data_4HQI # _entry.id 4HQI # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4HQI pdb_00004hqi 10.2210/pdb4hqi/pdb NDB NA2104 ? ? RCSB RCSB075793 ? ? WWPDB D_1000075793 ? ? # 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 2013-07-10 2 'Structure model' 1 1 2013-09-11 3 'Structure model' 1 2 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_conn 5 3 'Structure model' struct_conn_type 6 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.conn_type_id' 4 3 'Structure model' '_struct_conn.id' 5 3 'Structure model' '_struct_conn.pdbx_dist_value' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 15 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 16 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 19 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 20 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 21 3 'Structure model' '_struct_conn_type.id' 22 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 23 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 24 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4HQI _pdbx_database_status.recvd_initial_deposition_date 2012-10-25 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kowal, E.A.' 1 'Lad, R.' 2 'Pallan, P.S.' 3 'Muffly, E.' 4 'Wawrzak, Z.' 5 'Egli, M.' 6 'Sturla, S.J.' 7 'Stone, M.P.' 8 # _citation.id primary _citation.title ;Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 41 _citation.page_first 7566 _citation.page_last 7576 _citation.year 2013 _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 23748954 _citation.pdbx_database_id_DOI 10.1093/nar/gkt488 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kowal, E.A.' 1 ? primary 'Lad, R.R.' 2 ? primary 'Pallan, P.S.' 3 ? primary 'Dhummakupt, E.' 4 ? primary 'Wawrzak, Z.' 5 ? primary 'Egli, M.' 6 ? primary 'Sturla, S.J.' 7 ? primary 'Stone, M.P.' 8 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'Short modified nucleic acids' 3826.607 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 non-polymer syn 'STRONTIUM ION' 87.620 1 ? ? ? ? 4 water nat water 18.015 49 ? ? ? ? # _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 '(DC)(DG)(DC)(BZG)(DA)(DA)(DT)(DT)(D3N)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCNAATTXGCG _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 SPERMINE SPM 3 'STRONTIUM ION' SR 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 BZG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 D3N n 1 10 DG n 1 11 DC n 1 12 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'SYNTHETIC CONSTRUCT' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details 'Chemically synthesized modified oligonucleotides' # 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 BZG 'DNA linking' . '6-(BENZYLOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE' "O6-BENZYL-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" 'C17 H20 N5 O7 P' 437.344 D3N 'DNA linking' . '1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-perimidin-2(3H)-one' ? 'C16 H17 N2 O7 P' 380.289 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 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 # 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 ? ? ? A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 BZG 4 4 4 BZG BZG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 D3N 9 9 9 D3N D3N A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 13 13 DC DC B . n B 1 2 DG 2 14 14 DG DG B . n B 1 3 DC 3 15 15 DC DC B . n B 1 4 BZG 4 16 16 BZG BZG B . n B 1 5 DA 5 17 17 DA DA B . n B 1 6 DA 6 18 18 DA DA B . n B 1 7 DT 7 19 19 DT DT B . n B 1 8 DT 8 20 20 DT DT B . n B 1 9 D3N 9 21 21 D3N D3N B . n B 1 10 DG 10 22 22 DG DG B . n B 1 11 DC 11 23 23 DC DC B . n B 1 12 DG 12 24 24 DG DG 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 SPM 1 101 330 SPM SPM A . D 3 SR 1 102 1 SR SR A . E 4 HOH 1 201 4 HOH HOH A . E 4 HOH 2 202 7 HOH HOH A . E 4 HOH 3 203 11 HOH HOH A . E 4 HOH 4 204 12 HOH HOH A . E 4 HOH 5 205 13 HOH HOH A . E 4 HOH 6 206 19 HOH HOH A . E 4 HOH 7 207 20 HOH HOH A . E 4 HOH 8 208 21 HOH HOH A . E 4 HOH 9 209 22 HOH HOH A . E 4 HOH 10 210 23 HOH HOH A . E 4 HOH 11 211 24 HOH HOH A . E 4 HOH 12 212 25 HOH HOH A . E 4 HOH 13 213 26 HOH HOH A . E 4 HOH 14 214 28 HOH HOH A . E 4 HOH 15 215 30 HOH HOH A . E 4 HOH 16 216 31 HOH HOH A . E 4 HOH 17 217 32 HOH HOH A . E 4 HOH 18 218 33 HOH HOH A . E 4 HOH 19 219 34 HOH HOH A . E 4 HOH 20 220 35 HOH HOH A . E 4 HOH 21 221 37 HOH HOH A . E 4 HOH 22 222 38 HOH HOH A . E 4 HOH 23 223 39 HOH HOH A . E 4 HOH 24 224 41 HOH HOH A . E 4 HOH 25 225 44 HOH HOH A . E 4 HOH 26 226 48 HOH HOH A . E 4 HOH 27 227 49 HOH HOH A . E 4 HOH 28 228 50 HOH HOH A . F 4 HOH 1 101 2 HOH HOH B . F 4 HOH 2 102 3 HOH HOH B . F 4 HOH 3 103 5 HOH HOH B . F 4 HOH 4 104 6 HOH HOH B . F 4 HOH 5 105 8 HOH HOH B . F 4 HOH 6 106 9 HOH HOH B . F 4 HOH 7 107 10 HOH HOH B . F 4 HOH 8 108 14 HOH HOH B . F 4 HOH 9 109 15 HOH HOH B . F 4 HOH 10 110 16 HOH HOH B . F 4 HOH 11 111 17 HOH HOH B . F 4 HOH 12 112 18 HOH HOH B . F 4 HOH 13 113 27 HOH HOH B . F 4 HOH 14 114 29 HOH HOH B . F 4 HOH 15 115 36 HOH HOH B . F 4 HOH 16 116 40 HOH HOH B . F 4 HOH 17 117 42 HOH HOH B . F 4 HOH 18 118 43 HOH HOH B . F 4 HOH 19 119 45 HOH HOH B . F 4 HOH 20 120 46 HOH HOH B . F 4 HOH 21 121 47 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 B DC 13 ? "O5'" ? B DC 1 "O5'" 2 1 Y 1 B DC 13 ? "C5'" ? B DC 1 "C5'" 3 1 Y 1 B DC 13 ? "C4'" ? B DC 1 "C4'" 4 1 Y 1 B DC 13 ? "O4'" ? B DC 1 "O4'" 5 1 Y 1 B DC 13 ? "C3'" ? B DC 1 "C3'" 6 1 Y 1 B DC 13 ? "C2'" ? B DC 1 "C2'" 7 1 Y 1 B DC 13 ? "C1'" ? B DC 1 "C1'" 8 1 Y 1 B DC 13 ? N1 ? B DC 1 N1 9 1 Y 1 B DC 13 ? C2 ? B DC 1 C2 10 1 Y 1 B DC 13 ? O2 ? B DC 1 O2 11 1 Y 1 B DC 13 ? N3 ? B DC 1 N3 12 1 Y 1 B DC 13 ? C4 ? B DC 1 C4 13 1 Y 1 B DC 13 ? N4 ? B DC 1 N4 14 1 Y 1 B DC 13 ? C5 ? B DC 1 C5 15 1 Y 1 B DC 13 ? C6 ? B DC 1 C6 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MD2 'data collection' 'diffractometer software from EMBL (with LS-CAT developed extensions)' ? 1 PHENIX 'model building' . ? 2 REFMAC refinement 5.7.0029 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 4HQI _cell.length_a 26.384 _cell.length_b 36.774 _cell.length_c 77.653 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4HQI _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4HQI _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # loop_ _exptl_crystal.id _exptl_crystal.density_meas _exptl_crystal.density_Matthews _exptl_crystal.density_percent_sol _exptl_crystal.description _exptl_crystal.F_000 _exptl_crystal.preparation 1 ? 2.46 50.02 ? ? ? 2 ? ? ? ? ? ? # loop_ _exptl_crystal_grow.crystal_id _exptl_crystal_grow.method _exptl_crystal_grow.temp _exptl_crystal_grow.temp_details _exptl_crystal_grow.pH _exptl_crystal_grow.pdbx_details _exptl_crystal_grow.pdbx_pH_range 1 'VAPOR DIFFUSION, HANGING DROP' 291 ? 7.0 ;20 mM sodium cacodylate (pH 7.0), 6 mM spermine tetra-HCl, 20 mM LiCl, 40 mM SrCl2 and 5% v/v 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K ; ? 2 'VAPOR DIFFUSION, HANGING DROP' 291 ? 7.0 ;20 mM sodium cacodylate (pH 7.0), 6 mM spermine tetra-HCl, 40 mM KCl, 10 mM BaCl2 and 5% v/v 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K ; ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 2 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'MARMOSAIC 300 mm CCD' 2009-07-17 'Si(111)' 2 CCD 'MARMOSAIC 300 mm CCD' 2008-07-18 'C(111)' # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M 'Si(111)' 'SINGLE WAVELENGTH' x-ray 2 1 M 'C(111)' 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.60499 1.0 2 0.97857 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'APS BEAMLINE 21-ID-D' APS 21-ID-D ? 1.60499 2 SYNCHROTRON 'APS BEAMLINE 21-ID-G' APS 21-ID-G ? 0.97857 # _reflns.entry_id 4HQI _reflns.observed_criterion_sigma_I 5 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 30.0 _reflns.d_resolution_high 1.70 _reflns.number_obs 8236 _reflns.number_all 8811 _reflns.percent_possible_obs 93.4 _reflns.pdbx_Rmerge_I_obs 0.044 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 52.33 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.4 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1,2 # _reflns_shell.d_res_high 1.70 _reflns_shell.d_res_low 1.76 _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs 0.228 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.65 _reflns_shell.pdbx_redundancy 4 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 524 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1,2 # _refine.entry_id 4HQI _refine.ls_number_reflns_obs 7486 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.67 _refine.ls_d_res_high 1.70 _refine.ls_percent_reflns_obs 93.39 _refine.ls_R_factor_obs 0.26227 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.25885 _refine.ls_R_factor_R_free 0.29823 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 8.9 _refine.ls_number_reflns_R_free 734 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.954 _refine.correlation_coeff_Fo_to_Fc_free 0.940 _refine.B_iso_mean 44.140 _refine.aniso_B[1][1] 3.33 _refine.aniso_B[2][2] 1.38 _refine.aniso_B[3][3] -4.71 _refine.aniso_B[1][2] -0.00 _refine.aniso_B[1][3] -0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.149 _refine.pdbx_overall_ESU_R_Free 0.144 _refine.overall_SU_ML 0.130 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 4.224 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1,2 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 481 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 49 _refine_hist.number_atoms_total 545 _refine_hist.d_res_high 1.70 _refine_hist.d_res_low 20.67 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.011 0.013 ? 554 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.652 1.578 ? 833 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.125 0.200 ? 66 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.023 0.020 ? 260 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.70 _refine_ls_shell.d_res_low 1.745 _refine_ls_shell.number_reflns_R_work 338 _refine_ls_shell.R_factor_R_work 0.336 _refine_ls_shell.percent_reflns_obs 57.01 _refine_ls_shell.R_factor_R_free 0.336 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 36 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 4HQI _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 4HQI _struct.title ;Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4HQI _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;B-form DNA, O6-Benzyl-2'-deoxyguanosine, dPer, Perimidinone-Derived Nucleoside, Dickerson-Drew Dodecamer, DNA ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4HQI _struct_ref.pdbx_db_accession 4HQI _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 4HQI A 1 ? 12 ? 4HQI 1 ? 12 ? 1 12 2 1 4HQI B 1 ? 12 ? 4HQI 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1890 ? 1 MORE -24 ? 1 'SSA (A^2)' 4860 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DC 3 "O3'" ? ? ? 1_555 A BZG 4 P ? ? A DC 3 A BZG 4 1_555 ? ? ? ? ? ? ? 1.586 ? ? covale2 covale both ? A DT 8 "O3'" ? ? ? 1_555 A D3N 9 P ? ? A DT 8 A D3N 9 1_555 ? ? ? ? ? ? ? 1.578 ? ? covale3 covale both ? B DC 3 "O3'" ? ? ? 1_555 B BZG 4 P ? ? B DC 15 B BZG 16 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale4 covale both ? B DT 8 "O3'" ? ? ? 1_555 B D3N 9 P ? ? B DT 20 B D3N 21 1_555 ? ? ? ? ? ? ? 1.591 ? ? metalc1 metalc ? ? A DG 12 O6 ? ? ? 1_555 D SR . SR ? ? A DG 12 A SR 102 1_555 ? ? ? ? ? ? ? 2.690 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SPM 101 ? 6 'BINDING SITE FOR RESIDUE SPM A 101' AC2 Software A SR 102 ? 1 'BINDING SITE FOR RESIDUE SR A 102' # 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 6 DG A 2 ? DG A 2 . ? 1_555 ? 2 AC1 6 D3N A 9 ? D3N A 9 . ? 2_555 ? 3 AC1 6 D3N A 9 ? D3N A 9 . ? 3_645 ? 4 AC1 6 DG A 10 ? DG A 10 . ? 2_555 ? 5 AC1 6 DG B 2 ? DG B 14 . ? 2_555 ? 6 AC1 6 DG B 10 ? DG B 22 . ? 1_555 ? 7 AC2 1 DG A 12 ? DG A 12 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 225 ? ? O A HOH 226 ? ? 2.09 2 1 O B HOH 103 ? ? O B HOH 104 ? ? 2.19 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 DC _pdbx_validate_rmsd_angle.auth_seq_id_1 3 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 DC _pdbx_validate_rmsd_angle.auth_seq_id_2 3 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 "C4'" _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 DC _pdbx_validate_rmsd_angle.auth_seq_id_3 3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 103.88 _pdbx_validate_rmsd_angle.angle_target_value 110.10 _pdbx_validate_rmsd_angle.angle_deviation -6.22 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.00 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id DC _pdbx_unobs_or_zero_occ_residues.auth_seq_id 1 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id DC _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 # 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 BZG P P N N 1 BZG O1P O N N 2 BZG O2P O N N 3 BZG "O5'" O N N 4 BZG CZ1 C Y N 5 BZG CT1 C Y N 6 BZG CI C Y N 7 BZG CT2 C Y N 8 BZG CZ2 C Y N 9 BZG CE C Y N 10 BZG CW C N N 11 BZG OL O N N 12 BZG CK C Y N 13 BZG NJ N Y N 14 BZG CH C Y N 15 BZG NI N N N 16 BZG NG N Y N 17 BZG CF C Y N 18 BZG CM C Y N 19 BZG NN N Y N 20 BZG CO C Y N 21 BZG NE N Y N 22 BZG "CT'" C N R 23 BZG "OS'" O N N 24 BZG "CP'" C N N 25 BZG "C5'" C N N 26 BZG "C4'" C N R 27 BZG "C3'" C N S 28 BZG "O3'" O N N 29 BZG OXT O N N 30 BZG H1P H N N 31 BZG HOT H N N 32 BZG "H5'1" H N N 33 BZG "H5'2" H N N 34 BZG HZ1 H N N 35 BZG HT1 H N N 36 BZG HI H N N 37 BZG HT2 H N N 38 BZG HZ2 H N N 39 BZG HWC1 H N N 40 BZG HWC2 H N N 41 BZG HIN1 H N N 42 BZG HIN2 H N N 43 BZG HO H N N 44 BZG "HT'" H N N 45 BZG "HP'1" H N N 46 BZG "HP'2" H N N 47 BZG "H4'" H N N 48 BZG "H3'" H N N 49 BZG HA H N N 50 D3N O1P O N N 51 D3N P P N N 52 D3N O2P O N N 53 D3N "O5'" O N N 54 D3N "C5'" C N N 55 D3N "C4'" C N R 56 D3N "O4'" O N N 57 D3N "C3'" C N S 58 D3N "O3'" O N N 59 D3N "C2'" C N N 60 D3N "C1'" C N R 61 D3N N1 N N N 62 D3N C2 C N N 63 D3N O2 O N N 64 D3N N3 N N N 65 D3N C4 C Y N 66 D3N C5 C Y N 67 D3N C6 C Y N 68 D3N C7 C Y N 69 D3N C8 C Y N 70 D3N C9 C Y N 71 D3N C10 C Y N 72 D3N C11 C Y N 73 D3N C12 C Y N 74 D3N C13 C Y N 75 D3N H1 H N N 76 D3N H3 H N N 77 D3N H4 H N N 78 D3N H5 H N N 79 D3N H6 H N N 80 D3N H7 H N N 81 D3N H8 H N N 82 D3N H9 H N N 83 D3N H10 H N N 84 D3N H11 H N N 85 D3N H12 H N N 86 D3N H13 H N N 87 D3N H14 H N N 88 D3N H15 H N N 89 D3N H16 H N N 90 D3N H17 H N N 91 D3N OP3 O N N 92 D3N H2 H N N 93 DA OP3 O N N 94 DA P P N N 95 DA OP1 O N N 96 DA OP2 O N N 97 DA "O5'" O N N 98 DA "C5'" C N N 99 DA "C4'" C N R 100 DA "O4'" O N N 101 DA "C3'" C N S 102 DA "O3'" O N N 103 DA "C2'" C N N 104 DA "C1'" C N R 105 DA N9 N Y N 106 DA C8 C Y N 107 DA N7 N Y N 108 DA C5 C Y N 109 DA C6 C Y N 110 DA N6 N N N 111 DA N1 N Y N 112 DA C2 C Y N 113 DA N3 N Y N 114 DA C4 C Y N 115 DA HOP3 H N N 116 DA HOP2 H N N 117 DA "H5'" H N N 118 DA "H5''" H N N 119 DA "H4'" H N N 120 DA "H3'" H N N 121 DA "HO3'" H N N 122 DA "H2'" H N N 123 DA "H2''" H N N 124 DA "H1'" H N N 125 DA H8 H N N 126 DA H61 H N N 127 DA H62 H N N 128 DA H2 H N N 129 DC OP3 O N N 130 DC P P N N 131 DC OP1 O N N 132 DC OP2 O N N 133 DC "O5'" O N N 134 DC "C5'" C N N 135 DC "C4'" C N R 136 DC "O4'" O N N 137 DC "C3'" C N S 138 DC "O3'" O N N 139 DC "C2'" C N N 140 DC "C1'" C N R 141 DC N1 N N N 142 DC C2 C N N 143 DC O2 O N N 144 DC N3 N N N 145 DC C4 C N N 146 DC N4 N N N 147 DC C5 C N N 148 DC C6 C N N 149 DC HOP3 H N N 150 DC HOP2 H N N 151 DC "H5'" H N N 152 DC "H5''" H N N 153 DC "H4'" H N N 154 DC "H3'" H N N 155 DC "HO3'" H N N 156 DC "H2'" H N N 157 DC "H2''" H N N 158 DC "H1'" H N N 159 DC H41 H N N 160 DC H42 H N N 161 DC H5 H N N 162 DC H6 H N N 163 DG OP3 O N N 164 DG P P N N 165 DG OP1 O N N 166 DG OP2 O N N 167 DG "O5'" O N N 168 DG "C5'" C N N 169 DG "C4'" C N R 170 DG "O4'" O N N 171 DG "C3'" C N S 172 DG "O3'" O N N 173 DG "C2'" C N N 174 DG "C1'" C N R 175 DG N9 N Y N 176 DG C8 C Y N 177 DG N7 N Y N 178 DG C5 C Y N 179 DG C6 C N N 180 DG O6 O N N 181 DG N1 N N N 182 DG C2 C N N 183 DG N2 N N N 184 DG N3 N N N 185 DG C4 C Y N 186 DG HOP3 H N N 187 DG HOP2 H N N 188 DG "H5'" H N N 189 DG "H5''" H N N 190 DG "H4'" H N N 191 DG "H3'" H N N 192 DG "HO3'" H N N 193 DG "H2'" H N N 194 DG "H2''" H N N 195 DG "H1'" H N N 196 DG H8 H N N 197 DG H1 H N N 198 DG H21 H N N 199 DG H22 H N N 200 DT OP3 O N N 201 DT P P N N 202 DT OP1 O N N 203 DT OP2 O N N 204 DT "O5'" O N N 205 DT "C5'" C N N 206 DT "C4'" C N R 207 DT "O4'" O N N 208 DT "C3'" C N S 209 DT "O3'" O N N 210 DT "C2'" C N N 211 DT "C1'" C N R 212 DT N1 N N N 213 DT C2 C N N 214 DT O2 O N N 215 DT N3 N N N 216 DT C4 C N N 217 DT O4 O N N 218 DT C5 C N N 219 DT C7 C N N 220 DT C6 C N N 221 DT HOP3 H N N 222 DT HOP2 H N N 223 DT "H5'" H N N 224 DT "H5''" H N N 225 DT "H4'" H N N 226 DT "H3'" H N N 227 DT "HO3'" H N N 228 DT "H2'" H N N 229 DT "H2''" H N N 230 DT "H1'" H N N 231 DT H3 H N N 232 DT H71 H N N 233 DT H72 H N N 234 DT H73 H N N 235 DT H6 H N N 236 HOH O O N N 237 HOH H1 H N N 238 HOH H2 H N N 239 SPM N1 N N N 240 SPM C2 C N N 241 SPM C3 C N N 242 SPM C4 C N N 243 SPM N5 N N N 244 SPM C6 C N N 245 SPM C7 C N N 246 SPM C8 C N N 247 SPM C9 C N N 248 SPM N10 N N N 249 SPM C11 C N N 250 SPM C12 C N N 251 SPM C13 C N N 252 SPM N14 N N N 253 SPM HN11 H N N 254 SPM HN12 H N N 255 SPM H21 H N N 256 SPM H22 H N N 257 SPM H31 H N N 258 SPM H32 H N N 259 SPM H41 H N N 260 SPM H42 H N N 261 SPM HN5 H N N 262 SPM H61 H N N 263 SPM H62 H N N 264 SPM H71 H N N 265 SPM H72 H N N 266 SPM H81 H N N 267 SPM H82 H N N 268 SPM H91 H N N 269 SPM H92 H N N 270 SPM HN0 H N N 271 SPM H111 H N N 272 SPM H112 H N N 273 SPM H121 H N N 274 SPM H122 H N N 275 SPM H131 H N N 276 SPM H132 H N N 277 SPM HN41 H N N 278 SPM HN42 H N N 279 SR SR SR N N 280 # 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 BZG P O1P sing N N 1 BZG P O2P doub N N 2 BZG P "O5'" sing N N 3 BZG P OXT sing N N 4 BZG O1P H1P sing N N 5 BZG "O5'" "C5'" sing N N 6 BZG CZ1 CT1 sing Y N 7 BZG CZ1 CE doub Y N 8 BZG CZ1 HZ1 sing N N 9 BZG CT1 CI doub Y N 10 BZG CT1 HT1 sing N N 11 BZG CI CT2 sing Y N 12 BZG CI HI sing N N 13 BZG CT2 CZ2 doub Y N 14 BZG CT2 HT2 sing N N 15 BZG CZ2 CE sing Y N 16 BZG CZ2 HZ2 sing N N 17 BZG CE CW sing N N 18 BZG CW OL sing N N 19 BZG CW HWC1 sing N N 20 BZG CW HWC2 sing N N 21 BZG OL CK sing N N 22 BZG CK NJ sing Y N 23 BZG CK CM doub Y N 24 BZG NJ CH doub Y N 25 BZG CH NI sing N N 26 BZG CH NG sing Y N 27 BZG NI HIN1 sing N N 28 BZG NI HIN2 sing N N 29 BZG NG CF doub Y N 30 BZG CF CM sing Y N 31 BZG CF NE sing Y N 32 BZG CM NN sing Y N 33 BZG NN CO doub Y N 34 BZG CO NE sing Y N 35 BZG CO HO sing N N 36 BZG NE "CT'" sing N N 37 BZG "CT'" "OS'" sing N N 38 BZG "CT'" "CP'" sing N N 39 BZG "CT'" "HT'" sing N N 40 BZG "OS'" "C4'" sing N N 41 BZG "CP'" "C3'" sing N N 42 BZG "CP'" "HP'1" sing N N 43 BZG "CP'" "HP'2" sing N N 44 BZG "C5'" "C4'" sing N N 45 BZG "C5'" "H5'1" sing N N 46 BZG "C5'" "H5'2" sing N N 47 BZG "C4'" "C3'" sing N N 48 BZG "C4'" "H4'" sing N N 49 BZG "C3'" "O3'" sing N N 50 BZG "C3'" "H3'" sing N N 51 BZG "O3'" HA sing N N 52 BZG OXT HOT sing N N 53 D3N "O3'" "C3'" sing N N 54 D3N "C2'" "C3'" sing N N 55 D3N "C2'" "C1'" sing N N 56 D3N "C3'" "C4'" sing N N 57 D3N "C1'" N1 sing N N 58 D3N "C1'" "O4'" sing N N 59 D3N O2 C2 doub N N 60 D3N N1 C2 sing N N 61 D3N N1 C6 sing N N 62 D3N C2 N3 sing N N 63 D3N C7 C6 doub Y N 64 D3N C7 C8 sing Y N 65 D3N C6 C5 sing Y N 66 D3N "C4'" "O4'" sing N N 67 D3N "C4'" "C5'" sing N N 68 D3N C8 C9 doub Y N 69 D3N N3 C4 sing N N 70 D3N C5 C4 doub Y N 71 D3N C5 C10 sing Y N 72 D3N C4 C13 sing Y N 73 D3N C9 C10 sing Y N 74 D3N C10 C11 doub Y N 75 D3N C13 C12 doub Y N 76 D3N "C5'" "O5'" sing N N 77 D3N C11 C12 sing Y N 78 D3N "O5'" P sing N N 79 D3N O2P P doub N N 80 D3N P O1P sing N N 81 D3N O1P H1 sing N N 82 D3N "C5'" H3 sing N N 83 D3N "C5'" H4 sing N N 84 D3N "C4'" H5 sing N N 85 D3N "C3'" H6 sing N N 86 D3N "O3'" H7 sing N N 87 D3N "C2'" H8 sing N N 88 D3N "C2'" H9 sing N N 89 D3N "C1'" H10 sing N N 90 D3N N3 H11 sing N N 91 D3N C7 H12 sing N N 92 D3N C8 H13 sing N N 93 D3N C9 H14 sing N N 94 D3N C11 H15 sing N N 95 D3N C12 H16 sing N N 96 D3N C13 H17 sing N N 97 D3N P OP3 sing N N 98 D3N OP3 H2 sing N N 99 DA OP3 P sing N N 100 DA OP3 HOP3 sing N N 101 DA P OP1 doub N N 102 DA P OP2 sing N N 103 DA P "O5'" sing N N 104 DA OP2 HOP2 sing N N 105 DA "O5'" "C5'" sing N N 106 DA "C5'" "C4'" sing N N 107 DA "C5'" "H5'" sing N N 108 DA "C5'" "H5''" sing N N 109 DA "C4'" "O4'" sing N N 110 DA "C4'" "C3'" sing N N 111 DA "C4'" "H4'" sing N N 112 DA "O4'" "C1'" sing N N 113 DA "C3'" "O3'" sing N N 114 DA "C3'" "C2'" sing N N 115 DA "C3'" "H3'" sing N N 116 DA "O3'" "HO3'" sing N N 117 DA "C2'" "C1'" sing N N 118 DA "C2'" "H2'" sing N N 119 DA "C2'" "H2''" sing N N 120 DA "C1'" N9 sing N N 121 DA "C1'" "H1'" sing N N 122 DA N9 C8 sing Y N 123 DA N9 C4 sing Y N 124 DA C8 N7 doub Y N 125 DA C8 H8 sing N N 126 DA N7 C5 sing Y N 127 DA C5 C6 sing Y N 128 DA C5 C4 doub Y N 129 DA C6 N6 sing N N 130 DA C6 N1 doub Y N 131 DA N6 H61 sing N N 132 DA N6 H62 sing N N 133 DA N1 C2 sing Y N 134 DA C2 N3 doub Y N 135 DA C2 H2 sing N N 136 DA N3 C4 sing Y N 137 DC OP3 P sing N N 138 DC OP3 HOP3 sing N N 139 DC P OP1 doub N N 140 DC P OP2 sing N N 141 DC P "O5'" sing N N 142 DC OP2 HOP2 sing N N 143 DC "O5'" "C5'" sing N N 144 DC "C5'" "C4'" sing N N 145 DC "C5'" "H5'" sing N N 146 DC "C5'" "H5''" sing N N 147 DC "C4'" "O4'" sing N N 148 DC "C4'" "C3'" sing N N 149 DC "C4'" "H4'" sing N N 150 DC "O4'" "C1'" sing N N 151 DC "C3'" "O3'" sing N N 152 DC "C3'" "C2'" sing N N 153 DC "C3'" "H3'" sing N N 154 DC "O3'" "HO3'" sing N N 155 DC "C2'" "C1'" sing N N 156 DC "C2'" "H2'" sing N N 157 DC "C2'" "H2''" sing N N 158 DC "C1'" N1 sing N N 159 DC "C1'" "H1'" sing N N 160 DC N1 C2 sing N N 161 DC N1 C6 sing N N 162 DC C2 O2 doub N N 163 DC C2 N3 sing N N 164 DC N3 C4 doub N N 165 DC C4 N4 sing N N 166 DC C4 C5 sing N N 167 DC N4 H41 sing N N 168 DC N4 H42 sing N N 169 DC C5 C6 doub N N 170 DC C5 H5 sing N N 171 DC C6 H6 sing N N 172 DG OP3 P sing N N 173 DG OP3 HOP3 sing N N 174 DG P OP1 doub N N 175 DG P OP2 sing N N 176 DG P "O5'" sing N N 177 DG OP2 HOP2 sing N N 178 DG "O5'" "C5'" sing N N 179 DG "C5'" "C4'" sing N N 180 DG "C5'" "H5'" sing N N 181 DG "C5'" "H5''" sing N N 182 DG "C4'" "O4'" sing N N 183 DG "C4'" "C3'" sing N N 184 DG "C4'" "H4'" sing N N 185 DG "O4'" "C1'" sing N N 186 DG "C3'" "O3'" sing N N 187 DG "C3'" "C2'" sing N N 188 DG "C3'" "H3'" sing N N 189 DG "O3'" "HO3'" sing N N 190 DG "C2'" "C1'" sing N N 191 DG "C2'" "H2'" sing N N 192 DG "C2'" "H2''" sing N N 193 DG "C1'" N9 sing N N 194 DG "C1'" "H1'" sing N N 195 DG N9 C8 sing Y N 196 DG N9 C4 sing Y N 197 DG C8 N7 doub Y N 198 DG C8 H8 sing N N 199 DG N7 C5 sing Y N 200 DG C5 C6 sing N N 201 DG C5 C4 doub Y N 202 DG C6 O6 doub N N 203 DG C6 N1 sing N N 204 DG N1 C2 sing N N 205 DG N1 H1 sing N N 206 DG C2 N2 sing N N 207 DG C2 N3 doub N N 208 DG N2 H21 sing N N 209 DG N2 H22 sing N N 210 DG N3 C4 sing N N 211 DT OP3 P sing N N 212 DT OP3 HOP3 sing N N 213 DT P OP1 doub N N 214 DT P OP2 sing N N 215 DT P "O5'" sing N N 216 DT OP2 HOP2 sing N N 217 DT "O5'" "C5'" sing N N 218 DT "C5'" "C4'" sing N N 219 DT "C5'" "H5'" sing N N 220 DT "C5'" "H5''" sing N N 221 DT "C4'" "O4'" sing N N 222 DT "C4'" "C3'" sing N N 223 DT "C4'" "H4'" sing N N 224 DT "O4'" "C1'" sing N N 225 DT "C3'" "O3'" sing N N 226 DT "C3'" "C2'" sing N N 227 DT "C3'" "H3'" sing N N 228 DT "O3'" "HO3'" sing N N 229 DT "C2'" "C1'" sing N N 230 DT "C2'" "H2'" sing N N 231 DT "C2'" "H2''" sing N N 232 DT "C1'" N1 sing N N 233 DT "C1'" "H1'" sing N N 234 DT N1 C2 sing N N 235 DT N1 C6 sing N N 236 DT C2 O2 doub N N 237 DT C2 N3 sing N N 238 DT N3 C4 sing N N 239 DT N3 H3 sing N N 240 DT C4 O4 doub N N 241 DT C4 C5 sing N N 242 DT C5 C7 sing N N 243 DT C5 C6 doub N N 244 DT C7 H71 sing N N 245 DT C7 H72 sing N N 246 DT C7 H73 sing N N 247 DT C6 H6 sing N N 248 HOH O H1 sing N N 249 HOH O H2 sing N N 250 SPM N1 C2 sing N N 251 SPM N1 HN11 sing N N 252 SPM N1 HN12 sing N N 253 SPM C2 C3 sing N N 254 SPM C2 H21 sing N N 255 SPM C2 H22 sing N N 256 SPM C3 C4 sing N N 257 SPM C3 H31 sing N N 258 SPM C3 H32 sing N N 259 SPM C4 N5 sing N N 260 SPM C4 H41 sing N N 261 SPM C4 H42 sing N N 262 SPM N5 C6 sing N N 263 SPM N5 HN5 sing N N 264 SPM C6 C7 sing N N 265 SPM C6 H61 sing N N 266 SPM C6 H62 sing N N 267 SPM C7 C8 sing N N 268 SPM C7 H71 sing N N 269 SPM C7 H72 sing N N 270 SPM C8 C9 sing N N 271 SPM C8 H81 sing N N 272 SPM C8 H82 sing N N 273 SPM C9 N10 sing N N 274 SPM C9 H91 sing N N 275 SPM C9 H92 sing N N 276 SPM N10 C11 sing N N 277 SPM N10 HN0 sing N N 278 SPM C11 C12 sing N N 279 SPM C11 H111 sing N N 280 SPM C11 H112 sing N N 281 SPM C12 C13 sing N N 282 SPM C12 H121 sing N N 283 SPM C12 H122 sing N N 284 SPM C13 N14 sing N N 285 SPM C13 H131 sing N N 286 SPM C13 H132 sing N N 287 SPM N14 HN41 sing N N 288 SPM N14 HN42 sing N N 289 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4HQI 'b-form double helix' 4HQI 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 2 1_555 B DC 11 1_555 -0.125 -0.253 -0.220 -11.324 3.168 -1.868 1 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.199 -0.225 -0.317 2.151 10.773 -1.099 2 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 -0.236 -0.008 -0.460 -12.406 0.879 1.251 3 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 -0.009 -0.142 -0.125 -5.111 -11.621 0.172 4 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 0.132 -0.121 -0.126 2.516 -6.703 1.351 5 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 0.024 -0.181 -0.510 8.065 -0.035 4.832 6 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DG 10 1_555 B DC 3 1_555 -0.259 -0.158 -0.143 -0.234 8.429 0.472 7 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.194 -0.224 -0.063 10.713 2.217 -1.590 8 A_DC11:DG14_B A 11 ? B 14 ? 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 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.825 -0.036 3.016 -1.267 -2.600 30.408 0.405 -1.796 2.973 -4.943 2.408 30.542 1 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.057 -0.095 3.259 -2.570 8.650 26.842 -2.189 -0.476 3.072 18.000 5.348 28.292 2 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 -0.148 -0.601 3.135 0.082 6.206 27.711 -2.567 0.320 2.933 12.755 -0.169 28.384 3 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 1.209 0.289 3.235 6.047 7.993 32.969 -0.800 -1.070 3.374 13.696 -10.360 34.418 4 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -0.894 0.014 3.141 0.568 -2.918 30.844 0.565 1.778 3.110 -5.470 -1.064 30.984 5 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? # _atom_sites.entry_id 4HQI _atom_sites.fract_transf_matrix[1][1] 0.037902 _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] 0.027193 _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] 0.012878 _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 SR # loop_