data_5VY7 # _entry.id 5VY7 # _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 5VY7 pdb_00005vy7 10.2210/pdb5vy7/pdb WWPDB D_1000228142 ? ? # 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 2017-08-09 2 'Structure model' 1 1 2017-08-23 3 'Structure model' 1 2 2024-03-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation_author.name' 5 3 'Structure model' '_database_2.pdbx_DOI' 6 3 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5VY7 _pdbx_database_status.recvd_initial_deposition_date 2017-05-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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.content_type unspecified _pdbx_database_related.db_id 5VY6 _pdbx_database_related.db_name PDB _pdbx_database_related.details . # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Simmons, C.R.' 1 ? 'Yan, H.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'J. Am. Chem. Soc.' _citation.journal_id_ASTM JACSAT _citation.journal_id_CSD ? _citation.journal_id_ISSN 1520-5126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 139 _citation.language ? _citation.page_first 11254 _citation.page_last 11260 _citation.title 'Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacs.7b06485 _citation.pdbx_database_id_PubMed 28731332 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Simmons, C.R.' 1 ? primary 'Zhang, F.' 2 ? primary 'MacCulloch, T.' 3 ? primary 'Fahmi, N.' 4 ? primary 'Stephanopoulos, N.' 5 ? primary 'Liu, Y.' 6 ? primary 'Seeman, N.C.' 7 ? primary 'Yan, H.' 8 ? # 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*AP*CP*CP*TP*GP*AP*CP*GP*GP*AP*AP*CP*TP*CP*A)-3') ; 6466.201 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3') ; 1769.193 1 ? ? ? ? 3 polymer syn ;DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*T)-3') ; 2432.614 1 ? ? ? ? 4 polymer syn ;DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3') ; 2129.409 1 ? ? ? ? # 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 yes ;(0DG)(0DA)(0DG)(0DC)(0DA)(0DG)(0DA)(0DC)(0DC)(0DT)(0DG)(0DA)(0DC)(0DG)(0DG)(0DA) (0DA)(0DC)(0DT)(0DC)(0DA) ; GAGCAGACCTGACGGAACTCA A ? 2 polydeoxyribonucleotide no yes '(0DC)(0DC)(0DG)(0DT)(0DC)(0DA)' CCGTCA B ? 3 polydeoxyribonucleotide no yes '(0DT)(0DC)(0DT)(0DG)(0DA)(0DG)(0DT)(0DT)' TCTGAGTT C ? 4 polydeoxyribonucleotide no yes '(0DG)(0DG)(0DT)(0DC)(0DT)(0DG)(0DC)' GGTCTGC D ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 0DG n 1 2 0DA n 1 3 0DG n 1 4 0DC n 1 5 0DA n 1 6 0DG n 1 7 0DA n 1 8 0DC n 1 9 0DC n 1 10 0DT n 1 11 0DG n 1 12 0DA n 1 13 0DC n 1 14 0DG n 1 15 0DG n 1 16 0DA n 1 17 0DA n 1 18 0DC n 1 19 0DT n 1 20 0DC n 1 21 0DA n 2 1 0DC n 2 2 0DC n 2 3 0DG n 2 4 0DT n 2 5 0DC n 2 6 0DA n 3 1 0DT n 3 2 0DC n 3 3 0DT n 3 4 0DG n 3 5 0DA n 3 6 0DG n 3 7 0DT n 3 8 0DT n 4 1 0DG n 4 2 0DG n 4 3 0DT n 4 4 0DC n 4 5 0DT n 4 6 0DG n 4 7 0DC 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 1 21 'synthetic construct' ? 32630 ? 2 1 sample 1 6 'synthetic construct' ? 32630 ? 3 1 sample 1 8 'synthetic construct' ? 32630 ? 4 1 sample 1 7 'synthetic construct' ? 32630 ? # 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 0DA 'L-DNA linking' . ;2'-DEOXY-L-RIBO-FURANOSYL ADENOSINE-5'-MONOPHOSPHATE ; ? 'C10 H14 N5 O6 P' 331.222 0DC 'L-DNA linking' . ;2'-DEOXY-L-RIBO-FURANOSYL CYTOSINE-5'-MONOPHOSPHATE ; ? 'C9 H14 N3 O7 P' 307.197 0DG 'L-DNA linking' . ;2'-DEOXY-L-RIBO-FURANOSYL GUANINE-5'-MONOPHOSPHATE ; ? 'C10 H14 N5 O7 P' 347.221 0DT 'L-DNA linking' . ;2'-DEOXY-L-RIBO-FURANOSYL 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 0DG 1 1 1 0DG 0DG A . n A 1 2 0DA 2 2 2 0DA 0DA A . n A 1 3 0DG 3 3 3 0DG 0DG A . n A 1 4 0DC 4 4 4 0DC 0DC A . n A 1 5 0DA 5 5 5 0DA 0DA A . n A 1 6 0DG 6 6 6 0DG 0DG A . n A 1 7 0DA 7 7 7 0DA 0DA A . n A 1 8 0DC 8 8 8 0DC 0DC A . n A 1 9 0DC 9 9 9 0DC 0DC A . n A 1 10 0DT 10 10 10 0DT 0DT A . n A 1 11 0DG 11 11 11 0DG 0DG A . n A 1 12 0DA 12 12 12 0DA 0DA A . n A 1 13 0DC 13 13 13 0DC 0DC A . n A 1 14 0DG 14 14 14 0DG 0DG A . n A 1 15 0DG 15 15 15 0DG 0DG A . n A 1 16 0DA 16 16 16 0DA 0DA A . n A 1 17 0DA 17 17 17 0DA 0DA A . n A 1 18 0DC 18 18 18 0DC 0DC A . n A 1 19 0DT 19 19 19 0DT 0DT A . n A 1 20 0DC 20 20 20 0DC 0DC A . n A 1 21 0DA 21 21 21 0DA 0DA A . n B 2 1 0DC 1 0 0 0DC 0DC B . n B 2 2 0DC 2 1 1 0DC 0DC B . n B 2 3 0DG 3 2 2 0DG 0DG B . n B 2 4 0DT 4 3 3 0DT 0DT B . n B 2 5 0DC 5 4 4 0DC 0DC B . n B 2 6 0DA 6 5 5 0DA 0DA B . n C 3 1 0DT 1 1 1 0DT 0DT C . n C 3 2 0DC 2 2 2 0DC 0DC C . n C 3 3 0DT 3 3 3 0DT 0DT C . n C 3 4 0DG 4 4 4 0DG 0DG C . n C 3 5 0DA 5 5 5 0DA 0DA C . n C 3 6 0DG 6 6 6 0DG 0DG C . n C 3 7 0DT 7 7 7 0DT 0DT C . n C 3 8 0DT 8 8 8 0DT 0DT C . n D 4 1 0DG 1 10 10 0DG 0DG D . n D 4 2 0DG 2 11 11 0DG 0DG D . n D 4 3 0DT 3 12 12 0DT 0DT D . n D 4 4 0DC 4 13 13 0DC 0DC D . n D 4 5 0DT 5 14 14 0DT 0DT D . n D 4 6 0DG 6 15 15 0DG 0DG D . n D 4 7 0DC 7 16 16 0DC 0DC D . n # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A 0DG 1 ? "O5'" ? A 0DG 1 "O5'" 2 1 Y 1 A 0DG 1 ? "C5'" ? A 0DG 1 "C5'" 3 1 Y 1 C 0DT 1 ? "O5'" ? C 0DT 1 "O5'" 4 1 Y 1 C 0DT 1 ? "C5'" ? C 0DT 1 "C5'" # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.11.1_2575 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _cell.entry_id 5VY7 _cell.length_a 68.584 _cell.length_b 68.584 _cell.length_c 55.737 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VY7 _symmetry.space_group_name_H-M 'P 31' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5VY7 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 5.91 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 79.20 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '50 mM cacodylate pH 6.5, 50 mM MgCl2, 2.0 mM cobalt(III)hexamine, and 1.5 M lithium sulfate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-01-13 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.0 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 5VY7 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 34.292 _reflns.d_resolution_high 3.000 _reflns.number_obs 4949 _reflns.number_all ? _reflns.percent_possible_obs 86.1 _reflns.pdbx_Rmerge_I_obs 0.11 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 23.9000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 10.70 _reflns.pdbx_CC_half ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _reflns_shell.d_res_high 3.0 _reflns_shell.d_res_low 3.05 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.6 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 53.7 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.467 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 9.5 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5VY7 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 4949 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.010 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 34.29 _refine.ls_d_res_high 3.00 _refine.ls_percent_reflns_obs 84.2 _refine.ls_R_factor_obs 0.238 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.238 _refine.ls_R_factor_R_free 0.246 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.230 _refine.ls_number_reflns_R_free 259 _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] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.250 _refine.pdbx_overall_phase_error 37.700 _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_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 851 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 851 _refine_hist.d_res_high 3.00 _refine_hist.d_res_low 34.29 # 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 ? ? 952 'X-RAY DIFFRACTION' ? f_angle_d 1.332 ? ? 1461 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 39.865 ? ? 400 'X-RAY DIFFRACTION' ? f_chiral_restr 4.408 ? ? 164 'X-RAY DIFFRACTION' ? f_plane_restr 0.007 ? ? 42 '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.R_factor_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 3.0004 3.7794 1948 0.2701 70.00 0.2491 . . 116 . . . . 'X-RAY DIFFRACTION' . 3.7794 34.0000 2742 0.2291 99.00 0.2447 . . 143 . . . . # _struct.entry_id 5VY7 _struct.title 'A self-assembling L-form DNA crystal lattice' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 5VY7 _struct_keywords.text 'DNA nanotechnology, self-assembly, DNA structure, DNA' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 5VY7 5VY7 ? 1 ? 1 2 PDB 5VY7 5VY7 ? 2 ? 1 3 PDB 5VY7 5VY7 ? 3 ? 1 4 PDB 5VY7 5VY7 ? 4 ? 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 5VY7 A 1 ? 21 ? 5VY7 1 ? 21 ? 1 21 2 2 5VY7 B 1 ? 6 ? 5VY7 0 ? 5 ? 0 5 3 3 5VY7 C 1 ? 8 ? 5VY7 1 ? 8 ? 1 8 4 4 5VY7 D 1 ? 7 ? 5VY7 10 ? 16 ? 10 16 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # 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 ? A 0DG 1 "O3'" ? ? ? 1_555 A 0DA 2 P ? ? A 0DG 1 A 0DA 2 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale2 covale both ? A 0DA 2 "O3'" ? ? ? 1_555 A 0DG 3 P ? ? A 0DA 2 A 0DG 3 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale3 covale both ? A 0DG 3 "O3'" ? ? ? 1_555 A 0DC 4 P ? ? A 0DG 3 A 0DC 4 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? A 0DC 4 "O3'" ? ? ? 1_555 A 0DA 5 P ? ? A 0DC 4 A 0DA 5 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale5 covale both ? A 0DA 5 "O3'" ? ? ? 1_555 A 0DG 6 P ? ? A 0DA 5 A 0DG 6 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale6 covale both ? A 0DG 6 "O3'" ? ? ? 1_555 A 0DA 7 P ? ? A 0DG 6 A 0DA 7 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale7 covale both ? A 0DA 7 "O3'" ? ? ? 1_555 A 0DC 8 P ? ? A 0DA 7 A 0DC 8 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale8 covale both ? A 0DC 8 "O3'" ? ? ? 1_555 A 0DC 9 P ? ? A 0DC 8 A 0DC 9 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale9 covale both ? A 0DC 9 "O3'" ? ? ? 1_555 A 0DT 10 P ? ? A 0DC 9 A 0DT 10 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale10 covale both ? A 0DT 10 "O3'" ? ? ? 1_555 A 0DG 11 P ? ? A 0DT 10 A 0DG 11 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale11 covale both ? A 0DG 11 "O3'" ? ? ? 1_555 A 0DA 12 P ? ? A 0DG 11 A 0DA 12 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale12 covale both ? A 0DA 12 "O3'" ? ? ? 1_555 A 0DC 13 P ? ? A 0DA 12 A 0DC 13 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale13 covale both ? A 0DC 13 "O3'" ? ? ? 1_555 A 0DG 14 P ? ? A 0DC 13 A 0DG 14 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale14 covale both ? A 0DG 14 "O3'" ? ? ? 1_555 A 0DG 15 P ? ? A 0DG 14 A 0DG 15 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale15 covale both ? A 0DG 15 "O3'" ? ? ? 1_555 A 0DA 16 P ? ? A 0DG 15 A 0DA 16 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale16 covale both ? A 0DA 16 "O3'" ? ? ? 1_555 A 0DA 17 P ? ? A 0DA 16 A 0DA 17 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale17 covale both ? A 0DA 17 "O3'" ? ? ? 1_555 A 0DC 18 P ? ? A 0DA 17 A 0DC 18 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale18 covale both ? A 0DC 18 "O3'" ? ? ? 1_555 A 0DT 19 P ? ? A 0DC 18 A 0DT 19 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale19 covale both ? A 0DT 19 "O3'" ? ? ? 1_555 A 0DC 20 P ? ? A 0DT 19 A 0DC 20 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale20 covale both ? A 0DC 20 "O3'" ? ? ? 1_555 A 0DA 21 P ? ? A 0DC 20 A 0DA 21 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale21 covale both ? B 0DC 1 "O3'" ? ? ? 1_555 B 0DC 2 P ? ? B 0DC 0 B 0DC 1 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale22 covale both ? B 0DC 2 "O3'" ? ? ? 1_555 B 0DG 3 P ? ? B 0DC 1 B 0DG 2 1_555 ? ? ? ? ? ? ? 1.589 ? ? covale23 covale both ? B 0DG 3 "O3'" ? ? ? 1_555 B 0DT 4 P ? ? B 0DG 2 B 0DT 3 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale24 covale both ? B 0DT 4 "O3'" ? ? ? 1_555 B 0DC 5 P ? ? B 0DT 3 B 0DC 4 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale25 covale both ? B 0DC 5 "O3'" ? ? ? 1_555 B 0DA 6 P ? ? B 0DC 4 B 0DA 5 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale26 covale both ? C 0DT 1 "O3'" ? ? ? 1_555 C 0DC 2 P ? ? C 0DT 1 C 0DC 2 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale27 covale both ? C 0DC 2 "O3'" ? ? ? 1_555 C 0DT 3 P ? ? C 0DC 2 C 0DT 3 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale28 covale both ? C 0DT 3 "O3'" ? ? ? 1_555 C 0DG 4 P ? ? C 0DT 3 C 0DG 4 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale29 covale both ? C 0DG 4 "O3'" ? ? ? 1_555 C 0DA 5 P ? ? C 0DG 4 C 0DA 5 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale30 covale both ? C 0DA 5 "O3'" ? ? ? 1_555 C 0DG 6 P ? ? C 0DA 5 C 0DG 6 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale31 covale both ? C 0DG 6 "O3'" ? ? ? 1_555 C 0DT 7 P ? ? C 0DG 6 C 0DT 7 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale32 covale both ? C 0DT 7 "O3'" ? ? ? 1_555 C 0DT 8 P ? ? C 0DT 7 C 0DT 8 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale33 covale both ? D 0DG 1 "O3'" ? ? ? 1_555 D 0DG 2 P ? ? D 0DG 10 D 0DG 11 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale34 covale both ? D 0DG 2 "O3'" ? ? ? 1_555 D 0DT 3 P ? ? D 0DG 11 D 0DT 12 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale35 covale both ? D 0DT 3 "O3'" ? ? ? 1_555 D 0DC 4 P ? ? D 0DT 12 D 0DC 13 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale36 covale both ? D 0DC 4 "O3'" ? ? ? 1_555 D 0DT 5 P ? ? D 0DC 13 D 0DT 14 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale37 covale both ? D 0DT 5 "O3'" ? ? ? 1_555 D 0DG 6 P ? ? D 0DT 14 D 0DG 15 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale38 covale both ? D 0DG 6 "O3'" ? ? ? 1_555 D 0DC 7 P ? ? D 0DG 15 D 0DC 16 1_555 ? ? ? ? ? ? ? 1.619 ? ? hydrog1 hydrog ? ? A 0DG 3 N1 ? ? ? 1_555 D 0DC 7 N3 ? ? A 0DG 3 D 0DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A 0DG 3 N2 ? ? ? 1_555 D 0DC 7 O2 ? ? A 0DG 3 D 0DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A 0DG 3 O6 ? ? ? 1_555 D 0DC 7 N4 ? ? A 0DG 3 D 0DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A 0DC 4 N3 ? ? ? 1_555 D 0DG 6 N1 ? ? A 0DC 4 D 0DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A 0DC 4 N4 ? ? ? 1_555 D 0DG 6 O6 ? ? A 0DC 4 D 0DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A 0DC 4 O2 ? ? ? 1_555 D 0DG 6 N2 ? ? A 0DC 4 D 0DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A 0DG 6 N1 ? ? ? 1_555 D 0DC 4 O2 ? ? A 0DG 6 D 0DC 13 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog8 hydrog ? ? A 0DG 6 N2 ? ? ? 1_555 D 0DC 4 N3 ? ? A 0DG 6 D 0DC 13 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog9 hydrog ? ? A 0DC 8 N3 ? ? ? 1_555 D 0DG 2 N1 ? ? A 0DC 8 D 0DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 0DC 8 N4 ? ? ? 1_555 D 0DG 2 O6 ? ? A 0DC 8 D 0DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A 0DC 8 O2 ? ? ? 1_555 D 0DG 2 N2 ? ? A 0DC 8 D 0DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A 0DC 9 N3 ? ? ? 1_555 D 0DG 1 N1 ? ? A 0DC 9 D 0DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A 0DC 9 N4 ? ? ? 1_555 D 0DG 1 O6 ? ? A 0DC 9 D 0DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 0DC 9 O2 ? ? ? 1_555 D 0DG 1 N2 ? ? A 0DC 9 D 0DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 0DG 11 N1 ? ? ? 1_555 B 0DC 5 N3 ? ? A 0DG 11 B 0DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A 0DG 11 N2 ? ? ? 1_555 B 0DC 5 O2 ? ? A 0DG 11 B 0DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A 0DG 11 O6 ? ? ? 1_555 B 0DC 5 N4 ? ? A 0DG 11 B 0DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A 0DC 13 N3 ? ? ? 1_555 B 0DG 3 N1 ? ? A 0DC 13 B 0DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A 0DC 13 N4 ? ? ? 1_555 B 0DG 3 O6 ? ? A 0DC 13 B 0DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A 0DC 13 O2 ? ? ? 1_555 B 0DG 3 N2 ? ? A 0DC 13 B 0DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A 0DG 14 N1 ? ? ? 1_555 B 0DC 2 N3 ? ? A 0DG 14 B 0DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A 0DG 14 N2 ? ? ? 1_555 B 0DC 2 O2 ? ? A 0DG 14 B 0DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A 0DG 14 O6 ? ? ? 1_555 B 0DC 2 N4 ? ? A 0DG 14 B 0DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A 0DG 15 N1 ? ? ? 1_555 B 0DC 1 O2 ? ? A 0DG 15 B 0DC 0 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog25 hydrog ? ? A 0DG 15 N2 ? ? ? 1_555 B 0DC 1 N3 ? ? A 0DG 15 B 0DC 0 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog26 hydrog ? ? A 0DC 18 N3 ? ? ? 1_555 C 0DG 6 N1 ? ? A 0DC 18 C 0DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A 0DC 18 N4 ? ? ? 1_555 C 0DG 6 O6 ? ? A 0DC 18 C 0DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A 0DC 18 O2 ? ? ? 1_555 C 0DG 6 N2 ? ? A 0DC 18 C 0DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A 0DC 20 N3 ? ? ? 1_555 C 0DG 4 N1 ? ? A 0DC 20 C 0DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A 0DC 20 N4 ? ? ? 1_555 C 0DG 4 O6 ? ? A 0DC 20 C 0DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A 0DC 20 O2 ? ? ? 1_555 C 0DG 4 N2 ? ? A 0DC 20 C 0DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O6 A 0DG 6 ? ? N4 D 0DC 13 ? ? 2.17 2 1 N2 A 0DG 15 ? ? O2 B 0DC 0 ? ? 2.17 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 OP2 B 0DC 0 ? ? 1_555 "O3'" B 0DA 5 ? ? 3_654 1.54 2 1 "C3'" C 0DT 8 ? ? 1_555 OP2 D 0DG 10 ? ? 3_654 1.83 3 1 "C4'" C 0DT 8 ? ? 1_555 OP2 D 0DG 10 ? ? 3_654 1.93 4 1 "O3'" C 0DT 8 ? ? 1_555 OP2 D 0DG 10 ? ? 3_654 1.94 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" B 0DC 1 ? ? "C3'" B 0DC 1 ? ? 1.379 1.419 -0.040 0.006 N 2 1 "O5'" B 0DG 2 ? ? "C5'" B 0DG 2 ? ? 1.208 1.418 -0.210 0.025 N 3 1 "O5'" C 0DA 5 ? ? "C5'" C 0DA 5 ? ? 1.568 1.440 0.128 0.016 N 4 1 "O5'" D 0DG 15 ? ? "C5'" D 0DG 15 ? ? 1.552 1.440 0.112 0.016 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 "O5'" B 0DC 0 ? ? P B 0DC 0 ? ? OP1 B 0DC 0 ? ? 96.63 105.70 -9.07 0.90 N 2 1 "O4'" B 0DC 0 ? ? "C4'" B 0DC 0 ? ? "C3'" B 0DC 0 ? ? 101.19 104.50 -3.31 0.40 N 3 1 "C1'" B 0DC 0 ? ? "O4'" B 0DC 0 ? ? "C4'" B 0DC 0 ? ? 103.33 110.10 -6.77 1.00 N 4 1 "O4'" B 0DC 0 ? ? "C1'" B 0DC 0 ? ? N1 B 0DC 0 ? ? 111.62 108.30 3.32 0.30 N 5 1 "O5'" B 0DC 1 ? ? "C5'" B 0DC 1 ? ? "C4'" B 0DC 1 ? ? 103.11 109.40 -6.29 0.80 N 6 1 "O4'" B 0DC 1 ? ? "C4'" B 0DC 1 ? ? "C3'" B 0DC 1 ? ? 101.73 104.50 -2.77 0.40 N 7 1 "O5'" B 0DG 2 ? ? "C5'" B 0DG 2 ? ? "C4'" B 0DG 2 ? ? 102.78 109.40 -6.62 0.80 N 8 1 P D 0DT 12 ? ? "O5'" D 0DT 12 ? ? "C5'" D 0DT 12 ? ? 108.15 120.90 -12.75 1.60 N # 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 0DA C8A C Y N 1 0DA N9A N Y N 2 0DA C4A C Y N 3 0DA C5A C Y N 4 0DA N7A N Y N 5 0DA N3A N Y N 6 0DA C2A C Y N 7 0DA N1A N Y N 8 0DA C6A C Y N 9 0DA N6A N N N 10 0DA "C4'" C N S 11 0DA "O4'" O N N 12 0DA "C3'" C N R 13 0DA "C2'" C N N 14 0DA "C1'" C N S 15 0DA "O3'" O N N 16 0DA "C5'" C N N 17 0DA "O5'" O N N 18 0DA P P N N 19 0DA OP2 O N N 20 0DA OP3 O N N 21 0DA OP1 O N N 22 0DA H8A H N N 23 0DA H2A H N N 24 0DA HN61 H N N 25 0DA HN62 H N N 26 0DA "H4'" H N N 27 0DA "H3'" H N N 28 0DA "H2'" H N N 29 0DA "H2''" H N N 30 0DA "H1'" H N N 31 0DA "HO3'" H N N 32 0DA "H5'" H N N 33 0DA "H5''" H N N 34 0DA H2P H N N 35 0DA HOP3 H N N 36 0DC OP3 O N N 37 0DC P P N N 38 0DC OP1 O N N 39 0DC OP2 O N N 40 0DC "O5'" O N N 41 0DC "C5'" C N N 42 0DC "C4'" C N S 43 0DC "O4'" O N N 44 0DC "C3'" C N R 45 0DC "O3'" O N N 46 0DC "C2'" C N N 47 0DC "C1'" C N S 48 0DC N1 N N N 49 0DC C2 C N N 50 0DC O2 O N N 51 0DC N3 N N N 52 0DC C4 C N N 53 0DC N4 N N N 54 0DC C5 C N N 55 0DC C6 C N N 56 0DC HOP3 H N N 57 0DC HOP2 H N N 58 0DC "H5'" H N N 59 0DC "H5''" H N N 60 0DC "H4'" H N N 61 0DC "H3'" H N N 62 0DC "HO3'" H N N 63 0DC "H2'" H N N 64 0DC "H2''" H N N 65 0DC "H1'" H N N 66 0DC H41 H N N 67 0DC H42 H N N 68 0DC H5 H N N 69 0DC H6 H N N 70 0DG OP3 O N N 71 0DG P P N N 72 0DG OP1 O N N 73 0DG OP2 O N N 74 0DG "O5'" O N N 75 0DG "C5'" C N N 76 0DG "C4'" C N S 77 0DG "O4'" O N N 78 0DG "C3'" C N R 79 0DG "O3'" O N N 80 0DG "C2'" C N N 81 0DG "C1'" C N S 82 0DG N9 N Y N 83 0DG C8 C Y N 84 0DG N7 N Y N 85 0DG C5 C Y N 86 0DG C6 C N N 87 0DG O6 O N N 88 0DG N1 N N N 89 0DG C2 C N N 90 0DG N2 N N N 91 0DG N3 N N N 92 0DG C4 C Y N 93 0DG HOP3 H N N 94 0DG HOP2 H N N 95 0DG "H5'" H N N 96 0DG "H5''" H N N 97 0DG "H4'" H N N 98 0DG "H3'" H N N 99 0DG "HO3'" H N N 100 0DG "H2'" H N N 101 0DG "H2''" H N N 102 0DG "H1'" H N N 103 0DG H8 H N N 104 0DG H1 H N N 105 0DG H21 H N N 106 0DG H22 H N N 107 0DT OP3 O N N 108 0DT P P N N 109 0DT OP1 O N N 110 0DT OP2 O N N 111 0DT "O5'" O N N 112 0DT "C5'" C N N 113 0DT "C4'" C N S 114 0DT "O4'" O N N 115 0DT "C3'" C N R 116 0DT "O3'" O N N 117 0DT "C2'" C N N 118 0DT "C1'" C N S 119 0DT N1 N N N 120 0DT C2 C N N 121 0DT O2 O N N 122 0DT N3 N N N 123 0DT C4 C N N 124 0DT O4 O N N 125 0DT C5 C N N 126 0DT C5M C N N 127 0DT C6 C N N 128 0DT HOP3 H N N 129 0DT HOP2 H N N 130 0DT "H5'" H N N 131 0DT "H5''" H N N 132 0DT "H4'" H N N 133 0DT "H3'" H N N 134 0DT "HO3'" H N N 135 0DT "H2'" H N N 136 0DT "H2''" H N N 137 0DT "H1'" H N N 138 0DT H3 H N N 139 0DT H71 H N N 140 0DT H72 H N N 141 0DT H73 H N N 142 0DT 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 0DA C8A N9A sing Y N 1 0DA C8A N7A doub Y N 2 0DA N9A C4A sing Y N 3 0DA N9A "C1'" sing N N 4 0DA C4A C5A doub Y N 5 0DA C4A N3A sing Y N 6 0DA C5A N7A sing Y N 7 0DA C5A C6A sing Y N 8 0DA N3A C2A doub Y N 9 0DA C2A N1A sing Y N 10 0DA N1A C6A doub Y N 11 0DA C6A N6A sing N N 12 0DA "C4'" "O4'" sing N N 13 0DA "C4'" "C3'" sing N N 14 0DA "O4'" "C1'" sing N N 15 0DA "C3'" "C2'" sing N N 16 0DA "C2'" "C1'" sing N N 17 0DA "C3'" "O3'" sing N N 18 0DA "C4'" "C5'" sing N N 19 0DA "C5'" "O5'" sing N N 20 0DA "O5'" P sing N N 21 0DA P OP2 sing N N 22 0DA P OP3 sing N N 23 0DA P OP1 doub N N 24 0DA C8A H8A sing N N 25 0DA C2A H2A sing N N 26 0DA N6A HN61 sing N N 27 0DA N6A HN62 sing N N 28 0DA "C4'" "H4'" sing N N 29 0DA "C3'" "H3'" sing N N 30 0DA "C2'" "H2'" sing N N 31 0DA "C2'" "H2''" sing N N 32 0DA "C1'" "H1'" sing N N 33 0DA "O3'" "HO3'" sing N N 34 0DA "C5'" "H5'" sing N N 35 0DA "C5'" "H5''" sing N N 36 0DA OP2 H2P sing N N 37 0DA OP3 HOP3 sing N N 38 0DC OP3 P sing N N 39 0DC OP3 HOP3 sing N N 40 0DC P OP1 doub N N 41 0DC P OP2 sing N N 42 0DC P "O5'" sing N N 43 0DC OP2 HOP2 sing N N 44 0DC "O5'" "C5'" sing N N 45 0DC "C5'" "C4'" sing N N 46 0DC "C5'" "H5'" sing N N 47 0DC "C5'" "H5''" sing N N 48 0DC "C4'" "O4'" sing N N 49 0DC "C4'" "C3'" sing N N 50 0DC "C4'" "H4'" sing N N 51 0DC "O4'" "C1'" sing N N 52 0DC "C3'" "O3'" sing N N 53 0DC "C3'" "C2'" sing N N 54 0DC "C3'" "H3'" sing N N 55 0DC "O3'" "HO3'" sing N N 56 0DC "C2'" "C1'" sing N N 57 0DC "C2'" "H2'" sing N N 58 0DC "C2'" "H2''" sing N N 59 0DC "C1'" N1 sing N N 60 0DC "C1'" "H1'" sing N N 61 0DC N1 C2 sing N N 62 0DC N1 C6 sing N N 63 0DC C2 O2 doub N N 64 0DC C2 N3 sing N N 65 0DC N3 C4 doub N N 66 0DC C4 N4 sing N N 67 0DC C4 C5 sing N N 68 0DC N4 H41 sing N N 69 0DC N4 H42 sing N N 70 0DC C5 C6 doub N N 71 0DC C5 H5 sing N N 72 0DC C6 H6 sing N N 73 0DG OP3 P sing N N 74 0DG OP3 HOP3 sing N N 75 0DG P OP1 doub N N 76 0DG P OP2 sing N N 77 0DG P "O5'" sing N N 78 0DG OP2 HOP2 sing N N 79 0DG "O5'" "C5'" sing N N 80 0DG "C5'" "C4'" sing N N 81 0DG "C5'" "H5'" sing N N 82 0DG "C5'" "H5''" sing N N 83 0DG "C4'" "O4'" sing N N 84 0DG "C4'" "C3'" sing N N 85 0DG "C4'" "H4'" sing N N 86 0DG "O4'" "C1'" sing N N 87 0DG "C3'" "O3'" sing N N 88 0DG "C3'" "C2'" sing N N 89 0DG "C3'" "H3'" sing N N 90 0DG "O3'" "HO3'" sing N N 91 0DG "C2'" "C1'" sing N N 92 0DG "C2'" "H2'" sing N N 93 0DG "C2'" "H2''" sing N N 94 0DG "C1'" N9 sing N N 95 0DG "C1'" "H1'" sing N N 96 0DG N9 C8 sing Y N 97 0DG N9 C4 sing Y N 98 0DG C8 N7 doub Y N 99 0DG C8 H8 sing N N 100 0DG N7 C5 sing Y N 101 0DG C5 C6 sing N N 102 0DG C5 C4 doub Y N 103 0DG C6 O6 doub N N 104 0DG C6 N1 sing N N 105 0DG N1 C2 sing N N 106 0DG N1 H1 sing N N 107 0DG C2 N2 sing N N 108 0DG C2 N3 doub N N 109 0DG N2 H21 sing N N 110 0DG N2 H22 sing N N 111 0DG N3 C4 sing N N 112 0DT OP3 P sing N N 113 0DT OP3 HOP3 sing N N 114 0DT P OP1 doub N N 115 0DT P OP2 sing N N 116 0DT P "O5'" sing N N 117 0DT OP2 HOP2 sing N N 118 0DT "O5'" "C5'" sing N N 119 0DT "C5'" "C4'" sing N N 120 0DT "C5'" "H5'" sing N N 121 0DT "C5'" "H5''" sing N N 122 0DT "C4'" "O4'" sing N N 123 0DT "C4'" "C3'" sing N N 124 0DT "C4'" "H4'" sing N N 125 0DT "O4'" "C1'" sing N N 126 0DT "C3'" "O3'" sing N N 127 0DT "C3'" "C2'" sing N N 128 0DT "C3'" "H3'" sing N N 129 0DT "O3'" "HO3'" sing N N 130 0DT "C2'" "C1'" sing N N 131 0DT "C2'" "H2'" sing N N 132 0DT "C2'" "H2''" sing N N 133 0DT "C1'" N1 sing N N 134 0DT "C1'" "H1'" sing N N 135 0DT N1 C2 sing N N 136 0DT N1 C6 sing N N 137 0DT C2 O2 doub N N 138 0DT C2 N3 sing N N 139 0DT N3 C4 sing N N 140 0DT N3 H3 sing N N 141 0DT C4 O4 doub N N 142 0DT C4 C5 sing N N 143 0DT C5 C5M sing N N 144 0DT C5 C6 doub N N 145 0DT C5M H71 sing N N 146 0DT C5M H72 sing N N 147 0DT C5M H73 sing N N 148 0DT C6 H6 sing N N 149 # _ndb_struct_conf_na.entry_id 5VY7 _ndb_struct_conf_na.feature 'z-form double helix' # 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 0DG 3 1_555 D 0DC 7 1_555 -1.273 -0.067 0.754 -0.648 11.126 3.522 1 A_0DG3:0DC16_D A 3 ? D 16 ? 19 1 1 A 0DC 4 1_555 D 0DG 6 1_555 1.004 0.107 0.458 -6.496 3.208 -2.057 2 A_0DC4:0DG15_D A 4 ? D 15 ? 19 1 1 A 0DG 6 1_555 D 0DC 4 1_555 -0.276 -0.486 0.214 -2.931 3.570 11.490 3 A_0DG6:0DC13_D A 6 ? D 13 ? 22 1 1 A 0DC 8 1_555 D 0DG 2 1_555 -0.654 -0.604 -0.315 12.262 -0.291 4.843 4 A_0DC8:0DG11_D A 8 ? D 11 ? 19 1 1 A 0DC 9 1_555 D 0DG 1 1_555 0.283 -0.503 0.038 7.740 4.299 0.949 5 A_0DC9:0DG10_D A 9 ? D 10 ? 19 1 1 A 0DG 11 1_555 B 0DC 5 1_555 -0.520 0.185 0.452 12.098 -1.579 -3.854 6 A_0DG11:0DC4_B A 11 ? B 4 ? 19 1 1 A 0DC 13 1_555 B 0DG 3 1_555 -0.138 -0.516 0.648 0.293 2.703 9.166 7 A_0DC13:0DG2_B A 13 ? B 2 ? 19 1 1 A 0DG 14 1_555 B 0DC 2 1_555 -0.341 -0.434 0.573 5.456 21.989 12.223 8 A_0DG14:0DC1_B A 14 ? B 1 ? 19 1 1 A 0DG 15 1_555 B 0DC 1 1_555 -0.091 -0.296 -0.065 -5.457 7.564 -9.130 9 A_0DG15:0DC0_B A 15 ? B 0 ? 22 1 1 A 0DC 18 1_555 C 0DG 6 1_555 0.722 -0.492 0.159 -3.326 -3.747 0.012 10 A_0DC18:0DG6_C A 18 ? C 6 ? 19 1 1 A 0DC 20 1_555 C 0DG 4 1_555 -0.197 -0.423 -0.145 -10.998 -4.410 6.541 11 A_0DC20:0DG4_C A 20 ? C 4 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A 0DG 3 1_555 D 0DC 7 1_555 A 0DC 4 1_555 D 0DG 6 1_555 -0.697 -0.929 3.320 4.704 -2.889 -26.432 2.742 -0.271 3.274 6.233 10.147 -26.992 1 AA_0DG30DC4:0DG150DC16_DD A 3 ? D 16 ? A 4 ? D 15 ? 1 A 0DC 4 1_555 D 0DG 6 1_555 A 0DG 6 1_555 D 0DC 4 1_555 -0.285 -0.225 6.747 1.607 0.801 -67.751 0.139 -0.129 6.754 -0.718 1.441 -67.772 2 AA_0DC40DG6:0DC130DG15_DD A 4 ? D 15 ? A 6 ? D 13 ? 1 A 0DG 6 1_555 D 0DC 4 1_555 A 0DC 8 1_555 D 0DG 2 1_555 -1.051 -2.016 5.820 1.148 -10.007 -73.318 2.229 -0.811 5.559 8.342 0.957 -73.911 3 AA_0DG60DC8:0DG110DC13_DD A 6 ? D 13 ? A 8 ? D 11 ? 1 A 0DC 8 1_555 D 0DG 2 1_555 A 0DC 9 1_555 D 0DG 1 1_555 0.254 -2.012 3.632 -5.120 3.021 -31.010 3.056 -0.623 3.798 -5.585 -9.467 -31.561 4 AA_0DC80DC9:0DG100DG11_DD A 8 ? D 11 ? A 9 ? D 10 ? 1 A 0DC 9 1_555 D 0DG 1 1_555 A 0DG 11 1_555 B 0DC 5 1_555 1.435 -0.850 6.867 -1.550 -1.141 -55.571 1.050 1.349 6.884 1.223 -1.662 -55.601 5 AA_0DC90DG11:0DC40DG10_BD A 9 ? D 10 ? A 11 ? B 4 ? 1 A 0DG 11 1_555 B 0DC 5 1_555 A 0DC 13 1_555 B 0DG 3 1_555 -0.409 -1.005 6.649 0.450 -10.791 -74.310 1.492 -0.308 6.477 8.888 0.370 -74.978 6 AA_0DG110DC13:0DG20DC4_BB A 11 ? B 4 ? A 13 ? B 2 ? 1 A 0DC 13 1_555 B 0DG 3 1_555 A 0DG 14 1_555 B 0DC 2 1_555 0.593 -0.387 3.215 -1.336 -5.837 -30.521 1.813 0.856 3.112 10.955 -2.507 -31.089 7 AA_0DC130DG14:0DC10DG2_BB A 13 ? B 2 ? A 14 ? B 1 ? 1 A 0DG 14 1_555 B 0DC 2 1_555 A 0DG 15 1_555 B 0DC 1 1_555 -0.699 -0.009 3.791 -2.683 -0.574 -34.946 0.113 -1.625 3.728 0.954 -4.459 -35.050 8 AA_0DG140DG15:0DC00DC1_BB A 14 ? B 1 ? A 15 ? B 0 ? 1 A 0DC 18 1_555 C 0DG 6 1_555 A 0DC 20 1_555 C 0DG 4 1_555 0.368 0.902 7.028 7.065 -2.114 -80.752 -0.577 0.674 7.001 1.628 5.443 -81.031 9 AA_0DC180DC20:0DG40DG6_CC A 18 ? C 6 ? A 20 ? C 4 ? # _atom_sites.entry_id 5VY7 _atom_sites.fract_transf_matrix[1][1] 0.014581 _atom_sites.fract_transf_matrix[1][2] 0.008418 _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] 0.016836 _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] 0.017941 _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_