data_9V87 # _entry.id 9V87 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.413 _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 9V87 pdb_00009v87 10.2210/pdb9v87/pdb WWPDB D_1300058293 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2026-06-03 _pdbx_audit_revision_history.part_number ? # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9V87 _pdbx_database_status.recvd_initial_deposition_date 2025-05-29 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 3 _pdbx_contact_author.email mhho@nchu.edu.tw _pdbx_contact_author.name_first Ming-Hon _pdbx_contact_author.name_last Hou _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-4170-1527 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Yuan, Y.C.' 1 0009-0003-9945-372X 'Wang, S.C.' 2 0000-0001-5617-8447 'Hou, M.H.' 3 0000-0003-4170-1527 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Crystal structure of d(CGTTAACG)2' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yuan, Y.C.' 1 0009-0003-9945-372X primary 'Wang, S.C.' 2 0000-0001-5617-8447 primary 'Hou, M.H.' 3 0000-0003-4170-1527 # 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(P*CP*GP*TP*TP*AP*AP*CP*G)-3') ; 2426.617 4 ? ? ? ? 2 non-polymer syn 'SPERMINE (FULLY PROTONATED FORM)' 206.372 2 ? ? ? ? 3 non-polymer syn 'COBALT (II) ION' 58.933 7 ? ? ? ? 4 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 5 water nat water 18.015 66 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DT)(DT)(DA)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTTAACG _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SPERMINE (FULLY PROTONATED FORM)' SPK 3 'COBALT (II) ION' CO 4 'CHLORIDE ION' CL 5 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 DT n 1 4 DT n 1 5 DA n 1 6 DA n 1 7 DC n 1 8 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 8 _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 ? # 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 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 CO non-polymer . 'COBALT (II) ION' ? 'Co 2' 58.933 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 SPK non-polymer . 'SPERMINE (FULLY PROTONATED FORM)' ? 'C10 H30 N4 4' 206.372 # 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 DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DT 4 4 4 DT DT 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 DC 7 7 7 DC DC A . n A 1 8 DG 8 8 8 DG DG A . n B 1 1 DC 1 1 ? ? ? B . n B 1 2 DG 2 2 2 DG DG B . n B 1 3 DT 3 3 3 DT DT B . n B 1 4 DT 4 4 4 DT DT B . n B 1 5 DA 5 5 5 DA DA B . n B 1 6 DA 6 6 6 DA DA B . n B 1 7 DC 7 7 7 DC DC B . n B 1 8 DG 8 8 8 DG DG B . n C 1 1 DC 1 1 ? ? ? C . n C 1 2 DG 2 2 2 DG DG C . n C 1 3 DT 3 3 3 DT DT C . n C 1 4 DT 4 4 4 DT DT C . n C 1 5 DA 5 5 5 DA DA C . n C 1 6 DA 6 6 6 DA DA C . n C 1 7 DC 7 7 7 DC DC C . n C 1 8 DG 8 8 8 DG DG C . n D 1 1 DC 1 1 ? ? ? D . n D 1 2 DG 2 2 2 DG DG D . n D 1 3 DT 3 3 3 DT DT D . n D 1 4 DT 4 4 4 DT DT D . n D 1 5 DA 5 5 5 DA DA D . n D 1 6 DA 6 6 6 DA DA D . n D 1 7 DC 7 7 7 DC DC D . n D 1 8 DG 8 8 8 DG DG D . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id SPK _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id SPK _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # 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 E 2 SPK 1 101 101 SPK SPE A . F 3 CO 1 102 4 CO CO A . G 3 CO 1 101 1 CO CO B . H 3 CO 1 102 7 CO CO B . I 4 CL 1 103 2 CL CL B . J 2 SPK 1 201 201 SPK SPE C . K 3 CO 1 202 2 CO CO C . L 3 CO 1 203 6 CO CO C . M 3 CO 1 101 3 CO CO D . N 3 CO 1 102 8 CO CO D . O 5 HOH 1 201 63 HOH HOH A . O 5 HOH 2 202 74 HOH HOH A . O 5 HOH 3 203 39 HOH HOH A . O 5 HOH 4 204 82 HOH HOH A . O 5 HOH 5 205 31 HOH HOH A . O 5 HOH 6 206 16 HOH HOH A . O 5 HOH 7 207 29 HOH HOH A . O 5 HOH 8 208 25 HOH HOH A . O 5 HOH 9 209 32 HOH HOH A . O 5 HOH 10 210 40 HOH HOH A . O 5 HOH 11 211 72 HOH HOH A . O 5 HOH 12 212 33 HOH HOH A . O 5 HOH 13 213 53 HOH HOH A . O 5 HOH 14 214 38 HOH HOH A . O 5 HOH 15 215 35 HOH HOH A . O 5 HOH 16 216 41 HOH HOH A . P 5 HOH 1 201 49 HOH HOH B . P 5 HOH 2 202 9 HOH HOH B . P 5 HOH 3 203 8 HOH HOH B . P 5 HOH 4 204 11 HOH HOH B . P 5 HOH 5 205 77 HOH HOH B . P 5 HOH 6 206 7 HOH HOH B . P 5 HOH 7 207 34 HOH HOH B . P 5 HOH 8 208 70 HOH HOH B . P 5 HOH 9 209 81 HOH HOH B . P 5 HOH 10 210 17 HOH HOH B . P 5 HOH 11 211 22 HOH HOH B . Q 5 HOH 1 301 56 HOH HOH C . Q 5 HOH 2 302 51 HOH HOH C . Q 5 HOH 3 303 24 HOH HOH C . Q 5 HOH 4 304 2 HOH HOH C . Q 5 HOH 5 305 30 HOH HOH C . Q 5 HOH 6 306 1 HOH HOH C . Q 5 HOH 7 307 20 HOH HOH C . Q 5 HOH 8 308 79 HOH HOH C . Q 5 HOH 9 309 5 HOH HOH C . Q 5 HOH 10 310 26 HOH HOH C . Q 5 HOH 11 311 19 HOH HOH C . Q 5 HOH 12 312 43 HOH HOH C . Q 5 HOH 13 313 12 HOH HOH C . Q 5 HOH 14 314 6 HOH HOH C . Q 5 HOH 15 315 10 HOH HOH C . Q 5 HOH 16 316 65 HOH HOH C . Q 5 HOH 17 317 80 HOH HOH C . Q 5 HOH 18 318 47 HOH HOH C . Q 5 HOH 19 319 42 HOH HOH C . Q 5 HOH 20 320 36 HOH HOH C . Q 5 HOH 21 321 28 HOH HOH C . Q 5 HOH 22 322 27 HOH HOH C . R 5 HOH 1 201 13 HOH HOH D . R 5 HOH 2 202 44 HOH HOH D . R 5 HOH 3 203 54 HOH HOH D . R 5 HOH 4 204 3 HOH HOH D . R 5 HOH 5 205 37 HOH HOH D . R 5 HOH 6 206 78 HOH HOH D . R 5 HOH 7 207 21 HOH HOH D . R 5 HOH 8 208 52 HOH HOH D . R 5 HOH 9 209 76 HOH HOH D . R 5 HOH 10 210 71 HOH HOH D . R 5 HOH 11 211 62 HOH HOH D . R 5 HOH 12 212 67 HOH HOH D . R 5 HOH 13 213 48 HOH HOH D . R 5 HOH 14 214 45 HOH HOH D . R 5 HOH 15 215 75 HOH HOH D . R 5 HOH 16 216 14 HOH HOH D . R 5 HOH 17 217 18 HOH HOH D . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_reference_DOI _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.21.1_5286: ???)' ? 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . ? 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . ? 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . ? 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 9V87 _cell.details ? _cell.formula_units_Z ? _cell.length_a 45.447 _cell.length_a_esd ? _cell.length_b 45.447 _cell.length_b_esd ? _cell.length_c 71.352 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 24 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9V87 _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 2' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9V87 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.19 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 43.87 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.6mM Oligonucleotide, 50mM HEPES pH 7.5, 2mM Spermine tetrahydrochloride, 8.5mM Cobalt(II) chloride, 5% MPD' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'RAYONIX MX300HE' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-06-12 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'NSRRC BEAMLINE BL15A1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.00000 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL15A1 _diffrn_source.pdbx_synchrotron_site NSRRC # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 9V87 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.61 _reflns.d_resolution_low 30.00 _reflns.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.number_all ? _reflns.number_obs 11151 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.7 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 5.5 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 14.8 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.044 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 1.61 1.67 ? ? ? ? ? ? 1108 ? ? ? ? ? ? ? ? ? ? ? 5.3 1.068 ? ? 0.380 0.165 ? 1 1 0.993 0.998 ? 100.0 ? 0.342 ? ? ? ? ? ? ? ? ? 1.67 1.73 ? ? ? ? ? ? 1101 ? ? ? ? ? ? ? ? ? ? ? 5.5 1.051 ? ? 0.492 0.207 ? 2 1 0.923 0.980 ? 100.0 ? 0.445 ? ? ? ? ? ? ? ? ? 1.73 1.81 ? ? ? ? ? ? 1103 ? ? ? ? ? ? ? ? ? ? ? 5.5 1.085 ? ? 0.338 0.143 ? 3 1 0.953 0.988 ? 99.9 ? 0.306 ? ? ? ? ? ? ? ? ? 1.81 1.91 ? ? ? ? ? ? 1103 ? ? ? ? ? ? ? ? ? ? ? 5.5 1.095 ? ? 0.265 0.111 ? 4 1 0.975 0.994 ? 100.0 ? 0.240 ? ? ? ? ? ? ? ? ? 1.91 2.03 ? ? ? ? ? ? 1111 ? ? ? ? ? ? ? ? ? ? ? 5.5 1.085 ? ? 0.201 0.085 ? 5 1 0.976 0.994 ? 100.0 ? 0.182 ? ? ? ? ? ? ? ? ? 2.03 2.18 ? ? ? ? ? ? 1104 ? ? ? ? ? ? ? ? ? ? ? 5.5 1.093 ? ? 0.139 0.058 ? 6 1 0.987 0.997 ? 99.9 ? 0.125 ? ? ? ? ? ? ? ? ? 2.18 2.40 ? ? ? ? ? ? 1122 ? ? ? ? ? ? ? ? ? ? ? 5.5 1.049 ? ? 0.096 0.040 ? 7 1 0.995 0.999 ? 100.0 ? 0.087 ? ? ? ? ? ? ? ? ? 2.40 2.75 ? ? ? ? ? ? 1109 ? ? ? ? ? ? ? ? ? ? ? 5.5 1.044 ? ? 0.054 0.023 ? 8 1 0.997 0.999 ? 100.0 ? 0.049 ? ? ? ? ? ? ? ? ? 2.75 3.47 ? ? ? ? ? ? 1128 ? ? ? ? ? ? ? ? ? ? ? 5.5 1.043 ? ? 0.030 0.013 ? 9 1 1.000 1.000 ? 99.1 ? 0.027 ? ? ? ? ? ? ? ? ? 2.75 3.47 ? ? ? ? ? ? 1162 ? ? ? ? ? ? ? ? ? ? ? 5.3 1.064 ? ? 0.025 0.011 ? 10 1 0.999 1.000 ? 98.3 ? 0.022 ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9V87 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.61 _refine.ls_d_res_low 18.97 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 11122 _refine.ls_number_reflns_R_free 1108 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.77 _refine.ls_percent_reflns_R_free 9.96 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2565 _refine.ls_R_factor_R_free 0.2539 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2130 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.35 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method NONE _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values TWIN_LSQ_F _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.10 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 35.49 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 1.61 _refine_hist.d_res_low 18.97 _refine_hist.number_atoms_solvent 66 _refine_hist.number_atoms_total 701 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 599 _refine_hist.pdbx_number_atoms_ligand 36 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_Zscore _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.008 ? 695 ? f_bond_d ? ? ? 'X-RAY DIFFRACTION' ? 0.838 ? 1048 ? f_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 32.529 ? 332 ? f_dihedral_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 0.045 ? 116 ? f_chiral_restr ? ? ? 'X-RAY DIFFRACTION' ? 0.005 ? 29 ? f_plane_restr ? ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.correlation_coeff_Fo_to_Fc _refine_ls_shell.correlation_coeff_Fo_to_Fc_free _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 1.61 1.68 . . 139 1255 90.00 . . . . 0.4271 . . . . . . . . . . . . . . . 0.4225 'X-RAY DIFFRACTION' 1.68 1.77 . . 134 1221 90.00 . . . . 0.3864 . . . . . . . . . . . . . . . 0.3952 'X-RAY DIFFRACTION' 1.77 1.88 . . 140 1248 90.00 . . . . 0.3900 . . . . . . . . . . . . . . . 0.3417 'X-RAY DIFFRACTION' 1.88 2.03 . . 134 1237 90.00 . . . . 0.3483 . . . . . . . . . . . . . . . 0.3351 'X-RAY DIFFRACTION' 2.03 2.23 . . 139 1250 90.00 . . . . 0.2983 . . . . . . . . . . . . . . . 0.3520 'X-RAY DIFFRACTION' 2.23 2.55 . . 140 1255 90.00 . . . . 0.2969 . . . . . . . . . . . . . . . 0.3096 'X-RAY DIFFRACTION' 2.55 3.21 . . 140 1258 90.00 . . . . 0.2436 . . . . . . . . . . . . . . . 0.2642 'X-RAY DIFFRACTION' 3.22 18.97 . . 141 1291 89.00 . . . . 0.1698 . . . . . . . . . . . . . . . 0.2412 # _struct.entry_id 9V87 _struct.title 'Crystal structure of d(CGTTAACG)2' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9V87 _struct_keywords.text 'DNA perfectly matched, Watson and Crick base pairing, DNA' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 4 ? J N N 2 ? K N N 3 ? L N N 3 ? M N N 3 ? N N N 3 ? O N N 5 ? P N N 5 ? Q N N 5 ? R N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9V87 _struct_ref.pdbx_db_accession 9V87 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 9V87 A 1 ? 8 ? 9V87 1 ? 8 ? 1 8 2 1 9V87 B 1 ? 8 ? 9V87 1 ? 8 ? 1 8 3 1 9V87 C 1 ? 8 ? 9V87 1 ? 8 ? 1 8 4 1 9V87 D 1 ? 8 ? 9V87 1 ? 8 ? 1 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A DG 2 N7 ? ? ? 1_555 F CO . CO ? ? A DG 2 A CO 102 1_555 ? ? ? ? ? ? ? 2.114 ? ? metalc2 metalc ? ? B DG 2 N7 ? ? ? 1_555 H CO . CO ? ? B DG 2 B CO 102 1_555 ? ? ? ? ? ? ? 1.922 ? ? metalc3 metalc ? ? B DG 8 N7 ? ? ? 1_555 G CO . CO ? ? B DG 8 B CO 101 1_555 ? ? ? ? ? ? ? 2.094 ? ? metalc4 metalc ? ? G CO . CO ? ? ? 1_555 P HOH . O ? ? B CO 101 B HOH 205 1_555 ? ? ? ? ? ? ? 1.972 ? ? metalc5 metalc ? ? G CO . CO ? ? ? 1_555 P HOH . O ? ? B CO 101 B HOH 206 1_555 ? ? ? ? ? ? ? 2.275 ? ? metalc6 metalc ? ? G CO . CO ? ? ? 1_555 R HOH . O ? ? B CO 101 D HOH 206 6_545 ? ? ? ? ? ? ? 1.907 ? ? metalc7 metalc ? ? C DG 2 N7 ? ? ? 1_555 L CO . CO ? ? C DG 2 C CO 203 1_555 ? ? ? ? ? ? ? 2.211 ? ? metalc8 metalc ? ? C DG 8 N7 ? ? ? 1_555 K CO . CO ? ? C DG 8 C CO 202 1_555 ? ? ? ? ? ? ? 2.298 ? ? metalc9 metalc ? ? C DG 8 N7 ? ? ? 1_555 K CO . CO ? ? C DG 8 C CO 202 4_554 ? ? ? ? ? ? ? 2.351 ? ? metalc10 metalc ? ? K CO . CO ? ? ? 1_555 Q HOH . O ? ? C CO 202 C HOH 302 1_555 ? ? ? ? ? ? ? 1.982 ? ? metalc11 metalc ? ? K CO . CO ? ? ? 1_555 Q HOH . O ? ? C CO 202 C HOH 302 4_554 ? ? ? ? ? ? ? 1.974 ? ? metalc12 metalc ? ? K CO . CO ? ? ? 1_555 Q HOH . O ? ? C CO 202 C HOH 308 1_555 ? ? ? ? ? ? ? 2.190 ? ? metalc13 metalc ? ? K CO . CO ? ? ? 1_555 Q HOH . O ? ? C CO 202 C HOH 308 4_554 ? ? ? ? ? ? ? 2.190 ? ? metalc14 metalc ? ? L CO . CO ? ? ? 1_555 Q HOH . O ? ? C CO 203 C HOH 317 1_555 ? ? ? ? ? ? ? 1.934 ? ? metalc15 metalc ? ? D DG 2 N7 ? ? ? 1_555 M CO . CO ? ? D DG 2 D CO 101 1_555 ? ? ? ? ? ? ? 1.989 ? ? metalc16 metalc ? ? M CO . CO ? ? ? 1_555 R HOH . O ? ? D CO 101 D HOH 209 1_555 ? ? ? ? ? ? ? 2.028 ? ? metalc17 metalc ? ? M CO . CO ? ? ? 1_555 R HOH . O ? ? D CO 101 D HOH 215 1_555 ? ? ? ? ? ? ? 1.948 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 C DG 8 N1 ? ? A DC 1 C DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 C DG 8 O6 ? ? A DC 1 C DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 C DG 8 N2 ? ? A DC 1 C DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 2 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 2 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 2 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 2 N2 ? ? ? 1_555 C DG 8 N3 ? ? A DG 2 C DG 8 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog8 hydrog ? ? A DG 2 N3 ? ? ? 1_555 C DG 8 N2 ? ? A DG 2 C DG 8 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog9 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 3 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 3 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 4 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 4 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 5 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 5 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 6 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 6 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 7 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 7 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 7 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? B DG 8 N2 ? ? ? 1_555 D DG 2 N3 ? ? B DG 8 D DG 2 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog21 hydrog ? ? B DG 8 N3 ? ? ? 1_555 D DG 2 N2 ? ? B DG 8 D DG 2 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog22 hydrog ? ? C DG 2 N1 ? ? ? 1_555 D DC 7 N3 ? ? C DG 2 D DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C DG 2 N2 ? ? ? 1_555 D DC 7 O2 ? ? C DG 2 D DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C DG 2 O6 ? ? ? 1_555 D DC 7 N4 ? ? C DG 2 D DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C DT 3 N3 ? ? ? 1_555 D DA 6 N1 ? ? C DT 3 D DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C DT 3 O4 ? ? ? 1_555 D DA 6 N6 ? ? C DT 3 D DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C DT 4 N3 ? ? ? 1_555 D DA 5 N1 ? ? C DT 4 D DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C DT 4 O4 ? ? ? 1_555 D DA 5 N6 ? ? C DT 4 D DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C DA 5 N1 ? ? ? 1_555 D DT 4 N3 ? ? C DA 5 D DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C DA 5 N6 ? ? ? 1_555 D DT 4 O4 ? ? C DA 5 D DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C DA 6 N1 ? ? ? 1_555 D DT 3 N3 ? ? C DA 6 D DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DA 6 N6 ? ? ? 1_555 D DT 3 O4 ? ? C DA 6 D DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C DC 7 N3 ? ? ? 1_555 D DG 2 N1 ? ? C DC 7 D DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C DC 7 N4 ? ? ? 1_555 D DG 2 O6 ? ? C DC 7 D DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C DC 7 O2 ? ? ? 1_555 D DG 2 N2 ? ? C DC 7 D DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N7 ? B DG 8 ? B DG 8 ? 1_555 CO ? G CO . ? B CO 101 ? 1_555 O ? P HOH . ? B HOH 205 ? 1_555 89.3 ? 2 N7 ? B DG 8 ? B DG 8 ? 1_555 CO ? G CO . ? B CO 101 ? 1_555 O ? P HOH . ? B HOH 206 ? 1_555 83.0 ? 3 O ? P HOH . ? B HOH 205 ? 1_555 CO ? G CO . ? B CO 101 ? 1_555 O ? P HOH . ? B HOH 206 ? 1_555 85.0 ? 4 N7 ? B DG 8 ? B DG 8 ? 1_555 CO ? G CO . ? B CO 101 ? 1_555 O ? R HOH . ? D HOH 206 ? 6_545 86.8 ? 5 O ? P HOH . ? B HOH 205 ? 1_555 CO ? G CO . ? B CO 101 ? 1_555 O ? R HOH . ? D HOH 206 ? 6_545 170.9 ? 6 O ? P HOH . ? B HOH 206 ? 1_555 CO ? G CO . ? B CO 101 ? 1_555 O ? R HOH . ? D HOH 206 ? 6_545 102.6 ? 7 N7 ? C DG 2 ? C DG 2 ? 1_555 CO ? L CO . ? C CO 203 ? 1_555 O ? Q HOH . ? C HOH 317 ? 1_555 96.9 ? 8 N7 ? C DG 8 ? C DG 8 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 N7 ? C DG 8 ? C DG 8 ? 1_555 0.0 ? 9 N7 ? C DG 8 ? C DG 8 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 302 ? 1_555 88.5 ? 10 N7 ? C DG 8 ? C DG 8 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 302 ? 1_555 88.5 ? 11 N7 ? C DG 8 ? C DG 8 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 302 ? 4_554 91.1 ? 12 N7 ? C DG 8 ? C DG 8 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 302 ? 4_554 91.1 ? 13 O ? Q HOH . ? C HOH 302 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 302 ? 4_554 146.5 ? 14 N7 ? C DG 8 ? C DG 8 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 308 ? 1_555 93.9 ? 15 N7 ? C DG 8 ? C DG 8 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 308 ? 1_555 93.9 ? 16 O ? Q HOH . ? C HOH 302 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 308 ? 1_555 106.6 ? 17 O ? Q HOH . ? C HOH 302 ? 4_554 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 308 ? 1_555 106.8 ? 18 N7 ? C DG 8 ? C DG 8 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 308 ? 4_554 93.9 ? 19 N7 ? C DG 8 ? C DG 8 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 308 ? 4_554 93.9 ? 20 O ? Q HOH . ? C HOH 302 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 308 ? 4_554 106.6 ? 21 O ? Q HOH . ? C HOH 302 ? 4_554 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 308 ? 4_554 106.9 ? 22 O ? Q HOH . ? C HOH 308 ? 1_555 CO ? K CO . ? C CO 202 ? 1_555 O ? Q HOH . ? C HOH 308 ? 4_554 0.0 ? 23 N7 ? D DG 2 ? D DG 2 ? 1_555 CO ? M CO . ? D CO 101 ? 1_555 O ? R HOH . ? D HOH 209 ? 1_555 105.4 ? 24 N7 ? D DG 2 ? D DG 2 ? 1_555 CO ? M CO . ? D CO 101 ? 1_555 O ? R HOH . ? D HOH 215 ? 1_555 147.2 ? 25 O ? R HOH . ? D HOH 209 ? 1_555 CO ? M CO . ? D CO 101 ? 1_555 O ? R HOH . ? D HOH 215 ? 1_555 105.1 ? # _pdbx_entry_details.entry_id 9V87 _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 B CL 103 ? I CL . 2 1 C CO 202 ? K CO . 3 1 A HOH 204 ? O HOH . 4 1 A HOH 207 ? O HOH . 5 1 A HOH 211 ? O HOH . 6 1 A HOH 215 ? O HOH . 7 1 B HOH 211 ? P HOH . 8 1 C HOH 308 ? Q HOH . 9 1 C HOH 318 ? Q HOH . # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 B DC 1 ? B DC 1 2 1 Y 1 C DC 1 ? C DC 1 3 1 Y 1 D DC 1 ? D DC 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 CL CL CL N N 1 CO CO CO N N 2 DA OP3 O N N 3 DA P P N N 4 DA OP1 O N N 5 DA OP2 O N N 6 DA "O5'" O N N 7 DA "C5'" C N N 8 DA "C4'" C N R 9 DA "O4'" O N N 10 DA "C3'" C N S 11 DA "O3'" O N N 12 DA "C2'" C N N 13 DA "C1'" C N R 14 DA N9 N Y N 15 DA C8 C Y N 16 DA N7 N Y N 17 DA C5 C Y N 18 DA C6 C Y N 19 DA N6 N N N 20 DA N1 N Y N 21 DA C2 C Y N 22 DA N3 N Y N 23 DA C4 C Y N 24 DA HOP3 H N N 25 DA HOP2 H N N 26 DA "H5'" H N N 27 DA "H5''" H N N 28 DA "H4'" H N N 29 DA "H3'" H N N 30 DA "HO3'" H N N 31 DA "H2'" H N N 32 DA "H2''" H N N 33 DA "H1'" H N N 34 DA H8 H N N 35 DA H61 H N N 36 DA H62 H N N 37 DA H2 H N N 38 DC OP3 O N N 39 DC P P N N 40 DC OP1 O N N 41 DC OP2 O N N 42 DC "O5'" O N N 43 DC "C5'" C N N 44 DC "C4'" C N R 45 DC "O4'" O N N 46 DC "C3'" C N S 47 DC "O3'" O N N 48 DC "C2'" C N N 49 DC "C1'" C N R 50 DC N1 N N N 51 DC C2 C N N 52 DC O2 O N N 53 DC N3 N N N 54 DC C4 C N N 55 DC N4 N N N 56 DC C5 C N N 57 DC C6 C N N 58 DC HOP3 H N N 59 DC HOP2 H N N 60 DC "H5'" H N N 61 DC "H5''" H N N 62 DC "H4'" H N N 63 DC "H3'" H N N 64 DC "HO3'" H N N 65 DC "H2'" H N N 66 DC "H2''" H N N 67 DC "H1'" H N N 68 DC H41 H N N 69 DC H42 H N N 70 DC H5 H N N 71 DC H6 H N N 72 DG OP3 O N N 73 DG P P N N 74 DG OP1 O N N 75 DG OP2 O N N 76 DG "O5'" O N N 77 DG "C5'" C N N 78 DG "C4'" C N R 79 DG "O4'" O N N 80 DG "C3'" C N S 81 DG "O3'" O N N 82 DG "C2'" C N N 83 DG "C1'" C N R 84 DG N9 N Y N 85 DG C8 C Y N 86 DG N7 N Y N 87 DG C5 C Y N 88 DG C6 C N N 89 DG O6 O N N 90 DG N1 N N N 91 DG C2 C N N 92 DG N2 N N N 93 DG N3 N N N 94 DG C4 C Y N 95 DG HOP3 H N N 96 DG HOP2 H N N 97 DG "H5'" H N N 98 DG "H5''" H N N 99 DG "H4'" H N N 100 DG "H3'" H N N 101 DG "HO3'" H N N 102 DG "H2'" H N N 103 DG "H2''" H N N 104 DG "H1'" H N N 105 DG H8 H N N 106 DG H1 H N N 107 DG H21 H N N 108 DG H22 H N N 109 DT OP3 O N N 110 DT P P N N 111 DT OP1 O N N 112 DT OP2 O N N 113 DT "O5'" O N N 114 DT "C5'" C N N 115 DT "C4'" C N R 116 DT "O4'" O N N 117 DT "C3'" C N S 118 DT "O3'" O N N 119 DT "C2'" C N N 120 DT "C1'" C N R 121 DT N1 N N N 122 DT C2 C N N 123 DT O2 O N N 124 DT N3 N N N 125 DT C4 C N N 126 DT O4 O N N 127 DT C5 C N N 128 DT C7 C N N 129 DT C6 C N N 130 DT HOP3 H N N 131 DT HOP2 H N N 132 DT "H5'" H N N 133 DT "H5''" H N N 134 DT "H4'" H N N 135 DT "H3'" H N N 136 DT "HO3'" H N N 137 DT "H2'" H N N 138 DT "H2''" H N N 139 DT "H1'" H N N 140 DT H3 H N N 141 DT H71 H N N 142 DT H72 H N N 143 DT H73 H N N 144 DT H6 H N N 145 HOH O O N N 146 HOH H1 H N N 147 HOH H2 H N N 148 SPK N1 N N N 149 SPK C2 C N N 150 SPK C3 C N N 151 SPK C4 C N N 152 SPK N5 N N N 153 SPK C6 C N N 154 SPK C7 C N N 155 SPK C8 C N N 156 SPK C9 C N N 157 SPK N10 N N N 158 SPK C11 C N N 159 SPK C12 C N N 160 SPK C13 C N N 161 SPK N14 N N N 162 SPK H1A H N N 163 SPK H1B H N N 164 SPK H1C H N N 165 SPK H2A H N N 166 SPK H2B H N N 167 SPK H3A H N N 168 SPK H3B H N N 169 SPK H4A H N N 170 SPK H4B H N N 171 SPK H5A H N N 172 SPK H5B H N N 173 SPK H6A H N N 174 SPK H6B H N N 175 SPK H7A H N N 176 SPK H7B H N N 177 SPK H8A H N N 178 SPK H8B H N N 179 SPK H9A H N N 180 SPK H9B H N N 181 SPK H101 H N N 182 SPK H102 H N N 183 SPK H111 H N N 184 SPK H112 H N N 185 SPK H121 H N N 186 SPK H122 H N N 187 SPK H131 H N N 188 SPK H132 H N N 189 SPK H141 H N N 190 SPK H142 H N N 191 SPK H143 H N N 192 # 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 SPK N1 C2 sing N N 152 SPK N1 H1A sing N N 153 SPK N1 H1B sing N N 154 SPK N1 H1C sing N N 155 SPK C2 C3 sing N N 156 SPK C2 H2A sing N N 157 SPK C2 H2B sing N N 158 SPK C3 C4 sing N N 159 SPK C3 H3A sing N N 160 SPK C3 H3B sing N N 161 SPK C4 N5 sing N N 162 SPK C4 H4A sing N N 163 SPK C4 H4B sing N N 164 SPK N5 C6 sing N N 165 SPK N5 H5A sing N N 166 SPK N5 H5B sing N N 167 SPK C6 C7 sing N N 168 SPK C6 H6A sing N N 169 SPK C6 H6B sing N N 170 SPK C7 C8 sing N N 171 SPK C7 H7A sing N N 172 SPK C7 H7B sing N N 173 SPK C8 C9 sing N N 174 SPK C8 H8A sing N N 175 SPK C8 H8B sing N N 176 SPK C9 N10 sing N N 177 SPK C9 H9A sing N N 178 SPK C9 H9B sing N N 179 SPK N10 C11 sing N N 180 SPK N10 H101 sing N N 181 SPK N10 H102 sing N N 182 SPK C11 C12 sing N N 183 SPK C11 H111 sing N N 184 SPK C11 H112 sing N N 185 SPK C12 C13 sing N N 186 SPK C12 H121 sing N N 187 SPK C12 H122 sing N N 188 SPK C13 N14 sing N N 189 SPK C13 H131 sing N N 190 SPK C13 H132 sing N N 191 SPK N14 H141 sing N N 192 SPK N14 H142 sing N N 193 SPK N14 H143 sing N N 194 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9V87 'double helix' 9V87 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 C DG 8 1_555 0.232 -0.101 0.433 -3.069 -27.113 -1.100 1 A_DC1:DG8_C A 1 ? C 8 ? 19 1 1 B DG 2 1_555 A DC 7 1_555 -0.516 -0.081 0.071 -4.762 3.713 2.094 2 B_DG2:DC7_A B 2 ? A 7 ? 19 1 1 B DT 3 1_555 A DA 6 1_555 0.029 -0.127 0.777 1.712 -7.252 2.253 3 B_DT3:DA6_A B 3 ? A 6 ? 20 1 1 B DT 4 1_555 A DA 5 1_555 -0.167 -0.283 -0.037 15.913 -21.939 1.764 4 B_DT4:DA5_A B 4 ? A 5 ? 20 1 1 B DA 5 1_555 A DT 4 1_555 0.461 0.227 -0.232 -20.375 -18.964 7.599 5 B_DA5:DT4_A B 5 ? A 4 ? 20 1 1 B DA 6 1_555 A DT 3 1_555 -0.120 -0.221 0.223 -6.988 -4.682 -1.423 6 B_DA6:DT3_A B 6 ? A 3 ? 20 1 1 B DC 7 1_555 A DG 2 1_555 0.202 -0.231 -0.261 4.012 9.840 -0.449 7 B_DC7:DG2_A B 7 ? A 2 ? 19 1 1 D DG 2 1_555 C DC 7 1_555 -0.284 -0.222 0.175 -11.440 0.219 3.691 8 D_DG2:DC7_C D 2 ? C 7 ? 19 1 1 D DT 3 1_555 C DA 6 1_555 -0.249 0.080 0.573 -1.709 -14.003 -0.009 9 D_DT3:DA6_C D 3 ? C 6 ? 20 1 1 D DT 4 1_555 C DA 5 1_555 0.102 -0.086 -0.236 16.755 -11.072 3.752 10 D_DT4:DA5_C D 4 ? C 5 ? 20 1 1 D DA 5 1_555 C DT 4 1_555 0.203 -0.100 -0.434 -10.125 -16.392 1.436 11 D_DA5:DT4_C D 5 ? C 4 ? 20 1 1 D DA 6 1_555 C DT 3 1_555 -0.161 -0.139 0.559 -0.342 -4.732 2.751 12 D_DA6:DT3_C D 6 ? C 3 ? 20 1 1 D DC 7 1_555 C DG 2 1_555 0.337 -0.199 0.113 5.363 5.364 4.180 13 D_DC7:DG2_C D 7 ? C 2 ? 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 B DG 2 1_555 A DC 7 1_555 B DT 3 1_555 A DA 6 1_555 0.052 -0.427 3.280 -5.712 3.404 27.907 -1.627 -1.386 3.134 6.934 11.636 28.673 1 BB_DG2DT3:DA6DC7_AA B 2 ? A 7 ? B 3 ? A 6 ? 1 B DT 3 1_555 A DA 6 1_555 B DT 4 1_555 A DA 5 1_555 -0.168 -0.331 2.898 7.661 -8.154 32.347 0.590 1.370 2.787 -14.119 -13.265 34.178 2 BB_DT3DT4:DA5DA6_AA B 3 ? A 6 ? B 4 ? A 5 ? 1 B DT 4 1_555 A DA 5 1_555 B DA 5 1_555 A DT 4 1_555 -0.055 0.162 4.117 1.806 3.322 50.205 -0.109 0.227 4.115 3.909 -2.125 50.338 3 BB_DT4DA5:DT4DA5_AA B 4 ? A 5 ? B 5 ? A 4 ? 1 B DA 5 1_555 A DT 4 1_555 B DA 6 1_555 A DT 3 1_555 0.035 -0.214 2.923 -6.651 -6.217 28.927 0.720 -1.276 2.829 -12.073 12.917 30.296 4 BB_DA5DA6:DT3DT4_AA B 5 ? A 4 ? B 6 ? A 3 ? 1 B DA 6 1_555 A DT 3 1_555 B DC 7 1_555 A DG 2 1_555 0.014 -0.466 3.110 2.980 4.166 29.966 -1.675 0.537 3.006 7.983 -5.710 30.391 5 BB_DA6DC7:DG2DT3_AA B 6 ? A 3 ? B 7 ? A 2 ? 1 B DC 7 1_555 A DG 2 1_555 D DG 2 1_555 C DC 7 1_555 -0.200 0.924 3.627 -6.060 -0.149 -79.575 -0.716 -0.335 3.608 0.116 -4.728 -79.768 6 BD_DC7DG2:DC7DG2_CA B 7 ? A 2 ? D 2 ? C 7 ? 1 D DG 2 1_555 C DC 7 1_555 D DT 3 1_555 C DA 6 1_555 -0.104 0.025 3.203 -3.675 1.695 25.905 -0.396 -0.746 3.181 3.753 8.135 26.214 7 DD_DG2DT3:DA6DC7_CC D 2 ? C 7 ? D 3 ? C 6 ? 1 D DT 3 1_555 C DA 6 1_555 D DT 4 1_555 C DA 5 1_555 -0.004 -0.319 2.837 6.238 -4.940 36.173 0.079 0.739 2.815 -7.840 -9.899 37.009 8 DD_DT3DT4:DA5DA6_CC D 3 ? C 6 ? D 4 ? C 5 ? 1 D DT 4 1_555 C DA 5 1_555 D DA 5 1_555 C DT 4 1_555 -0.172 0.379 3.885 2.584 1.344 47.492 0.342 0.460 3.880 1.668 -3.204 47.576 9 DD_DT4DA5:DT4DA5_CC D 4 ? C 5 ? D 5 ? C 4 ? 1 D DA 5 1_555 C DT 4 1_555 D DA 6 1_555 C DT 3 1_555 0.168 -0.370 2.844 -8.393 -2.865 33.383 -0.238 -1.415 2.744 -4.880 14.299 34.508 10 DD_DA5DA6:DT3DT4_CC D 5 ? C 4 ? D 6 ? C 3 ? 1 D DA 6 1_555 C DT 3 1_555 D DC 7 1_555 C DG 2 1_555 -0.011 -0.237 3.397 3.775 4.954 26.437 -1.794 1.005 3.266 10.645 -8.113 27.148 11 DD_DA6DC7:DG2DT3_CC D 6 ? C 3 ? D 7 ? C 2 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Ministry of Science and Technology (MoST, Taiwan)' Taiwan '109-2628-M- 005-001-MY4' 1 'Ministry of Science and Technology (MoST, Taiwan)' Taiwan 109-2311-B-005-007-MY3 2 # loop_ _pdbx_initial_refinement_model.id _pdbx_initial_refinement_model.entity_id_list _pdbx_initial_refinement_model.type _pdbx_initial_refinement_model.source_name _pdbx_initial_refinement_model.accession_code _pdbx_initial_refinement_model.details 1 ? 'experimental model' PDB 237D ? 2 ? 'in silico model' Other ? 'BIOVIA Discovery Studio' # _atom_sites.entry_id 9V87 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.022004 _atom_sites.fract_transf_matrix[1][2] 0.012704 _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] 0.025408 _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] 0.014015 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C CL CO N O P # loop_ #