data_307D # _entry.id 307D # _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 307D pdb_0000307d 10.2210/pdb307d/pdb RCSB BDJ081 ? ? WWPDB D_1000178775 ? ? # 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 1997-01-27 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-04-04 5 'Structure model' 1 4 2024-02-21 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' 'Data collection' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 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' diffrn_source 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 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 4 'Structure model' '_diffrn_source.type' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 307D _pdbx_database_status.recvd_initial_deposition_date 1997-01-07 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Han, G.W.' 1 'Kopka, M.L.' 2 'Cascio, D.' 3 'Grzeskowiak, K.' 4 'Dickerson, R.E.' 5 # _citation.id primary _citation.title 'Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 269 _citation.page_first 811 _citation.page_last 826 _citation.year 1997 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9223643 _citation.pdbx_database_id_DOI 10.1006/jmbi.1997.1085 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Han, G.W.' 1 ? primary 'Kopka, M.L.' 2 ? primary 'Cascio, D.' 3 ? primary 'Grzeskowiak, K.' 4 ? primary 'Dickerson, R.E.' 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 ;DNA (5'-D(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3') ; 3095.083 3 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3') ; 2991.961 3 ? ? ? ? 3 water nat water 18.015 138 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DC)(DA)(DA)(DA)(DG)(DA)(DA)(DA)(DA)(DG)' CAAAGAAAAG A,C,E ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DT)(DT)(DT)(DC)(DT)(DT)(DT)(DG)' CTTTTCTTTG B,D,F ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 DA n 1 3 DA n 1 4 DA n 1 5 DG n 1 6 DA n 1 7 DA n 1 8 DA n 1 9 DA n 1 10 DG n 2 1 DC n 2 2 DT n 2 3 DT n 2 4 DT n 2 5 DT n 2 6 DC n 2 7 DT n 2 8 DT n 2 9 DT n 2 10 DG 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 DA 2 2 2 DA A A . n A 1 3 DA 3 3 3 DA A 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 DA 7 7 7 DA A A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DA 9 9 9 DA A A . n A 1 10 DG 10 10 10 DG G A . n B 2 1 DC 1 11 11 DC C B . n B 2 2 DT 2 12 12 DT T B . n B 2 3 DT 3 13 13 DT T B . n B 2 4 DT 4 14 14 DT T B . n B 2 5 DT 5 15 15 DT T B . n B 2 6 DC 6 16 16 DC C B . n B 2 7 DT 7 17 17 DT T B . n B 2 8 DT 8 18 18 DT T B . n B 2 9 DT 9 19 19 DT T B . n B 2 10 DG 10 20 20 DG G B . n C 1 1 DC 1 21 21 DC C C . n C 1 2 DA 2 22 22 DA A C . n C 1 3 DA 3 23 23 DA A C . n C 1 4 DA 4 24 24 DA A C . n C 1 5 DG 5 25 25 DG G C . n C 1 6 DA 6 26 26 DA A C . n C 1 7 DA 7 27 27 DA A C . n C 1 8 DA 8 28 28 DA A C . n C 1 9 DA 9 29 29 DA A C . n C 1 10 DG 10 30 30 DG G C . n D 2 1 DC 1 31 31 DC C D . n D 2 2 DT 2 32 32 DT T D . n D 2 3 DT 3 33 33 DT T D . n D 2 4 DT 4 34 34 DT T D . n D 2 5 DT 5 35 35 DT T D . n D 2 6 DC 6 36 36 DC C D . n D 2 7 DT 7 37 37 DT T D . n D 2 8 DT 8 38 38 DT T D . n D 2 9 DT 9 39 39 DT T D . n D 2 10 DG 10 40 40 DG G D . n E 1 1 DC 1 41 121 DC C E . n E 1 2 DA 2 42 122 DA A E . n E 1 3 DA 3 43 123 DA A E . n E 1 4 DA 4 44 124 DA A E . n E 1 5 DG 5 45 125 DG G E . n E 1 6 DA 6 46 126 DA A E . n E 1 7 DA 7 47 127 DA A E . n E 1 8 DA 8 48 128 DA A E . n E 1 9 DA 9 49 129 DA A E . n E 1 10 DG 10 50 130 DG G E . n F 2 1 DC 1 51 131 DC C F . n F 2 2 DT 2 52 132 DT T F . n F 2 3 DT 3 53 133 DT T F . n F 2 4 DT 4 54 134 DT T F . n F 2 5 DT 5 55 135 DT T F . n F 2 6 DC 6 56 136 DC C F . n F 2 7 DT 7 57 137 DT T F . n F 2 8 DT 8 58 138 DT T F . n F 2 9 DT 9 59 139 DT T F . n F 2 10 DG 10 60 140 DG G F . 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 G 3 HOH 1 63 63 HOH HOH A . G 3 HOH 2 64 64 HOH HOH A . G 3 HOH 3 67 67 HOH HOH A . G 3 HOH 4 71 71 HOH HOH A . G 3 HOH 5 73 73 HOH HOH A . G 3 HOH 6 74 74 HOH HOH A . G 3 HOH 7 78 78 HOH HOH A . G 3 HOH 8 80 80 HOH HOH A . G 3 HOH 9 81 81 HOH HOH A . G 3 HOH 10 83 83 HOH HOH A . G 3 HOH 11 86 86 HOH HOH A . G 3 HOH 12 87 87 HOH HOH A . G 3 HOH 13 89 89 HOH HOH A . G 3 HOH 14 90 90 HOH HOH A . G 3 HOH 15 95 95 HOH HOH A . G 3 HOH 16 96 96 HOH HOH A . G 3 HOH 17 99 99 HOH HOH A . G 3 HOH 18 102 102 HOH HOH A . G 3 HOH 19 106 106 HOH HOH A . G 3 HOH 20 114 114 HOH HOH A . G 3 HOH 21 116 116 HOH HOH A . G 3 HOH 22 117 117 HOH HOH A . G 3 HOH 23 120 120 HOH HOH A . G 3 HOH 24 124 124 HOH HOH A . G 3 HOH 25 126 126 HOH HOH A . G 3 HOH 26 128 128 HOH HOH A . G 3 HOH 27 129 129 HOH HOH A . G 3 HOH 28 131 131 HOH HOH A . G 3 HOH 29 133 133 HOH HOH A . G 3 HOH 30 134 134 HOH HOH A . G 3 HOH 31 135 135 HOH HOH A . G 3 HOH 32 136 136 HOH HOH A . G 3 HOH 33 140 140 HOH HOH A . G 3 HOH 34 143 143 HOH HOH A . G 3 HOH 35 145 145 HOH HOH A . G 3 HOH 36 146 146 HOH HOH A . G 3 HOH 37 147 147 HOH HOH A . G 3 HOH 38 148 148 HOH HOH A . G 3 HOH 39 149 149 HOH HOH A . G 3 HOH 40 154 154 HOH HOH A . G 3 HOH 41 156 156 HOH HOH A . G 3 HOH 42 158 158 HOH HOH A . G 3 HOH 43 162 162 HOH HOH A . G 3 HOH 44 167 167 HOH HOH A . G 3 HOH 45 169 169 HOH HOH A . G 3 HOH 46 170 170 HOH HOH A . G 3 HOH 47 172 172 HOH HOH A . G 3 HOH 48 173 173 HOH HOH A . G 3 HOH 49 176 176 HOH HOH A . G 3 HOH 50 177 177 HOH HOH A . G 3 HOH 51 178 178 HOH HOH A . G 3 HOH 52 179 179 HOH HOH A . G 3 HOH 53 192 192 HOH HOH A . H 3 HOH 1 61 61 HOH HOH B . H 3 HOH 2 62 62 HOH HOH B . H 3 HOH 3 65 65 HOH HOH B . H 3 HOH 4 66 66 HOH HOH B . H 3 HOH 5 69 69 HOH HOH B . H 3 HOH 6 70 70 HOH HOH B . H 3 HOH 7 72 72 HOH HOH B . H 3 HOH 8 75 75 HOH HOH B . H 3 HOH 9 76 76 HOH HOH B . H 3 HOH 10 79 79 HOH HOH B . H 3 HOH 11 82 82 HOH HOH B . H 3 HOH 12 85 85 HOH HOH B . H 3 HOH 13 92 92 HOH HOH B . H 3 HOH 14 93 93 HOH HOH B . H 3 HOH 15 94 94 HOH HOH B . H 3 HOH 16 97 97 HOH HOH B . H 3 HOH 17 98 98 HOH HOH B . H 3 HOH 18 100 100 HOH HOH B . H 3 HOH 19 101 101 HOH HOH B . H 3 HOH 20 103 103 HOH HOH B . H 3 HOH 21 104 104 HOH HOH B . H 3 HOH 22 105 105 HOH HOH B . H 3 HOH 23 107 107 HOH HOH B . H 3 HOH 24 108 108 HOH HOH B . H 3 HOH 25 109 109 HOH HOH B . H 3 HOH 26 111 111 HOH HOH B . H 3 HOH 27 118 118 HOH HOH B . H 3 HOH 28 119 119 HOH HOH B . H 3 HOH 29 121 121 HOH HOH B . H 3 HOH 30 122 122 HOH HOH B . H 3 HOH 31 123 123 HOH HOH B . H 3 HOH 32 125 125 HOH HOH B . H 3 HOH 33 127 127 HOH HOH B . H 3 HOH 34 130 130 HOH HOH B . H 3 HOH 35 132 132 HOH HOH B . H 3 HOH 36 137 137 HOH HOH B . H 3 HOH 37 138 138 HOH HOH B . H 3 HOH 38 139 139 HOH HOH B . H 3 HOH 39 141 141 HOH HOH B . H 3 HOH 40 144 144 HOH HOH B . H 3 HOH 41 150 150 HOH HOH B . H 3 HOH 42 151 151 HOH HOH B . H 3 HOH 43 153 153 HOH HOH B . H 3 HOH 44 157 157 HOH HOH B . H 3 HOH 45 160 160 HOH HOH B . H 3 HOH 46 161 161 HOH HOH B . H 3 HOH 47 163 163 HOH HOH B . H 3 HOH 48 164 164 HOH HOH B . H 3 HOH 49 175 175 HOH HOH B . I 3 HOH 1 68 68 HOH HOH C . I 3 HOH 2 77 77 HOH HOH C . I 3 HOH 3 91 91 HOH HOH C . I 3 HOH 4 113 113 HOH HOH C . I 3 HOH 5 142 142 HOH HOH C . I 3 HOH 6 159 159 HOH HOH C . I 3 HOH 7 171 171 HOH HOH C . I 3 HOH 8 181 181 HOH HOH C . I 3 HOH 9 188 188 HOH HOH C . I 3 HOH 10 195 195 HOH HOH C . I 3 HOH 11 198 198 HOH HOH C . J 3 HOH 1 88 88 HOH HOH D . J 3 HOH 2 110 110 HOH HOH D . J 3 HOH 3 112 112 HOH HOH D . J 3 HOH 4 115 115 HOH HOH D . J 3 HOH 5 182 182 HOH HOH D . J 3 HOH 6 187 187 HOH HOH D . J 3 HOH 7 189 189 HOH HOH D . J 3 HOH 8 191 191 HOH HOH D . K 3 HOH 1 84 84 HOH HOH E . K 3 HOH 2 152 152 HOH HOH E . K 3 HOH 3 155 155 HOH HOH E . K 3 HOH 4 165 165 HOH HOH E . K 3 HOH 5 168 168 HOH HOH E . K 3 HOH 6 184 184 HOH HOH E . K 3 HOH 7 185 185 HOH HOH E . K 3 HOH 8 190 190 HOH HOH E . K 3 HOH 9 193 193 HOH HOH E . L 3 HOH 1 166 166 HOH HOH F . L 3 HOH 2 174 174 HOH HOH F . L 3 HOH 3 180 180 HOH HOH F . L 3 HOH 4 183 183 HOH HOH F . L 3 HOH 5 186 186 HOH HOH F . L 3 HOH 6 194 194 HOH HOH F . L 3 HOH 7 196 196 HOH HOH F . L 3 HOH 8 197 197 HOH HOH F . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MLPHARE phasing . ? 1 TNT refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _cell.entry_id 307D _cell.length_a 59.820 _cell.length_b 28.280 _cell.length_c 72.490 _cell.angle_alpha 90.00 _cell.angle_beta 103.87 _cell.angle_gamma 90.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 307D _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # _exptl.entry_id 307D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.63 _exptl_crystal.density_percent_sol 50.0000 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'VAPOR DIFFUSION, SITTING DROP, temperature 277.00K' _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 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'MG ACETATE' ? ? ? 1 4 1 SPERMIDINE ? ? ? 1 5 1 BETA-OCTAGLUCOSIDE ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 93.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS II' _diffrn_detector.pdbx_collection_date 1996-09-01 _diffrn_detector.details 'MIRROR MSC-YALE' # _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 ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 307D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 100.000 _reflns.d_resolution_high 1.850 _reflns.number_obs 9686 _reflns.number_all ? _reflns.percent_possible_obs 93.800 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.0580000 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 24.60 _reflns.pdbx_redundancy ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.850 _reflns_shell.d_res_low 1.920 _reflns_shell.percent_possible_all 91.00 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.2400000 _reflns_shell.meanI_over_sigI_obs 5.000 _reflns_shell.pdbx_redundancy 3.000 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 307D _refine.ls_number_reflns_obs 9630 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 1.850 _refine.ls_percent_reflns_obs 93.000 _refine.ls_R_factor_obs 0.2330000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ;THIS ENTRY PRESENTS THE COORDINATES OF THE CRYSTAL STRUCTURE OF CAAAGAAAAG AND ITS COMPLEMENTARY STRAND. THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. HOWEVER, THE FIRST MOLECULE (HELIX #1 WITH STRANDS A AND B) IS ORDERED, AND THE SECOND MOLECULE IS DISORDERED WITH HELIX #2 (STRANDS C AND D) AND HELIX #3 (STRANDS E AND F). THIS IS EVIDENCED BY THE MULTIPLE ISOMORPHOUS REPLACEMENT METHOD FROM ONE BROMINE AND ONE IODINE ISOMORPHOUS DERIVATIVE PLUS ANOMALOUS DATA. HELICES IN THE SECOND MOLECULE ARE DISORDERED END-FOR-END WITH HALF-WEIGHT HELICES #2 AND #3 BEING RELATED BY A TWOFOLD AXIS THROUGH THEIR CENTERS, NORMAL TO THE HELICAL AXIS. THE OCCUPANCY FOR THE HELIX #2 IS 0.52 AND FOR THE HELIX #3 IS 0.46. ; _refine.pdbx_starting_model 'IDEAL B-DNA HELIX OF SEQUENCE CAAAGAAAAG' _refine.pdbx_method_to_determine_struct 'MIR PHASE ANALYSIS' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1212 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 138 _refine_hist.number_atoms_total 1350 _refine_hist.d_res_high 1.850 _refine_hist.d_res_low 8.000 # 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 t_bond_d 0.015 ? 0.450 ? 'X-RAY DIFFRACTION' ? t_angle_deg 2.134 ? 1.000 ? 'X-RAY DIFFRACTION' ? t_dihedral_angle_d 15.95 ? 1.000 ? 'X-RAY DIFFRACTION' ? t_incorr_chiral_ct ? ? ? ? 'X-RAY DIFFRACTION' ? t_pseud_angle ? ? ? ? 'X-RAY DIFFRACTION' ? t_trig_c_planes ? ? ? ? 'X-RAY DIFFRACTION' ? t_gen_planes 0.007 ? 10.00 ? 'X-RAY DIFFRACTION' ? t_it 4.500 ? ? ? 'X-RAY DIFFRACTION' ? t_nbd 0.016 ? 10.00 ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 307D _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 307D _struct.title 'Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 307D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 1 ? D N N 2 ? E N N 1 ? F N N 2 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 3 ? K N N 3 ? L N N 3 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 307D 307D ? ? ? 2 2 PDB 307D 307D ? ? ? # 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 307D A 1 ? 10 ? 307D 1 ? 10 ? 1 10 2 2 307D B 1 ? 10 ? 307D 11 ? 20 ? 11 20 3 1 307D C 1 ? 10 ? 307D 21 ? 30 ? 21 30 4 2 307D D 1 ? 10 ? 307D 31 ? 40 ? 31 40 5 1 307D E 1 ? 10 ? 307D 41 ? 50 ? 41 50 6 2 307D F 1 ? 10 ? 307D 51 ? 60 ? 51 60 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 3 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,G,H 2 1 C,D,I,J 3 1 E,F,K,L # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_biol.id 1 2 3 # 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 hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 2 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 2 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 3 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 5 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 8 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 8 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 9 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 9 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 10 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C DC 1 N3 ? ? ? 1_555 D DG 10 N1 ? ? C DC 21 D DG 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C DC 1 N4 ? ? ? 1_555 D DG 10 O6 ? ? C DC 21 D DG 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C DC 1 O2 ? ? ? 1_555 D DG 10 N2 ? ? C DC 21 D DG 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C DA 2 N6 ? ? ? 1_555 D DT 8 O4 ? ? C DA 22 D DT 38 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog28 hydrog ? ? C DA 2 N1 ? ? ? 1_555 D DT 9 N3 ? ? C DA 22 D DT 39 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog29 hydrog ? ? C DA 3 N1 ? ? ? 1_555 D DT 8 N3 ? ? C DA 23 D DT 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C DA 3 N6 ? ? ? 1_555 D DT 8 O4 ? ? C DA 23 D DT 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C DA 4 N1 ? ? ? 1_555 D DT 7 N3 ? ? C DA 24 D DT 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DA 4 N6 ? ? ? 1_555 D DT 7 O4 ? ? C DA 24 D DT 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C DG 5 N1 ? ? ? 1_555 D DC 6 N3 ? ? C DG 25 D DC 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C DG 5 N2 ? ? ? 1_555 D DC 6 O2 ? ? C DG 25 D DC 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C DG 5 O6 ? ? ? 1_555 D DC 6 N4 ? ? C DG 25 D DC 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C DA 6 N1 ? ? ? 1_555 D DT 5 N3 ? ? C DA 26 D DT 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C DA 6 N6 ? ? ? 1_555 D DT 5 O4 ? ? C DA 26 D DT 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C DA 7 N1 ? ? ? 1_555 D DT 4 N3 ? ? C DA 27 D DT 34 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog39 hydrog ? ? C DA 8 N1 ? ? ? 1_555 D DT 3 N3 ? ? C DA 28 D DT 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C DA 8 N6 ? ? ? 1_555 D DT 3 O4 ? ? C DA 28 D DT 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C DA 9 N6 ? ? ? 1_555 D DC 1 N3 ? ? C DA 29 D DC 31 1_555 ? ? ? ? ? ? 'DA-DC MISPAIR' ? ? ? hydrog42 hydrog ? ? C DA 9 N1 ? ? ? 1_555 D DT 2 N3 ? ? C DA 29 D DT 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C DA 9 N6 ? ? ? 1_555 D DT 2 O4 ? ? C DA 29 D DT 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C DG 10 N1 ? ? ? 1_555 D DC 1 N3 ? ? C DG 30 D DC 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C DG 10 N2 ? ? ? 1_555 D DC 1 O2 ? ? C DG 30 D DC 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C DG 10 O6 ? ? ? 1_555 D DC 1 N4 ? ? C DG 30 D DC 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? E DC 1 N3 ? ? ? 1_555 F DG 10 N1 ? ? E DC 41 F DG 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? E DC 1 N4 ? ? ? 1_555 F DG 10 O6 ? ? E DC 41 F DG 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? E DC 1 O2 ? ? ? 1_555 F DG 10 N2 ? ? E DC 41 F DG 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? E DA 2 N1 ? ? ? 1_555 F DT 9 N3 ? ? E DA 42 F DT 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? E DA 2 N6 ? ? ? 1_555 F DT 9 O4 ? ? E DA 42 F DT 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? E DA 3 N1 ? ? ? 1_555 F DT 8 N3 ? ? E DA 43 F DT 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? E DA 3 N6 ? ? ? 1_555 F DT 8 O4 ? ? E DA 43 F DT 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? E DA 4 N1 ? ? ? 1_555 F DT 7 N3 ? ? E DA 44 F DT 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? E DA 4 N6 ? ? ? 1_555 F DT 7 O4 ? ? E DA 44 F DT 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? E DG 5 N1 ? ? ? 1_555 F DC 6 N3 ? ? E DG 45 F DC 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? E DG 5 N2 ? ? ? 1_555 F DC 6 O2 ? ? E DG 45 F DC 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? E DG 5 O6 ? ? ? 1_555 F DC 6 N4 ? ? E DG 45 F DC 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? E DA 6 N1 ? ? ? 1_555 F DT 5 N3 ? ? E DA 46 F DT 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? E DA 6 N6 ? ? ? 1_555 F DT 5 O4 ? ? E DA 46 F DT 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? E DA 7 N1 ? ? ? 1_555 F DT 4 N3 ? ? E DA 47 F DT 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? E DA 7 N6 ? ? ? 1_555 F DT 4 O4 ? ? E DA 47 F DT 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? E DA 8 N6 ? ? ? 1_555 F DT 2 O4 ? ? E DA 48 F DT 52 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog64 hydrog ? ? E DA 8 N1 ? ? ? 1_555 F DT 3 N3 ? ? E DA 48 F DT 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? E DA 8 N6 ? ? ? 1_555 F DT 3 O4 ? ? E DA 48 F DT 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? E DA 9 N1 ? ? ? 1_555 F DT 2 N3 ? ? E DA 49 F DT 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? E DA 9 N6 ? ? ? 1_555 F DT 2 O4 ? ? E DA 49 F DT 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? E DG 10 N1 ? ? ? 1_555 F DC 1 N3 ? ? E DG 50 F DC 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? E DG 10 N2 ? ? ? 1_555 F DC 1 O2 ? ? E DG 50 F DC 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? E DG 10 O6 ? ? ? 1_555 F DC 1 N4 ? ? E DG 50 F DC 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DC 1 ? ? "C3'" A DC 1 ? ? 1.363 1.419 -0.056 0.006 N 2 1 N1 A DC 1 ? ? C2 A DC 1 ? ? 1.335 1.397 -0.062 0.010 N 3 1 N9 A DA 2 ? ? C4 A DA 2 ? ? 1.332 1.374 -0.042 0.006 N 4 1 "O3'" A DG 5 ? ? "C3'" A DG 5 ? ? 1.374 1.419 -0.045 0.006 N 5 1 "O3'" A DA 8 ? ? "C3'" A DA 8 ? ? 1.379 1.419 -0.040 0.006 N 6 1 "O3'" A DA 9 ? ? "C3'" A DA 9 ? ? 1.383 1.419 -0.036 0.006 N 7 1 C6 A DG 10 ? ? N1 A DG 10 ? ? 1.347 1.391 -0.044 0.007 N 8 1 "O3'" B DT 13 ? ? "C3'" B DT 13 ? ? 1.379 1.419 -0.040 0.006 N 9 1 "C1'" B DT 19 ? ? N1 B DT 19 ? ? 1.383 1.468 -0.085 0.014 N 10 1 N1 B DT 19 ? ? C2 B DT 19 ? ? 1.322 1.376 -0.054 0.008 N 11 1 "O3'" C DC 21 ? ? "C3'" C DC 21 ? ? 1.370 1.419 -0.049 0.006 N 12 1 "O3'" C DA 26 ? ? "C3'" C DA 26 ? ? 1.381 1.419 -0.038 0.006 N 13 1 N9 C DA 29 ? ? C4 C DA 29 ? ? 1.329 1.374 -0.045 0.006 N 14 1 "O3'" D DG 40 ? ? "C3'" D DG 40 ? ? 1.381 1.419 -0.038 0.006 N 15 1 "O3'" E DC 41 ? ? "C3'" E DC 41 ? ? 1.383 1.419 -0.036 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 110.40 106.80 3.60 0.50 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.62 108.30 4.32 0.30 N 3 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? "C2'" A DG 5 ? ? 111.34 106.80 4.54 0.50 N 4 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.33 108.30 2.03 0.30 N 5 1 "O4'" A DA 9 ? ? "C4'" A DA 9 ? ? "C3'" A DA 9 ? ? 109.63 106.00 3.63 0.60 N 6 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? "C2'" A DG 10 ? ? 110.86 106.80 4.06 0.50 N 7 1 "O4'" B DT 12 ? ? "C1'" B DT 12 ? ? "C2'" B DT 12 ? ? 110.61 106.80 3.81 0.50 N 8 1 "O4'" B DT 12 ? ? "C1'" B DT 12 ? ? N1 B DT 12 ? ? 112.37 108.30 4.07 0.30 N 9 1 "O4'" B DT 17 ? ? "C1'" B DT 17 ? ? N1 B DT 17 ? ? 111.19 108.30 2.89 0.30 N 10 1 C4 B DT 19 ? ? C5 B DT 19 ? ? C7 B DT 19 ? ? 122.72 119.00 3.72 0.60 N 11 1 "O4'" B DG 20 ? ? "C1'" B DG 20 ? ? N9 B DG 20 ? ? 102.36 108.00 -5.64 0.70 N 12 1 "O4'" C DC 21 ? ? "C1'" C DC 21 ? ? "C2'" C DC 21 ? ? 109.97 106.80 3.17 0.50 N 13 1 "O4'" C DC 21 ? ? "C1'" C DC 21 ? ? N1 C DC 21 ? ? 111.18 108.30 2.88 0.30 N 14 1 "O4'" C DA 22 ? ? "C1'" C DA 22 ? ? N9 C DA 22 ? ? 111.74 108.30 3.44 0.30 N 15 1 "O4'" C DA 23 ? ? "C1'" C DA 23 ? ? "C2'" C DA 23 ? ? 109.92 106.80 3.12 0.50 N 16 1 "O4'" C DG 25 ? ? "C1'" C DG 25 ? ? N9 C DG 25 ? ? 111.68 108.30 3.38 0.30 N 17 1 "O4'" C DA 27 ? ? "C1'" C DA 27 ? ? N9 C DA 27 ? ? 111.31 108.30 3.01 0.30 N 18 1 P C DA 29 ? ? "O5'" C DA 29 ? ? "C5'" C DA 29 ? ? 110.60 120.90 -10.30 1.60 N 19 1 "C5'" C DA 29 ? ? "C4'" C DA 29 ? ? "O4'" C DA 29 ? ? 97.67 109.30 -11.63 1.90 N 20 1 "O4'" C DA 29 ? ? "C1'" C DA 29 ? ? "C2'" C DA 29 ? ? 110.11 106.80 3.31 0.50 N 21 1 "O4'" C DA 29 ? ? "C1'" C DA 29 ? ? N9 C DA 29 ? ? 111.07 108.30 2.77 0.30 N 22 1 "O4'" C DG 30 ? ? "C1'" C DG 30 ? ? N9 C DG 30 ? ? 110.59 108.30 2.29 0.30 N 23 1 "O4'" D DC 31 ? ? "C1'" D DC 31 ? ? "C2'" D DC 31 ? ? 110.37 106.80 3.57 0.50 N 24 1 "O4'" D DC 31 ? ? "C1'" D DC 31 ? ? N1 D DC 31 ? ? 112.59 108.30 4.29 0.30 N 25 1 "O4'" D DT 32 ? ? "C1'" D DT 32 ? ? N1 D DT 32 ? ? 112.05 108.30 3.75 0.30 N 26 1 "O4'" D DT 33 ? ? "C1'" D DT 33 ? ? N1 D DT 33 ? ? 114.41 108.30 6.11 0.30 N 27 1 "C3'" D DT 33 ? ? "O3'" D DT 33 ? ? P D DT 34 ? ? 130.20 119.70 10.50 1.20 Y 28 1 "O4'" D DT 35 ? ? "C1'" D DT 35 ? ? N1 D DT 35 ? ? 111.47 108.30 3.17 0.30 N 29 1 "O4'" D DT 39 ? ? "C1'" D DT 39 ? ? "C2'" D DT 39 ? ? 109.94 106.80 3.14 0.50 N 30 1 "O4'" D DT 39 ? ? "C1'" D DT 39 ? ? N1 D DT 39 ? ? 113.33 108.30 5.03 0.30 N 31 1 "O4'" D DG 40 ? ? "C1'" D DG 40 ? ? N9 D DG 40 ? ? 112.55 108.30 4.25 0.30 N 32 1 "O4'" E DC 41 ? ? "C1'" E DC 41 ? ? N1 E DC 41 ? ? 112.78 108.30 4.48 0.30 N 33 1 "O4'" E DA 44 ? ? "C1'" E DA 44 ? ? N9 E DA 44 ? ? 111.85 108.30 3.55 0.30 N 34 1 "O4'" E DG 45 ? ? "C1'" E DG 45 ? ? "C2'" E DG 45 ? ? 110.08 106.80 3.28 0.50 N 35 1 "O4'" E DG 45 ? ? "C1'" E DG 45 ? ? N9 E DG 45 ? ? 112.69 108.30 4.39 0.30 N 36 1 "O4'" E DA 47 ? ? "C1'" E DA 47 ? ? N9 E DA 47 ? ? 111.71 108.30 3.41 0.30 N 37 1 "O4'" E DG 50 ? ? "C1'" E DG 50 ? ? "C2'" E DG 50 ? ? 110.05 106.80 3.25 0.50 N 38 1 "O4'" E DG 50 ? ? "C1'" E DG 50 ? ? N9 E DG 50 ? ? 114.60 108.30 6.30 0.30 N 39 1 "O4'" F DC 51 ? ? "C1'" F DC 51 ? ? N1 F DC 51 ? ? 113.25 108.30 4.95 0.30 N 40 1 "O4'" F DT 52 ? ? "C1'" F DT 52 ? ? N1 F DT 52 ? ? 111.07 108.30 2.77 0.30 N 41 1 "O4'" F DT 53 ? ? "C1'" F DT 53 ? ? N1 F DT 53 ? ? 111.08 108.30 2.78 0.30 N 42 1 "C3'" F DT 53 ? ? "O3'" F DT 53 ? ? P F DT 54 ? ? 127.18 119.70 7.48 1.20 Y 43 1 "C5'" F DT 54 ? ? "C4'" F DT 54 ? ? "C3'" F DT 54 ? ? 123.99 115.70 8.29 1.20 N 44 1 "O4'" F DT 54 ? ? "C1'" F DT 54 ? ? N1 F DT 54 ? ? 110.32 108.30 2.02 0.30 N 45 1 "O4'" F DT 55 ? ? "C1'" F DT 55 ? ? N1 F DT 55 ? ? 114.02 108.30 5.72 0.30 N 46 1 "O4'" F DT 57 ? ? "C1'" F DT 57 ? ? N1 F DT 57 ? ? 110.43 108.30 2.13 0.30 N 47 1 "O4'" F DT 59 ? ? "C1'" F DT 59 ? ? N1 F DT 59 ? ? 119.69 108.30 11.39 0.30 N # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 307D 'double helix' 307D 'b-form double helix' 307D 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 10 1_555 0.558 -0.492 0.699 -3.192 -15.203 0.034 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DA 2 1_555 B DT 9 1_555 0.171 -0.165 0.152 -2.541 -11.964 -5.892 2 A_DA2:DT19_B A 2 ? B 19 ? 20 1 1 A DA 3 1_555 B DT 8 1_555 0.049 -0.276 0.011 1.467 -15.496 -1.079 3 A_DA3:DT18_B A 3 ? B 18 ? 20 1 1 A DA 4 1_555 B DT 7 1_555 -0.092 -0.135 0.474 8.068 -2.468 -1.185 4 A_DA4:DT17_B A 4 ? B 17 ? 20 1 1 A DG 5 1_555 B DC 6 1_555 -0.026 -0.060 0.263 9.938 -5.287 -1.072 5 A_DG5:DC16_B A 5 ? B 16 ? 19 1 1 A DA 6 1_555 B DT 5 1_555 0.188 -0.079 0.075 1.382 -11.949 4.213 6 A_DA6:DT15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.071 -0.056 -0.176 2.215 -17.725 2.796 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DA 8 1_555 B DT 3 1_555 -0.185 -0.161 -0.114 0.119 -16.914 2.452 8 A_DA8:DT13_B A 8 ? B 13 ? 20 1 1 A DA 9 1_555 B DT 2 1_555 0.008 -0.272 0.239 4.813 -12.561 4.482 9 A_DA9:DT12_B A 9 ? B 12 ? 20 1 1 A DG 10 1_555 B DC 1 1_555 -0.308 -0.112 0.348 10.193 -13.874 0.010 10 A_DG10:DC11_B A 10 ? B 11 ? 19 1 1 C DC 1 1_555 D DG 10 1_555 0.353 -0.005 0.698 -9.840 -5.653 4.456 11 C_DC21:DG40_D C 21 ? D 40 ? 19 1 1 C DA 2 1_555 D DT 9 1_555 -0.632 0.460 1.257 9.489 -26.801 21.416 12 C_DA22:DT39_D C 22 ? D 39 ? ? 1 1 C DA 3 1_555 D DT 8 1_555 -0.340 -0.295 0.728 11.931 -14.754 10.044 13 C_DA23:DT38_D C 23 ? D 38 ? 20 1 1 C DA 4 1_555 D DT 7 1_555 -0.186 -0.223 0.847 14.739 -8.846 13.106 14 C_DA24:DT37_D C 24 ? D 37 ? 20 1 1 C DG 5 1_555 D DC 6 1_555 -0.759 -0.813 0.505 4.596 -17.494 0.277 15 C_DG25:DC36_D C 25 ? D 36 ? 19 1 1 C DA 6 1_555 D DT 5 1_555 -0.472 -0.056 0.406 3.718 -0.609 4.495 16 C_DA26:DT35_D C 26 ? D 35 ? 20 1 1 C DA 7 1_555 D DT 4 1_555 -0.695 0.116 0.294 -6.719 -29.302 6.323 17 C_DA27:DT34_D C 27 ? D 34 ? ? ? 1 C DA 8 1_555 D DT 3 1_555 0.588 -0.590 0.029 -8.096 -14.774 2.989 18 C_DA28:DT33_D C 28 ? D 33 ? 20 1 1 C DA 9 1_555 D DT 2 1_555 -0.336 -0.661 -0.045 -2.540 -20.215 -9.413 19 C_DA29:DT32_D C 29 ? D 32 ? 20 1 1 C DG 10 1_555 D DC 1 1_555 -0.546 -1.125 1.342 12.776 -8.859 -8.266 20 C_DG30:DC31_D C 30 ? D 31 ? 19 1 1 E DC 1 1_555 F DG 10 1_555 -1.117 0.178 0.235 0.363 -2.875 0.776 21 E_DC41:DG60_F E 41 ? F 60 ? 19 1 1 E DA 2 1_555 F DT 9 1_555 0.888 -0.670 0.439 -21.119 -9.461 -5.502 22 E_DA42:DT59_F E 42 ? F 59 ? 20 1 1 E DA 3 1_555 F DT 8 1_555 0.551 -0.679 -0.144 0.607 -26.425 2.378 23 E_DA43:DT58_F E 43 ? F 58 ? 20 1 1 E DA 4 1_555 F DT 7 1_555 -0.024 0.022 -0.063 -8.299 -12.297 6.682 24 E_DA44:DT57_F E 44 ? F 57 ? 20 1 1 E DG 5 1_555 F DC 6 1_555 0.160 -0.019 -0.124 -6.894 -30.862 10.411 25 E_DG45:DC56_F E 45 ? F 56 ? 19 1 1 E DA 6 1_555 F DT 5 1_555 0.522 -0.359 0.151 -11.061 -10.920 -3.622 26 E_DA46:DT55_F E 46 ? F 55 ? 20 1 1 E DA 7 1_555 F DT 4 1_555 0.355 -0.332 -0.032 -5.258 -11.126 -15.201 27 E_DA47:DT54_F E 47 ? F 54 ? 20 1 1 E DA 8 1_555 F DT 3 1_555 -1.425 -0.810 0.553 -16.735 -9.970 -3.802 28 E_DA48:DT53_F E 48 ? F 53 ? 20 1 1 E DA 9 1_555 F DT 2 1_555 -0.133 -1.088 1.424 1.345 -0.939 5.585 29 E_DA49:DT52_F E 49 ? F 52 ? 20 1 1 E DG 10 1_555 F DC 1 1_555 1.274 -0.502 0.041 -18.177 -3.692 1.705 30 E_DG50:DC51_F E 50 ? F 51 ? 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 DA 2 1_555 B DT 9 1_555 0.037 2.086 3.352 3.390 -12.242 45.208 3.584 0.220 2.726 -15.565 -4.310 46.868 1 AA_DC1DA2:DT19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DA 2 1_555 B DT 9 1_555 A DA 3 1_555 B DT 8 1_555 -0.115 0.225 3.221 -1.458 6.090 33.485 -0.577 -0.033 3.213 10.457 2.504 34.049 2 AA_DA2DA3:DT18DT19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DA 3 1_555 B DT 8 1_555 A DA 4 1_555 B DT 7 1_555 0.190 -0.357 3.080 -5.131 1.589 30.360 -0.961 -1.293 2.986 3.005 9.702 30.820 3 AA_DA3DA4:DT17DT18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DA 4 1_555 B DT 7 1_555 A DG 5 1_555 B DC 6 1_555 0.119 -0.682 3.349 0.873 1.796 31.833 -1.574 -0.055 3.309 3.270 -1.590 31.894 4 AA_DA4DG5:DC16DT17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DG 5 1_555 B DC 6 1_555 A DA 6 1_555 B DT 5 1_555 -0.174 -0.371 3.457 2.015 -4.381 39.451 -0.004 0.505 3.464 -6.461 -2.971 39.733 5 AA_DG5DA6:DT15DC16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DA 6 1_555 B DT 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.093 -0.445 3.154 2.149 -1.324 36.004 -0.537 0.443 3.158 -2.138 -3.471 36.089 6 AA_DA6DA7:DT14DT15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B DT 4 1_555 A DA 8 1_555 B DT 3 1_555 -0.125 -0.293 3.253 -1.997 -2.164 36.373 -0.169 -0.077 3.266 -3.460 3.193 36.488 7 AA_DA7DA8:DT13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DA 8 1_555 B DT 3 1_555 A DA 9 1_555 B DT 2 1_555 0.405 -0.338 3.041 -3.084 -0.921 35.789 -0.427 -1.064 3.004 -1.496 5.006 35.928 8 AA_DA8DA9:DT12DT13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DA 9 1_555 B DT 2 1_555 A DG 10 1_555 B DC 1 1_555 0.099 -0.104 3.312 -0.178 11.215 28.475 -2.441 -0.223 3.053 21.763 0.345 30.562 9 AA_DA9DG10:DC11DT12_BB A 9 ? B 12 ? A 10 ? B 11 ? 1 C DC 1 1_555 D DG 10 1_555 C DA 2 1_555 D DT 9 1_555 0.938 0.151 2.956 1.127 -2.218 25.704 0.900 -1.815 2.970 -4.972 -2.525 25.822 10 CC_DC21DA22:DT39DG40_DD C 21 ? D 40 ? C 22 ? D 39 ? 1 C DA 2 1_555 D DT 9 1_555 C DA 3 1_555 D DT 8 1_555 -0.452 0.200 3.202 -0.366 2.270 35.083 -0.002 0.695 3.212 3.761 0.607 35.156 11 CC_DA22DA23:DT38DT39_DD C 22 ? D 39 ? C 23 ? D 38 ? 1 C DA 3 1_555 D DT 8 1_555 C DA 4 1_555 D DT 7 1_555 0.462 -0.440 3.351 -1.917 -8.216 34.372 0.532 -1.055 3.335 -13.650 3.185 35.362 12 CC_DA23DA24:DT37DT38_DD C 23 ? D 38 ? C 24 ? D 37 ? 1 C DA 4 1_555 D DT 7 1_555 C DG 5 1_555 D DC 6 1_555 -0.452 -0.822 3.521 1.428 -3.315 33.932 -0.831 1.016 3.562 -5.661 -2.438 34.117 13 CC_DA24DG25:DC36DT37_DD C 24 ? D 37 ? C 25 ? D 36 ? 1 C DG 5 1_555 D DC 6 1_555 C DA 6 1_555 D DT 5 1_555 0.687 -0.538 3.038 3.251 -1.260 38.589 -0.667 -0.661 3.099 -1.901 -4.907 38.740 14 CC_DG25DA26:DT35DC36_DD C 25 ? D 36 ? C 26 ? D 35 ? 1 C DA 6 1_555 D DT 5 1_555 C DA 7 1_555 D DT 4 1_555 -0.176 0.071 3.578 4.214 -5.753 36.593 0.943 0.884 3.487 -9.056 -6.635 37.258 15 CC_DA26DA27:DT34DT35_DD C 26 ? D 35 ? C 27 ? D 34 ? 1 C DA 7 1_555 D DT 4 1_555 C DA 8 1_555 D DT 3 1_555 -0.231 0.143 3.269 2.854 -0.076 45.909 0.189 0.541 3.250 -0.097 -3.655 45.992 16 CC_DA27DA28:DT33DT34_DD C 27 ? D 34 ? C 28 ? D 33 ? 1 C DA 8 1_555 D DT 3 1_555 C DA 9 1_555 D DT 2 1_555 -0.186 0.107 3.103 1.053 -4.112 29.903 0.996 0.560 3.053 -7.918 -2.027 30.196 17 CC_DA28DA29:DT32DT33_DD C 28 ? D 33 ? C 29 ? D 32 ? 1 C DA 9 1_555 D DT 2 1_555 C DG 10 1_555 D DC 1 1_555 0.553 -0.229 2.913 -9.022 3.218 36.487 -0.717 -1.872 2.677 5.033 14.112 37.682 18 CC_DA29DG30:DC31DT32_DD C 29 ? D 32 ? C 30 ? D 31 ? 1 E DC 1 1_555 F DG 10 1_555 E DA 2 1_555 F DT 9 1_555 -0.246 0.416 3.861 -2.119 0.302 49.842 0.467 0.109 3.870 0.359 2.513 49.885 19 EE_DC41DA42:DT59DG60_FF E 41 ? F 60 ? E 42 ? F 59 ? 1 E DA 2 1_555 F DT 9 1_555 E DA 3 1_555 F DT 8 1_555 -0.537 -0.528 2.954 6.545 -4.600 25.852 -0.080 2.641 2.787 -9.982 -14.202 27.041 20 EE_DA42DA43:DT58DT59_FF E 42 ? F 59 ? E 43 ? F 58 ? 1 E DA 3 1_555 F DT 8 1_555 E DA 4 1_555 F DT 7 1_555 0.626 0.041 3.386 -1.020 -2.172 35.259 0.399 -1.187 3.359 -3.581 1.682 35.338 21 EE_DA43DA44:DT57DT58_FF E 43 ? F 58 ? E 44 ? F 57 ? 1 E DA 4 1_555 F DT 7 1_555 E DG 5 1_555 F DC 6 1_555 0.070 -0.116 3.157 5.711 4.095 32.874 -0.848 0.781 3.089 7.134 -9.950 33.597 22 EE_DA44DG45:DC56DT57_FF E 44 ? F 57 ? E 45 ? F 56 ? 1 E DG 5 1_555 F DC 6 1_555 E DA 6 1_555 F DT 5 1_555 -0.447 -0.625 3.118 -8.142 10.313 39.766 -1.899 -0.182 2.909 14.683 11.592 41.797 23 EE_DG45DA46:DT55DC56_FF E 45 ? F 56 ? E 46 ? F 55 ? 1 E DA 6 1_555 F DT 5 1_555 E DA 7 1_555 F DT 4 1_555 -1.057 -0.196 3.061 -2.001 -10.240 35.127 1.033 1.420 3.051 -16.521 3.229 36.597 24 EE_DA46DA47:DT54DT55_FF E 46 ? F 55 ? E 47 ? F 54 ? 1 E DA 7 1_555 F DT 4 1_555 E DA 8 1_555 F DT 3 1_555 0.796 -0.438 3.726 0.406 -1.609 29.633 -0.468 -1.456 3.754 -3.144 -0.794 29.678 25 EE_DA47DA48:DT53DT54_FF E 47 ? F 54 ? E 48 ? F 53 ? 1 E DA 8 1_555 F DT 3 1_555 E DA 9 1_555 F DT 2 1_555 0.540 -0.210 2.666 -10.227 -5.866 39.814 0.205 -1.637 2.466 -8.394 14.633 41.455 26 EE_DA48DA49:DT52DT53_FF E 48 ? F 53 ? E 49 ? F 52 ? 1 E DA 9 1_555 F DT 2 1_555 E DG 10 1_555 F DC 1 1_555 0.068 -0.800 3.887 8.417 -1.183 35.503 -1.082 1.286 3.827 -1.906 -13.564 36.474 27 EE_DA49DG50:DC51DT52_FF E 49 ? F 52 ? E 50 ? F 51 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'IDEAL B-DNA HELIX OF SEQUENCE CAAAGAAAAG' # _atom_sites.entry_id 307D _atom_sites.fract_transf_matrix[1][1] 0.016717 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.004128 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.035361 _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] 0.014209 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_ #