data_9KBR # _entry.id 9KBR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.404 _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 9KBR pdb_00009kbr 10.2210/pdb9kbr/pdb WWPDB D_1300052947 ? ? # _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 2025-09-17 _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 9KBR _pdbx_database_status.recvd_initial_deposition_date 2024-10-31 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBC _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 huanglin36@mail.sysu.edu.cn _pdbx_contact_author.name_first Lin _pdbx_contact_author.name_last Huang _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-2121-365X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'He, Y.' 1 ? 'Yan, K.' 2 ? 'Lilley, D.M.J.' 3 ? 'Huang, L.' 4 ? # _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 the methyltransferase ribozyme MTR1 bound to DNA substrate' _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 'He, Y.' 1 ? primary 'Yan, K.' 2 ? primary 'Lilley, D.M.J.' 3 ? primary 'Huang, L.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*CP*AP*CP*TP*GP*(MA7)P*GP*AP*GP*CP*TP*TP*C)-3') ; 4255.801 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3') ; 7641.636 1 ? ? ? ? 3 polymer syn ;RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3') ; 7755.703 1 ? ? ? ? 4 non-polymer syn 'SODIUM ION' 22.990 4 ? ? ? ? 5 non-polymer syn GUANINE 151.126 1 ? ? ? ? 6 water nat water 18.015 1 ? ? ? ? # 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 yes '(DC)(DC)(DA)(DC)(DT)(DG)(MA7)(DG)(DA)(DG)(DC)(DT)(DT)(DC)' CCACTGAGAGCTTC A ? 2 polyribonucleotide no no GGAAGCUCUGACCGACCCCCAGCC GGAAGCUCUGACCGACCCCCAGCC B ? 3 polyribonucleotide no no GCUGGGACAACUAGACAUACAGUG GCUGGGACAACUAGACAUACAGUG C ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'SODIUM ION' NA 5 GUANINE GUN 6 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 DC n 1 3 DA n 1 4 DC n 1 5 DT n 1 6 DG n 1 7 MA7 n 1 8 DG n 1 9 DA n 1 10 DG n 1 11 DC n 1 12 DT n 1 13 DT n 1 14 DC n 2 1 G n 2 2 G n 2 3 A n 2 4 A n 2 5 G n 2 6 C n 2 7 U n 2 8 C n 2 9 U n 2 10 G n 2 11 A n 2 12 C n 2 13 C n 2 14 G n 2 15 A n 2 16 C n 2 17 C n 2 18 C n 2 19 C n 2 20 C n 2 21 A n 2 22 G n 2 23 C n 2 24 C n 3 1 G n 3 2 C n 3 3 U n 3 4 G n 3 5 G n 3 6 G n 3 7 A n 3 8 C n 3 9 A n 3 10 A n 3 11 C n 3 12 U n 3 13 A n 3 14 G n 3 15 A n 3 16 C n 3 17 A n 3 18 U n 3 19 A n 3 20 C n 3 21 A n 3 22 G n 3 23 U n 3 24 G n # 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 14 'synthetic construct' ? 32630 ? 2 1 sample 1 24 'synthetic construct' ? 32630 ? 3 1 sample 1 24 '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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GUN non-polymer . GUANINE ? 'C5 H5 N5 O' 151.126 HOH non-polymer . WATER ? 'H2 O' 18.015 MA7 'DNA linking' n "1N-METHYLADENOSINE-5'-MONOPHOSPHATE" ? 'C11 H17 N5 O6 P 1' 346.256 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 DC 2 2 2 DC DC A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DT 5 5 5 DT DT A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 MA7 7 7 7 MA7 MA7 A . n A 1 8 DG 8 8 8 DG DG A . n A 1 9 DA 9 9 9 DA DA A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DT 12 12 12 DT DT A . n A 1 13 DT 13 13 13 DT DT A . n A 1 14 DC 14 14 14 DC DC A . n B 2 1 G 1 1 1 G G B . n B 2 2 G 2 2 2 G G B . n B 2 3 A 3 3 3 A A B . n B 2 4 A 4 4 4 A A B . n B 2 5 G 5 5 5 G G B . n B 2 6 C 6 6 6 C C B . n B 2 7 U 7 7 7 U U B . n B 2 8 C 8 8 8 C C B . n B 2 9 U 9 9 9 U U B . n B 2 10 G 10 10 10 G G B . n B 2 11 A 11 11 11 A A B . n B 2 12 C 12 12 12 C C B . n B 2 13 C 13 13 13 C C B . n B 2 14 G 14 14 14 G G B . n B 2 15 A 15 15 15 A A B . n B 2 16 C 16 16 16 C C B . n B 2 17 C 17 17 17 C C B . n B 2 18 C 18 18 18 C C B . n B 2 19 C 19 19 19 C C B . n B 2 20 C 20 20 20 C C B . n B 2 21 A 21 21 21 A A B . n B 2 22 G 22 22 22 G G B . n B 2 23 C 23 23 23 C C B . n B 2 24 C 24 24 24 C C B . n C 3 1 G 1 25 25 G G C . n C 3 2 C 2 26 26 C C C . n C 3 3 U 3 27 27 U U C . n C 3 4 G 4 28 28 G G C . n C 3 5 G 5 29 29 G G C . n C 3 6 G 6 30 30 G G C . n C 3 7 A 7 31 31 A A C . n C 3 8 C 8 32 32 C C C . n C 3 9 A 9 33 33 A A C . n C 3 10 A 10 34 34 A A C . n C 3 11 C 11 35 35 C C C . n C 3 12 U 12 36 36 U U C . n C 3 13 A 13 37 37 A A C . n C 3 14 G 14 38 38 G G C . n C 3 15 A 15 39 39 A A C . n C 3 16 C 16 40 40 C C C . n C 3 17 A 17 41 41 A A C . n C 3 18 U 18 42 42 U U C . n C 3 19 A 19 43 43 A A C . n C 3 20 C 20 44 44 C C C . n C 3 21 A 21 45 45 A A C . n C 3 22 G 22 46 46 G G C . n C 3 23 U 23 47 47 U U C . n C 3 24 G 24 48 48 G G C . n # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 GUN ? ? GUN ? ? 'SUBJECT OF INVESTIGATION' ? 2 MA7 ? ? MA7 ? ? 'SUBJECT OF INVESTIGATION' ? # 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 D 4 NA 1 101 5 NA NA B . E 5 GUN 1 101 101 GUN GUN C . F 4 NA 1 102 1 NA NA C . G 4 NA 1 103 2 NA NA C . H 4 NA 1 104 4 NA NA C . I 6 HOH 1 201 1 HOH HOH C . # 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 reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 9KBR _cell.details ? _cell.formula_units_Z ? _cell.length_a 69.196 _cell.length_a_esd ? _cell.length_b 69.196 _cell.length_b_esd ? _cell.length_c 65.597 _cell.length_c_esd ? _cell.volume 314084.105 _cell.volume_esd ? _cell.Z_PDB 4 _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 9KBR _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall 'P 4w' _symmetry.space_group_name_H-M 'P 41' _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 9KBR _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 4.00 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 69.21 _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, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _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 ;100mM NaCl, 100mM LiCl, 10mM MgCl2, 34% MPD ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 291 # _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 PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER2 S 9M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2024-03-24 _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 0.97918 _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 'SSRF BEAMLINE BL02U1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97918 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL02U1 _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate 88.88 _reflns.entry_id 9KBR _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.65 _reflns.d_resolution_low 48.93 _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 9120 _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 99.9 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 13.9 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 15.4 _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 0.038 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.093 _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 ? # _reflns_shell.d_res_high 2.65 _reflns_shell.d_res_low 2.79 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 0.8 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 1315 _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 2.303 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.389 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all 99.8 _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 5.850 _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 ? # _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 110.23 _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 9KBR _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 2.65 _refine.ls_d_res_low 34.60 _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 8893 _refine.ls_number_reflns_R_free 455 _refine.ls_number_reflns_R_work 8438 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 97.59 _refine.ls_percent_reflns_R_free 5.12 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1905 _refine.ls_R_factor_R_free 0.2231 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1887 _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 1.35 _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 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _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 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _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 33.9320 _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 0.3966 _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 2.65 _refine_hist.d_res_low 34.60 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 1317 _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 1301 _refine_hist.pdbx_number_atoms_ligand 15 _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' ? 0.0080 ? 1466 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.2036 ? 2273 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0452 ? 292 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0057 ? 63 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 13.9165 ? 700 ? f_dihedral_angle_d ? ? # 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' 2.65 3.03 . . 154 2648 92.90 . . . . 0.3535 . . . . . . . . . . . 0.3704 'X-RAY DIFFRACTION' 3.03 3.82 . . 154 2876 99.93 . . . . 0.2299 . . . . . . . . . . . 0.2697 'X-RAY DIFFRACTION' 3.82 34.60 . . 147 2914 99.87 . . . . 0.1580 . . . . . . . . . . . 0.1863 # _struct.entry_id 9KBR _struct.title 'Crystal structure of the methyltransferase-ribozyme 1 bound to DNA substrate (with 1-methyl-adenosine)' _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 9KBR _struct_keywords.text 'Ribozyme, Methyltransferase, MTR1, O6-methylguanine, DNA-RNA HYBRID' _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' # 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 4 ? E N N 5 ? F N N 4 ? G N N 4 ? H N N 4 ? I 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 9KBR 9KBR ? 1 ? 1 2 PDB 9KBR 9KBR ? 2 ? 1 3 PDB 9KBR 9KBR ? 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 9KBR A 1 ? 14 ? 9KBR 1 ? 14 ? 1 14 2 2 9KBR B 1 ? 24 ? 9KBR 1 ? 24 ? 1 24 3 3 9KBR C 1 ? 24 ? 9KBR 25 ? 48 ? 25 48 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 5320 ? 1 MORE -35 ? 1 'SSA (A^2)' 10040 ? # _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 # _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 covale1 covale both ? A DG 6 "O3'" ? ? ? 1_555 A MA7 7 P ? ? A DG 6 A MA7 7 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A MA7 7 "O3'" ? ? ? 1_555 A DG 8 P ? ? A MA7 7 A DG 8 1_555 ? ? ? ? ? ? ? 1.608 ? ? metalc1 metalc ? ? C C 8 O2 ? ? ? 1_555 F NA . NA ? ? C C 32 C NA 102 1_555 ? ? ? ? ? ? ? 2.225 ? ? metalc2 metalc ? ? C A 10 OP2 ? ? ? 1_555 H NA . NA ? ? C A 34 C NA 104 1_555 ? ? ? ? ? ? ? 2.780 ? ? hydrog1 hydrog ? ? A DC 2 N3 ? ? ? 1_555 C G 24 N1 ? ? A DC 2 C G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 2 N4 ? ? ? 1_555 C G 24 O6 ? ? A DC 2 C G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 O2 ? ? ? 1_555 C G 24 N2 ? ? A DC 2 C G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 3 N1 ? ? ? 1_555 C U 23 N3 ? ? A DA 3 C U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 3 N6 ? ? ? 1_555 C U 23 O4 ? ? A DA 3 C U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 N3 ? ? ? 1_555 C G 22 N1 ? ? A DC 4 C G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C G 22 O6 ? ? A DC 4 C G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 4 O2 ? ? ? 1_555 C G 22 N2 ? ? A DC 4 C G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 5 N3 ? ? ? 1_555 C A 21 N1 ? ? A DT 5 C A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 5 O4 ? ? ? 1_555 C A 21 N6 ? ? A DT 5 C A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 6 N1 ? ? ? 1_555 C C 20 N3 ? ? A DG 6 C C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 6 N2 ? ? ? 1_555 C C 20 O2 ? ? A DG 6 C C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 O6 ? ? ? 1_555 C C 20 N4 ? ? A DG 6 C C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 8 N1 ? ? ? 1_555 B C 8 N3 ? ? A DG 8 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 8 N2 ? ? ? 1_555 B C 8 O2 ? ? A DG 8 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 8 O6 ? ? ? 1_555 B C 8 N4 ? ? A DG 8 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B U 7 N3 ? ? A DA 9 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B U 7 O4 ? ? A DA 9 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B C 6 N3 ? ? A DG 10 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B C 6 O2 ? ? A DG 10 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B C 6 N4 ? ? A DG 10 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B G 5 N1 ? ? A DC 11 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B G 5 O6 ? ? A DC 11 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B G 5 N2 ? ? A DC 11 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 12 N3 ? ? ? 1_555 B A 4 N1 ? ? A DT 12 B A 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 12 O4 ? ? ? 1_555 B A 4 N6 ? ? A DT 12 B A 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DT 13 N3 ? ? ? 1_555 B A 3 N1 ? ? A DT 13 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DT 13 O4 ? ? ? 1_555 B A 3 N6 ? ? A DT 13 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 14 N3 ? ? ? 1_555 B G 2 N1 ? ? A DC 14 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 14 N4 ? ? ? 1_555 B G 2 O6 ? ? A DC 14 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DC 14 O2 ? ? ? 1_555 B G 2 N2 ? ? A DC 14 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B U 9 N3 ? ? ? 1_555 C A 10 N7 ? ? B U 9 C A 34 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog33 hydrog ? ? B U 9 O2 ? ? ? 1_555 C A 10 N6 ? ? B U 9 C A 34 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog34 hydrog ? ? B A 11 N6 ? ? ? 1_555 C A 19 N3 ? ? B A 11 C A 43 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog35 hydrog ? ? B C 13 N3 ? ? ? 1_555 C G 14 N1 ? ? B C 13 C G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B C 13 N4 ? ? ? 1_555 C G 14 O6 ? ? B C 13 C G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B C 13 O2 ? ? ? 1_555 C G 14 N2 ? ? B C 13 C G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B C 13 O2 ? ? ? 1_555 C A 17 N6 ? ? B C 13 C A 41 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog39 hydrog ? ? B G 14 N1 ? ? ? 1_555 C C 11 N3 ? ? B G 14 C C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B G 14 N2 ? ? ? 1_555 C C 11 O2 ? ? B G 14 C C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B G 14 O6 ? ? ? 1_555 C C 11 N4 ? ? B G 14 C C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B C 17 N4 ? ? ? 1_555 C A 7 N1 ? ? B C 17 C A 31 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog43 hydrog ? ? B C 18 N3 ? ? ? 1_555 C G 6 N1 ? ? B C 18 C G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B C 18 N4 ? ? ? 1_555 C G 6 O6 ? ? B C 18 C G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? B C 18 O2 ? ? ? 1_555 C G 6 N2 ? ? B C 18 C G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? B C 19 N3 ? ? ? 1_555 C G 5 N1 ? ? B C 19 C G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? B C 19 N4 ? ? ? 1_555 C G 5 O6 ? ? B C 19 C G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? B C 19 O2 ? ? ? 1_555 C G 5 N2 ? ? B C 19 C G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? B C 20 N3 ? ? ? 1_555 C G 4 N1 ? ? B C 20 C G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? B C 20 N4 ? ? ? 1_555 C G 4 O6 ? ? B C 20 C G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? B C 20 O2 ? ? ? 1_555 C G 4 N2 ? ? B C 20 C G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? B A 21 N1 ? ? ? 1_555 C U 3 N3 ? ? B A 21 C U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? B A 21 N6 ? ? ? 1_555 C U 3 O4 ? ? B A 21 C U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? B G 22 N1 ? ? ? 1_555 C C 2 N3 ? ? B G 22 C C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? B G 22 N2 ? ? ? 1_555 C C 2 O2 ? ? B G 22 C C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? B G 22 O6 ? ? ? 1_555 C C 2 N4 ? ? B G 22 C C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? B C 23 N3 ? ? ? 1_555 C G 1 N1 ? ? B C 23 C G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? B C 23 N4 ? ? ? 1_555 C G 1 O6 ? ? B C 23 C G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? B C 23 O2 ? ? ? 1_555 C G 1 N2 ? ? B C 23 C G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C A 13 N3 ? ? ? 1_555 C A 19 N6 ? ? C A 37 C A 43 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _pdbx_entry_details.entry_id 9KBR _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 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 N3 _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 C _pdbx_validate_rmsd_bond.auth_seq_id_1 19 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 C4 _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 C _pdbx_validate_rmsd_bond.auth_seq_id_2 19 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.291 _pdbx_validate_rmsd_bond.bond_target_value 1.335 _pdbx_validate_rmsd_bond.bond_deviation -0.044 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.007 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N3 B C 16 ? ? C4 B C 16 ? ? N4 B C 16 ? ? 113.67 118.00 -4.33 0.70 N 2 1 "O5'" B C 19 ? ? P B C 19 ? ? OP2 B C 19 ? ? 100.05 105.70 -5.65 0.90 N 3 1 N1 B C 19 ? ? C2 B C 19 ? ? O2 B C 19 ? ? 122.56 118.90 3.66 0.60 N 4 1 N1 C G 29 ? ? C6 C G 29 ? ? O6 C G 29 ? ? 116.26 119.90 -3.64 0.60 N 5 1 N1 C C 32 ? ? C2 C C 32 ? ? O2 C C 32 ? ? 123.54 118.90 4.64 0.60 N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x,z+1/4 3 y,-x,z+3/4 4 -x,-y,z+1/2 # 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 16.5774746792 18.4477518993 -5.57000248704 1.47158387417 ? -0.354894100747 ? 0.204482613266 ? 1.43846914245 ? -0.226719089716 ? 1.58719988232 ? 1.06588128564 ? -0.649457432092 ? 0.744267019103 ? 1.28120786469 ? -1.70154086849 ? 2.00551725377 ? -1.23225905026 ? -0.785790185169 ? -2.01928133945 ? -0.407460745022 ? -0.226946375958 ? 1.05560301055 ? 1.25281468412 ? -0.143992879766 ? 0.003356657663 ? 2 'X-RAY DIFFRACTION' ? refined 27.3923328801 32.6973346792 -2.80052767527 0.80777227358 ? 0.0830511402362 ? -0.0850483990824 ? 0.582737062859 ? 0.0319156313833 ? 0.643190455386 ? 7.43599976417 ? 1.52123914256 ? -0.204021927038 ? 2.38906992515 ? 0.326802846245 ? 5.17314314085 ? -0.22968157908 ? -0.126931526766 ? -0.646122363305 ? -0.59090540469 ? -0.218819113844 ? 0.23107161016 ? -0.299441847713 ? -0.407201715865 ? -0.00805697787397 ? 3 'X-RAY DIFFRACTION' ? refined 17.8359911287 32.2313523288 1.87865042126 0.713429485329 ? 0.143780922176 ? -0.0983017667298 ? 0.923837268909 ? -0.145904879343 ? 0.864061321269 ? 4.42799665568 ? -0.0909214749137 ? -2.38098855099 ? 2.81723523488 ? -0.812755090014 ? 4.21636026002 ? -0.406666483009 ? 0.160135232867 ? -0.550966826059 ? -0.0771357104388 ? -0.0552563401988 ? 0.830632572133 ? 0.146423747827 ? -1.03615043693 ? 0.00011540634622 ? # 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 A ? A 1 ? A ? A 14 ? ? '(chain A and resseq 1:14)' 2 'X-RAY DIFFRACTION' 2 B ? B 1 ? B ? B 24 ? ? '(chain B and resseq 1:24)' 3 'X-RAY DIFFRACTION' 3 C ? C 25 ? C ? C 48 ? ? '(chain C and resseq 25:48)' # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DA OP3 O N N 73 DA P P N N 74 DA OP1 O N N 75 DA OP2 O N N 76 DA "O5'" O N N 77 DA "C5'" C N N 78 DA "C4'" C N R 79 DA "O4'" O N N 80 DA "C3'" C N S 81 DA "O3'" O N N 82 DA "C2'" C N N 83 DA "C1'" C N R 84 DA N9 N Y N 85 DA C8 C Y N 86 DA N7 N Y N 87 DA C5 C Y N 88 DA C6 C Y N 89 DA N6 N N N 90 DA N1 N Y N 91 DA C2 C Y N 92 DA N3 N Y N 93 DA C4 C Y N 94 DA HOP3 H N N 95 DA HOP2 H N N 96 DA "H5'" H N N 97 DA "H5''" H N N 98 DA "H4'" H N N 99 DA "H3'" H N N 100 DA "HO3'" H N N 101 DA "H2'" H N N 102 DA "H2''" H N N 103 DA "H1'" H N N 104 DA H8 H N N 105 DA H61 H N N 106 DA H62 H N N 107 DA H2 H N N 108 DC OP3 O N N 109 DC P P N N 110 DC OP1 O N N 111 DC OP2 O N N 112 DC "O5'" O N N 113 DC "C5'" C N N 114 DC "C4'" C N R 115 DC "O4'" O N N 116 DC "C3'" C N S 117 DC "O3'" O N N 118 DC "C2'" C N N 119 DC "C1'" C N R 120 DC N1 N N N 121 DC C2 C N N 122 DC O2 O N N 123 DC N3 N N N 124 DC C4 C N N 125 DC N4 N N N 126 DC C5 C N N 127 DC C6 C N N 128 DC HOP3 H N N 129 DC HOP2 H N N 130 DC "H5'" H N N 131 DC "H5''" H N N 132 DC "H4'" H N N 133 DC "H3'" H N N 134 DC "HO3'" H N N 135 DC "H2'" H N N 136 DC "H2''" H N N 137 DC "H1'" H N N 138 DC H41 H N N 139 DC H42 H N N 140 DC H5 H N N 141 DC H6 H N N 142 DG OP3 O N N 143 DG P P N N 144 DG OP1 O N N 145 DG OP2 O N N 146 DG "O5'" O N N 147 DG "C5'" C N N 148 DG "C4'" C N R 149 DG "O4'" O N N 150 DG "C3'" C N S 151 DG "O3'" O N N 152 DG "C2'" C N N 153 DG "C1'" C N R 154 DG N9 N Y N 155 DG C8 C Y N 156 DG N7 N Y N 157 DG C5 C Y N 158 DG C6 C N N 159 DG O6 O N N 160 DG N1 N N N 161 DG C2 C N N 162 DG N2 N N N 163 DG N3 N N N 164 DG C4 C Y N 165 DG HOP3 H N N 166 DG HOP2 H N N 167 DG "H5'" H N N 168 DG "H5''" H N N 169 DG "H4'" H N N 170 DG "H3'" H N N 171 DG "HO3'" H N N 172 DG "H2'" H N N 173 DG "H2''" H N N 174 DG "H1'" H N N 175 DG H8 H N N 176 DG H1 H N N 177 DG H21 H N N 178 DG H22 H N N 179 DT OP3 O N N 180 DT P P N N 181 DT OP1 O N N 182 DT OP2 O N N 183 DT "O5'" O N N 184 DT "C5'" C N N 185 DT "C4'" C N R 186 DT "O4'" O N N 187 DT "C3'" C N S 188 DT "O3'" O N N 189 DT "C2'" C N N 190 DT "C1'" C N R 191 DT N1 N N N 192 DT C2 C N N 193 DT O2 O N N 194 DT N3 N N N 195 DT C4 C N N 196 DT O4 O N N 197 DT C5 C N N 198 DT C7 C N N 199 DT C6 C N N 200 DT HOP3 H N N 201 DT HOP2 H N N 202 DT "H5'" H N N 203 DT "H5''" H N N 204 DT "H4'" H N N 205 DT "H3'" H N N 206 DT "HO3'" H N N 207 DT "H2'" H N N 208 DT "H2''" H N N 209 DT "H1'" H N N 210 DT H3 H N N 211 DT H71 H N N 212 DT H72 H N N 213 DT H73 H N N 214 DT H6 H N N 215 G OP3 O N N 216 G P P N N 217 G OP1 O N N 218 G OP2 O N N 219 G "O5'" O N N 220 G "C5'" C N N 221 G "C4'" C N R 222 G "O4'" O N N 223 G "C3'" C N S 224 G "O3'" O N N 225 G "C2'" C N R 226 G "O2'" O N N 227 G "C1'" C N R 228 G N9 N Y N 229 G C8 C Y N 230 G N7 N Y N 231 G C5 C Y N 232 G C6 C N N 233 G O6 O N N 234 G N1 N N N 235 G C2 C N N 236 G N2 N N N 237 G N3 N N N 238 G C4 C Y N 239 G HOP3 H N N 240 G HOP2 H N N 241 G "H5'" H N N 242 G "H5''" H N N 243 G "H4'" H N N 244 G "H3'" H N N 245 G "HO3'" H N N 246 G "H2'" H N N 247 G "HO2'" H N N 248 G "H1'" H N N 249 G H8 H N N 250 G H1 H N N 251 G H21 H N N 252 G H22 H N N 253 GUN N9 N Y N 254 GUN C8 C Y N 255 GUN N7 N Y N 256 GUN C5 C Y N 257 GUN C6 C N N 258 GUN O6 O N N 259 GUN N1 N N N 260 GUN C2 C N N 261 GUN N2 N N N 262 GUN N3 N N N 263 GUN C4 C Y N 264 GUN HN9 H N N 265 GUN H8 H N N 266 GUN HN1 H N N 267 GUN HN21 H N N 268 GUN HN22 H N N 269 HOH O O N N 270 HOH H1 H N N 271 HOH H2 H N N 272 MA7 C2 C Y N 273 MA7 C4 C Y N 274 MA7 C5 C Y N 275 MA7 C6 C Y N 276 MA7 C8 C Y N 277 MA7 P P N N 278 MA7 OP1 O N N 279 MA7 OP2 O N N 280 MA7 "O5'" O N N 281 MA7 N9 N Y N 282 MA7 N3 N Y N 283 MA7 N1 N Y N 284 MA7 N6 N N N 285 MA7 N7 N Y N 286 MA7 CN C N N 287 MA7 "C2'" C N N 288 MA7 "C5'" C N N 289 MA7 "C4'" C N R 290 MA7 "O4'" O N N 291 MA7 "C1'" C N R 292 MA7 "C3'" C N S 293 MA7 "O3'" O N N 294 MA7 OP3 O N N 295 MA7 H2 H N N 296 MA7 H8 H N N 297 MA7 HOP2 H N N 298 MA7 H61 H N N 299 MA7 H62 H N N 300 MA7 HN1 H N N 301 MA7 HN2 H N N 302 MA7 HN3 H N N 303 MA7 "H2'" H N N 304 MA7 "H2''" H N N 305 MA7 "H5'" H N N 306 MA7 "H5''" H N N 307 MA7 "H4'" H N N 308 MA7 "H1'" H N N 309 MA7 "H3'" H N N 310 MA7 "HO3'" H N N 311 MA7 HOP3 H N N 312 NA NA NA N N 313 U OP3 O N N 314 U P P N N 315 U OP1 O N N 316 U OP2 O N N 317 U "O5'" O N N 318 U "C5'" C N N 319 U "C4'" C N R 320 U "O4'" O N N 321 U "C3'" C N S 322 U "O3'" O N N 323 U "C2'" C N R 324 U "O2'" O N N 325 U "C1'" C N R 326 U N1 N N N 327 U C2 C N N 328 U O2 O N N 329 U N3 N N N 330 U C4 C N N 331 U O4 O N N 332 U C5 C N N 333 U C6 C N N 334 U HOP3 H N N 335 U HOP2 H N N 336 U "H5'" H N N 337 U "H5''" H N N 338 U "H4'" H N N 339 U "H3'" H N N 340 U "HO3'" H N N 341 U "H2'" H N N 342 U "HO2'" H N N 343 U "H1'" H N N 344 U H3 H N N 345 U H5 H N N 346 U H6 H N N 347 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DA OP3 P sing N N 76 DA OP3 HOP3 sing N N 77 DA P OP1 doub N N 78 DA P OP2 sing N N 79 DA P "O5'" sing N N 80 DA OP2 HOP2 sing N N 81 DA "O5'" "C5'" sing N N 82 DA "C5'" "C4'" sing N N 83 DA "C5'" "H5'" sing N N 84 DA "C5'" "H5''" sing N N 85 DA "C4'" "O4'" sing N N 86 DA "C4'" "C3'" sing N N 87 DA "C4'" "H4'" sing N N 88 DA "O4'" "C1'" sing N N 89 DA "C3'" "O3'" sing N N 90 DA "C3'" "C2'" sing N N 91 DA "C3'" "H3'" sing N N 92 DA "O3'" "HO3'" sing N N 93 DA "C2'" "C1'" sing N N 94 DA "C2'" "H2'" sing N N 95 DA "C2'" "H2''" sing N N 96 DA "C1'" N9 sing N N 97 DA "C1'" "H1'" sing N N 98 DA N9 C8 sing Y N 99 DA N9 C4 sing Y N 100 DA C8 N7 doub Y N 101 DA C8 H8 sing N N 102 DA N7 C5 sing Y N 103 DA C5 C6 sing Y N 104 DA C5 C4 doub Y N 105 DA C6 N6 sing N N 106 DA C6 N1 doub Y N 107 DA N6 H61 sing N N 108 DA N6 H62 sing N N 109 DA N1 C2 sing Y N 110 DA C2 N3 doub Y N 111 DA C2 H2 sing N N 112 DA N3 C4 sing Y N 113 DC OP3 P sing N N 114 DC OP3 HOP3 sing N N 115 DC P OP1 doub N N 116 DC P OP2 sing N N 117 DC P "O5'" sing N N 118 DC OP2 HOP2 sing N N 119 DC "O5'" "C5'" sing N N 120 DC "C5'" "C4'" sing N N 121 DC "C5'" "H5'" sing N N 122 DC "C5'" "H5''" sing N N 123 DC "C4'" "O4'" sing N N 124 DC "C4'" "C3'" sing N N 125 DC "C4'" "H4'" sing N N 126 DC "O4'" "C1'" sing N N 127 DC "C3'" "O3'" sing N N 128 DC "C3'" "C2'" sing N N 129 DC "C3'" "H3'" sing N N 130 DC "O3'" "HO3'" sing N N 131 DC "C2'" "C1'" sing N N 132 DC "C2'" "H2'" sing N N 133 DC "C2'" "H2''" sing N N 134 DC "C1'" N1 sing N N 135 DC "C1'" "H1'" sing N N 136 DC N1 C2 sing N N 137 DC N1 C6 sing N N 138 DC C2 O2 doub N N 139 DC C2 N3 sing N N 140 DC N3 C4 doub N N 141 DC C4 N4 sing N N 142 DC C4 C5 sing N N 143 DC N4 H41 sing N N 144 DC N4 H42 sing N N 145 DC C5 C6 doub N N 146 DC C5 H5 sing N N 147 DC C6 H6 sing N N 148 DG OP3 P sing N N 149 DG OP3 HOP3 sing N N 150 DG P OP1 doub N N 151 DG P OP2 sing N N 152 DG P "O5'" sing N N 153 DG OP2 HOP2 sing N N 154 DG "O5'" "C5'" sing N N 155 DG "C5'" "C4'" sing N N 156 DG "C5'" "H5'" sing N N 157 DG "C5'" "H5''" sing N N 158 DG "C4'" "O4'" sing N N 159 DG "C4'" "C3'" sing N N 160 DG "C4'" "H4'" sing N N 161 DG "O4'" "C1'" sing N N 162 DG "C3'" "O3'" sing N N 163 DG "C3'" "C2'" sing N N 164 DG "C3'" "H3'" sing N N 165 DG "O3'" "HO3'" sing N N 166 DG "C2'" "C1'" sing N N 167 DG "C2'" "H2'" sing N N 168 DG "C2'" "H2''" sing N N 169 DG "C1'" N9 sing N N 170 DG "C1'" "H1'" sing N N 171 DG N9 C8 sing Y N 172 DG N9 C4 sing Y N 173 DG C8 N7 doub Y N 174 DG C8 H8 sing N N 175 DG N7 C5 sing Y N 176 DG C5 C6 sing N N 177 DG C5 C4 doub Y N 178 DG C6 O6 doub N N 179 DG C6 N1 sing N N 180 DG N1 C2 sing N N 181 DG N1 H1 sing N N 182 DG C2 N2 sing N N 183 DG C2 N3 doub N N 184 DG N2 H21 sing N N 185 DG N2 H22 sing N N 186 DG N3 C4 sing N N 187 DT OP3 P sing N N 188 DT OP3 HOP3 sing N N 189 DT P OP1 doub N N 190 DT P OP2 sing N N 191 DT P "O5'" sing N N 192 DT OP2 HOP2 sing N N 193 DT "O5'" "C5'" sing N N 194 DT "C5'" "C4'" sing N N 195 DT "C5'" "H5'" sing N N 196 DT "C5'" "H5''" sing N N 197 DT "C4'" "O4'" sing N N 198 DT "C4'" "C3'" sing N N 199 DT "C4'" "H4'" sing N N 200 DT "O4'" "C1'" sing N N 201 DT "C3'" "O3'" sing N N 202 DT "C3'" "C2'" sing N N 203 DT "C3'" "H3'" sing N N 204 DT "O3'" "HO3'" sing N N 205 DT "C2'" "C1'" sing N N 206 DT "C2'" "H2'" sing N N 207 DT "C2'" "H2''" sing N N 208 DT "C1'" N1 sing N N 209 DT "C1'" "H1'" sing N N 210 DT N1 C2 sing N N 211 DT N1 C6 sing N N 212 DT C2 O2 doub N N 213 DT C2 N3 sing N N 214 DT N3 C4 sing N N 215 DT N3 H3 sing N N 216 DT C4 O4 doub N N 217 DT C4 C5 sing N N 218 DT C5 C7 sing N N 219 DT C5 C6 doub N N 220 DT C7 H71 sing N N 221 DT C7 H72 sing N N 222 DT C7 H73 sing N N 223 DT C6 H6 sing N N 224 G OP3 P sing N N 225 G OP3 HOP3 sing N N 226 G P OP1 doub N N 227 G P OP2 sing N N 228 G P "O5'" sing N N 229 G OP2 HOP2 sing N N 230 G "O5'" "C5'" sing N N 231 G "C5'" "C4'" sing N N 232 G "C5'" "H5'" sing N N 233 G "C5'" "H5''" sing N N 234 G "C4'" "O4'" sing N N 235 G "C4'" "C3'" sing N N 236 G "C4'" "H4'" sing N N 237 G "O4'" "C1'" sing N N 238 G "C3'" "O3'" sing N N 239 G "C3'" "C2'" sing N N 240 G "C3'" "H3'" sing N N 241 G "O3'" "HO3'" sing N N 242 G "C2'" "O2'" sing N N 243 G "C2'" "C1'" sing N N 244 G "C2'" "H2'" sing N N 245 G "O2'" "HO2'" sing N N 246 G "C1'" N9 sing N N 247 G "C1'" "H1'" sing N N 248 G N9 C8 sing Y N 249 G N9 C4 sing Y N 250 G C8 N7 doub Y N 251 G C8 H8 sing N N 252 G N7 C5 sing Y N 253 G C5 C6 sing N N 254 G C5 C4 doub Y N 255 G C6 O6 doub N N 256 G C6 N1 sing N N 257 G N1 C2 sing N N 258 G N1 H1 sing N N 259 G C2 N2 sing N N 260 G C2 N3 doub N N 261 G N2 H21 sing N N 262 G N2 H22 sing N N 263 G N3 C4 sing N N 264 GUN N9 C8 sing Y N 265 GUN N9 C4 sing Y N 266 GUN N9 HN9 sing N N 267 GUN C8 N7 doub Y N 268 GUN C8 H8 sing N N 269 GUN N7 C5 sing Y N 270 GUN C5 C6 sing N N 271 GUN C5 C4 doub Y N 272 GUN C6 O6 doub N N 273 GUN C6 N1 sing N N 274 GUN N1 C2 sing N N 275 GUN N1 HN1 sing N N 276 GUN C2 N2 sing N N 277 GUN C2 N3 doub N N 278 GUN N2 HN21 sing N N 279 GUN N2 HN22 sing N N 280 GUN N3 C4 sing N N 281 HOH O H1 sing N N 282 HOH O H2 sing N N 283 MA7 C2 N3 doub Y N 284 MA7 C2 N1 sing Y N 285 MA7 C2 H2 sing N N 286 MA7 C4 C5 doub Y N 287 MA7 C4 N9 sing Y N 288 MA7 C4 N3 sing Y N 289 MA7 C5 C6 sing Y N 290 MA7 C5 N7 sing Y N 291 MA7 C6 N1 doub Y N 292 MA7 C6 N6 sing N N 293 MA7 C8 N9 sing Y N 294 MA7 C8 N7 doub Y N 295 MA7 C8 H8 sing N N 296 MA7 P OP1 doub N N 297 MA7 P OP2 sing N N 298 MA7 P "O5'" sing N N 299 MA7 P OP3 sing N N 300 MA7 OP2 HOP2 sing N N 301 MA7 "O5'" "C5'" sing N N 302 MA7 N9 "C1'" sing N N 303 MA7 N1 CN sing N N 304 MA7 N6 H61 sing N N 305 MA7 N6 H62 sing N N 306 MA7 CN HN1 sing N N 307 MA7 CN HN2 sing N N 308 MA7 CN HN3 sing N N 309 MA7 "C2'" "C1'" sing N N 310 MA7 "C2'" "C3'" sing N N 311 MA7 "C2'" "H2'" sing N N 312 MA7 "C2'" "H2''" sing N N 313 MA7 "C5'" "C4'" sing N N 314 MA7 "C5'" "H5'" sing N N 315 MA7 "C5'" "H5''" sing N N 316 MA7 "C4'" "O4'" sing N N 317 MA7 "C4'" "C3'" sing N N 318 MA7 "C4'" "H4'" sing N N 319 MA7 "O4'" "C1'" sing N N 320 MA7 "C1'" "H1'" sing N N 321 MA7 "C3'" "O3'" sing N N 322 MA7 "C3'" "H3'" sing N N 323 MA7 "O3'" "HO3'" sing N N 324 MA7 OP3 HOP3 sing N N 325 U OP3 P sing N N 326 U OP3 HOP3 sing N N 327 U P OP1 doub N N 328 U P OP2 sing N N 329 U P "O5'" sing N N 330 U OP2 HOP2 sing N N 331 U "O5'" "C5'" sing N N 332 U "C5'" "C4'" sing N N 333 U "C5'" "H5'" sing N N 334 U "C5'" "H5''" sing N N 335 U "C4'" "O4'" sing N N 336 U "C4'" "C3'" sing N N 337 U "C4'" "H4'" sing N N 338 U "O4'" "C1'" sing N N 339 U "C3'" "O3'" sing N N 340 U "C3'" "C2'" sing N N 341 U "C3'" "H3'" sing N N 342 U "O3'" "HO3'" sing N N 343 U "C2'" "O2'" sing N N 344 U "C2'" "C1'" sing N N 345 U "C2'" "H2'" sing N N 346 U "O2'" "HO2'" sing N N 347 U "C1'" N1 sing N N 348 U "C1'" "H1'" sing N N 349 U N1 C2 sing N N 350 U N1 C6 sing N N 351 U C2 O2 doub N N 352 U C2 N3 sing N N 353 U N3 C4 sing N N 354 U N3 H3 sing N N 355 U C4 O4 doub N N 356 U C4 C5 sing N N 357 U C5 C6 doub N N 358 U C5 H5 sing N N 359 U C6 H6 sing N N 360 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9KBR 'double helix' 9KBR 'a-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 2 1_555 C G 24 1_555 0.129 -0.236 0.262 0.629 -11.593 2.235 1 A_DC2:G48_C A 2 ? C 48 ? 19 1 1 A DA 3 1_555 C U 23 1_555 -0.041 -0.083 -0.026 -4.360 -7.229 2.054 2 A_DA3:U47_C A 3 ? C 47 ? 20 1 1 A DC 4 1_555 C G 22 1_555 0.145 -0.089 0.354 -2.984 -6.993 0.079 3 A_DC4:G46_C A 4 ? C 46 ? 19 1 1 A DT 5 1_555 C A 21 1_555 -0.141 -0.243 0.681 1.230 -8.651 -4.275 4 A_DT5:A45_C A 5 ? C 45 ? 20 1 1 A DG 6 1_555 C C 20 1_555 -0.275 -0.198 -0.012 -1.886 -15.298 -1.236 5 A_DG6:C44_C A 6 ? C 44 ? 19 1 1 C A 13 1_555 C A 19 1_555 1.998 -4.065 0.859 -24.137 4.682 -102.142 6 C_A37:A43_C C 37 ? C 43 ? ? 6 1 B G 2 1_555 A DC 14 1_555 -0.081 -0.190 0.585 -0.202 -4.201 0.310 7 B_G2:DC14_A B 2 ? A 14 ? 19 1 1 B A 3 1_555 A DT 13 1_555 0.073 -0.134 0.440 -1.496 -2.475 -0.803 8 B_A3:DT13_A B 3 ? A 13 ? 20 1 1 B A 4 1_555 A DT 12 1_555 0.182 -0.169 0.355 1.537 1.304 1.628 9 B_A4:DT12_A B 4 ? A 12 ? 20 1 1 B G 5 1_555 A DC 11 1_555 -0.141 -0.108 -0.036 2.976 6.274 0.766 10 B_G5:DC11_A B 5 ? A 11 ? 19 1 1 B C 6 1_555 A DG 10 1_555 0.224 -0.269 0.159 0.991 3.983 2.557 11 B_C6:DG10_A B 6 ? A 10 ? 19 1 1 B U 7 1_555 A DA 9 1_555 0.069 -0.091 0.012 3.131 0.538 6.772 12 B_U7:DA9_A B 7 ? A 9 ? 20 1 1 B C 8 1_555 A DG 8 1_555 0.295 -0.195 -0.008 -5.788 -2.122 0.916 13 B_C8:DG8_A B 8 ? A 8 ? 19 1 1 B U 9 1_555 C A 10 1_555 4.151 -2.615 -0.073 -8.812 -3.458 -92.472 14 B_U9:A34_C B 9 ? C 34 ? 24 4 1 B C 13 1_555 C G 14 1_555 0.305 -0.213 -0.053 -3.650 -11.861 0.934 15 B_C13:G38_C B 13 ? C 38 ? 19 1 1 B G 14 1_555 C C 11 1_555 -0.097 -0.110 -0.627 -10.581 -11.879 3.267 16 B_G14:C35_C B 14 ? C 35 ? 19 1 1 B C 17 1_555 C A 7 1_555 -2.393 0.828 0.225 23.419 -0.660 -0.498 17 B_C17:A31_C B 17 ? C 31 ? ? ? 1 B C 18 1_555 C G 6 1_555 0.149 0.002 -0.008 11.308 -10.287 5.526 18 B_C18:G30_C B 18 ? C 30 ? 19 1 1 B C 19 1_555 C G 5 1_555 -0.219 -0.204 -0.167 2.056 -7.107 1.040 19 B_C19:G29_C B 19 ? C 29 ? 19 1 1 B C 20 1_555 C G 4 1_555 0.084 -0.024 -0.080 -0.675 -7.373 2.850 20 B_C20:G28_C B 20 ? C 28 ? 19 1 1 B A 21 1_555 C U 3 1_555 -0.018 0.011 -0.015 -2.929 -4.730 7.511 21 B_A21:U27_C B 21 ? C 27 ? 20 1 1 B G 22 1_555 C C 2 1_555 -0.247 -0.181 -0.364 -2.073 -7.145 4.953 22 B_G22:C26_C B 22 ? C 26 ? 19 1 1 B C 23 1_555 C G 1 1_555 0.167 -0.103 0.106 1.644 -1.534 1.270 23 B_C23:G25_C B 23 ? C 25 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 2 1_555 C G 24 1_555 A DA 3 1_555 C U 23 1_555 -0.642 -1.746 3.149 -3.808 12.662 27.433 -5.524 0.565 2.214 24.945 7.502 30.398 1 AA_DC2DA3:U47G48_CC A 2 ? C 48 ? A 3 ? C 47 ? 1 A DA 3 1_555 C U 23 1_555 A DC 4 1_555 C G 22 1_555 -0.153 -1.312 3.213 -3.924 2.257 30.880 -2.856 -0.440 3.107 4.211 7.319 31.202 2 AA_DA3DC4:G46U47_CC A 3 ? C 47 ? A 4 ? C 46 ? 1 A DC 4 1_555 C G 22 1_555 A DT 5 1_555 C A 21 1_555 -0.478 -1.729 3.146 -2.236 0.105 30.860 -3.260 0.477 3.166 0.197 4.196 30.940 3 AA_DC4DT5:A45G46_CC A 4 ? C 46 ? A 5 ? C 45 ? 1 A DT 5 1_555 C A 21 1_555 A DG 6 1_555 C C 20 1_555 0.242 -1.546 3.225 5.570 8.170 31.174 -4.073 0.473 2.745 14.744 -10.052 32.667 4 AA_DT5DG6:C44A45_CC A 5 ? C 45 ? A 6 ? C 44 ? 1 A DG 6 1_555 C C 20 1_555 C A 13 1_555 C A 19 1_555 1.688 -2.560 -1.655 -122.007 -123.505 -144.668 1.091 1.031 -1.770 61.860 -61.109 -178.061 5 AC_DG6A37:A43C44_CC A 6 ? C 44 ? C 37 ? C 43 ? 1 B G 2 1_555 A DC 14 1_555 B A 3 1_555 A DT 13 1_555 -0.110 -1.622 2.998 0.015 5.604 34.075 -3.496 0.187 2.705 9.483 -0.025 34.519 6 BB_G2A3:DT13DC14_AA B 2 ? A 14 ? B 3 ? A 13 ? 1 B A 3 1_555 A DT 13 1_555 B A 4 1_555 A DT 12 1_555 -0.153 -1.417 3.152 -2.869 0.482 30.074 -2.813 -0.267 3.130 0.927 5.512 30.211 7 BB_A3A4:DT12DT13_AA B 3 ? A 13 ? B 4 ? A 12 ? 1 B A 4 1_555 A DT 12 1_555 B G 5 1_555 A DC 11 1_555 -0.655 -1.832 3.232 -1.673 6.608 28.834 -4.886 0.951 2.785 13.041 3.301 29.612 8 BB_A4G5:DC11DT12_AA B 4 ? A 12 ? B 5 ? A 11 ? 1 B G 5 1_555 A DC 11 1_555 B C 6 1_555 A DG 10 1_555 -0.323 -1.620 3.289 -3.546 7.661 35.979 -3.552 0.049 2.913 12.196 5.645 36.924 9 BB_G5C6:DG10DC11_AA B 5 ? A 11 ? B 6 ? A 10 ? 1 B C 6 1_555 A DG 10 1_555 B U 7 1_555 A DA 9 1_555 0.333 -1.603 3.041 0.916 8.010 30.150 -4.309 -0.468 2.550 15.063 -1.722 31.185 10 BB_C6U7:DA9DG10_AA B 6 ? A 10 ? B 7 ? A 9 ? 1 B U 7 1_555 A DA 9 1_555 B C 8 1_555 A DG 8 1_555 0.178 -1.833 3.466 1.490 5.911 33.432 -4.097 -0.062 3.110 10.169 -2.563 33.967 11 BB_U7C8:DG8DA9_AA B 7 ? A 9 ? B 8 ? A 8 ? 1 B C 8 1_555 A DG 8 1_555 B U 9 1_555 C A 10 1_555 -2.765 -1.818 3.303 5.732 8.567 82.341 -1.575 2.224 2.974 6.484 -4.338 82.869 12 BB_C8U9:A34DG8_CA B 8 ? A 8 ? B 9 ? C 34 ? 1 B C 13 1_555 C G 14 1_555 B G 14 1_555 C C 11 1_555 -0.352 -1.515 3.329 3.619 15.591 25.158 -5.846 1.357 2.001 31.992 -7.427 29.749 13 BB_C13G14:C35G38_CC B 13 ? C 38 ? B 14 ? C 35 ? 1 B C 17 1_555 C A 7 1_555 B C 18 1_555 C G 6 1_555 0.149 -1.233 3.317 -4.038 8.805 44.003 -2.387 -0.550 3.005 11.585 5.313 45.005 14 BB_C17C18:G30A31_CC B 17 ? C 31 ? B 18 ? C 30 ? 1 B C 18 1_555 C G 6 1_555 B C 19 1_555 C G 5 1_555 -0.748 -2.150 3.443 -4.689 6.298 34.371 -4.498 0.532 3.086 10.488 7.808 35.230 15 BB_C18C19:G29G30_CC B 18 ? C 30 ? B 19 ? C 29 ? 1 B C 19 1_555 C G 5 1_555 B C 20 1_555 C G 4 1_555 -0.178 -1.780 3.299 -1.199 2.601 29.630 -4.003 0.099 3.139 5.072 2.338 29.765 16 BB_C19C20:G28G29_CC B 19 ? C 29 ? B 20 ? C 28 ? 1 B C 20 1_555 C G 4 1_555 B A 21 1_555 C U 3 1_555 0.210 -1.558 3.120 1.052 11.880 29.723 -4.695 -0.216 2.346 22.073 -1.954 31.976 17 BB_C20A21:U27G28_CC B 20 ? C 28 ? B 21 ? C 27 ? 1 B A 21 1_555 C U 3 1_555 B G 22 1_555 C C 2 1_555 0.292 -1.537 3.316 3.336 5.044 26.866 -4.438 0.185 2.996 10.685 -7.067 27.526 18 BB_A21G22:C26U27_CC B 21 ? C 27 ? B 22 ? C 26 ? 1 B G 22 1_555 C C 2 1_555 B C 23 1_555 C G 1 1_555 0.301 -1.500 3.130 -2.747 2.582 35.211 -2.823 -0.873 2.985 4.254 4.525 35.406 19 BB_G22C23:G25C26_CC B 22 ? C 26 ? B 23 ? C 25 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Natural Science Foundation of China (NSFC)' China 32171191 1 'Cancer Research UK' 'United Kingdom' A18604 2 # _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 7Q7X _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'P 41' _space_group.name_Hall 'P 4w' _space_group.IT_number 76 _space_group.crystal_system tetragonal _space_group.id 1 # _atom_sites.entry_id 9KBR _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] 0.014452 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.014452 _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] 0.015245 _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 _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? NA ? ? ? ? ? ? ? ? ? ? ? ? ? NA1+ ? ? 9.95753 ? ? ? 4.19129 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 7.96527 ? ? ? 9.05267 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O1- ? ? 5.12366 3.84317 ? ? 3.49406 27.47979 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ # loop_ #