data_8XPB # _entry.id 8XPB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.395 _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 8XPB pdb_00008xpb 10.2210/pdb8xpb/pdb WWPDB D_1300043912 ? ? # 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 2024-05-29 2 'Structure model' 1 1 2024-08-14 3 'Structure model' 1 2 2024-08-28 # _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' 'Database references' # 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' citation 4 3 'Structure model' citation_author # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.pdbx_database_id_PubMed' 8 2 'Structure model' '_citation.title' 9 2 'Structure model' '_citation.year' 10 3 'Structure model' '_citation.journal_volume' 11 3 'Structure model' '_citation.page_first' 12 3 'Structure model' '_citation.page_last' 13 3 'Structure model' '_citation_author.identifier_ORCID' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8XPB _pdbx_database_status.recvd_initial_deposition_date 2024-01-03 _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 2 _pdbx_contact_author.email mhho@dragon.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 'Hou, M.H.' 1 0000-0003-4170-1527 'Huang, H.T.' 2 ? 'Lin, S.M.' 3 0000-0001-7813-9000 'Neidle, S.' 4 0000-0003-0622-6548 # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 52 _citation.language ? _citation.page_first 8566 _citation.page_last 8579 _citation.title 'Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkae594 _citation.pdbx_database_id_PubMed 38989613 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lin, S.M.' 1 ? primary 'Huang, H.T.' 2 ? primary 'Fang, P.J.' 3 ? primary 'Chang, C.F.' 4 ? primary 'Satange, R.' 5 ? primary 'Chang, C.K.' 6 ? primary 'Chou, S.H.' 7 ? primary 'Neidle, S.' 8 ? primary 'Hou, M.H.' 9 ? # 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*AP*CP*GP*GP*CP*GP*T)-3') ; 2138.423 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*AP*CP*GP*CP*CP*GP*T)-3') ; 2098.399 1 ? ? ? ? 3 polymer nat Echinomycin 809.008 2 ? ? ? ? 4 non-polymer syn 'MANGANESE (II) ION' 54.938 3 ? ? ? ? 5 non-polymer syn 2-CARBOXYQUINOXALINE 174.156 4 ? ? ? ? 6 water nat water 18.015 20 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DA)(DC)(DG)(DG)(DC)(DG)(DT)' ACGGCGT A ? 2 polydeoxyribonucleotide no no '(DA)(DC)(DG)(DC)(DC)(DG)(DT)' ACGCCGT B ? 3 'polypeptide(L)' no yes '(DSN)A(N2C)(MVA)(DSN)A(NCY)(MVA)' SAXVSAXV D,E ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'MANGANESE (II) ION' MN 5 2-CARBOXYQUINOXALINE QUI 6 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DC n 1 3 DG n 1 4 DG n 1 5 DC n 1 6 DG n 1 7 DT n 2 1 DA n 2 2 DC n 2 3 DG n 2 4 DC n 2 5 DC n 2 6 DG n 2 7 DT n 3 1 DSN n 3 2 ALA n 3 3 N2C n 3 4 MVA n 3 5 DSN n 3 6 ALA n 3 7 NCY n 3 8 MVA n # _entity_src_nat.entity_id 3 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num 1 _entity_src_nat.pdbx_end_seq_num 8 _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Streptomyces echinatus.' _entity_src_nat.pdbx_ncbi_taxonomy_id 67293 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 7 'synthetic construct' ? 32630 ? 2 1 sample 1 7 'synthetic construct' ? 32630 ? # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DSN 'D-peptide linking' . D-SERINE ? 'C3 H7 N O3' 105.093 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 MVA 'L-peptide linking' n N-METHYLVALINE ? 'C6 H13 N O2' 131.173 N2C 'L-peptide linking' . N,S-DIMETHYLCYSTEINE ? 'C5 H11 N O2 S' 149.211 NCY 'L-peptide linking' . N-METHYLCYSTEINE ? 'C4 H9 N O2 S' 135.185 QUI non-polymer . 2-CARBOXYQUINOXALINE ? 'C9 H6 N2 O2' 174.156 # 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 DA 1 1 1 DA DA A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DT 7 7 7 DT DT A . n B 2 1 DA 1 1 1 DA DA B . n B 2 2 DC 2 2 2 DC DC B . n B 2 3 DG 3 3 3 DG DG B . n B 2 4 DC 4 4 4 DC DC B . n B 2 5 DC 5 5 5 DC DC B . n B 2 6 DG 6 6 6 DG DG B . n B 2 7 DT 7 7 7 DT DT B . n C 3 1 DSN 1 1 101 DSN LIG D . n C 3 2 ALA 2 2 101 ALA LIG D . n C 3 3 N2C 3 3 101 N2C LIG D . n C 3 4 MVA 4 4 101 MVA LIG D . n C 3 5 DSN 5 5 101 DSN LIG D . n C 3 6 ALA 6 6 101 ALA LIG D . n C 3 7 NCY 7 7 101 NCY LIG D . n C 3 8 MVA 8 8 101 MVA LIG D . n D 3 1 DSN 1 1 101 DSN LIG E . n D 3 2 ALA 2 2 101 ALA LIG E . n D 3 3 N2C 3 3 101 N2C LIG E . n D 3 4 MVA 4 4 101 MVA LIG E . n D 3 5 DSN 5 5 101 DSN LIG E . n D 3 6 ALA 6 6 101 ALA LIG E . n D 3 7 NCY 7 7 101 NCY LIG E . n D 3 8 MVA 8 8 101 MVA LIG E . 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 E 4 MN 1 101 3 MN MN A . F 4 MN 1 102 5 MN MN A . G 4 MN 1 101 4 MN MN B . H 5 QUI 1 101 101 QUI LIG D . I 5 QUI 1 102 101 QUI LIG D . J 5 QUI 1 101 101 QUI LIG E . K 5 QUI 1 102 101 QUI LIG E . L 6 HOH 1 201 6 HOH HOH A . L 6 HOH 2 202 7 HOH HOH A . L 6 HOH 3 203 1 HOH HOH A . L 6 HOH 4 204 5 HOH HOH A . L 6 HOH 5 205 22 HOH HOH A . L 6 HOH 6 206 11 HOH HOH A . L 6 HOH 7 207 10 HOH HOH A . L 6 HOH 8 208 21 HOH HOH A . L 6 HOH 9 209 3 HOH HOH A . L 6 HOH 10 210 19 HOH HOH A . M 6 HOH 1 201 13 HOH HOH B . M 6 HOH 2 202 4 HOH HOH B . M 6 HOH 3 203 9 HOH HOH B . M 6 HOH 4 204 23 HOH HOH B . M 6 HOH 5 205 12 HOH HOH B . M 6 HOH 6 206 14 HOH HOH B . M 6 HOH 7 207 2 HOH HOH B . M 6 HOH 8 208 20 HOH HOH B . M 6 HOH 9 209 17 HOH HOH B . N 6 HOH 1 201 8 HOH HOH E . # 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_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.20.1_4487: ???)' 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 8XPB _cell.details ? _cell.formula_units_Z ? _cell.length_a 46.317 _cell.length_a_esd ? _cell.length_b 46.317 _cell.length_b_esd ? _cell.length_c 47.971 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _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 8XPB _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 8XPB _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 2.54 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 51.52 _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 ? _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 '20mM MES (pH 6), 10mM Spermine HCl, 1% PEG 200, 10mM MnCl2' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293.15 # _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 2018-05-20 _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 8XPB _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.00 _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 4107 _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 100.0 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.8 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 11.6 _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 0.049 _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 2.00 2.07 ? ? ? ? ? ? 410 ? ? ? ? ? ? ? ? ? ? ? 10.4 1.089 ? ? 0.508 0.156 ? 1 1 0.978 0.994 ? 100.0 ? 0.483 ? ? ? ? ? ? ? ? ? 2.07 2.15 ? ? ? ? ? ? 403 ? ? ? ? ? ? ? ? ? ? ? 10.8 1.131 ? ? 0.406 0.123 ? 2 1 0.980 0.995 ? 100.0 ? 0.387 ? ? ? ? ? ? ? ? ? 2.15 2.25 ? ? ? ? ? ? 398 ? ? ? ? ? ? ? ? ? ? ? 11.1 1.141 ? ? 0.319 0.095 ? 3 1 0.990 0.998 ? 100.0 ? 0.304 ? ? ? ? ? ? ? ? ? 2.25 2.37 ? ? ? ? ? ? 410 ? ? ? ? ? ? ? ? ? ? ? 11.1 1.147 ? ? 0.201 0.061 ? 4 1 0.995 0.999 ? 100.0 ? 0.191 ? ? ? ? ? ? ? ? ? 2.37 2.52 ? ? ? ? ? ? 406 ? ? ? ? ? ? ? ? ? ? ? 11.0 1.179 ? ? 0.140 0.042 ? 5 1 0.998 1.000 ? 100.0 ? 0.133 ? ? ? ? ? ? ? ? ? 2.52 2.71 ? ? ? ? ? ? 401 ? ? ? ? ? ? ? ? ? ? ? 11.1 1.091 ? ? 0.139 0.042 ? 6 1 0.997 0.999 ? 100.0 ? 0.133 ? ? ? ? ? ? ? ? ? 2.71 2.99 ? ? ? ? ? ? 416 ? ? ? ? ? ? ? ? ? ? ? 11.0 0.989 ? ? 0.076 0.023 ? 7 1 0.999 1.000 ? 100.0 ? 0.072 ? ? ? ? ? ? ? ? ? 2.99 3.42 ? ? ? ? ? ? 404 ? ? ? ? ? ? ? ? ? ? ? 10.9 1.057 ? ? 0.036 0.011 ? 8 1 1.000 1.000 ? 100.0 ? 0.035 ? ? ? ? ? ? ? ? ? 3.42 4.31 ? ? ? ? ? ? 418 ? ? ? ? ? ? ? ? ? ? ? 10.8 0.906 ? ? 0.045 0.014 ? 9 1 0.999 1.000 ? 100.0 ? 0.043 ? ? ? ? ? ? ? ? ? 4.31 30.00 ? ? ? ? ? ? 441 ? ? ? ? ? ? ? ? ? ? ? 10.2 0.969 ? ? 0.027 0.008 ? 10 1 1.000 1.000 ? 99.5 ? 0.026 ? ? ? ? ? ? ? ? ? # _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 8XPB _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 2.00 _refine.ls_d_res_low 20.86 _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 4052 _refine.ls_number_reflns_R_free 404 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.90 _refine.ls_percent_reflns_R_free 9.97 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2116 _refine.ls_R_factor_R_free 0.2159 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2107 _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.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 1.39 _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 ML _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 28.12 _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 0.22 _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 2.00 _refine_hist.d_res_low 20.86 _refine_hist.number_atoms_solvent 20 _refine_hist.number_atoms_total 458 _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 281 _refine_hist.pdbx_number_atoms_ligand 157 _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_restraint_function 'X-RAY DIFFRACTION' ? 0.011 ? ? ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 2.061 ? ? ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 32.355 ? 146 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.173 ? 72 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.009 ? 38 ? 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.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' 2.00 2.29 . . 129 1213 99.00 . . . . 0.2693 . . . . . . . . . . . 0.3300 'X-RAY DIFFRACTION' 2.29 2.88 . . 136 1206 99.00 . . . . 0.2709 . . . . . . . . . . . 0.2784 'X-RAY DIFFRACTION' 2.89 10 . . 139 1229 98.00 . . . . 0.1763 . . . . . . . . . . . 0.1763 # _struct.entry_id 8XPB _struct.title 'Crystal structure of d(ACGCCGT/ACGGCGT) in complex with Echinomycin' _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 8XPB _struct_keywords.text 'complex, DNA, DNA-ANTIBIOTIC complex' _struct_keywords.pdbx_keywords DNA/ANTIBIOTIC # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 4 ? F N N 4 ? G N N 4 ? H N N 5 ? I N N 5 ? J N N 5 ? K N N 5 ? L N N 6 ? M N N 6 ? N N N 6 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 8XPB 8XPB ? 1 ? 1 2 PDB 8XPB 8XPB ? 2 ? 1 3 PDB 8XPB 8XPB ? 3 ? 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 8XPB A 1 ? 7 ? 8XPB 1 ? 7 ? 1 7 2 2 8XPB B 1 ? 7 ? 8XPB 1 ? 7 ? 1 7 3 3 8XPB D 1 ? 8 ? 8XPB 1 ? 8 ? 1 8 4 3 8XPB E 1 ? 8 ? 8XPB 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 # _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 disulf1 disulf ? ? C N2C 3 SG ? ? ? 1_555 C NCY 7 SG ? ? D N2C 3 D NCY 7 1_555 ? ? ? ? ? ? ? 2.892 ? ? disulf2 disulf ? ? D N2C 3 SG ? ? ? 1_555 D NCY 7 SG ? ? E N2C 3 E NCY 7 1_555 ? ? ? ? ? ? ? 2.900 ? ? covale1 covale both ? C DSN 1 C ? ? ? 1_555 C ALA 2 N ? ? D DSN 1 D ALA 2 1_555 ? ? ? ? ? ? ? 1.455 ? ? covale2 covale one ? C DSN 1 OG ? ? ? 1_555 C MVA 8 C ? ? D DSN 1 D MVA 8 1_555 ? ? ? ? ? ? ? 1.407 ? ? covale3 covale both ? C DSN 1 N ? ? ? 1_555 H QUI . C ? ? D DSN 1 D QUI 101 1_555 ? ? ? ? ? ? ? 1.458 ? ? covale4 covale both ? C ALA 2 C ? ? ? 1_555 C N2C 3 N ? ? D ALA 2 D N2C 3 1_555 ? ? ? ? ? ? ? 1.471 ? ? covale5 covale both ? C N2C 3 C ? ? ? 1_555 C MVA 4 N ? ? D N2C 3 D MVA 4 1_555 ? ? ? ? ? ? ? 1.480 ? ? covale6 covale both ? C N2C 3 CB ? ? ? 1_555 C NCY 7 SG ? ? D N2C 3 D NCY 7 1_555 ? ? ? ? ? ? ? 1.835 ? ? covale7 covale one ? C MVA 4 C ? ? ? 1_555 C DSN 5 OG ? ? D MVA 4 D DSN 5 1_555 ? ? ? ? ? ? ? 1.415 ? ? covale8 covale both ? C DSN 5 C ? ? ? 1_555 C ALA 6 N ? ? D DSN 5 D ALA 6 1_555 ? ? ? ? ? ? ? 1.459 ? ? covale9 covale both ? C DSN 5 N ? ? ? 1_555 I QUI . C ? ? D DSN 5 D QUI 102 1_555 ? ? ? ? ? ? ? 1.448 ? ? covale10 covale both ? C ALA 6 C ? ? ? 1_555 C NCY 7 N ? ? D ALA 6 D NCY 7 1_555 ? ? ? ? ? ? ? 1.454 ? ? covale11 covale both ? C NCY 7 C ? ? ? 1_555 C MVA 8 N ? ? D NCY 7 D MVA 8 1_555 ? ? ? ? ? ? ? 1.473 ? ? covale12 covale both ? D DSN 1 C ? ? ? 1_555 D ALA 2 N ? ? E DSN 1 E ALA 2 1_555 ? ? ? ? ? ? ? 1.463 ? ? covale13 covale one ? D DSN 1 OG ? ? ? 1_555 D MVA 8 C ? ? E DSN 1 E MVA 8 1_555 ? ? ? ? ? ? ? 1.414 ? ? covale14 covale both ? D DSN 1 N ? ? ? 1_555 J QUI . C ? ? E DSN 1 E QUI 101 1_555 ? ? ? ? ? ? ? 1.448 ? ? covale15 covale both ? D ALA 2 C ? ? ? 1_555 D N2C 3 N ? ? E ALA 2 E N2C 3 1_555 ? ? ? ? ? ? ? 1.474 ? ? covale16 covale both ? D N2C 3 C ? ? ? 1_555 D MVA 4 N ? ? E N2C 3 E MVA 4 1_555 ? ? ? ? ? ? ? 1.472 ? ? covale17 covale both ? D N2C 3 CB ? ? ? 1_555 D NCY 7 SG ? ? E N2C 3 E NCY 7 1_555 ? ? ? ? ? ? ? 1.834 ? ? covale18 covale one ? D MVA 4 C ? ? ? 1_555 D DSN 5 OG ? ? E MVA 4 E DSN 5 1_555 ? ? ? ? ? ? ? 1.411 ? ? covale19 covale both ? D DSN 5 C ? ? ? 1_555 D ALA 6 N ? ? E DSN 5 E ALA 6 1_555 ? ? ? ? ? ? ? 1.454 ? ? covale20 covale both ? D DSN 5 N ? ? ? 1_555 K QUI . C ? ? E DSN 5 E QUI 102 1_555 ? ? ? ? ? ? ? 1.454 ? ? covale21 covale both ? D ALA 6 C ? ? ? 1_555 D NCY 7 N ? ? E ALA 6 E NCY 7 1_555 ? ? ? ? ? ? ? 1.457 ? ? covale22 covale both ? D NCY 7 C ? ? ? 1_555 D MVA 8 N ? ? E NCY 7 E MVA 8 1_555 ? ? ? ? ? ? ? 1.475 ? ? metalc1 metalc ? ? A DG 3 N7 ? ? ? 1_555 E MN . MN ? ? A DG 3 A MN 101 1_555 ? ? ? ? ? ? ? 2.211 ? ? metalc2 metalc ? ? A DG 6 N7 ? ? ? 1_555 F MN . MN ? ? A DG 6 A MN 102 1_555 ? ? ? ? ? ? ? 2.329 ? ? metalc3 metalc ? ? E MN . MN ? ? ? 1_555 L HOH . O ? ? A MN 101 A HOH 203 1_555 ? ? ? ? ? ? ? 2.173 ? ? metalc4 metalc ? ? E MN . MN ? ? ? 1_555 L HOH . O ? ? A MN 101 A HOH 209 1_555 ? ? ? ? ? ? ? 2.393 ? ? metalc5 metalc ? ? E MN . MN ? ? ? 6_557 B DG 3 N7 ? ? A MN 101 B DG 3 1_555 ? ? ? ? ? ? ? 2.183 ? ? metalc6 metalc ? ? E MN . MN ? ? ? 1_555 M HOH . O ? ? A MN 101 B HOH 202 6_557 ? ? ? ? ? ? ? 2.094 ? ? metalc7 metalc ? ? E MN . MN ? ? ? 1_555 M HOH . O ? ? A MN 101 B HOH 207 6_557 ? ? ? ? ? ? ? 2.539 ? ? metalc8 metalc ? ? B DG 6 N7 ? ? ? 1_555 G MN . MN ? ? B DG 6 B MN 101 1_555 ? ? ? ? ? ? ? 2.330 ? ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 1 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 1 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 3 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 3 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 3 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 4 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 4 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 4 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 5 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 5 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 5 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 7 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 7 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 203 ? 1_555 90.2 ? 2 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 209 ? 1_555 89.7 ? 3 O ? L HOH . ? A HOH 203 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 209 ? 1_555 177.0 ? 4 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 N7 ? B DG 3 ? B DG 3 ? 1_555 82.4 ? 5 O ? L HOH . ? A HOH 203 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 N7 ? B DG 3 ? B DG 3 ? 1_555 136.9 ? 6 O ? L HOH . ? A HOH 209 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 N7 ? B DG 3 ? B DG 3 ? 1_555 40.1 ? 7 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? M HOH . ? B HOH 202 ? 6_557 87.4 ? 8 O ? L HOH . ? A HOH 203 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? M HOH . ? B HOH 202 ? 6_557 95.0 ? 9 O ? L HOH . ? A HOH 209 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? M HOH . ? B HOH 202 ? 6_557 88.0 ? 10 N7 ? B DG 3 ? B DG 3 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? M HOH . ? B HOH 202 ? 6_557 126.7 ? 11 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? M HOH . ? B HOH 207 ? 6_557 99.3 ? 12 O ? L HOH . ? A HOH 203 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? M HOH . ? B HOH 207 ? 6_557 99.8 ? 13 O ? L HOH . ? A HOH 209 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? M HOH . ? B HOH 207 ? 6_557 77.3 ? 14 N7 ? B DG 3 ? B DG 3 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? M HOH . ? B HOH 207 ? 6_557 41.0 ? 15 O ? M HOH . ? B HOH 202 ? 6_557 MN ? E MN . ? A MN 101 ? 1_555 O ? M HOH . ? B HOH 207 ? 6_557 163.7 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 C D N2C 3 ? ? N D MVA 4 ? ? 1.480 1.336 0.144 0.023 Y 2 1 C E ALA 2 ? ? N E N2C 3 ? ? 1.474 1.336 0.138 0.023 Y 3 1 C E NCY 7 ? ? N E MVA 8 ? ? 1.475 1.336 0.139 0.023 Y # _pdbx_molecule_features.prd_id PRD_000491 _pdbx_molecule_features.name Echinomycin _pdbx_molecule_features.type 'Cyclic depsipeptide' _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000491 C 1 PRD_000491 H 1 PRD_000491 I 2 PRD_000491 D 2 PRD_000491 J 2 PRD_000491 K # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[1][1]_esd _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][2]_esd _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[1][3]_esd _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[2][2]_esd _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.T[2][3]_esd _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[3][3]_esd _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[1][1]_esd _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][2]_esd _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[1][3]_esd _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[2][2]_esd _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.L[2][3]_esd _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[3][3]_esd _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][1]_esd _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][2]_esd _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[1][3]_esd _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][1]_esd _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][2]_esd _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][3]_esd _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][1]_esd _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][2]_esd _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[3][3]_esd 1 'X-RAY DIFFRACTION' ? refined 33.8672 12.2919 46.1410 0.3911 ? -0.0803 ? 0.0161 ? 0.3407 ? -0.0597 ? 0.3294 ? 6.4159 ? 0.6419 ? -0.7466 ? 4.9849 ? -1.1383 ? 4.1104 ? 0.3512 ? 0.7325 ? -0.2793 ? 0.4190 ? 0.0316 ? 0.2276 ? 0.6611 ? -0.5123 ? -0.2919 ? 2 'X-RAY DIFFRACTION' ? refined 41.9518 16.9561 49.8410 0.2659 ? -0.0307 ? -0.0399 ? 0.4628 ? 0.0614 ? 0.3639 ? 5.5720 ? 0.9937 ? -1.9312 ? 5.0113 ? -0.0914 ? 4.9029 ? 0.7617 ? 0.2078 ? 0.1953 ? 0.5332 ? -0.2506 ? -0.3128 ? -0.0526 ? 0.7474 ? -0.5141 ? # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_PDB_ins_code _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_PDB_ins_code _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 ? ? ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 1 through 7 ) ; 2 'X-RAY DIFFRACTION' 2 ? ? ? ? ? ? ? ? ? ? ? ;chain 'B' and (resid 1 through 7 ) ; # _pdbx_entry_details.entry_id 8XPB _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ;THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.has_protein_modification ? # 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 ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 DA OP3 O N N 14 DA P P N N 15 DA OP1 O N N 16 DA OP2 O N N 17 DA "O5'" O N N 18 DA "C5'" C N N 19 DA "C4'" C N R 20 DA "O4'" O N N 21 DA "C3'" C N S 22 DA "O3'" O N N 23 DA "C2'" C N N 24 DA "C1'" C N R 25 DA N9 N Y N 26 DA C8 C Y N 27 DA N7 N Y N 28 DA C5 C Y N 29 DA C6 C Y N 30 DA N6 N N N 31 DA N1 N Y N 32 DA C2 C Y N 33 DA N3 N Y N 34 DA C4 C Y N 35 DA HOP3 H N N 36 DA HOP2 H N N 37 DA "H5'" H N N 38 DA "H5''" H N N 39 DA "H4'" H N N 40 DA "H3'" H N N 41 DA "HO3'" H N N 42 DA "H2'" H N N 43 DA "H2''" H N N 44 DA "H1'" H N N 45 DA H8 H N N 46 DA H61 H N N 47 DA H62 H N N 48 DA H2 H N N 49 DC OP3 O N N 50 DC P P N N 51 DC OP1 O N N 52 DC OP2 O N N 53 DC "O5'" O N N 54 DC "C5'" C N N 55 DC "C4'" C N R 56 DC "O4'" O N N 57 DC "C3'" C N S 58 DC "O3'" O N N 59 DC "C2'" C N N 60 DC "C1'" C N R 61 DC N1 N N N 62 DC C2 C N N 63 DC O2 O N N 64 DC N3 N N N 65 DC C4 C N N 66 DC N4 N N N 67 DC C5 C N N 68 DC C6 C N N 69 DC HOP3 H N N 70 DC HOP2 H N N 71 DC "H5'" H N N 72 DC "H5''" H N N 73 DC "H4'" H N N 74 DC "H3'" H N N 75 DC "HO3'" H N N 76 DC "H2'" H N N 77 DC "H2''" H N N 78 DC "H1'" H N N 79 DC H41 H N N 80 DC H42 H N N 81 DC H5 H N N 82 DC H6 H N N 83 DG OP3 O N N 84 DG P P N N 85 DG OP1 O N N 86 DG OP2 O N N 87 DG "O5'" O N N 88 DG "C5'" C N N 89 DG "C4'" C N R 90 DG "O4'" O N N 91 DG "C3'" C N S 92 DG "O3'" O N N 93 DG "C2'" C N N 94 DG "C1'" C N R 95 DG N9 N Y N 96 DG C8 C Y N 97 DG N7 N Y N 98 DG C5 C Y N 99 DG C6 C N N 100 DG O6 O N N 101 DG N1 N N N 102 DG C2 C N N 103 DG N2 N N N 104 DG N3 N N N 105 DG C4 C Y N 106 DG HOP3 H N N 107 DG HOP2 H N N 108 DG "H5'" H N N 109 DG "H5''" H N N 110 DG "H4'" H N N 111 DG "H3'" H N N 112 DG "HO3'" H N N 113 DG "H2'" H N N 114 DG "H2''" H N N 115 DG "H1'" H N N 116 DG H8 H N N 117 DG H1 H N N 118 DG H21 H N N 119 DG H22 H N N 120 DSN N N N N 121 DSN CA C N R 122 DSN C C N N 123 DSN O O N N 124 DSN OXT O N N 125 DSN CB C N N 126 DSN OG O N N 127 DSN H H N N 128 DSN H2 H N N 129 DSN HA H N N 130 DSN HXT H N N 131 DSN HB2 H N N 132 DSN HB3 H N N 133 DSN HG H N N 134 DT OP3 O N N 135 DT P P N N 136 DT OP1 O N N 137 DT OP2 O N N 138 DT "O5'" O N N 139 DT "C5'" C N N 140 DT "C4'" C N R 141 DT "O4'" O N N 142 DT "C3'" C N S 143 DT "O3'" O N N 144 DT "C2'" C N N 145 DT "C1'" C N R 146 DT N1 N N N 147 DT C2 C N N 148 DT O2 O N N 149 DT N3 N N N 150 DT C4 C N N 151 DT O4 O N N 152 DT C5 C N N 153 DT C7 C N N 154 DT C6 C N N 155 DT HOP3 H N N 156 DT HOP2 H N N 157 DT "H5'" H N N 158 DT "H5''" H N N 159 DT "H4'" H N N 160 DT "H3'" H N N 161 DT "HO3'" H N N 162 DT "H2'" H N N 163 DT "H2''" H N N 164 DT "H1'" H N N 165 DT H3 H N N 166 DT H71 H N N 167 DT H72 H N N 168 DT H73 H N N 169 DT H6 H N N 170 HOH O O N N 171 HOH H1 H N N 172 HOH H2 H N N 173 MN MN MN N N 174 MVA N N N N 175 MVA CN C N N 176 MVA CA C N S 177 MVA CB C N N 178 MVA CG1 C N N 179 MVA CG2 C N N 180 MVA C C N N 181 MVA O O N N 182 MVA OXT O N N 183 MVA H H N N 184 MVA HN1 H N N 185 MVA HN2 H N N 186 MVA HN3 H N N 187 MVA HA H N N 188 MVA HB H N N 189 MVA HG11 H N N 190 MVA HG12 H N N 191 MVA HG13 H N N 192 MVA HG21 H N N 193 MVA HG22 H N N 194 MVA HG23 H N N 195 MVA HXT H N N 196 N2C N N N N 197 N2C CA C N R 198 N2C CB C N N 199 N2C SG S N N 200 N2C CD C N N 201 N2C CN C N N 202 N2C C C N N 203 N2C O O N N 204 N2C OXT O N N 205 N2C H H N N 206 N2C HA H N N 207 N2C HB2 H N N 208 N2C HB3 H N N 209 N2C HD1 H N N 210 N2C HD2 H N N 211 N2C HD3 H N N 212 N2C HN1 H N N 213 N2C HN2 H N N 214 N2C HN3 H N N 215 N2C HXT H N N 216 NCY N N N N 217 NCY CA C N R 218 NCY CB C N N 219 NCY SG S N N 220 NCY CN C N N 221 NCY C C N N 222 NCY O O N N 223 NCY OXT O N N 224 NCY H H N N 225 NCY HA H N N 226 NCY HB2 H N N 227 NCY HB3 H N N 228 NCY HG H N N 229 NCY HCN1 H N N 230 NCY HCN2 H N N 231 NCY HCN3 H N N 232 NCY HXT H N N 233 QUI N1 N Y N 234 QUI C2 C Y N 235 QUI C3 C Y N 236 QUI N4 N Y N 237 QUI C5 C Y N 238 QUI C6 C Y N 239 QUI C7 C Y N 240 QUI C8 C Y N 241 QUI C9 C Y N 242 QUI C10 C Y N 243 QUI C C N N 244 QUI O1 O N N 245 QUI O2 O N N 246 QUI H3 H N N 247 QUI H5 H N N 248 QUI H6 H N N 249 QUI H7 H N N 250 QUI H8 H N N 251 QUI HO2 H N N 252 # 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 ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 DA OP3 P sing N N 13 DA OP3 HOP3 sing N N 14 DA P OP1 doub N N 15 DA P OP2 sing N N 16 DA P "O5'" sing N N 17 DA OP2 HOP2 sing N N 18 DA "O5'" "C5'" sing N N 19 DA "C5'" "C4'" sing N N 20 DA "C5'" "H5'" sing N N 21 DA "C5'" "H5''" sing N N 22 DA "C4'" "O4'" sing N N 23 DA "C4'" "C3'" sing N N 24 DA "C4'" "H4'" sing N N 25 DA "O4'" "C1'" sing N N 26 DA "C3'" "O3'" sing N N 27 DA "C3'" "C2'" sing N N 28 DA "C3'" "H3'" sing N N 29 DA "O3'" "HO3'" sing N N 30 DA "C2'" "C1'" sing N N 31 DA "C2'" "H2'" sing N N 32 DA "C2'" "H2''" sing N N 33 DA "C1'" N9 sing N N 34 DA "C1'" "H1'" sing N N 35 DA N9 C8 sing Y N 36 DA N9 C4 sing Y N 37 DA C8 N7 doub Y N 38 DA C8 H8 sing N N 39 DA N7 C5 sing Y N 40 DA C5 C6 sing Y N 41 DA C5 C4 doub Y N 42 DA C6 N6 sing N N 43 DA C6 N1 doub Y N 44 DA N6 H61 sing N N 45 DA N6 H62 sing N N 46 DA N1 C2 sing Y N 47 DA C2 N3 doub Y N 48 DA C2 H2 sing N N 49 DA N3 C4 sing Y N 50 DC OP3 P sing N N 51 DC OP3 HOP3 sing N N 52 DC P OP1 doub N N 53 DC P OP2 sing N N 54 DC P "O5'" sing N N 55 DC OP2 HOP2 sing N N 56 DC "O5'" "C5'" sing N N 57 DC "C5'" "C4'" sing N N 58 DC "C5'" "H5'" sing N N 59 DC "C5'" "H5''" sing N N 60 DC "C4'" "O4'" sing N N 61 DC "C4'" "C3'" sing N N 62 DC "C4'" "H4'" sing N N 63 DC "O4'" "C1'" sing N N 64 DC "C3'" "O3'" sing N N 65 DC "C3'" "C2'" sing N N 66 DC "C3'" "H3'" sing N N 67 DC "O3'" "HO3'" sing N N 68 DC "C2'" "C1'" sing N N 69 DC "C2'" "H2'" sing N N 70 DC "C2'" "H2''" sing N N 71 DC "C1'" N1 sing N N 72 DC "C1'" "H1'" sing N N 73 DC N1 C2 sing N N 74 DC N1 C6 sing N N 75 DC C2 O2 doub N N 76 DC C2 N3 sing N N 77 DC N3 C4 doub N N 78 DC C4 N4 sing N N 79 DC C4 C5 sing N N 80 DC N4 H41 sing N N 81 DC N4 H42 sing N N 82 DC C5 C6 doub N N 83 DC C5 H5 sing N N 84 DC C6 H6 sing N N 85 DG OP3 P sing N N 86 DG OP3 HOP3 sing N N 87 DG P OP1 doub N N 88 DG P OP2 sing N N 89 DG P "O5'" sing N N 90 DG OP2 HOP2 sing N N 91 DG "O5'" "C5'" sing N N 92 DG "C5'" "C4'" sing N N 93 DG "C5'" "H5'" sing N N 94 DG "C5'" "H5''" sing N N 95 DG "C4'" "O4'" sing N N 96 DG "C4'" "C3'" sing N N 97 DG "C4'" "H4'" sing N N 98 DG "O4'" "C1'" sing N N 99 DG "C3'" "O3'" sing N N 100 DG "C3'" "C2'" sing N N 101 DG "C3'" "H3'" sing N N 102 DG "O3'" "HO3'" sing N N 103 DG "C2'" "C1'" sing N N 104 DG "C2'" "H2'" sing N N 105 DG "C2'" "H2''" sing N N 106 DG "C1'" N9 sing N N 107 DG "C1'" "H1'" sing N N 108 DG N9 C8 sing Y N 109 DG N9 C4 sing Y N 110 DG C8 N7 doub Y N 111 DG C8 H8 sing N N 112 DG N7 C5 sing Y N 113 DG C5 C6 sing N N 114 DG C5 C4 doub Y N 115 DG C6 O6 doub N N 116 DG C6 N1 sing N N 117 DG N1 C2 sing N N 118 DG N1 H1 sing N N 119 DG C2 N2 sing N N 120 DG C2 N3 doub N N 121 DG N2 H21 sing N N 122 DG N2 H22 sing N N 123 DG N3 C4 sing N N 124 DSN N CA sing N N 125 DSN N H sing N N 126 DSN N H2 sing N N 127 DSN CA C sing N N 128 DSN CA CB sing N N 129 DSN CA HA sing N N 130 DSN C O doub N N 131 DSN C OXT sing N N 132 DSN OXT HXT sing N N 133 DSN CB OG sing N N 134 DSN CB HB2 sing N N 135 DSN CB HB3 sing N N 136 DSN OG HG sing N N 137 DT OP3 P sing N N 138 DT OP3 HOP3 sing N N 139 DT P OP1 doub N N 140 DT P OP2 sing N N 141 DT P "O5'" sing N N 142 DT OP2 HOP2 sing N N 143 DT "O5'" "C5'" sing N N 144 DT "C5'" "C4'" sing N N 145 DT "C5'" "H5'" sing N N 146 DT "C5'" "H5''" sing N N 147 DT "C4'" "O4'" sing N N 148 DT "C4'" "C3'" sing N N 149 DT "C4'" "H4'" sing N N 150 DT "O4'" "C1'" sing N N 151 DT "C3'" "O3'" sing N N 152 DT "C3'" "C2'" sing N N 153 DT "C3'" "H3'" sing N N 154 DT "O3'" "HO3'" sing N N 155 DT "C2'" "C1'" sing N N 156 DT "C2'" "H2'" sing N N 157 DT "C2'" "H2''" sing N N 158 DT "C1'" N1 sing N N 159 DT "C1'" "H1'" sing N N 160 DT N1 C2 sing N N 161 DT N1 C6 sing N N 162 DT C2 O2 doub N N 163 DT C2 N3 sing N N 164 DT N3 C4 sing N N 165 DT N3 H3 sing N N 166 DT C4 O4 doub N N 167 DT C4 C5 sing N N 168 DT C5 C7 sing N N 169 DT C5 C6 doub N N 170 DT C7 H71 sing N N 171 DT C7 H72 sing N N 172 DT C7 H73 sing N N 173 DT C6 H6 sing N N 174 HOH O H1 sing N N 175 HOH O H2 sing N N 176 MVA N CN sing N N 177 MVA N CA sing N N 178 MVA N H sing N N 179 MVA CN HN1 sing N N 180 MVA CN HN2 sing N N 181 MVA CN HN3 sing N N 182 MVA CA CB sing N N 183 MVA CA C sing N N 184 MVA CA HA sing N N 185 MVA CB CG1 sing N N 186 MVA CB CG2 sing N N 187 MVA CB HB sing N N 188 MVA CG1 HG11 sing N N 189 MVA CG1 HG12 sing N N 190 MVA CG1 HG13 sing N N 191 MVA CG2 HG21 sing N N 192 MVA CG2 HG22 sing N N 193 MVA CG2 HG23 sing N N 194 MVA C O doub N N 195 MVA C OXT sing N N 196 MVA OXT HXT sing N N 197 N2C N CA sing N N 198 N2C N CN sing N N 199 N2C N H sing N N 200 N2C CA CB sing N N 201 N2C CA C sing N N 202 N2C CA HA sing N N 203 N2C CB SG sing N N 204 N2C CB HB2 sing N N 205 N2C CB HB3 sing N N 206 N2C SG CD sing N N 207 N2C CD HD1 sing N N 208 N2C CD HD2 sing N N 209 N2C CD HD3 sing N N 210 N2C CN HN1 sing N N 211 N2C CN HN2 sing N N 212 N2C CN HN3 sing N N 213 N2C C O doub N N 214 N2C C OXT sing N N 215 N2C OXT HXT sing N N 216 NCY N CA sing N N 217 NCY N CN sing N N 218 NCY N H sing N N 219 NCY CA CB sing N N 220 NCY CA C sing N N 221 NCY CA HA sing N N 222 NCY CB SG sing N N 223 NCY CB HB2 sing N N 224 NCY CB HB3 sing N N 225 NCY SG HG sing N N 226 NCY CN HCN1 sing N N 227 NCY CN HCN2 sing N N 228 NCY CN HCN3 sing N N 229 NCY C O doub N N 230 NCY C OXT sing N N 231 NCY OXT HXT sing N N 232 QUI N1 C2 doub Y N 233 QUI N1 C9 sing Y N 234 QUI C2 C3 sing Y N 235 QUI C2 C sing N N 236 QUI C3 N4 doub Y N 237 QUI C3 H3 sing N N 238 QUI N4 C10 sing Y N 239 QUI C5 C6 doub Y N 240 QUI C5 C10 sing Y N 241 QUI C5 H5 sing N N 242 QUI C6 C7 sing Y N 243 QUI C6 H6 sing N N 244 QUI C7 C8 doub Y N 245 QUI C7 H7 sing N N 246 QUI C8 C9 sing Y N 247 QUI C8 H8 sing N N 248 QUI C9 C10 doub Y N 249 QUI C O1 doub N N 250 QUI C O2 sing N N 251 QUI O2 HO2 sing N N 252 # _ndb_struct_conf_na.entry_id 8XPB _ndb_struct_conf_na.feature '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 DA 1 1_555 B DT 7 1_555 0.008 -0.339 0.144 3.293 2.437 -2.266 1 A_DA1:DT7_B A 1 ? B 7 ? 20 1 1 A DC 2 1_555 B DG 6 1_555 0.262 -0.265 -0.192 -13.786 4.862 -0.849 2 A_DC2:DG6_B A 2 ? B 6 ? 19 1 1 A DG 3 1_555 B DC 5 1_555 -0.303 -0.170 0.032 17.779 4.078 -3.259 3 A_DG3:DC5_B A 3 ? B 5 ? 19 1 1 A DG 4 1_555 B DC 4 1_555 0.069 -0.399 0.235 1.018 2.269 -1.825 4 A_DG4:DC4_B A 4 ? B 4 ? 19 1 1 A DC 5 1_555 B DG 3 1_555 0.161 -0.210 0.003 -18.991 2.770 -3.426 5 A_DC5:DG3_B A 5 ? B 3 ? 19 1 1 A DG 6 1_555 B DC 2 1_555 -0.241 -0.204 0.111 17.479 4.160 -3.635 6 A_DG6:DC2_B A 6 ? B 2 ? 19 1 1 A DT 7 1_555 B DA 1 1_555 -0.095 -0.320 0.022 -3.003 3.187 -1.800 7 A_DT7:DA1_B A 7 ? B 1 ? 20 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 DA 1 1_555 B DT 7 1_555 A DC 2 1_555 B DG 6 1_555 0.480 1.018 6.708 12.024 -1.458 16.525 4.224 9.856 5.635 -4.385 -36.170 20.464 1 AA_DA1DC2:DG6DT7_BB A 1 ? B 7 ? A 2 ? B 6 ? 1 A DC 2 1_555 B DG 6 1_555 A DG 3 1_555 B DC 5 1_555 -0.055 2.789 2.744 -0.644 1.493 11.779 11.699 -0.495 3.070 7.227 3.117 11.891 2 AA_DC2DG3:DC5DG6_BB A 2 ? B 6 ? A 3 ? B 5 ? 1 A DG 3 1_555 B DC 5 1_555 A DG 4 1_555 B DC 4 1_555 -0.483 1.008 6.905 -12.103 -5.560 17.193 7.336 -8.863 5.490 -15.861 34.526 21.717 3 AA_DG3DG4:DC4DC5_BB A 3 ? B 5 ? A 4 ? B 4 ? 1 A DG 4 1_555 B DC 4 1_555 A DC 5 1_555 B DG 3 1_555 0.611 0.889 6.954 12.667 -2.123 16.160 4.516 10.422 5.744 -6.394 -38.155 20.616 4 AA_DG4DC5:DG3DC4_BB A 4 ? B 4 ? A 5 ? B 3 ? 1 A DC 5 1_555 B DG 3 1_555 A DG 6 1_555 B DC 2 1_555 -0.056 2.700 2.638 -1.486 -0.749 10.999 14.814 -1.466 2.435 -3.877 7.695 11.124 5 AA_DC5DG6:DC2DG3_BB A 5 ? B 3 ? A 6 ? B 2 ? 1 A DG 6 1_555 B DC 2 1_555 A DT 7 1_555 B DA 1 1_555 -0.233 0.895 6.813 -9.297 0.156 17.356 2.460 -8.754 6.134 0.476 28.319 19.673 6 AA_DG6DT7:DA1DC2_BB A 6 ? B 2 ? A 7 ? B 1 ? # _pdbx_audit_support.funding_organization 'Ministry of Science and Technology (MoST, Taiwan)' _pdbx_audit_support.country Taiwan _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 5YTZ _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 8XPB _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] 0.021590 _atom_sites.fract_transf_matrix[1][2] 0.012465 _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] 0.024930 _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] 0.020846 _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 MN N O P S # loop_