data_1ZF9 # _entry.id 1ZF9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 1ZF9 pdb_00001zf9 10.2210/pdb1zf9/pdb NDB AD0051 ? ? RCSB RCSB032652 ? ? WWPDB D_1000032652 ? ? # 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 2005-05-10 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-11 5 'Structure model' 1 4 2024-02-14 6 'Structure model' 1 5 2024-04-03 # _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' 'Version format compliance' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_struct_conn_angle 6 5 'Structure model' struct_conn 7 5 'Structure model' struct_site 8 6 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.value' 17 5 'Structure model' '_struct_conn.pdbx_dist_value' 18 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 19 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 26 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 32 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 33 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 34 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 1ZF9 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2005-04-20 _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_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1P4Y . unspecified PDB 1P4Z . unspecified PDB 1DCW . unspecified PDB 1DCV . unspecified PDB 1ZEW . unspecified PDB 1ZEX . unspecified PDB 1ZEY . unspecified PDB 1ZEZ . unspecified PDB 1ZF0 . unspecified PDB 1ZF1 . unspecified PDB 1ZF2 . unspecified PDB 1ZF3 . unspecified PDB 1ZF4 . unspecified PDB 1ZF5 . unspecified PDB 1ZF6 . unspecified PDB 1ZF7 . unspecified PDB 1ZF8 . unspecified PDB 1ZFA . unspecified PDB 1ZFB . unspecified PDB 1ZFC . unspecified PDB 1ZFE . unspecified PDB 1ZFF . unspecified PDB 1ZFG . unspecified PDB 1ZFH . unspecified PDB 1ZFM . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hays, F.A.' 1 'Teegarden, A.T.' 2 'Jones, Z.J.R.' 3 'Harms, M.' 4 'Raup, D.' 5 'Watson, J.' 6 'Cavaliere, E.' 7 'Ho, P.S.' 8 # _citation.id primary _citation.title 'How sequence defines structure: a crystallographic map of DNA structure and conformation.' _citation.journal_abbrev Proc.Natl.Acad.Sci.Usa _citation.journal_volume 102 _citation.page_first 7157 _citation.page_last 7162 _citation.year 2005 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15870206 _citation.pdbx_database_id_DOI 10.1073/pnas.0409455102 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hays, F.A.' 1 ? primary 'Teegarden, A.' 2 ? primary 'Jones, Z.J.' 3 ? primary 'Harms, M.' 4 ? primary 'Raup, D.' 5 ? primary 'Watson, J.' 6 ? primary 'Cavaliere, E.' 7 ? primary 'Ho, P.S.' 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 "5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'" 3046.980 2 ? ? ? ? 2 non-polymer syn 'SODIUM ION' 22.990 2 ? ? ? ? 3 water nat water 18.015 94 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DC)(DC)(DC)(DC)(DG)(DG)(DG)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCCCCGGGGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SODIUM ION' NA 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DC n 1 4 DC n 1 5 DC n 1 6 DG n 1 7 DG n 1 8 DG n 1 9 DG n 1 10 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details ;DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. ; # 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # 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 DC 1 1 1 DC C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DC 1 11 11 DC C B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DC 3 13 13 DC C B . n B 1 4 DC 4 14 14 DC C B . n B 1 5 DC 5 15 15 DC C B . n B 1 6 DG 6 16 16 DG G B . n B 1 7 DG 7 17 17 DG G B . n B 1 8 DG 8 18 18 DG G B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DG 10 20 20 DG G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 NA 1 64 64 NA NA A . D 2 NA 1 35 35 NA NA B . E 3 HOH 1 21 21 HOH HOH A . E 3 HOH 2 22 22 HOH HOH A . E 3 HOH 3 23 23 HOH HOH A . E 3 HOH 4 25 25 HOH HOH A . E 3 HOH 5 26 26 HOH HOH A . E 3 HOH 6 30 30 HOH HOH A . E 3 HOH 7 31 31 HOH HOH A . E 3 HOH 8 32 32 HOH HOH A . E 3 HOH 9 34 34 HOH HOH A . E 3 HOH 10 36 36 HOH HOH A . E 3 HOH 11 39 39 HOH HOH A . E 3 HOH 12 40 40 HOH HOH A . E 3 HOH 13 41 41 HOH HOH A . E 3 HOH 14 42 42 HOH HOH A . E 3 HOH 15 43 43 HOH HOH A . E 3 HOH 16 44 44 HOH HOH A . E 3 HOH 17 48 48 HOH HOH A . E 3 HOH 18 50 50 HOH HOH A . E 3 HOH 19 51 51 HOH HOH A . E 3 HOH 20 54 54 HOH HOH A . E 3 HOH 21 55 55 HOH HOH A . E 3 HOH 22 58 58 HOH HOH A . E 3 HOH 23 59 59 HOH HOH A . E 3 HOH 24 60 60 HOH HOH A . E 3 HOH 25 63 63 HOH HOH A . E 3 HOH 26 65 65 HOH HOH A . E 3 HOH 27 68 68 HOH HOH A . E 3 HOH 28 71 71 HOH HOH A . E 3 HOH 29 72 72 HOH HOH A . E 3 HOH 30 79 79 HOH HOH A . E 3 HOH 31 83 83 HOH HOH A . E 3 HOH 32 84 84 HOH HOH A . E 3 HOH 33 87 87 HOH HOH A . E 3 HOH 34 88 88 HOH HOH A . E 3 HOH 35 89 89 HOH HOH A . E 3 HOH 36 91 91 HOH HOH A . E 3 HOH 37 97 97 HOH HOH A . E 3 HOH 38 100 100 HOH HOH A . E 3 HOH 39 103 103 HOH HOH A . E 3 HOH 40 105 105 HOH HOH A . E 3 HOH 41 107 107 HOH HOH A . E 3 HOH 42 108 108 HOH HOH A . E 3 HOH 43 109 109 HOH HOH A . E 3 HOH 44 110 110 HOH HOH A . E 3 HOH 45 111 111 HOH HOH A . E 3 HOH 46 112 112 HOH HOH A . E 3 HOH 47 114 114 HOH HOH A . E 3 HOH 48 115 115 HOH HOH A . E 3 HOH 49 116 116 HOH HOH A . E 3 HOH 50 117 117 HOH HOH A . E 3 HOH 51 118 118 HOH HOH A . F 3 HOH 1 24 24 HOH HOH B . F 3 HOH 2 27 27 HOH HOH B . F 3 HOH 3 28 28 HOH HOH B . F 3 HOH 4 29 29 HOH HOH B . F 3 HOH 5 33 33 HOH HOH B . F 3 HOH 6 37 37 HOH HOH B . F 3 HOH 7 38 38 HOH HOH B . F 3 HOH 8 45 45 HOH HOH B . F 3 HOH 9 46 46 HOH HOH B . F 3 HOH 10 47 47 HOH HOH B . F 3 HOH 11 49 49 HOH HOH B . F 3 HOH 12 52 52 HOH HOH B . F 3 HOH 13 53 53 HOH HOH B . F 3 HOH 14 56 56 HOH HOH B . F 3 HOH 15 57 57 HOH HOH B . F 3 HOH 16 61 61 HOH HOH B . F 3 HOH 17 62 62 HOH HOH B . F 3 HOH 18 66 66 HOH HOH B . F 3 HOH 19 67 67 HOH HOH B . F 3 HOH 20 69 69 HOH HOH B . F 3 HOH 21 70 70 HOH HOH B . F 3 HOH 22 73 73 HOH HOH B . F 3 HOH 23 74 74 HOH HOH B . F 3 HOH 24 75 75 HOH HOH B . F 3 HOH 25 76 76 HOH HOH B . F 3 HOH 26 77 77 HOH HOH B . F 3 HOH 27 78 78 HOH HOH B . F 3 HOH 28 80 80 HOH HOH B . F 3 HOH 29 81 81 HOH HOH B . F 3 HOH 30 82 82 HOH HOH B . F 3 HOH 31 85 85 HOH HOH B . F 3 HOH 32 86 86 HOH HOH B . F 3 HOH 33 90 90 HOH HOH B . F 3 HOH 34 92 92 HOH HOH B . F 3 HOH 35 93 93 HOH HOH B . F 3 HOH 36 96 96 HOH HOH B . F 3 HOH 37 98 98 HOH HOH B . F 3 HOH 38 99 99 HOH HOH B . F 3 HOH 39 104 104 HOH HOH B . F 3 HOH 40 106 106 HOH HOH B . F 3 HOH 41 113 113 HOH HOH B . F 3 HOH 42 119 119 HOH HOH B . F 3 HOH 43 121 121 HOH HOH B . # 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 DENZO . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data reduction' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 2 CNS 1.1 ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 3 EPMR . ? ? ? ? phasing ? ? ? 4 # _cell.entry_id 1ZF9 _cell.length_a 23.280 _cell.length_b 45.310 _cell.length_c 47.550 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZF9 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1ZF9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.06 _exptl_crystal.density_percent_sol 40.22 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 'Na Cacodylate' ? ? ? 1 2 1 CaCl2 ? ? ? 1 3 1 Spermine ? ? ? 1 4 1 MPD ? ? ? 1 5 1 H2O ? ? ? 1 6 2 'Na Cacodylate' ? ? ? 1 7 2 CaCl2 ? ? ? 1 8 2 MPD ? ? ? 1 9 2 H2O ? ? ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 103 ? 1 2 103 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD MARRESEARCH 2003-06-14 ? 2 'IMAGE PLATE' 'RIGAKU RAXIS IV' 2003-02-02 ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.972 1.0 2 1.542 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_wavelength_list _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline 1 SYNCHROTRON 'APS BEAMLINE 14-ID-B' 0.972 ? APS 14-ID-B 2 'ROTATING ANODE' 'RIGAKU RUH3R' 1.542 ? ? ? # _reflns.entry_id 1ZF9 _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 99.000 _reflns.d_resolution_high 1.350 _reflns.number_obs 10745 _reflns.number_all ? _reflns.percent_possible_obs 92.2 _reflns.pdbx_Rmerge_I_obs 0.037 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 29.4000 _reflns.B_iso_Wilson_estimate 5.0 _reflns.pdbx_redundancy ? _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 1.35 _reflns_shell.d_res_low 1.40 _reflns_shell.percent_possible_all 48.2 _reflns_shell.Rmerge_I_obs 0.297 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.000 _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.entry_id 1ZF9 _refine.ls_number_reflns_obs 10051 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF 53828.80 _refine.pdbx_data_cutoff_low_absF 0.00 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 18.99 _refine.ls_d_res_high 1.38 _refine.ls_percent_reflns_obs 92.5 _refine.ls_R_factor_obs 0.237 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.237 _refine.ls_R_factor_R_free 0.259 _refine.ls_R_factor_R_free_error 0.008 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.3 _refine.ls_number_reflns_R_free 1034 _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 6.1 _refine.aniso_B[1][1] -1.25000 _refine.aniso_B[2][2] 0.13900 _refine.aniso_B[3][3] 1.11100 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.7443 _refine.solvent_model_param_bsol 80.17 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'STRUCTURE NOT REFINED TO ITS LOWEST R AND RFREE VALUES. PLEASE REFER TO CITATION ABOVE FOR MORE DETAILS.' _refine.pdbx_starting_model 'ndb entry ADJ049' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _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 ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1ZF9 _refine_analyze.Luzzati_coordinate_error_obs 0.18 _refine_analyze.Luzzati_sigma_a_obs 0.08 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.21 _refine_analyze.Luzzati_sigma_a_free 0.16 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 404 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 94 _refine_hist.number_atoms_total 500 _refine_hist.d_res_high 1.38 _refine_hist.d_res_low 18.99 # 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 c_bond_d 0.028 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 2.9 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 35.9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 2.74 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 0.464 ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 0.613 0.000 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 0.964 0.000 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 1.426 0.000 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.38 _refine_ls_shell.d_res_low 1.47 _refine_ls_shell.number_reflns_R_work 1234 _refine_ls_shell.R_factor_R_work 0.253 _refine_ls_shell.percent_reflns_obs 76.9 _refine_ls_shell.R_factor_R_free 0.312 _refine_ls_shell.R_factor_R_free_error 0.028 _refine_ls_shell.percent_reflns_R_free 9.1 _refine_ls_shell.number_reflns_R_free 124 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 CNS_TOPPAR:DNA-RNA_REP.PARAM CNS_TOPPAR:DNA-RNA.TOP 'X-RAY DIFFRACTION' 2 CNS_TOPPAR:WATER_REP.PARAM CNS_TOPPAR:DNA-RNA.LINK 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:ION.PARAM CNS_TOPPAR:WATER.TOP 'X-RAY DIFFRACTION' 4 ? CNS_TOPPAR:ION.TOP 'X-RAY DIFFRACTION' # _struct.entry_id 1ZF9 _struct.title 'GGG Duplex A-DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text 'Crystallographic Screen, DNA Structure, Holliday Junction, Molecular Structure, DNA' _struct_keywords.entry_id 1ZF9 _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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1ZF9 _struct_ref.pdbx_db_accession 1ZF9 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1ZF9 A 1 ? 10 ? 1ZF9 1 ? 10 ? 1 10 2 1 1ZF9 B 1 ? 10 ? 1ZF9 11 ? 20 ? 11 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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,E,F # _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 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # 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 metalc1 metalc ? ? C NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 64 A HOH 79 1_555 ? ? ? ? ? ? ? 2.854 ? ? metalc2 metalc ? ? C NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 64 A HOH 88 1_555 ? ? ? ? ? ? ? 2.618 ? ? metalc3 metalc ? ? B DG 7 O6 ? ? ? 1_555 D NA . NA ? ? B DG 17 B NA 35 1_555 ? ? ? ? ? ? ? 2.502 ? ? metalc4 metalc ? ? D NA . NA ? ? ? 1_555 F HOH . O ? ? B NA 35 B HOH 37 1_555 ? ? ? ? ? ? ? 2.280 ? ? metalc5 metalc ? ? D NA . NA ? ? ? 1_555 F HOH . O ? ? B NA 35 B HOH 47 1_555 ? ? ? ? ? ? ? 2.531 ? ? metalc6 metalc ? ? D NA . NA ? ? ? 1_555 F HOH . O ? ? B NA 35 B HOH 73 1_555 ? ? ? ? ? ? ? 2.263 ? ? metalc7 metalc ? ? D NA . NA ? ? ? 1_555 F HOH . O ? ? B NA 35 B HOH 81 1_555 ? ? ? ? ? ? ? 2.494 ? ? hydrog1 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog2 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 8 N1 ? ? A DC 3 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 8 O6 ? ? A DC 3 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 8 N2 ? ? A DC 3 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 7 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 7 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 7 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 8 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 8 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 8 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 8 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 8 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 8 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? A HOH 79 ? 1_555 NA ? C NA . ? A NA 64 ? 1_555 O ? E HOH . ? A HOH 88 ? 1_555 112.3 ? 2 O6 ? B DG 7 ? B DG 17 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 37 ? 1_555 73.8 ? 3 O6 ? B DG 7 ? B DG 17 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 47 ? 1_555 71.0 ? 4 O ? F HOH . ? B HOH 37 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 47 ? 1_555 113.1 ? 5 O6 ? B DG 7 ? B DG 17 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 73 ? 1_555 159.7 ? 6 O ? F HOH . ? B HOH 37 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 73 ? 1_555 99.7 ? 7 O ? F HOH . ? B HOH 47 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 73 ? 1_555 95.0 ? 8 O6 ? B DG 7 ? B DG 17 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 81 ? 1_555 107.3 ? 9 O ? F HOH . ? B HOH 37 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 81 ? 1_555 169.7 ? 10 O ? F HOH . ? B HOH 47 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 81 ? 1_555 58.9 ? 11 O ? F HOH . ? B HOH 73 ? 1_555 NA ? D NA . ? B NA 35 ? 1_555 O ? F HOH . ? B HOH 81 ? 1_555 75.7 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B NA 35 ? 5 'BINDING SITE FOR RESIDUE NA B 35' AC2 Software A NA 64 ? 4 'BINDING SITE FOR RESIDUE NA A 64' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 5 DG B 7 ? DG B 17 . ? 1_555 ? 2 AC1 5 HOH F . ? HOH B 37 . ? 1_555 ? 3 AC1 5 HOH F . ? HOH B 47 . ? 1_555 ? 4 AC1 5 HOH F . ? HOH B 73 . ? 1_555 ? 5 AC1 5 HOH F . ? HOH B 81 . ? 1_555 ? 6 AC2 4 DC A 1 ? DC A 1 . ? 1_555 ? 7 AC2 4 DG A 7 ? DG A 7 . ? 2_555 ? 8 AC2 4 HOH E . ? HOH A 79 . ? 1_555 ? 9 AC2 4 HOH E . ? HOH A 88 . ? 1_555 ? # 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 O A HOH 41 ? ? O A HOH 54 ? ? 1.61 2 1 OP2 B DG 18 ? ? O B HOH 49 ? ? 1.89 3 1 "C4'" A DC 1 ? ? O A HOH 79 ? ? 2.01 4 1 O A HOH 89 ? ? O B HOH 75 ? ? 2.01 5 1 O A HOH 58 ? ? O A HOH 72 ? ? 2.05 6 1 O A HOH 111 ? ? O B HOH 75 ? ? 2.06 7 1 O A HOH 50 ? ? O A HOH 91 ? ? 2.07 8 1 O A HOH 21 ? ? O A HOH 26 ? ? 2.09 9 1 OP1 A DC 4 ? ? O A HOH 116 ? ? 2.10 10 1 "O3'" B DG 19 ? ? O B HOH 99 ? ? 2.13 11 1 O A HOH 109 ? ? O A HOH 118 ? ? 2.16 # 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 "O5'" B DG 20 ? ? 1_555 O A HOH 63 ? ? 2_555 1.84 2 1 O A HOH 51 ? ? 1_555 O B HOH 99 ? ? 3_546 2.05 # 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 C2 A DC 3 ? ? O2 A DC 3 ? ? 1.176 1.240 -0.064 0.009 N 2 1 C2 A DC 4 ? ? N3 A DC 4 ? ? 1.411 1.353 0.058 0.008 N 3 1 C2 A DC 5 ? ? O2 A DC 5 ? ? 1.303 1.240 0.063 0.009 N 4 1 N1 A DC 5 ? ? C2 A DC 5 ? ? 1.321 1.397 -0.076 0.010 N 5 1 C2 A DC 5 ? ? N3 A DC 5 ? ? 1.415 1.353 0.062 0.008 N 6 1 N3 A DG 6 ? ? C4 A DG 6 ? ? 1.393 1.350 0.043 0.007 N 7 1 N1 A DG 7 ? ? C2 A DG 7 ? ? 1.303 1.373 -0.070 0.008 N 8 1 "O3'" A DG 10 ? ? "C3'" A DG 10 ? ? 1.342 1.419 -0.077 0.006 N 9 1 C2 B DC 11 ? ? O2 B DC 11 ? ? 1.178 1.240 -0.062 0.009 N 10 1 P B DC 13 ? ? OP2 B DC 13 ? ? 1.369 1.485 -0.116 0.017 N 11 1 "O3'" B DC 13 ? ? "C3'" B DC 13 ? ? 1.382 1.419 -0.037 0.006 N 12 1 C2 B DC 15 ? ? O2 B DC 15 ? ? 1.120 1.240 -0.120 0.009 N 13 1 "O3'" B DG 16 ? ? "C3'" B DG 16 ? ? 1.378 1.419 -0.041 0.006 N 14 1 C6 B DG 16 ? ? O6 B DG 16 ? ? 1.181 1.237 -0.056 0.009 N 15 1 N3 B DG 17 ? ? C4 B DG 17 ? ? 1.392 1.350 0.042 0.007 N 16 1 "O3'" B DG 18 ? ? "C3'" B DG 18 ? ? 1.367 1.419 -0.052 0.006 N 17 1 C8 B DG 18 ? ? N9 B DG 18 ? ? 1.332 1.374 -0.042 0.007 N 18 1 C4 B DG 19 ? ? C5 B DG 19 ? ? 1.337 1.379 -0.042 0.007 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O5'" A DC 1 ? ? "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 127.64 111.00 16.64 2.50 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 102.39 108.00 -5.61 0.70 N 3 1 "O3'" A DC 1 ? ? P A DC 2 ? ? OP2 A DC 2 ? ? 86.25 105.20 -18.95 2.20 Y 4 1 "O3'" A DC 1 ? ? P A DC 2 ? ? OP1 A DC 2 ? ? 127.08 110.50 16.58 1.10 Y 5 1 "O4'" A DC 3 ? ? "C4'" A DC 3 ? ? "C3'" A DC 3 ? ? 101.62 104.50 -2.88 0.40 N 6 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.41 108.30 2.11 0.30 N 7 1 "O5'" B DC 11 ? ? "C5'" B DC 11 ? ? "C4'" B DC 11 ? ? 104.41 109.40 -4.99 0.80 N 8 1 "O4'" B DC 13 ? ? "C1'" B DC 13 ? ? N1 B DC 13 ? ? 110.72 108.30 2.42 0.30 N 9 1 "O4'" B DG 16 ? ? "C1'" B DG 16 ? ? "C2'" B DG 16 ? ? 110.91 106.80 4.11 0.50 N 10 1 "O3'" B DG 16 ? ? P B DG 17 ? ? OP2 B DG 17 ? ? 117.11 110.50 6.61 1.10 Y 11 1 "O5'" B DG 17 ? ? P B DG 17 ? ? OP2 B DG 17 ? ? 97.26 105.70 -8.44 0.90 N 12 1 "C5'" B DG 17 ? ? "C4'" B DG 17 ? ? "C3'" B DG 17 ? ? 123.53 115.70 7.83 1.20 N 13 1 "O4'" B DG 17 ? ? "C1'" B DG 17 ? ? N9 B DG 17 ? ? 111.24 108.30 2.94 0.30 N 14 1 "O4'" B DG 19 ? ? "C4'" B DG 19 ? ? "C3'" B DG 19 ? ? 98.52 104.50 -5.98 0.40 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DC A 5 ? ? 0.079 'SIDE CHAIN' 2 1 DC B 12 ? ? 0.083 'SIDE CHAIN' 3 1 DC B 15 ? ? 0.080 'SIDE CHAIN' 4 1 DG B 16 ? ? 0.051 'SIDE CHAIN' # 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 HOH O O N N 72 HOH H1 H N N 73 HOH H2 H N N 74 NA NA NA N N 75 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 # _ndb_struct_conf_na.entry_id 1ZF9 _ndb_struct_conf_na.feature 'a-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 DC 1 1_555 B DG 10 1_555 2.391 -0.263 -0.115 -10.150 5.393 -0.198 1 A_DC1:DG20_B A 1 ? B 20 ? ? ? 1 A DC 2 1_555 B DG 9 1_555 0.186 -0.107 0.026 10.202 -7.850 -0.033 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DC 3 1_555 B DG 8 1_555 0.161 -0.083 -0.253 12.344 -15.975 -1.302 3 A_DC3:DG18_B A 3 ? B 18 ? 19 1 1 A DC 4 1_555 B DG 7 1_555 0.279 -0.137 -0.033 5.571 -8.609 0.431 4 A_DC4:DG17_B A 4 ? B 17 ? 19 1 1 A DC 5 1_555 B DG 6 1_555 0.162 -0.101 0.016 -5.169 -13.397 2.924 5 A_DC5:DG16_B A 5 ? B 16 ? 19 1 1 A DG 6 1_555 B DC 5 1_555 -0.217 -0.145 -0.067 -10.691 -14.624 -0.847 6 A_DG6:DC15_B A 6 ? B 15 ? 19 1 1 A DG 7 1_555 B DC 4 1_555 -0.074 0.014 -0.108 -17.290 -13.785 2.641 7 A_DG7:DC14_B A 7 ? B 14 ? 19 1 1 A DG 8 1_555 B DC 3 1_555 -0.219 -0.096 0.020 -8.363 -9.041 -0.331 8 A_DG8:DC13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.116 -0.163 0.181 -10.256 -12.677 -3.001 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DG 10 1_555 B DC 1 1_555 -0.061 -0.194 0.031 -6.091 -7.443 -0.044 10 A_DG10:DC11_B A 10 ? B 11 ? 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 DC 1 1_555 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 -0.139 -1.683 2.808 -1.734 8.725 20.028 -6.993 -0.142 1.918 23.638 4.698 21.896 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DC 3 1_555 B DG 8 1_555 0.249 -2.242 3.193 2.478 6.041 30.099 -5.303 -0.027 2.714 11.464 -4.703 30.783 2 AA_DC2DC3:DG18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DC 3 1_555 B DG 8 1_555 A DC 4 1_555 B DG 7 1_555 -0.361 -2.194 3.487 -4.914 6.533 27.352 -5.942 -0.388 2.915 13.439 10.108 28.525 3 AA_DC3DC4:DG17DG18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DC 4 1_555 B DG 7 1_555 A DC 5 1_555 B DG 6 1_555 -1.346 -1.729 3.462 -2.880 4.317 31.536 -3.956 1.902 3.309 7.876 5.253 31.950 4 AA_DC4DC5:DG16DG17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DC 5 1_555 B DG 6 1_555 A DG 6 1_555 B DC 5 1_555 0.837 -1.569 3.170 3.724 17.679 25.334 -5.804 -0.960 1.818 35.171 -7.408 31.031 5 AA_DC5DG6:DC15DG16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DG 6 1_555 B DC 5 1_555 A DG 7 1_555 B DC 4 1_555 0.728 -1.851 3.459 4.616 2.822 34.259 -3.561 -0.479 3.367 4.753 -7.775 34.671 6 AA_DG6DG7:DC14DC15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DG 7 1_555 B DC 4 1_555 A DG 8 1_555 B DC 3 1_555 0.161 -1.773 3.038 2.564 3.017 28.413 -4.193 0.197 2.842 6.109 -5.192 28.682 7 AA_DG7DG8:DC13DC14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DG 8 1_555 B DC 3 1_555 A DG 9 1_555 B DC 2 1_555 0.502 -1.982 3.291 2.740 3.560 26.392 -5.181 -0.392 3.038 7.725 -5.947 26.765 8 AA_DG8DG9:DC12DC13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DG 10 1_555 B DC 1 1_555 0.299 -1.877 3.134 5.737 5.196 36.103 -3.617 0.247 2.858 8.268 -9.128 36.896 9 AA_DG9DG10:DC11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _pdbx_initial_refinement_model.accession_code 160D _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details 'ndb entry ADJ049' # _atom_sites.entry_id 1ZF9 _atom_sites.fract_transf_matrix[1][1] 0.042955 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.022070 _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] 0.021030 _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 NA O P # loop_