data_1V3N # _entry.id 1V3N # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 1V3N pdb_00001v3n 10.2210/pdb1v3n/pdb NDB UD0046 ? ? RCSB RCSB006164 ? ? WWPDB D_1000006164 ? ? # 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 2004-06-08 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-12-27 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 19 4 'Structure model' '_pdbx_struct_conn_angle.value' 20 4 'Structure model' '_struct_conn.conn_type_id' 21 4 'Structure model' '_struct_conn.id' 22 4 'Structure model' '_struct_conn.pdbx_dist_value' 23 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 24 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 25 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 26 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 27 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 28 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 29 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 30 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 31 4 'Structure model' '_struct_conn.ptnr1_symmetry' 32 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 33 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 34 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 35 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 36 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 37 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 38 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 39 4 'Structure model' '_struct_conn.ptnr2_symmetry' 40 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 41 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 42 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1V3N _pdbx_database_status.recvd_initial_deposition_date 2003-11-03 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1V3O 'The same structure, I-derivative' unspecified PDB 1V3P 'The same structure, I-derivative, with I-motif of G-quartet' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Umeda, S.' 2 'Sunami, T.' 3 'Takenaka, A.' 4 # _citation.id primary _citation.title ;Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 32 _citation.page_first 2541 _citation.page_last 2549 _citation.year 2004 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15133122 _citation.pdbx_database_id_DOI 10.1093/nar/gkh575 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Adachi, W.' 2 ? primary 'Umeda, S.' 3 ? primary 'Sunami, T.' 4 ? primary 'Takenaka, A.' 5 ? # 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(*GP*(CBR)P*GP*AP*GP*AP*GP*C)-3'" 2555.539 2 ? ? ? ? 2 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 3 water nat water 18.015 110 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(CBR)(DG)(DA)(DG)(DA)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGAGAGC _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 'POTASSIUM ION' K 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 CBR n 1 3 DG n 1 4 DA n 1 5 DG n 1 6 DA n 1 7 DG n 1 8 DC n # 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 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 CBR 2 2 2 CBR CBR A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DC 8 8 8 DC C A . n B 1 1 DG 1 9 9 DG G B . n B 1 2 CBR 2 10 10 CBR CBR B . n B 1 3 DG 3 11 11 DG G B . n B 1 4 DA 4 12 12 DA A B . n B 1 5 DG 5 13 13 DG G B . n B 1 6 DA 6 14 14 DA A B . n B 1 7 DG 7 15 15 DG G B . n B 1 8 DC 8 16 16 DC C 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 K 1 127 127 K K A . D 3 HOH 1 17 17 HOH HOH A . D 3 HOH 2 20 20 HOH HOH A . D 3 HOH 3 21 21 HOH HOH A . D 3 HOH 4 24 24 HOH HOH A . D 3 HOH 5 26 26 HOH HOH A . D 3 HOH 6 28 28 HOH HOH A . D 3 HOH 7 30 30 HOH HOH A . D 3 HOH 8 34 34 HOH HOH A . D 3 HOH 9 36 36 HOH HOH A . D 3 HOH 10 37 37 HOH HOH A . D 3 HOH 11 40 40 HOH HOH A . D 3 HOH 12 41 41 HOH HOH A . D 3 HOH 13 43 43 HOH HOH A . D 3 HOH 14 46 46 HOH HOH A . D 3 HOH 15 47 47 HOH HOH A . D 3 HOH 16 48 48 HOH HOH A . D 3 HOH 17 49 49 HOH HOH A . D 3 HOH 18 51 51 HOH HOH A . D 3 HOH 19 53 53 HOH HOH A . D 3 HOH 20 54 54 HOH HOH A . D 3 HOH 21 57 57 HOH HOH A . D 3 HOH 22 58 58 HOH HOH A . D 3 HOH 23 60 60 HOH HOH A . D 3 HOH 24 61 61 HOH HOH A . D 3 HOH 25 63 63 HOH HOH A . D 3 HOH 26 64 64 HOH HOH A . D 3 HOH 27 67 67 HOH HOH A . D 3 HOH 28 69 69 HOH HOH A . D 3 HOH 29 70 70 HOH HOH A . D 3 HOH 30 71 71 HOH HOH A . D 3 HOH 31 72 72 HOH HOH A . D 3 HOH 32 73 73 HOH HOH A . D 3 HOH 33 74 74 HOH HOH A . D 3 HOH 34 75 75 HOH HOH A . D 3 HOH 35 78 78 HOH HOH A . D 3 HOH 36 82 82 HOH HOH A . D 3 HOH 37 83 83 HOH HOH A . D 3 HOH 38 86 86 HOH HOH A . D 3 HOH 39 89 89 HOH HOH A . D 3 HOH 40 91 91 HOH HOH A . D 3 HOH 41 94 94 HOH HOH A . D 3 HOH 42 97 97 HOH HOH A . D 3 HOH 43 98 98 HOH HOH A . D 3 HOH 44 101 101 HOH HOH A . D 3 HOH 45 102 102 HOH HOH A . D 3 HOH 46 103 103 HOH HOH A . D 3 HOH 47 104 104 HOH HOH A . D 3 HOH 48 110 110 HOH HOH A . D 3 HOH 49 111 111 HOH HOH A . D 3 HOH 50 113 113 HOH HOH A . D 3 HOH 51 116 116 HOH HOH A . D 3 HOH 52 117 117 HOH HOH A . D 3 HOH 53 123 123 HOH HOH A . E 3 HOH 1 18 18 HOH HOH B . E 3 HOH 2 19 19 HOH HOH B . E 3 HOH 3 22 22 HOH HOH B . E 3 HOH 4 23 23 HOH HOH B . E 3 HOH 5 25 25 HOH HOH B . E 3 HOH 6 27 27 HOH HOH B . E 3 HOH 7 29 29 HOH HOH B . E 3 HOH 8 31 31 HOH HOH B . E 3 HOH 9 32 32 HOH HOH B . E 3 HOH 10 33 33 HOH HOH B . E 3 HOH 11 35 35 HOH HOH B . E 3 HOH 12 38 38 HOH HOH B . E 3 HOH 13 39 39 HOH HOH B . E 3 HOH 14 42 42 HOH HOH B . E 3 HOH 15 44 44 HOH HOH B . E 3 HOH 16 45 45 HOH HOH B . E 3 HOH 17 50 50 HOH HOH B . E 3 HOH 18 52 52 HOH HOH B . E 3 HOH 19 55 55 HOH HOH B . E 3 HOH 20 56 56 HOH HOH B . E 3 HOH 21 59 59 HOH HOH B . E 3 HOH 22 62 62 HOH HOH B . E 3 HOH 23 65 65 HOH HOH B . E 3 HOH 24 66 66 HOH HOH B . E 3 HOH 25 68 68 HOH HOH B . E 3 HOH 26 76 76 HOH HOH B . E 3 HOH 27 77 77 HOH HOH B . E 3 HOH 28 79 79 HOH HOH B . E 3 HOH 29 80 80 HOH HOH B . E 3 HOH 30 81 81 HOH HOH B . E 3 HOH 31 84 84 HOH HOH B . E 3 HOH 32 85 85 HOH HOH B . E 3 HOH 33 87 87 HOH HOH B . E 3 HOH 34 88 88 HOH HOH B . E 3 HOH 35 90 90 HOH HOH B . E 3 HOH 36 92 92 HOH HOH B . E 3 HOH 37 93 93 HOH HOH B . E 3 HOH 38 95 95 HOH HOH B . E 3 HOH 39 96 96 HOH HOH B . E 3 HOH 40 99 99 HOH HOH B . E 3 HOH 41 100 100 HOH HOH B . E 3 HOH 42 105 105 HOH HOH B . E 3 HOH 43 106 106 HOH HOH B . E 3 HOH 44 107 107 HOH HOH B . E 3 HOH 45 108 108 HOH HOH B . E 3 HOH 46 109 109 HOH HOH B . E 3 HOH 47 112 112 HOH HOH B . E 3 HOH 48 114 114 HOH HOH B . E 3 HOH 49 115 115 HOH HOH B . E 3 HOH 50 118 118 HOH HOH B . E 3 HOH 51 119 119 HOH HOH B . E 3 HOH 52 120 120 HOH HOH B . E 3 HOH 53 121 121 HOH HOH B . E 3 HOH 54 122 122 HOH HOH B . E 3 HOH 55 124 124 HOH HOH B . E 3 HOH 56 125 125 HOH HOH B . E 3 HOH 57 126 126 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOSFLM 'data reduction' . ? 1 SCALA 'data scaling' . ? 2 SOLVE phasing . ? 3 CNS refinement 1.0 ? 4 CCP4 'data scaling' '(SCALA)' ? 5 # _cell.entry_id 1V3N _cell.length_a 33.810 _cell.length_b 43.470 _cell.length_c 64.200 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V3N _symmetry.space_group_name_H-M 'I 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 # _exptl.entry_id 1V3N _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 44.36 _exptl_crystal.description ? _exptl_crystal.density_Matthews 2.21 # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;2-methyl-2,4-pentanediol, spermine tetrahydrochloride, sodium chloride, potassium chloride, sodium cacodylate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 2-methyl-2,4-pentanediol ? ? ? 1 2 1 'spermine tetrahydrochloride' ? ? ? 1 3 1 'sodium chloride' ? ? ? 1 4 1 'potassium chloride' ? ? ? 1 5 1 'sodium cacodylate' ? ? ? 1 6 2 'sodium chloride' ? ? ? 1 7 2 'potassium chloride' ? ? ? 1 8 2 'sodium cacodylate' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2001-05-15 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.0 1.0 2 0.91961 1.0 3 0.92020 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-18B' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-18B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '1.0, 0.91961, 0.92020' # _reflns.entry_id 1V3N _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 1.8 _reflns.d_resolution_low 32 _reflns.number_all 4553 _reflns.number_obs 4543 _reflns.percent_possible_obs 98.1 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value 0.05 _reflns.pdbx_netI_over_sigmaI 7.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.2 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.8 _reflns_shell.d_res_low 1.89 _reflns_shell.percent_possible_all 88.6 _reflns_shell.Rmerge_I_obs 0.265 _reflns_shell.pdbx_Rsym_value 0.265 _reflns_shell.meanI_over_sigI_obs 2.6 _reflns_shell.pdbx_redundancy 3.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 583 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1V3N _refine.ls_d_res_high 1.8 _refine.ls_d_res_low 9.0 _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 4594 _refine.ls_number_reflns_obs 4227 _refine.ls_number_reflns_R_free 436 _refine.ls_percent_reflns_obs 92.0 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.225 _refine.ls_R_factor_R_free 0.249 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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 1V3N _refine_analyze.Luzzati_coordinate_error_obs 0.27 _refine_analyze.Luzzati_sigma_a_obs 0.32 _refine_analyze.Luzzati_d_res_low_obs 5.0 _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_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 332 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 110 _refine_hist.number_atoms_total 443 _refine_hist.d_res_high 1.8 _refine_hist.d_res_low 9.0 # 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 0.004 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 22.3 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.8 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.80 _refine_ls_shell.d_res_low 1.86 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.335 _refine_ls_shell.percent_reflns_obs 62.8 _refine_ls_shell.R_factor_R_free 0.331 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 35 _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 ? # _database_PDB_matrix.entry_id 1V3N _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1V3N _struct.title 'Crystal structure of d(GCGAGAGC): the DNA quadruplex structure split from the octaplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1V3N _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;octaplex, quadruplex, G-duet, base-intercalated duplex, base-intercalated motif, sheared G:A pair, DNA, deoxyribonucleic acid, X-ray analysis, crystal struture ; # 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 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1V3N _struct_ref.pdbx_db_accession 1V3N _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 1V3N A 1 ? 8 ? 1V3N 1 ? 8 ? 1 8 2 1 1V3N B 1 ? 8 ? 1V3N 9 ? 16 ? 9 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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 3_555 -x,y,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details ;The biological assembly is a quadruplex generated from the duplex in the asymmetric unit by the operations: x, y, z and -x, y, -z. ; _struct_biol.pdbx_parent_biol_id ? # 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 DG 1 "O3'" ? ? ? 1_555 A CBR 2 P ? ? A DG 1 A CBR 2 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale both ? A CBR 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A CBR 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale3 covale both ? B DG 1 "O3'" ? ? ? 1_555 B CBR 2 P ? ? B DG 9 B CBR 10 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale4 covale both ? B CBR 2 "O3'" ? ? ? 1_555 B DG 3 P ? ? B CBR 10 B DG 11 1_555 ? ? ? ? ? ? ? 1.607 ? ? metalc1 metalc ? ? A DG 5 O6 ? ? ? 1_555 C K . K ? ? A DG 5 A K 127 1_555 ? ? ? ? ? ? ? 2.776 ? ? metalc2 metalc ? ? A DG 5 O6 ? ? ? 3_555 C K . K ? ? A DG 5 A K 127 1_555 ? ? ? ? ? ? ? 2.776 ? ? metalc3 metalc ? ? D HOH . O ? ? ? 1_555 C K . K ? ? A HOH 21 A K 127 1_555 ? ? ? ? ? ? ? 3.094 ? ? metalc4 metalc ? ? D HOH . O ? ? ? 3_555 C K . K ? ? A HOH 21 A K 127 1_555 ? ? ? ? ? ? ? 3.094 ? ? metalc5 metalc ? ? C K . K ? ? ? 1_555 B DG 5 O6 ? ? A K 127 B DG 13 1_555 ? ? ? ? ? ? ? 2.897 ? ? metalc6 metalc ? ? C K . K ? ? ? 1_555 B DG 5 O6 ? ? A K 127 B DG 13 3_555 ? ? ? ? ? ? ? 2.897 ? ? metalc7 metalc ? ? C K . K ? ? ? 1_555 E HOH . O ? ? A K 127 B HOH 59 1_555 ? ? ? ? ? ? ? 2.852 ? ? metalc8 metalc ? ? C K . K ? ? ? 1_555 E HOH . O ? ? A K 127 B HOH 59 3_555 ? ? ? ? ? ? ? 2.852 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 1 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 1 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 1 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A CBR 2 N3 ? ? ? 1_555 B DG 7 N1 ? ? A CBR 2 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A CBR 2 N4 ? ? ? 1_555 B DG 7 O6 ? ? A CBR 2 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A CBR 2 O2 ? ? ? 1_555 B DG 7 N2 ? ? A CBR 2 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DA 6 N7 ? ? A DG 3 B DA 14 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog8 hydrog ? ? A DG 3 N3 ? ? ? 1_555 B DA 6 N6 ? ? A DG 3 B DA 14 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog9 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DG 3 N3 ? ? A DA 6 B DG 11 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog10 hydrog ? ? A DA 6 N7 ? ? ? 1_555 B DG 3 N2 ? ? A DA 6 B DG 11 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog11 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B CBR 2 N3 ? ? A DG 7 B CBR 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B CBR 2 O2 ? ? A DG 7 B CBR 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B CBR 2 N4 ? ? A DG 7 B CBR 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 127 ? 1_555 O6 ? A DG 5 ? A DG 5 ? 3_555 68.1 ? 2 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? D HOH . ? A HOH 21 ? 1_555 75.4 ? 3 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 127 ? 1_555 O ? D HOH . ? A HOH 21 ? 1_555 123.8 ? 4 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? D HOH . ? A HOH 21 ? 3_555 123.8 ? 5 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 127 ? 1_555 O ? D HOH . ? A HOH 21 ? 3_555 75.4 ? 6 O ? D HOH . ? A HOH 21 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? D HOH . ? A HOH 21 ? 3_555 158.8 ? 7 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 127 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 1_555 84.4 ? 8 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 127 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 1_555 71.3 ? 9 O ? D HOH . ? A HOH 21 ? 1_555 K ? C K . ? A K 127 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 1_555 63.8 ? 10 O ? D HOH . ? A HOH 21 ? 3_555 K ? C K . ? A K 127 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 1_555 122.3 ? 11 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 127 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 71.3 ? 12 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 127 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 84.4 ? 13 O ? D HOH . ? A HOH 21 ? 1_555 K ? C K . ? A K 127 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 122.3 ? 14 O ? D HOH . ? A HOH 21 ? 3_555 K ? C K . ? A K 127 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 63.8 ? 15 O6 ? B DG 5 ? B DG 13 ? 1_555 K ? C K . ? A K 127 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 150.7 ? 16 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 1_555 154.4 ? 17 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 1_555 107.4 ? 18 O ? D HOH . ? A HOH 21 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 1_555 88.1 ? 19 O ? D HOH . ? A HOH 21 ? 3_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 1_555 76.4 ? 20 O6 ? B DG 5 ? B DG 13 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 1_555 70.7 ? 21 O6 ? B DG 5 ? B DG 13 ? 3_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 1_555 134.2 ? 22 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 3_555 107.4 ? 23 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 3_555 154.4 ? 24 O ? D HOH . ? A HOH 21 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 3_555 76.4 ? 25 O ? D HOH . ? A HOH 21 ? 3_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 3_555 88.1 ? 26 O6 ? B DG 5 ? B DG 13 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 3_555 134.2 ? 27 O6 ? B DG 5 ? B DG 13 ? 3_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 3_555 70.7 ? 28 O ? E HOH . ? B HOH 59 ? 1_555 K ? C K . ? A K 127 ? 1_555 O ? E HOH . ? B HOH 59 ? 3_555 87.0 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id K _struct_site.pdbx_auth_seq_id 127 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 8 _struct_site.details 'BINDING SITE FOR RESIDUE K A 127' # 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 8 DG A 5 ? DG A 5 . ? 1_555 ? 2 AC1 8 DG A 5 ? DG A 5 . ? 3_555 ? 3 AC1 8 HOH D . ? HOH A 21 . ? 1_555 ? 4 AC1 8 HOH D . ? HOH A 21 . ? 3_555 ? 5 AC1 8 DG B 5 ? DG B 13 . ? 3_555 ? 6 AC1 8 DG B 5 ? DG B 13 . ? 1_555 ? 7 AC1 8 HOH E . ? HOH B 59 . ? 1_555 ? 8 AC1 8 HOH E . ? HOH B 59 . ? 3_555 ? # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A CBR 2 A CBR 2 ? DC ? 2 B CBR 2 B CBR 10 ? DC ? # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A K 127 ? C K . 2 1 A HOH 89 ? D HOH . 3 1 B HOH 55 ? E HOH . 4 1 B HOH 66 ? E HOH . 5 1 B HOH 84 ? E HOH . 6 1 B HOH 118 ? E HOH . # 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 CBR BR BR N N 1 CBR P P N N 2 CBR OP1 O N N 3 CBR OP2 O N N 4 CBR "O5'" O N N 5 CBR N1 N N N 6 CBR C6 C N N 7 CBR C2 C N N 8 CBR O2 O N N 9 CBR N3 N N N 10 CBR C4 C N N 11 CBR N4 N N N 12 CBR C5 C N N 13 CBR "C2'" C N N 14 CBR "C5'" C N N 15 CBR "C4'" C N R 16 CBR "O4'" O N N 17 CBR "C1'" C N R 18 CBR "C3'" C N S 19 CBR "O3'" O N N 20 CBR OP3 O N N 21 CBR HOP2 H N N 22 CBR H6 H N N 23 CBR H41 H N N 24 CBR H42 H N N 25 CBR "H2'" H N N 26 CBR "H2''" H N N 27 CBR "H5'" H N N 28 CBR "H5''" H N N 29 CBR "H4'" H N N 30 CBR "H1'" H N N 31 CBR "H3'" H N N 32 CBR "HO3'" H N N 33 CBR HOP3 H N N 34 DA OP3 O N N 35 DA P P N N 36 DA OP1 O N N 37 DA OP2 O N N 38 DA "O5'" O N N 39 DA "C5'" C N N 40 DA "C4'" C N R 41 DA "O4'" O N N 42 DA "C3'" C N S 43 DA "O3'" O N N 44 DA "C2'" C N N 45 DA "C1'" C N R 46 DA N9 N Y N 47 DA C8 C Y N 48 DA N7 N Y N 49 DA C5 C Y N 50 DA C6 C Y N 51 DA N6 N N N 52 DA N1 N Y N 53 DA C2 C Y N 54 DA N3 N Y N 55 DA C4 C Y N 56 DA HOP3 H N N 57 DA HOP2 H N N 58 DA "H5'" H N N 59 DA "H5''" H N N 60 DA "H4'" H N N 61 DA "H3'" H N N 62 DA "HO3'" H N N 63 DA "H2'" H N N 64 DA "H2''" H N N 65 DA "H1'" H N N 66 DA H8 H N N 67 DA H61 H N N 68 DA H62 H N N 69 DA H2 H N N 70 DC OP3 O N N 71 DC P P N N 72 DC OP1 O N N 73 DC OP2 O N N 74 DC "O5'" O N N 75 DC "C5'" C N N 76 DC "C4'" C N R 77 DC "O4'" O N N 78 DC "C3'" C N S 79 DC "O3'" O N N 80 DC "C2'" C N N 81 DC "C1'" C N R 82 DC N1 N N N 83 DC C2 C N N 84 DC O2 O N N 85 DC N3 N N N 86 DC C4 C N N 87 DC N4 N N N 88 DC C5 C N N 89 DC C6 C N N 90 DC HOP3 H N N 91 DC HOP2 H N N 92 DC "H5'" H N N 93 DC "H5''" H N N 94 DC "H4'" H N N 95 DC "H3'" H N N 96 DC "HO3'" H N N 97 DC "H2'" H N N 98 DC "H2''" H N N 99 DC "H1'" H N N 100 DC H41 H N N 101 DC H42 H N N 102 DC H5 H N N 103 DC H6 H N N 104 DG OP3 O N N 105 DG P P N N 106 DG OP1 O N N 107 DG OP2 O N N 108 DG "O5'" O N N 109 DG "C5'" C N N 110 DG "C4'" C N R 111 DG "O4'" O N N 112 DG "C3'" C N S 113 DG "O3'" O N N 114 DG "C2'" C N N 115 DG "C1'" C N R 116 DG N9 N Y N 117 DG C8 C Y N 118 DG N7 N Y N 119 DG C5 C Y N 120 DG C6 C N N 121 DG O6 O N N 122 DG N1 N N N 123 DG C2 C N N 124 DG N2 N N N 125 DG N3 N N N 126 DG C4 C Y N 127 DG HOP3 H N N 128 DG HOP2 H N N 129 DG "H5'" H N N 130 DG "H5''" H N N 131 DG "H4'" H N N 132 DG "H3'" H N N 133 DG "HO3'" H N N 134 DG "H2'" H N N 135 DG "H2''" H N N 136 DG "H1'" H N N 137 DG H8 H N N 138 DG H1 H N N 139 DG H21 H N N 140 DG H22 H N N 141 HOH O O N N 142 HOH H1 H N N 143 HOH H2 H N N 144 K K K N N 145 # 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 CBR BR C5 sing N N 1 CBR P OP1 doub N N 2 CBR P OP2 sing N N 3 CBR P "O5'" sing N N 4 CBR P OP3 sing N N 5 CBR OP2 HOP2 sing N N 6 CBR "O5'" "C5'" sing N N 7 CBR N1 C6 sing N N 8 CBR N1 C2 sing N N 9 CBR N1 "C1'" sing N N 10 CBR C6 C5 doub N N 11 CBR C6 H6 sing N N 12 CBR C2 O2 doub N N 13 CBR C2 N3 sing N N 14 CBR N3 C4 doub N N 15 CBR C4 N4 sing N N 16 CBR C4 C5 sing N N 17 CBR N4 H41 sing N N 18 CBR N4 H42 sing N N 19 CBR "C2'" "C1'" sing N N 20 CBR "C2'" "C3'" sing N N 21 CBR "C2'" "H2'" sing N N 22 CBR "C2'" "H2''" sing N N 23 CBR "C5'" "C4'" sing N N 24 CBR "C5'" "H5'" sing N N 25 CBR "C5'" "H5''" sing N N 26 CBR "C4'" "O4'" sing N N 27 CBR "C4'" "C3'" sing N N 28 CBR "C4'" "H4'" sing N N 29 CBR "O4'" "C1'" sing N N 30 CBR "C1'" "H1'" sing N N 31 CBR "C3'" "O3'" sing N N 32 CBR "C3'" "H3'" sing N N 33 CBR "O3'" "HO3'" sing N N 34 CBR OP3 HOP3 sing N N 35 DA OP3 P sing N N 36 DA OP3 HOP3 sing N N 37 DA P OP1 doub N N 38 DA P OP2 sing N N 39 DA P "O5'" sing N N 40 DA OP2 HOP2 sing N N 41 DA "O5'" "C5'" sing N N 42 DA "C5'" "C4'" sing N N 43 DA "C5'" "H5'" sing N N 44 DA "C5'" "H5''" sing N N 45 DA "C4'" "O4'" sing N N 46 DA "C4'" "C3'" sing N N 47 DA "C4'" "H4'" sing N N 48 DA "O4'" "C1'" sing N N 49 DA "C3'" "O3'" sing N N 50 DA "C3'" "C2'" sing N N 51 DA "C3'" "H3'" sing N N 52 DA "O3'" "HO3'" sing N N 53 DA "C2'" "C1'" sing N N 54 DA "C2'" "H2'" sing N N 55 DA "C2'" "H2''" sing N N 56 DA "C1'" N9 sing N N 57 DA "C1'" "H1'" sing N N 58 DA N9 C8 sing Y N 59 DA N9 C4 sing Y N 60 DA C8 N7 doub Y N 61 DA C8 H8 sing N N 62 DA N7 C5 sing Y N 63 DA C5 C6 sing Y N 64 DA C5 C4 doub Y N 65 DA C6 N6 sing N N 66 DA C6 N1 doub Y N 67 DA N6 H61 sing N N 68 DA N6 H62 sing N N 69 DA N1 C2 sing Y N 70 DA C2 N3 doub Y N 71 DA C2 H2 sing N N 72 DA N3 C4 sing Y N 73 DC OP3 P sing N N 74 DC OP3 HOP3 sing N N 75 DC P OP1 doub N N 76 DC P OP2 sing N N 77 DC P "O5'" sing N N 78 DC OP2 HOP2 sing N N 79 DC "O5'" "C5'" sing N N 80 DC "C5'" "C4'" sing N N 81 DC "C5'" "H5'" sing N N 82 DC "C5'" "H5''" sing N N 83 DC "C4'" "O4'" sing N N 84 DC "C4'" "C3'" sing N N 85 DC "C4'" "H4'" sing N N 86 DC "O4'" "C1'" sing N N 87 DC "C3'" "O3'" sing N N 88 DC "C3'" "C2'" sing N N 89 DC "C3'" "H3'" sing N N 90 DC "O3'" "HO3'" sing N N 91 DC "C2'" "C1'" sing N N 92 DC "C2'" "H2'" sing N N 93 DC "C2'" "H2''" sing N N 94 DC "C1'" N1 sing N N 95 DC "C1'" "H1'" sing N N 96 DC N1 C2 sing N N 97 DC N1 C6 sing N N 98 DC C2 O2 doub N N 99 DC C2 N3 sing N N 100 DC N3 C4 doub N N 101 DC C4 N4 sing N N 102 DC C4 C5 sing N N 103 DC N4 H41 sing N N 104 DC N4 H42 sing N N 105 DC C5 C6 doub N N 106 DC C5 H5 sing N N 107 DC C6 H6 sing N N 108 DG OP3 P sing N N 109 DG OP3 HOP3 sing N N 110 DG P OP1 doub N N 111 DG P OP2 sing N N 112 DG P "O5'" sing N N 113 DG OP2 HOP2 sing N N 114 DG "O5'" "C5'" sing N N 115 DG "C5'" "C4'" sing N N 116 DG "C5'" "H5'" sing N N 117 DG "C5'" "H5''" sing N N 118 DG "C4'" "O4'" sing N N 119 DG "C4'" "C3'" sing N N 120 DG "C4'" "H4'" sing N N 121 DG "O4'" "C1'" sing N N 122 DG "C3'" "O3'" sing N N 123 DG "C3'" "C2'" sing N N 124 DG "C3'" "H3'" sing N N 125 DG "O3'" "HO3'" sing N N 126 DG "C2'" "C1'" sing N N 127 DG "C2'" "H2'" sing N N 128 DG "C2'" "H2''" sing N N 129 DG "C1'" N9 sing N N 130 DG "C1'" "H1'" sing N N 131 DG N9 C8 sing Y N 132 DG N9 C4 sing Y N 133 DG C8 N7 doub Y N 134 DG C8 H8 sing N N 135 DG N7 C5 sing Y N 136 DG C5 C6 sing N N 137 DG C5 C4 doub Y N 138 DG C6 O6 doub N N 139 DG C6 N1 sing N N 140 DG N1 C2 sing N N 141 DG N1 H1 sing N N 142 DG C2 N2 sing N N 143 DG C2 N3 doub N N 144 DG N2 H21 sing N N 145 DG N2 H22 sing N N 146 DG N3 C4 sing N N 147 HOH O H1 sing N N 148 HOH O H2 sing N N 149 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1V3N 'b-form double helix' 1V3N 'mismatched base pair' 1V3N 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 B DC 8 1_555 -0.107 -0.014 0.010 -3.427 1.750 2.150 1 A_DG1:DC16_B A 1 ? B 16 ? 19 1 1 A CBR 2 1_555 B DG 7 1_555 0.168 -0.064 -0.105 17.516 7.131 -1.057 2 A_CBR2:DG15_B A 2 ? B 15 ? 19 1 1 A DG 3 1_555 B DA 6 1_555 6.349 -4.315 1.252 33.599 -14.032 13.271 3 A_DG3:DA14_B A 3 ? B 14 ? 11 9 1 A DA 6 1_555 B DG 3 1_555 -6.474 -4.285 1.395 -28.095 -11.570 15.470 4 A_DA6:DG11_B A 6 ? B 11 ? 11 9 1 A DG 7 1_555 B CBR 2 1_555 -0.214 -0.067 -0.220 -16.177 4.142 -0.395 5 A_DG7:CBR10_B A 7 ? B 10 ? 19 1 1 A DC 8 1_555 B DG 1 1_555 0.386 -0.069 0.167 -3.454 2.464 0.097 6 A_DC8:DG9_B A 8 ? B 9 ? 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 DG 1 1_555 B DC 8 1_555 A CBR 2 1_555 B DG 7 1_555 0.315 0.010 2.950 -0.040 0.284 24.441 -0.057 -0.756 2.950 0.672 0.095 24.443 1 AA_DG1CBR2:DG15DC16_BB A 1 ? B 16 ? A 2 ? B 15 ? 1 A CBR 2 1_555 B DG 7 1_555 A DG 3 1_555 B DA 6 1_555 0.255 1.891 3.150 2.290 5.414 56.634 1.688 -0.142 3.311 5.689 -2.406 56.913 2 AA_CBR2DG3:DA14DG15_BB A 2 ? B 15 ? A 3 ? B 14 ? 1 A DA 6 1_555 B DG 3 1_555 A DG 7 1_555 B CBR 2 1_555 -1.047 1.661 3.242 0.253 8.134 54.993 1.296 1.138 3.432 8.755 -0.272 55.546 3 AA_DA6DG7:CBR10DG11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A DG 7 1_555 B CBR 2 1_555 A DC 8 1_555 B DG 1 1_555 -0.387 -0.012 3.089 -2.194 -0.333 31.237 0.037 0.325 3.108 -0.618 4.069 31.314 4 AA_DG7DC8:DG9CBR10_BB A 7 ? B 10 ? A 8 ? B 9 ? # _atom_sites.entry_id 1V3N _atom_sites.fract_transf_matrix[1][1] 0.029577 _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] 0.023004 _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] 0.015576 _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 BR C K N O P # loop_