.oligomeric_count 7 # _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 # 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 ;Authors state that the crystal is an infinite network made from three DNA strands that self-associate. In the current entry the asymmetric unit is comprised of 4 chains, 3 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 the contents of the asymmetric unit generates one trimeric unit of the self-associated DNA network. Additional details about the chemical composition and association are included in remark 400. ; # 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 2_555 ? ? ? ? ? ? ? 1.612 ? ? covale2 covale both ? B DC 1 P ? ? ? 3_555 B DA 7 "O3'" ? ? B DC 119 B DA 125 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale3 covale both ? C DG 1 P ? ? ? 1_555 D DT 8 "O3'" ? ? C DG 209 D DT 108 3_555 ? ? ? ? ? ? ? 1.614 ? ? covale4 covale both ? C DG 1 P ? ? ? 2_555 D DT 8 "O3'" ? ? C DG 209 D DT 108 1_555 ? ? ? ? ? ? ? 1.614 ? ? hydrog1 hydrog ? ? A DG 3 N1 ? ? ? 1_555 C DC 6 N3 ? ? A DG 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 3 N2 ? ? ? 1_555 C DC 6 O2 ? ? A DG 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 3 O6 ? ? ? 1_555 C DC 6 N4 ? ? A DG 103 C DC 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 4 N3 ? ? ? 1_555 C DG 5 N1 ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DG 5 O6 ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 O2 ? ? ? 1_555 C DG 5 N2 ? ? A DC 104 C DG 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 5 N1 ? ? ? 1_555 C DT 4 N3 ? ? A DA 105 C DT 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 5 N6 ? ? ? 1_555 C DT 4 O4 ? ? A DA 105 C DT 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 6 N2 ? ? ? 1_555 C DC 3 N3 ? ? A DG 106 C DC 211 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog10 hydrog ? ? A DC 7 N3 ? ? ? 1_555 C DG 2 N1 ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 7 N4 ? ? ? 1_555 C DG 2 O6 ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 7 O2 ? ? ? 1_555 C DG 2 N2 ? ? A DC 107 C DG 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 8 N3 ? ? ? 1_555 C DG 1 N1 ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N4 ? ? ? 1_555 C DG 1 O6 ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 O2 ? ? ? 1_555 C DG 1 N2 ? ? A DC 108 C DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 109 B DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 109 B DA 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DA 5 N1 ? ? A DG 110 B DA 123 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog19 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DA 5 N6 ? ? A DG 110 B DA 123 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog20 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 110 B DC 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 11 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 111 B DA 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DT 11 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 111 B DA 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 112 B DT 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DC 2 N4 ? ? A DC 113 B DC 120 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog28 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 113 B DG 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 14 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 114 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 14 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 114 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DG 14 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 114 B DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DG 15 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DG 15 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DG 15 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 115 B DC 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DA 16 N1 ? ? ? 1_555 D DT 8 N3 ? ? A DA 116 D DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A DA 16 N6 ? ? ? 1_555 D DT 8 O4 ? ? A DA 116 D DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A DC 17 N3 ? ? ? 1_555 D DG 7 N1 ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A DC 17 N4 ? ? ? 1_555 D DG 7 O6 ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A DC 17 O2 ? ? ? 1_555 D DG 7 N2 ? ? A DC 117 D DG 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A DA 18 N1 ? ? ? 1_555 D DT 6 N3 ? ? A DA 118 D DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A DA 18 N6 ? ? ? 1_555 D DT 6 O4 ? ? A DA 118 D DT 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A DT 19 N3 ? ? ? 1_555 D DA 5 N1 ? ? A DT 119 D DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A DT 19 O4 ? ? ? 1_555 D DA 5 N6 ? ? A DT 119 D DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A DC 20 N3 ? ? ? 1_555 D DG 4 N1 ? ? A DC 120 D DG 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A DC 20 N4 ? ? ? 1_555 D DG 4 O6 ? ? A DC 120 D DG 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A DC 20 O2 ? ? ? 1_555 D DG 4 N2 ? ? A DC 120 D DG 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A DA 21 N1 ? ? ? 1_555 D DT 3 N3 ? ? A DA 121 D DT 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A DA 21 N6 ? ? ? 1_555 D DT 3 O4 ? ? A DA 121 D DT 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 C5 _pdbx_validate_rmsd_bond.auth_asym_id_1 D _pdbx_validate_rmsd_bond.auth_comp_id_1 DT _pdbx_validate_rmsd_bond.auth_seq_id_1 106 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 C7 _pdbx_validate_rmsd_bond.auth_asym_id_2 D _pdbx_validate_rmsd_bond.auth_comp_id_2 DT _pdbx_validate_rmsd_bond.auth_seq_id_2 106 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.532 _pdbx_validate_rmsd_bond.bond_target_value 1.496 _pdbx_validate_rmsd_bond.bond_deviation 0.036 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag 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'" A DA 102 ? ? "C1'" A DA 102 ? ? N9 A DA 102 ? ? 112.60 108.30 4.30 0.30 N 2 1 "O4'" A DG 103 ? ? "C1'" A DG 103 ? ? N9 A DG 103 ? ? 112.60 108.30 4.30 0.30 N 3 1 "C3'" A DA 105 ? ? "C2'" A DA 105 ? ? "C1'" A DA 105 ? ? 97.19 102.40 -5.21 0.80 N 4 1 "O4'" A DA 105 ? ? "C1'" A DA 105 ? ? N9 A DA 105 ? ? 110.89 108.30 2.59 0.30 N 5 1 "C1'" A DC 107 ? ? "O4'" A DC 107 ? ? "C4'" A DC 107 ? ? 103.88 110.10 -6.22 1.00 N 6 1 "C3'" A DC 107 ? ? "C2'" A DC 107 ? ? "C1'" A DC 107 ? ? 97.34 102.40 -5.06 0.80 N 7 1 "O4'" A DC 107 ? ? "C1'" A DC 107 ? ? N1 A DC 107 ? ? 112.74 108.30 4.44 0.30 N 8 1 "O4'" A DT 111 ? ? "C1'" A DT 111 ? ? N1 A DT 111 ? ? 110.17 108.30 1.87 0.30 N 9 1 "O4'" A DA 116 ? ? "C1'" A DA 116 ? ? N9 A DA 116 ? ? 111.99 108.30 3.69 0.30 N 10 1 "O4'" A DC 117 ? ? "C1'" A DC 117 ? ? N1 A DC 117 ? ? 111.08 108.30 2.78 0.30 N 11 1 "O4'" A DA 118 ? ? "C4'" A DA 118 ? ? "C3'" A DA 118 ? ? 101.45 104.50 -3.05 0.40 N 12 1 "O4'" A DT 119 ? ? "C1'" A DT 119 ? ? N1 A DT 119 ? ? 110.20 108.30 1.90 0.30 N 13 1 "C3'" A DA 121 ? ? "C2'" A DA 121 ? ? "C1'" A DA 121 ? ? 95.56 102.40 -6.84 0.80 N 14 1 "O4'" A DA 121 ? ? "C1'" A DA 121 ? ? N9 A DA 121 ? ? 110.21 108.30 1.91 0.30 N 15 1 "C3'" B DA 123 ? ? "C2'" B DA 123 ? ? "C1'" B DA 123 ? ? 95.50 102.40 -6.90 0.80 N 16 1 "O4'" B DA 123 ? ? "C1'" B DA 123 ? ? N9 B DA 123 ? ? 111.74 108.30 3.44 0.30 N 17 1 "O4'" C DG 210 ? ? "C1'" C DG 210 ? ? N9 C DG 210 ? ? 111.49 108.30 3.19 0.30 N 18 1 "O4'" C DC 211 ? ? "C1'" C DC 211 ? ? N1 C DC 211 ? ? 111.27 108.30 2.97 0.30 N 19 1 "O4'" C DG 213 ? ? "C1'" C DG 213 ? ? N9 C DG 213 ? ? 111.54 108.30 3.24 0.30 N 20 1 "O4'" D DC 102 ? ? "C1'" D DC 102 ? ? N1 D DC 102 ? ? 110.26 108.30 1.96 0.30 N 21 1 "O4'" D DT 103 ? ? "C1'" D DT 103 ? ? N1 D DT 103 ? ? 111.78 108.30 3.48 0.30 N 22 1 "C3'" D DG 104 ? ? "C2'" D DG 104 ? ? "C1'" D DG 104 ? ? 96.44 102.40 -5.96 0.80 N 23 1 "C3'" D DA 105 ? ? "C2'" D DA 105 ? ? "C1'" D DA 105 ? ? 97.27 102.40 -5.13 0.80 N 24 1 "C1'" D DT 106 ? ? "O4'" D DT 106 ? ? "C4'" D DT 106 ? ? 103.69 110.10 -6.41 1.00 N 25 1 "C3'" D DT 106 ? ? "C2'" D DT 106 ? ? "C1'" D DT 106 ? ? 97.28 102.40 -5.12 0.80 N 26 1 "O4'" D DT 106 ? ? "C1'" D DT 106 ? ? N1 D DT 106 ? ? 111.08 108.30 2.78 0.30 N 27 1 "O4'" D DT 108 ? ? "C1'" D DT 108 ? ? N1 D DT 108 ? ? 110.21 108.30 1.91 0.30 N # _pdbx_entry_details.entry_id 3GBI _pdbx_entry_details.compound_details ;THE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH INTERNAL 3-FOLD SYMMETRY. EXTENDING OF THE STRUCTURE UNIT IN 3-D SPACE RESULTS THE CRYSTAL AT R3 SPACE GROUP (REPRESENTED AS H3). THE DNA SEQUENCES OF THE 7 STRANDS ARE: (#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(*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP* CP*G)-3' (#3) 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 #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. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_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 3GBI 'double helix' 3GBI 'b-form double helix' 3GBI '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 DG 3 1_555 C DC 6 1_555 -0.339 -0.255 1.131 10.421 7.577 -3.950 1 A_DG103:DC214_C A 103 ? C 214 ? 19 1 1 A DC 4 1_555 C DG 5 1_555 0.198 -0.137 0.693 -8.699 -7.249 -8.925 2 A_DC104:DG213_C A 104 ? C 213 ? 19 1 1 A DA 5 1_555 C DT 4 1_555 -0.061 -0.184 0.385 -14.211 -18.029 -9.386 3 A_DA105:DT212_C A 105 ? C 212 ? 20 1 1 A DG 6 1_555 C DC 3 1_555 2.220 0.281 -0.081 0.211 -1.754 3.601 4 A_DG106:DC211_C A 106 ? C 211 ? ? ? 1 A DC 7 1_555 C DG 2 1_555 0.208 -0.306 -1.012 12.676 13.331 -12.689 5 A_DC107:DG210_C A 107 ? C 210 ? 19 1 1 A DC 8 1_555 C DG 1 1_555 0.291 -0.116 -0.324 -3.890 -8.958 -7.533 6 A_DC108:DG209_C A 108 ? C 209 ? 19 1 1 A DT 9 1_555 B DA 7 1_555 0.099 -0.155 0.880 -16.146 18.527 -0.152 7 A_DT109:DA125_B A 109 ? B 125 ? 20 1 1 A DG 10 1_555 B DC 6 1_555 -0.321 -0.259 0.575 -22.498 -9.596 -8.824 8 A_DG110:DC124_B A 110 ? B 124 ? 19 1 1 A DT 11 1_555 B DA 5 1_555 -0.012 -0.092 -0.087 -8.424 10.601 -12.047 9 A_DT111:DA123_B A 111 ? B 123 ? 20 1 1 A DA 12 1_555 B DT 4 1_555 -0.105 -0.020 -0.006 -27.279 -14.283 -10.041 10 A_DA112:DT122_B A 112 ? B 122 ? 20 1 1 A DC 13 1_555 B DG 3 1_555 0.219 -0.474 1.961 -27.559 7.372 -4.888 11 A_DC113:DG121_B A 113 ? B 121 ? 19 1 1 A DG 14 1_555 B DC 2 1_555 -0.284 -0.384 1.002 -24.398 -14.288 -11.026 12 A_DG114:DC120_B A 114 ? B 120 ? 19 1 1 A DG 15 1_555 B DC 1 1_555 -0.249 -0.088 0.173 -17.964 -3.624 -8.962 13 A_DG115:DC119_B A 115 ? B 119 ? 19 1 1 A DA 16 1_555 D DT 8 1_555 0.008 -0.216 0.832 3.294 3.092 -4.762 14 A_DA116:DT108_D A 116 ? D 108 ? 20 1 1 A DC 17 1_555 D DG 7 1_555 0.332 -0.154 0.441 7.501 -2.508 -7.189 15 A_DC117:DG107_D A 117 ? D 107 ? 19 1 1 A DA 18 1_555 D DT 6 1_555 -0.126 -0.103 -0.055 -18.801 -16.679 -5.067 16 A_DA118:DT106_D A 118 ? D 106 ? 20 1 1 A DT 19 1_555 D DA 5 1_555 -0.105 -0.008 0.301 -32.859 -10.734 -3.989 17 A_DT119:DA105_D A 119 ? D 105 ? 20 1 1 A DC 20 1_555 D DG 4 1_555 0.145 0.182 0.319 -23.669 -5.736 8.064 18 A_DC120:DG104_D A 120 ? D 104 ? 19 1 1 A DA 21 1_555 D DT 3 1_555 0.058 -0.141 0.244 1.063 9.309 -2.855 19 A_DA121:DT103_D A 121 ? D 103 ? 20 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 DG 3 1_555 C DC 6 1_555 A DC 4 1_555 C DG 5 1_555 -0.382 -0.876 3.788 2.297 12.267 45.968 -2.198 0.682 3.438 15.377 -2.880 47.543 1 AA_DG103DC104:DG213DC214_CC A 103 ? C 214 ? A 104 ? C 213 ? 1 A DC 4 1_555 C DG 5 1_555 A DA 5 1_555 C DT 4 1_555 -0.759 -0.015 3.678 -2.626 9.423 32.721 -1.722 0.821 3.585 16.278 4.536 34.114 2 AA_DC104DA105:DT212DG213_CC A 104 ? C 213 ? A 105 ? C 212 ? 1 A DA 5 1_555 C DT 4 1_555 A DG 6 1_555 C DC 3 1_555 -0.535 -0.840 2.912 1.562 -2.171 42.240 -0.965 0.884 2.929 -3.008 -2.165 42.321 3 AA_DA105DG106:DC211DT212_CC A 105 ? C 212 ? A 106 ? C 211 ? 1 A DG 6 1_555 C DC 3 1_555 A DC 7 1_555 C DG 2 1_555 0.277 -1.613 3.053 3.114 -7.578 22.499 -1.378 0.363 3.413 -18.647 -7.663 23.926 4 AA_DG106DC107:DG210DC211_CC A 106 ? C 211 ? A 107 ? C 210 ? 1 A DC 7 1_555 C DG 2 1_555 A DC 8 1_555 C DG 1 1_555 0.982 -0.174 3.681 -0.310 12.201 42.136 -1.536 -1.349 3.496 16.558 0.420 43.791 5 AA_DC107DC108:DG209DG210_CC A 107 ? C 210 ? A 108 ? C 209 ? 1 A DC 8 1_555 C DG 1 1_555 A DT 9 1_555 B DA 7 1_555 -0.698 -2.092 4.099 -12.822 -17.856 18.922 2.001 -3.048 4.283 -40.418 29.023 28.929 6 AA_DC108DT109:DA125DG209_BC A 108 ? C 209 ? A 109 ? B 125 ? 1 A DT 9 1_555 B DA 7 1_555 A DG 10 1_555 B DC 6 1_555 0.827 -1.579 3.185 7.574 19.013 28.849 -5.070 -0.385 1.960 33.379 -13.297 35.245 7 AA_DT109DG110:DC124DA125_BB A 109 ? B 125 ? A 110 ? B 124 ? 1 A DG 10 1_555 B DC 6 1_555 A DT 11 1_555 B DA 5 1_555 -0.143 0.010 2.732 5.757 1.869 37.675 -0.181 0.824 2.680 2.871 -8.844 38.140 8 AA_DG110DT111:DA123DC124_BB A 110 ? B 124 ? A 111 ? B 123 ? 1 A DT 11 1_555 B DA 5 1_555 A DA 12 1_555 B DT 4 1_555 -1.304 -0.247 3.749 -4.283 9.463 37.038 -1.744 1.362 3.701 14.549 6.584 38.418 9 AA_DT111DA112:DT122DA123_BB A 111 ? B 123 ? A 112 ? B 122 ? 1 A DA 12 1_555 B DT 4 1_555 A DC 13 1_555 B DG 3 1_555 -0.826 -0.083 3.581 -16.294 -3.269 33.569 0.371 -1.204 3.587 -5.278 26.304 37.351 10 AA_DA112DC113:DG121DT122_BB A 112 ? B 122 ? A 113 ? B 121 ? 1 A DC 13 1_555 B DG 3 1_555 A DG 14 1_555 B DC 2 1_555 -1.058 2.307 3.564 -1.130 -32.803 39.936 4.641 1.155 1.420 -40.753 1.403 51.264 11 AA_DC113DG114:DC120DG121_BB A 113 ? B 121 ? A 114 ? B 120 ? 1 A DG 14 1_555 B DC 2 1_555 A DG 15 1_555 B DC 1 1_555 0.464 0.415 3.555 2.011 -10.497 37.731 1.972 -0.434 3.345 -15.847 -3.036 39.163 12 AA_DG114DG115:DC119DC120_BB A 114 ? B 120 ? A 115 ? B 119 ? 1 A DG 15 1_555 B DC 1 1_555 A DA 16 1_555 D DT 8 1_555 0.018 -0.279 2.591 -6.779 3.891 30.399 -1.093 -1.037 2.475 7.270 12.667 31.365 13 AA_DG115DA116:DT108DC119_DB A 115 ? B 119 ? A 116 ? D 108 ? 1 A DA 16 1_555 D DT 8 1_555 A DC 17 1_555 D DG 7 1_555 -0.702 -1.622 3.141 5.345 -5.230 31.350 -2.006 2.202 3.203 -9.510 -9.718 32.208 14 AA_DA116DC117:DG107DT108_DD A 116 ? D 108 ? A 117 ? D 107 ? 1 A DC 17 1_555 D DG 7 1_555 A DA 18 1_555 D DT 6 1_555 -0.450 -0.339 3.344 3.337 9.510 42.407 -1.382 0.932 3.157 12.929 -4.537 43.535 15 AA_DC117DA118:DT106DG107_DD A 117 ? D 107 ? A 118 ? D 106 ? 1 A DA 18 1_555 D DT 6 1_555 A DT 19 1_555 D DA 5 1_555 -0.670 0.117 3.561 -3.579 -12.060 31.624 2.317 0.519 3.350 -21.113 6.267 33.975 16 AA_DA118DT119:DA105DT106_DD A 118 ? D 106 ? A 119 ? D 105 ? 1 A DT 19 1_555 D DA 5 1_555 A DC 20 1_555 D DG 4 1_555 -0.244 -1.099 2.684 4.558 -6.116 29.518 -1.055 1.237 2.782 -11.758 -8.763 30.466 17 AA_DT119DC120:DG104DA105_DD A 119 ? D 105 ? A 120 ? D 104 ? 1 A DC 20 1_555 D DG 4 1_555 A DA 21 1_555 D DT 3 1_555 0.200 0.200 2.495 2.319 -0.618 38.725 0.359 -0.085 2.499 -0.931 -3.493 38.797 18 AA_DC120DA121:DT103DG104_DD A 120 ? D 104 ? A 121 ? D 103 ? # _atom_sites.entry_id 3GBI _atom_sites.fract_transf_matrix[1][1] 0.009332 _atom_sites.fract_transf_matrix[1][2] 0.005388 _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] 0.010775 _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] 0.010736 _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_