data_5DI4 # _entry.id 5DI4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 5DI4 pdb_00005di4 10.2210/pdb5di4/pdb WWPDB D_1000213232 ? ? # 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 2015-10-07 2 'Structure model' 1 1 2015-11-04 3 'Structure model' 1 2 2017-09-27 4 'Structure model' 1 3 2019-12-25 5 'Structure model' 1 4 2024-03-06 # _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' 'Author supporting evidence' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Author supporting evidence' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Database references' 8 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' citation 2 3 'Structure model' pdbx_audit_support 3 3 'Structure model' pdbx_struct_oper_list 4 4 'Structure model' pdbx_audit_support 5 5 'Structure model' chem_comp_atom 6 5 'Structure model' chem_comp_bond 7 5 'Structure model' database_2 8 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_citation.journal_id_CSD' 2 3 'Structure model' '_pdbx_audit_support.funding_organization' 3 3 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 4 4 'Structure model' '_pdbx_audit_support.funding_organization' 5 5 'Structure model' '_database_2.pdbx_DOI' 6 5 'Structure model' '_database_2.pdbx_database_accession' 7 5 'Structure model' '_struct_conn.pdbx_dist_value' 8 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 5 'Structure model' '_struct_conn.ptnr2_symmetry' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5DI4 _pdbx_database_status.recvd_initial_deposition_date 2015-08-31 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB . 5DI2 unspecified PDB . 5DH8 unspecified PDB . 5DH7 unspecified PDB . 5DH6 unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mir, A.' 1 'Chen, J.' 2 'Neau, D.' 3 'Golden, B.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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Biochemistry _citation.journal_id_ASTM BICHAW _citation.journal_id_CSD 0033 _citation.journal_id_ISSN 0006-2960 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 54 _citation.language ? _citation.page_first 6369 _citation.page_last 6381 _citation.title 'Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.' _citation.year 2015 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.biochem.5b00824 _citation.pdbx_database_id_PubMed 26398724 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mir, A.' 1 ? primary 'Chen, J.' 2 ? primary 'Robinson, K.' 3 ? primary 'Lendy, E.' 4 ? primary 'Goodman, J.' 5 ? primary 'Neau, D.' 6 ? primary 'Golden, B.L.' 7 ? # 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 'RNA (48-MER)' 15500.287 1 ? ? ? ? 2 polymer syn "5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'" 6437.895 1 ? ? ? ? 3 non-polymer syn 'MANGANESE (II) ION' 54.938 11 ? ? ? ? # 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 polyribonucleotide no no GGGUACUUAAGCCCACUGAUGAGUCGCUGGGAUGCGACGAAACGCCCA GGGUACUUAAGCCCACUGAUGAGUCGCUGGGAUGCGACGAAACGCCCA A ? 2 'polydeoxyribonucleotide/polyribonucleotide hybrid' no no 'GGGCGU(DC)UGGGCAGUACCCA' GGGCGUCUGGGCAGUACCCA B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name 'MANGANESE (II) ION' _pdbx_entity_nonpoly.comp_id MN # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 G n 1 4 U n 1 5 A n 1 6 C n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 G n 1 12 C n 1 13 C n 1 14 C n 1 15 A n 1 16 C n 1 17 U n 1 18 G n 1 19 A n 1 20 U n 1 21 G n 1 22 A n 1 23 G n 1 24 U n 1 25 C n 1 26 G n 1 27 C n 1 28 U n 1 29 G n 1 30 G n 1 31 G n 1 32 A n 1 33 U n 1 34 G n 1 35 C n 1 36 G n 1 37 A n 1 38 C n 1 39 G n 1 40 A n 1 41 A n 1 42 A n 1 43 C n 1 44 G n 1 45 C n 1 46 C n 1 47 C n 1 48 A n 2 1 G n 2 2 G n 2 3 G n 2 4 C n 2 5 G n 2 6 U n 2 7 DC n 2 8 U n 2 9 G n 2 10 G n 2 11 G n 2 12 C n 2 13 A n 2 14 G n 2 15 U n 2 16 A n 2 17 C n 2 18 C n 2 19 C n 2 20 A 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 48 'synthetic construct' ? 32630 'This RNA was made by in vitro transcription' 2 1 sample 1 20 'synthetic construct' ? 32630 'synthesized oligonucleotide' # 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 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 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 G 3 3 3 G G A . n A 1 4 U 4 4 4 U U A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 C 12 12 12 C C A . n A 1 13 C 13 13 13 C C A . n A 1 14 C 14 14 14 C C A . n A 1 15 A 15 15 15 A A A . n A 1 16 C 16 16 16 C C A . n A 1 17 U 17 17 17 U U A . n A 1 18 G 18 18 18 G G A . n A 1 19 A 19 19 19 A A A . n A 1 20 U 20 20 20 U U A . n A 1 21 G 21 21 21 G G A . n A 1 22 A 22 22 22 A A A . n A 1 23 G 23 23 23 G G A . n A 1 24 U 24 24 24 U U A . n A 1 25 C 25 25 25 C C A . n A 1 26 G 26 26 26 G G A . n A 1 27 C 27 27 27 C C A . n A 1 28 U 28 28 28 U U A . n A 1 29 G 29 29 29 G G A . n A 1 30 G 30 30 30 G G A . n A 1 31 G 31 31 31 G G A . n A 1 32 A 32 32 32 A A A . n A 1 33 U 33 33 33 U U A . n A 1 34 G 34 34 34 G G A . n A 1 35 C 35 35 35 C C A . n A 1 36 G 36 36 36 G G A . n A 1 37 A 37 37 37 A A A . n A 1 38 C 38 38 38 C C A . n A 1 39 G 39 39 39 G G A . n A 1 40 A 40 40 40 A A A . n A 1 41 A 41 41 41 A A A . n A 1 42 A 42 42 42 A A A . n A 1 43 C 43 43 43 C C A . n A 1 44 G 44 44 44 G G A . n A 1 45 C 45 45 45 C C A . n A 1 46 C 46 46 46 C C A . n A 1 47 C 47 47 47 C C A . n A 1 48 A 48 48 48 A A 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 G 3 3 3 G G B . n B 2 4 C 4 4 4 C C B . n B 2 5 G 5 5 5 G G B . n B 2 6 U 6 6 6 U U B . n B 2 7 DC 7 7 7 DC DC B . n B 2 8 U 8 8 8 U U B . n B 2 9 G 9 9 9 G G B . n B 2 10 G 10 10 10 G G B . n B 2 11 G 11 11 11 G G B . n B 2 12 C 12 12 12 C C B . n B 2 13 A 13 13 13 A A B . n B 2 14 G 14 14 14 G G B . n B 2 15 U 15 15 15 U U B . n B 2 16 A 16 16 16 A A 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 A 20 20 20 A A B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 MN 1 101 1 MN MN A . D 3 MN 1 102 2 MN MN A . E 3 MN 1 103 3 MN MN A . F 3 MN 1 104 5 MN MN A . G 3 MN 1 105 6 MN MN A . H 3 MN 1 106 7 MN MN A . I 3 MN 1 107 8 MN MN A . J 3 MN 1 108 9 MN MN A . K 3 MN 1 109 10 MN MN A . L 3 MN 1 101 4 MN MN B . M 3 MN 1 102 11 MN MN B . # 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 ? ? ? 1.9_1692 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? 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 90.00 _cell.angle_gamma_esd ? _cell.entry_id 5DI4 _cell.details ? _cell.formula_units_Z ? _cell.length_a 80.169 _cell.length_a_esd ? _cell.length_b 85.923 _cell.length_b_esd ? _cell.length_c 104.258 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _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 ? # _symmetry.entry_id 5DI4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' _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 5DI4 _exptl.crystals_number ? _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 4.09 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 69.94 _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_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 ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '33 % MPD, 0.4 M potassium chloride, 50 mM potassium acetate pH 5.0, 10 mM MgCl2 and 0.5mM spermine' _exptl_crystal_grow.pdbx_pH_range ? # _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_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2013-11-12 # _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 1.5011 _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 'APS BEAMLINE 21-ID-D' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.5011 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 21-ID-D _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5DI4 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.94 _reflns.d_resolution_low 50.0 _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 14606 _reflns.number_obs 14606 _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 99.8 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 14.2 _reflns.pdbx_Rmerge_I_obs 0.076 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 36.9 _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_R_split ? # _reflns_shell.d_res_high 2.94 _reflns_shell.d_res_low 2.99 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 7.7 _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_all 100.0 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_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 37.9 _reflns_shell.pdbx_Rsym_value ? _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 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _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 5DI4 _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 2.948 _refine.ls_d_res_low 28.215 _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 14432 _refine.ls_number_reflns_R_free 1446 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.40 _refine.ls_percent_reflns_R_free 10.02 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2118 _refine.ls_R_factor_R_free 0.2330 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2094 _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.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 ? _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 1.11 _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 27.21 _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 0.32 _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.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1455 _refine_hist.pdbx_number_atoms_ligand 11 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1466 _refine_hist.d_res_high 2.948 _refine_hist.d_res_low 28.215 # 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' ? 0.001 ? 1627 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.388 ? 2534 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 10.735 ? 807 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.022 ? 338 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.002 ? 68 ? 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 _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_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.9484 3.0537 . . 136 1255 95.00 . . . 0.2965 . 0.3054 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.0537 3.1758 . . 142 1268 97.00 . . . 0.3283 . 0.2419 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.1758 3.3201 . . 152 1292 98.00 . . . 0.2621 . 0.2258 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.3201 3.4948 . . 135 1290 97.00 . . . 0.2631 . 0.2235 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.4948 3.7133 . . 150 1298 99.00 . . . 0.2864 . 0.2284 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.7133 3.9993 . . 140 1325 99.00 . . . 0.2592 . 0.2033 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.9993 4.4004 . . 159 1296 100.00 . . . 0.2312 . 0.2013 . . . . . . . . . . 'X-RAY DIFFRACTION' 4.4004 5.0341 . . 148 1329 100.00 . . . 0.2172 . 0.1889 . . . . . . . . . . 'X-RAY DIFFRACTION' 5.0341 6.3305 . . 139 1317 100.00 . . . 0.1733 . 0.1838 . . . . . . . . . . 'X-RAY DIFFRACTION' 6.3305 28.2160 . . 145 1316 99.00 . . . 0.2255 . 0.2148 . . . . . . . . . . # _struct.entry_id 5DI4 _struct.title ;Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mn2+ at low pH ; _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5DI4 _struct_keywords.text 'ribozyme, hammerhead, RNA' _struct_keywords.pdbx_keywords RNA # 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 3 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 3 ? K N N 3 ? L N N 3 ? M N N 3 ? # 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 5DI4 5DI4 ? 1 ? 1 2 PDB 5DI4 5DI4 ? 2 ? 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 5DI4 A 1 ? 48 ? 5DI4 1 ? 48 ? 1 48 2 2 5DI4 B 1 ? 19 ? 5DI4 1 ? 19 ? 1 19 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3190 ? 1 MORE -60 ? 1 'SSA (A^2)' 12130 ? # _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A G 1 N7 ? ? ? 1_555 C MN . MN ? ? A G 1 A MN 101 1_555 ? ? ? ? ? ? ? 2.566 ? ? metalc2 metalc ? ? A G 1 N7 ? ? ? 1_555 C MN . MN ? ? A G 1 A MN 101 3_455 ? ? ? ? ? ? ? 2.566 ? ? metalc3 metalc ? ? A G 18 N7 ? ? ? 1_555 D MN . MN ? ? A G 18 A MN 102 1_555 ? ? ? ? ? ? ? 2.456 ? ? metalc4 metalc ? ? A A 22 OP2 ? ? ? 1_555 H MN . MN ? ? A A 22 A MN 106 1_555 ? ? ? ? ? ? ? 1.947 ? ? metalc5 metalc ? ? A G 29 N7 ? ? ? 1_555 K MN . MN ? ? A G 29 A MN 109 1_555 ? ? ? ? ? ? ? 2.378 ? ? metalc6 metalc ? ? A G 30 N7 ? ? ? 1_555 E MN . MN ? ? A G 30 A MN 103 1_555 ? ? ? ? ? ? ? 2.248 ? ? metalc7 metalc ? ? A A 41 OP2 ? ? ? 1_555 I MN . MN ? ? A A 41 A MN 107 1_555 ? ? ? ? ? ? ? 2.198 ? ? hydrog1 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 13 N7 ? ? A U 7 B A 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog2 hydrog ? ? A U 7 O2 ? ? ? 1_555 B A 13 N6 ? ? A U 7 B A 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog3 hydrog ? ? A A 10 N1 ? ? ? 1_555 A G 29 N2 ? ? A A 10 A G 29 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog4 hydrog ? ? A A 10 N6 ? ? ? 1_555 A G 29 N3 ? ? A A 10 A G 29 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog5 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 11 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 11 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 11 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 12 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 12 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 12 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 13 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 13 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 13 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 14 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 14 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 14 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 14 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 14 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 14 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 15 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 15 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 15 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 15 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 16 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 16 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 16 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 22 N6 ? ? ? 1_555 A G 39 N3 ? ? A A 22 A G 39 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog23 hydrog ? ? A A 22 N7 ? ? ? 1_555 A G 39 N2 ? ? A A 22 A G 39 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog24 hydrog ? ? A G 23 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 23 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 23 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 23 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 23 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 23 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 24 N3 ? ? ? 1_555 A A 37 N1 ? ? A U 24 A A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 24 O4 ? ? ? 1_555 A A 37 N6 ? ? A U 24 A A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 36 N1 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 36 O6 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 36 N2 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 26 N1 ? ? ? 1_555 A C 35 N3 ? ? A G 26 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 26 N2 ? ? ? 1_555 A C 35 O2 ? ? A G 26 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 26 O6 ? ? ? 1_555 A C 35 N4 ? ? A G 26 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 27 N3 ? ? ? 1_555 A G 34 N1 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 27 N4 ? ? ? 1_555 A G 34 O6 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 27 O2 ? ? ? 1_555 A G 34 N2 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 28 N3 ? ? ? 1_555 A A 32 N7 ? ? A U 28 A A 32 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog39 hydrog ? ? A U 28 O2 ? ? ? 1_555 A A 32 N6 ? ? A U 28 A A 32 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog40 hydrog ? ? A A 40 N6 ? ? ? 1_555 B DC 7 O2 ? ? A A 40 B DC 7 1_555 ? ? ? ? ? ? 'A-DC MISPAIR' ? ? ? hydrog41 hydrog ? ? A A 41 N6 ? ? ? 1_555 B DC 7 O2 ? ? A A 41 B DC 7 1_555 ? ? ? ? ? ? 'A-DC MISPAIR' ? ? ? hydrog42 hydrog ? ? A A 42 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 42 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A A 42 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 42 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 43 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 43 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 43 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 43 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 43 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 43 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 44 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 44 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 44 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 44 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 44 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 44 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 45 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 45 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 45 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 45 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 45 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 45 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A C 46 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 46 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A C 46 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 46 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A C 46 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 46 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A C 47 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 47 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A C 47 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 47 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A C 47 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 47 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id N7 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id A _pdbx_struct_conn_angle.ptnr1_label_comp_id G _pdbx_struct_conn_angle.ptnr1_label_seq_id 1 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id G _pdbx_struct_conn_angle.ptnr1_auth_seq_id 1 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id MN _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id C _pdbx_struct_conn_angle.ptnr2_label_comp_id MN _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id MN _pdbx_struct_conn_angle.ptnr2_auth_seq_id 101 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id N7 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id A _pdbx_struct_conn_angle.ptnr3_label_comp_id G _pdbx_struct_conn_angle.ptnr3_label_seq_id 1 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id A _pdbx_struct_conn_angle.ptnr3_auth_comp_id G _pdbx_struct_conn_angle.ptnr3_auth_seq_id 1 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 0.0 _pdbx_struct_conn_angle.value_esd ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A MN 101 ? 2 'binding site for residue MN A 101' AC2 Software A MN 102 ? 1 'binding site for residue MN A 102' AC3 Software A MN 103 ? 1 'binding site for residue MN A 103' AC4 Software A MN 104 ? 1 'binding site for residue MN A 104' AC5 Software A MN 105 ? 1 'binding site for residue MN A 105' AC6 Software A MN 106 ? 2 'binding site for residue MN A 106' AC7 Software A MN 107 ? 1 'binding site for residue MN A 107' AC8 Software A MN 108 ? 1 'binding site for residue MN A 108' AC9 Software A MN 109 ? 1 'binding site for residue MN A 109' AD1 Software B MN 101 ? 1 'binding site for residue MN B 101' AD2 Software B MN 102 ? 2 'binding site for residue MN B 102' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 2 G A 1 ? G A 1 . ? 1_555 ? 2 AC1 2 G A 1 ? G A 1 . ? 3_455 ? 3 AC2 1 G A 18 ? G A 18 . ? 1_555 ? 4 AC3 1 G A 30 ? G A 30 . ? 1_555 ? 5 AC4 1 G A 2 ? G A 2 . ? 1_555 ? 6 AC5 1 A A 48 ? A A 48 . ? 1_555 ? 7 AC6 2 A A 22 ? A A 22 . ? 1_555 ? 8 AC6 2 G A 23 ? G A 23 . ? 1_555 ? 9 AC7 1 A A 41 ? A A 41 . ? 1_555 ? 10 AC8 1 G A 1 ? G A 1 . ? 1_555 ? 11 AC9 1 G A 29 ? G A 29 . ? 1_555 ? 12 AD1 1 G B 10 ? G B 10 . ? 1_555 ? 13 AD2 2 G B 2 ? G B 2 . ? 1_555 ? 14 AD2 2 G B 3 ? G B 3 . ? 1_555 ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id MN _pdbx_struct_special_symmetry.auth_seq_id 101 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id C _pdbx_struct_special_symmetry.label_comp_id MN _pdbx_struct_special_symmetry.label_seq_id . # 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 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 MN MN MN N N 145 U OP3 O N N 146 U P P N N 147 U OP1 O N N 148 U OP2 O N N 149 U "O5'" O N N 150 U "C5'" C N N 151 U "C4'" C N R 152 U "O4'" O N N 153 U "C3'" C N S 154 U "O3'" O N N 155 U "C2'" C N R 156 U "O2'" O N N 157 U "C1'" C N R 158 U N1 N N N 159 U C2 C N N 160 U O2 O N N 161 U N3 N N N 162 U C4 C N N 163 U O4 O N N 164 U C5 C N N 165 U C6 C N N 166 U HOP3 H N N 167 U HOP2 H N N 168 U "H5'" H N N 169 U "H5''" H N N 170 U "H4'" H N N 171 U "H3'" H N N 172 U "HO3'" H N N 173 U "H2'" H N N 174 U "HO2'" H N N 175 U "H1'" H N N 176 U H3 H N N 177 U H5 H N N 178 U H6 H N N 179 # 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 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 U OP3 P sing N N 151 U OP3 HOP3 sing N N 152 U P OP1 doub N N 153 U P OP2 sing N N 154 U P "O5'" sing N N 155 U OP2 HOP2 sing N N 156 U "O5'" "C5'" sing N N 157 U "C5'" "C4'" sing N N 158 U "C5'" "H5'" sing N N 159 U "C5'" "H5''" sing N N 160 U "C4'" "O4'" sing N N 161 U "C4'" "C3'" sing N N 162 U "C4'" "H4'" sing N N 163 U "O4'" "C1'" sing N N 164 U "C3'" "O3'" sing N N 165 U "C3'" "C2'" sing N N 166 U "C3'" "H3'" sing N N 167 U "O3'" "HO3'" sing N N 168 U "C2'" "O2'" sing N N 169 U "C2'" "C1'" sing N N 170 U "C2'" "H2'" sing N N 171 U "O2'" "HO2'" sing N N 172 U "C1'" N1 sing N N 173 U "C1'" "H1'" sing N N 174 U N1 C2 sing N N 175 U N1 C6 sing N N 176 U C2 O2 doub N N 177 U C2 N3 sing N N 178 U N3 C4 sing N N 179 U N3 H3 sing N N 180 U C4 O4 doub N N 181 U C4 C5 sing N N 182 U C5 C6 doub N N 183 U C5 H5 sing N N 184 U C6 H6 sing N N 185 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5DI4 'double helix' 5DI4 'a-form double helix' 5DI4 'hairpin loop' 5DI4 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A U 7 1_555 B A 13 1_555 4.381 -2.585 -0.450 -12.947 -7.772 -88.495 1 A_U7:A13_B A 7 ? B 13 ? 24 4 1 A A 10 1_555 A G 29 1_555 -3.628 3.751 0.229 -18.950 -7.536 69.873 2 A_A10:G29_A A 10 ? A 29 ? 10 6 1 A A 32 1_555 A U 28 1_555 -4.129 -2.201 0.876 -0.945 12.787 -87.328 3 A_A32:U28_A A 32 ? A 28 ? 24 4 1 A G 34 1_555 A C 27 1_555 -0.416 -0.090 0.408 11.530 -6.348 -4.477 4 A_G34:C27_A A 34 ? A 27 ? 19 1 1 A C 35 1_555 A G 26 1_555 0.188 -0.066 -0.058 9.161 -11.530 0.825 5 A_C35:G26_A A 35 ? A 26 ? 19 1 1 A G 36 1_555 A C 25 1_555 -0.168 -0.028 -0.133 -4.302 -5.744 2.795 6 A_G36:C25_A A 36 ? A 25 ? 19 1 1 A A 37 1_555 A U 24 1_555 -0.421 -0.072 -0.033 -10.322 -10.478 -1.055 7 A_A37:U24_A A 37 ? A 24 ? 20 1 1 A C 38 1_555 A G 23 1_555 0.361 -0.447 0.150 -0.328 -12.356 -9.712 8 A_C38:G23_A A 38 ? A 23 ? 19 1 1 A G 39 1_555 A A 22 1_555 6.695 -3.713 0.191 1.246 -10.762 -8.530 9 A_G39:A22_A A 39 ? A 22 ? 11 10 1 A A 41 1_555 B DC 7 1_555 -5.402 -1.348 1.498 -18.386 7.012 -3.608 10 A_A41:DC7_B A 41 ? B 7 ? ? ? 1 A A 42 1_555 B U 6 1_555 -0.121 0.164 1.187 9.271 -3.893 -0.409 11 A_A42:U6_B A 42 ? B 6 ? 20 1 1 A C 43 1_555 B G 5 1_555 0.009 -0.115 0.571 8.769 -11.494 1.919 12 A_C43:G5_B A 43 ? B 5 ? 19 1 1 A G 44 1_555 B C 4 1_555 -0.925 -0.316 0.153 5.418 -8.055 -0.599 13 A_G44:C4_B A 44 ? B 4 ? 19 1 1 A C 45 1_555 B G 3 1_555 -0.259 0.030 0.021 7.539 -12.703 3.665 14 A_C45:G3_B A 45 ? B 3 ? 19 1 1 A C 46 1_555 B G 2 1_555 -0.018 0.195 0.058 4.277 -10.014 7.957 15 A_C46:G2_B A 46 ? B 2 ? 19 1 1 A C 47 1_555 B G 1 1_555 0.277 -0.036 0.408 -3.644 -6.821 2.917 16 A_C47:G1_B A 47 ? B 1 ? 19 1 1 A G 11 1_555 B C 12 1_555 -0.737 0.008 -0.135 -6.373 -14.764 4.627 17 A_G11:C12_B A 11 ? B 12 ? 19 1 1 A C 12 1_555 B G 11 1_555 0.436 -0.163 -0.002 4.091 -9.019 1.364 18 A_C12:G11_B A 12 ? B 11 ? 19 1 1 A C 13 1_555 B G 10 1_555 -0.536 0.105 -0.227 5.641 -7.350 5.448 19 A_C13:G10_B A 13 ? B 10 ? 19 1 1 A C 14 1_555 B G 9 1_555 0.390 -0.282 -0.287 3.139 -12.664 -1.452 20 A_C14:G9_B A 14 ? B 9 ? 19 1 1 A A 15 1_555 B U 8 1_555 -0.054 -0.028 0.362 -4.150 -14.455 6.688 21 A_A15:U8_B A 15 ? B 8 ? 20 1 1 A C 16 1_555 A G 21 1_555 0.397 -0.222 0.400 7.352 -0.791 5.647 22 A_C16:G21_A A 16 ? A 21 ? 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 A 10 1_555 A G 29 1_555 A A 32 1_555 A U 28 1_555 -3.396 -2.276 -1.529 162.410 -46.938 -53.933 1.152 -1.669 1.646 24.298 84.072 -170.250 1 AA_A10A32:U28G29_AA A 10 ? A 29 ? A 32 ? A 28 ? 1 A A 32 1_555 A U 28 1_555 A G 34 1_555 A C 27 1_555 2.626 -1.782 2.996 -4.330 5.618 72.740 -1.657 -2.330 2.733 4.726 3.642 73.038 2 AA_A32G34:C27U28_AA A 32 ? A 28 ? A 34 ? A 27 ? 1 A G 34 1_555 A C 27 1_555 A C 35 1_555 A G 26 1_555 0.363 -1.707 3.252 2.699 2.935 37.592 -3.005 -0.220 3.133 4.539 -4.174 37.795 3 AA_G34C35:G26C27_AA A 34 ? A 27 ? A 35 ? A 26 ? 1 A C 35 1_555 A G 26 1_555 A G 36 1_555 A C 25 1_555 0.111 -1.780 3.445 0.303 12.466 29.638 -5.344 -0.149 2.512 23.123 -0.562 32.100 4 AA_C35G36:C25G26_AA A 35 ? A 26 ? A 36 ? A 25 ? 1 A G 36 1_555 A C 25 1_555 A A 37 1_555 A U 24 1_555 -0.088 -1.845 3.367 0.451 9.541 30.975 -4.904 0.234 2.693 17.355 -0.820 32.380 5 AA_G36A37:U24C25_AA A 36 ? A 25 ? A 37 ? A 24 ? 1 A A 37 1_555 A U 24 1_555 A C 38 1_555 A G 23 1_555 0.283 -1.741 3.029 1.557 0.252 33.685 -3.038 -0.254 3.026 0.434 -2.685 33.721 6 AA_A37C38:G23U24_AA A 37 ? A 24 ? A 38 ? A 23 ? 1 A C 38 1_555 A G 23 1_555 A G 39 1_555 A A 22 1_555 -0.523 -1.328 3.482 -0.735 2.855 52.753 -1.687 0.538 3.417 3.211 0.827 52.830 7 AA_C38G39:A22G23_AA A 38 ? A 23 ? A 39 ? A 22 ? 1 A G 39 1_555 A A 22 1_555 A A 41 1_555 B DC 7 1_555 1.269 -1.585 5.783 15.991 9.887 48.647 -2.998 0.474 5.522 11.516 -18.625 51.947 8 AA_G39A41:DC7A22_BA A 39 ? A 22 ? A 41 ? B 7 ? 1 A A 41 1_555 B DC 7 1_555 A A 42 1_555 B U 6 1_555 -0.187 -0.303 2.728 -7.654 17.393 48.010 -1.336 -0.219 2.488 20.468 9.007 51.426 9 AA_A41A42:U6DC7_BB A 41 ? B 7 ? A 42 ? B 6 ? 1 A A 42 1_555 B U 6 1_555 A C 43 1_555 B G 5 1_555 0.229 -1.572 3.403 2.718 6.542 31.828 -3.936 0.063 3.037 11.747 -4.881 32.587 10 AA_A42C43:G5U6_BB A 42 ? B 6 ? A 43 ? B 5 ? 1 A C 43 1_555 B G 5 1_555 A G 44 1_555 B C 4 1_555 -0.449 -1.800 2.916 -0.907 13.930 28.075 -5.368 0.700 1.850 26.725 1.741 31.291 11 AA_C43G44:C4G5_BB A 43 ? B 5 ? A 44 ? B 4 ? 1 A G 44 1_555 B C 4 1_555 A C 45 1_555 B G 3 1_555 0.192 -1.641 3.175 -1.325 2.736 35.053 -3.102 -0.505 3.034 4.532 2.195 35.180 12 AA_G44C45:G3C4_BB A 44 ? B 4 ? A 45 ? B 3 ? 1 A C 45 1_555 B G 3 1_555 A C 46 1_555 B G 2 1_555 0.212 -1.657 3.294 -1.749 5.478 32.058 -3.876 -0.672 2.962 9.820 3.136 32.556 13 AA_C45C46:G2G3_BB A 45 ? B 3 ? A 46 ? B 2 ? 1 A C 46 1_555 B G 2 1_555 A C 47 1_555 B G 1 1_555 -0.518 -1.854 3.291 -2.579 7.095 33.563 -4.195 0.491 2.881 12.097 4.397 34.377 14 AA_C46C47:G1G2_BB A 46 ? B 2 ? A 47 ? B 1 ? 1 A G 11 1_555 B C 12 1_555 A C 12 1_555 B G 11 1_555 -0.313 -1.259 3.067 -4.322 2.022 37.637 -2.179 -0.033 3.014 3.118 6.666 37.927 15 AA_G11C12:G11C12_BB A 11 ? B 12 ? A 12 ? B 11 ? 1 A C 12 1_555 B G 11 1_555 A C 13 1_555 B G 10 1_555 0.389 -1.946 3.211 2.289 5.531 26.202 -5.506 -0.292 2.772 12.002 -4.968 26.865 16 AA_C12C13:G10G11_BB A 12 ? B 11 ? A 13 ? B 10 ? 1 A C 13 1_555 B G 10 1_555 A C 14 1_555 B G 9 1_555 -0.516 -1.390 3.438 1.230 3.687 34.244 -2.935 1.067 3.255 6.236 -2.081 34.457 17 AA_C13C14:G9G10_BB A 13 ? B 10 ? A 14 ? B 9 ? 1 A C 14 1_555 B G 9 1_555 A A 15 1_555 B U 8 1_555 0.688 -1.555 3.257 -1.013 12.326 30.269 -4.701 -1.382 2.431 22.462 1.846 32.643 18 AA_C14A15:U8G9_BB A 14 ? B 9 ? A 15 ? B 8 ? 1 A A 15 1_555 B U 8 1_555 A C 16 1_555 A G 21 1_555 -1.429 -1.832 3.058 2.626 21.369 18.413 -7.052 3.332 0.499 49.546 -6.090 28.259 19 AA_A15C16:G21U8_AB A 15 ? B 8 ? A 16 ? A 21 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number R01GM095923 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 5DI4 _atom_sites.fract_transf_matrix[1][1] 0.012474 _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] 0.011638 _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] 0.009592 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H MN N O P # loop_