data_9S1D # _entry.id 9S1D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.416 _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 9S1D pdb_00009s1d 10.2210/pdb9s1d/pdb WWPDB D_1292145571 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2026-07-22 _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 9S1D _pdbx_database_status.recvd_initial_deposition_date 2025-07-18 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email claudia.hoebartner@uni-wuerzburg.de _pdbx_contact_author.name_first Claudia _pdbx_contact_author.name_last Hoebartner _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-4548-2299 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Chen, H.-A.' 1 0000-0002-0586-0742 'Scheitl, C.P.M.' 2 0009-0000-7822-2066 'Hoebartner, C.' 3 0000-0002-4548-2299 # loop_ _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 _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_patent _citation.unpublished_flag ? ? ? ? ? ? ? UK ? ? primary 'Nat Commun' ? ? 2041-1723 ? ? ? ? ? ? 'A magic methyl effect in the active site of a methyltransferase ribozyme' 2026 ? 10.1038/s41467-026-75575-8 ? ? ? ? ? ? ? ? ? ? US ? ? 1 'Nat Chem Biol' ? ? 1552-4469 ? ? 18 ? 547 555 'Structure and mechanism of the methyltransferase ribozyme MTR1.' 2022 ? 10.1038/s41589-022-00976-x 35301481 ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chen, H.-A.' 1 0000-0002-0586-0742 primary 'Scheitl, C.P.M.' 2 0009-0000-7822-2066 primary 'Hoebartner, C.' 3 0000-0002-4548-2299 1 'Scheitl, C.P.M.' 4 0009-0000-7822-2066 1 'Mieczkowski, M.' 5 ? 1 'Schindelin, H.' 6 0000-0002-2067-3187 1 'Hoebartner, C.' 7 0000-0002-4548-2299 # 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 'Chains: A' 4436.710 1 ? ? ? 'Chemically synthesized RNA oligonucleotide. N1-methylation of A7 occurred during crystallization process.' 2 polymer syn 'Chains: B' 7655.662 1 ? ? ? ;Chemically synthesized RNA oligonucleotide. 2'O-methyl modification at position 12 was introduced during solid-phase synthesis. ; 3 polymer syn 'Chains: C' 7769.729 1 ? ? ? ;Chemically synthesized RNA oligonucleotide. 2'O-methyl modification at position 42 was introduced during solid-phase synthesis. ; 4 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 5 non-polymer syn 'SODIUM ION' 22.990 2 ? ? ? ? 6 non-polymer syn GUANINE 151.126 1 ? ? ? ? 7 water nat water 18.015 45 ? ? ? ? # 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 yes 'CCACUG(1MA)GAGCUUC' CCACUGAGAGCUUC A ? 2 polyribonucleotide no yes 'GGAAGCUCUGA(OMC)CGACCCCCAGCC' GGAAGCUCUGACCGACCCCCAGCC B ? 3 polyribonucleotide no yes 'GCUGGGACAACUAGACA(OMU)ACAGUG' GCUGGGACAACUAGACAUACAGUG C ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'MAGNESIUM ION' MG 5 'SODIUM ION' NA 6 GUANINE GUN 7 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 C n 1 3 A n 1 4 C n 1 5 U n 1 6 G n 1 7 1MA n 1 8 G n 1 9 A n 1 10 G n 1 11 C n 1 12 U n 1 13 U n 1 14 C 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 OMC 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 OMU 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 1MA 'RNA linking' n "6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE" ? 'C11 H16 N5 O7 P' 361.248 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 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 OMC 'RNA linking' n "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O8 P' 337.223 OMU 'RNA linking' n ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; ? 'C10 H15 N2 O9 P' 338.208 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 C 1 1 1 C C A . n A 1 2 C 2 2 2 C C A . n A 1 3 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 U 5 5 5 U U A . n A 1 6 G 6 6 6 G G A . n A 1 7 1MA 7 7 7 1MA 1MA A . n A 1 8 G 8 8 8 G G A . n A 1 9 A 9 9 9 A A A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . n A 1 12 U 12 12 12 U U A . n A 1 13 U 13 13 13 U U A . n A 1 14 C 14 14 14 C C 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 OMC 12 12 12 OMC OMC 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 OMU 18 42 42 OMU OMU 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 1MA ? ? 1MA ? ? 'SUBJECT OF INVESTIGATION' ? 2 GUN ? ? GUN ? ? 'SUBJECT OF INVESTIGATION' ? 3 OMC ? ? OMC ? ? 'SUBJECT OF INVESTIGATION' ? 4 OMU ? ? OMU ? ? '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 MG 1 101 2 MG MG B . E 5 NA 1 102 1 NA NA B . F 6 GUN 1 101 101 GUN GUN C . G 4 MG 1 102 1 MG MG C . H 5 NA 1 103 2 NA NA C . I 7 HOH 1 101 7 HOH HOH A . I 7 HOH 2 102 40 HOH HOH A . I 7 HOH 3 103 38 HOH HOH A . J 7 HOH 1 201 24 HOH HOH B . J 7 HOH 2 202 11 HOH HOH B . J 7 HOH 3 203 20 HOH HOH B . J 7 HOH 4 204 30 HOH HOH B . J 7 HOH 5 205 28 HOH HOH B . J 7 HOH 6 206 13 HOH HOH B . J 7 HOH 7 207 27 HOH HOH B . J 7 HOH 8 208 17 HOH HOH B . J 7 HOH 9 209 29 HOH HOH B . J 7 HOH 10 210 31 HOH HOH B . J 7 HOH 11 211 19 HOH HOH B . J 7 HOH 12 212 9 HOH HOH B . J 7 HOH 13 213 2 HOH HOH B . J 7 HOH 14 214 35 HOH HOH B . J 7 HOH 15 215 3 HOH HOH B . J 7 HOH 16 216 39 HOH HOH B . J 7 HOH 17 217 36 HOH HOH B . J 7 HOH 18 218 41 HOH HOH B . J 7 HOH 19 219 34 HOH HOH B . J 7 HOH 20 220 23 HOH HOH B . J 7 HOH 21 221 37 HOH HOH B . J 7 HOH 22 222 45 HOH HOH B . K 7 HOH 1 201 5 HOH HOH C . K 7 HOH 2 202 16 HOH HOH C . K 7 HOH 3 203 4 HOH HOH C . K 7 HOH 4 204 33 HOH HOH C . K 7 HOH 5 205 26 HOH HOH C . K 7 HOH 6 206 43 HOH HOH C . K 7 HOH 7 207 10 HOH HOH C . K 7 HOH 8 208 22 HOH HOH C . K 7 HOH 9 209 6 HOH HOH C . K 7 HOH 10 210 15 HOH HOH C . K 7 HOH 11 211 8 HOH HOH C . K 7 HOH 12 212 18 HOH HOH C . K 7 HOH 13 213 32 HOH HOH C . K 7 HOH 14 214 44 HOH HOH C . K 7 HOH 15 215 21 HOH HOH C . K 7 HOH 16 216 14 HOH HOH C . K 7 HOH 17 217 42 HOH HOH C . K 7 HOH 18 218 25 HOH HOH C . K 7 HOH 19 219 1 HOH HOH C . K 7 HOH 20 220 12 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_reference_DOI _software.pdbx_ordinal ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? 'June 30 2024' ? 1 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? 2.8.3 ? 2 ? 'model building' ? ? ? ? ? ? ? ? ? ? ? Coot ? ? ? 0.9.8.95 ? 3 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.21.2_5419 ? 4 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . ? 5 # _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 9S1D _cell.details ? _cell.formula_units_Z ? _cell.length_a 71.323 _cell.length_a_esd ? _cell.length_b 71.323 _cell.length_b_esd ? _cell.length_c 83.512 _cell.length_c_esd ? _cell.volume 424823.066 _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 ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9S1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9S1D _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.53 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 67.16 _exptl_crystal.description '50-150 um short rod' _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 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details 'Growth in a thermally controlled cabinet' _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;200 uM RNA in a ratio of A:B:C=1:1:1 in 10 mM HEPES pH7.5, 50 mM potassium chloride, 5 mM magnesium chloride and 240 uM of O6-methylguanine Crystallization cocktail: 100 mM NaCl, 100 mM LiCl, 10 mM MgCl2, 50 mM MES pH 6.4-6.7, 36-42% MPD ; _exptl_crystal_grow.pdbx_pH_range 6.4-6.7 _exptl_crystal_grow.temp 293.15 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details 'cold nitrogen stream' _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 X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2021-06-06 _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 'Si-111 and Si-113 reflection' _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 1.0332 _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 'PETRA III, DESY BEAMLINE P11' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.0332 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline P11 _diffrn_source.pdbx_synchrotron_site 'PETRA III, DESY' # _reflns.B_iso_Wilson_estimate 76.8 _reflns.entry_id 9S1D _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.60 _reflns.d_resolution_low 43.17 _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 7084 _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 3.0 _reflns.percent_possible_obs 100 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 25.3 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 42.9 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.04 _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 0.045 _reflns.pdbx_Rpim_I_all 0.010 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.044 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 2.60 _reflns_shell.d_res_low 2.72 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.0 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 837 _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 27 _reflns_shell.pdbx_chi_squared 0.82 _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all 2.039 _reflns_shell.pdbx_Rpim_I_all 0.396 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.583 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 2.017 _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 44.34 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ;Hendrickson-Lattman coefficients were generated in Phenix Resolve based on a non-methylated 7Q7X model, which was used in Phenix Refine as phase restraints (target function: MLHL). Three methyl groups were introduced during following refinements according to the difference map peaks. ; _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 9S1D _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 2.60 _refine.ls_d_res_low 43.17 _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 7047 _refine.ls_number_reflns_R_free 347 _refine.ls_number_reflns_R_work 6700 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.96 _refine.ls_percent_reflns_R_free 4.92 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2216 _refine.ls_R_factor_R_free 0.2510 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2201 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.37 _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 26.8536 _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 0.3643 _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 2.60 _refine_hist.d_res_low 43.17 _refine_hist.number_atoms_solvent 45 _refine_hist.number_atoms_total 1374 _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 1314 _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_Zscore _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0053 ? 1479 ? f_bond_d ? ? ? 'X-RAY DIFFRACTION' ? 0.9398 ? 2297 ? f_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 0.0357 ? 304 ? f_chiral_restr ? ? ? 'X-RAY DIFFRACTION' ? 0.0049 ? 63 ? f_plane_restr ? ? ? 'X-RAY DIFFRACTION' ? 24.5219 ? 916 ? 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.correlation_coeff_Fo_to_Fc _refine_ls_shell.correlation_coeff_Fo_to_Fc_free _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 2.60 2.98 . . 107 2181 100.00 . . . . 0.3504 . . . . . . . . . . . . . . . 0.3742 'X-RAY DIFFRACTION' 2.98 3.75 . . 119 2195 99.96 . . . . 0.2259 . . . . . . . . . . . . . . . 0.2831 'X-RAY DIFFRACTION' 3.75 43.17 . . 121 2324 99.92 . . . . 0.1653 . . . . . . . . . . . . . . . 0.1822 # _struct.entry_id 9S1D _struct.title ;Crystal structure of the methyltransferase ribozyme 1 with two 2'O-methylation (MTR1m2) ; _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 9S1D _struct_keywords.text ;Ribozyme, methyltransferase, 2'O-methylation, accelerated catalysis, 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 4 ? E N N 5 ? F N N 6 ? G N N 4 ? H N N 5 ? I N N 7 ? J N N 7 ? K N N 7 ? # 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 9S1D 9S1D ? 1 ? 1 2 PDB 9S1D 9S1D ? 2 ? 1 3 PDB 9S1D 9S1D ? 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 9S1D A 1 ? 14 ? 9S1D 1 ? 14 ? 1 14 2 2 9S1D B 1 ? 24 ? 9S1D 1 ? 24 ? 1 24 3 3 9S1D C 1 ? 24 ? 9S1D 25 ? 48 ? 25 48 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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)' 6770 ? 1 MORE -20 ? 1 'SSA (A^2)' 9610 ? # _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 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'assay for oligomerization' _pdbx_struct_assembly_auth_evidence.details ;Dissolved crystals were injected into anion exchange HPLC to check the composition. Peak areas were integrated to calculate the ratio of the RNA species. ; # _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 G 6 "O3'" ? ? ? 1_555 A 1MA 7 P ? ? A G 6 A 1MA 7 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale2 covale both ? A 1MA 7 "O3'" ? ? ? 1_555 A G 8 P ? ? A 1MA 7 A G 8 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale3 covale both ? B A 11 "O3'" ? ? ? 1_555 B OMC 12 P ? ? B A 11 B OMC 12 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale4 covale both ? B OMC 12 "O3'" ? ? ? 1_555 B C 13 P ? ? B OMC 12 B C 13 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale5 covale both ? C A 17 "O3'" ? ? ? 1_555 C OMU 18 P ? ? C A 41 C OMU 42 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale6 covale both ? C OMU 18 "O3'" ? ? ? 1_555 C A 19 P ? ? C OMU 42 C A 43 1_555 ? ? ? ? ? ? ? 1.601 ? ? metalc1 metalc ? ? B G 14 OP1 ? ? ? 1_555 E NA . NA ? ? B G 14 B NA 102 1_555 ? ? ? ? ? ? ? 2.928 ? ? metalc2 metalc ? ? B A 15 OP1 ? ? ? 1_555 E NA . NA ? ? B A 15 B NA 102 1_555 ? ? ? ? ? ? ? 2.933 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 J HOH . O ? ? B MG 101 B HOH 222 1_555 ? ? ? ? ? ? ? 2.149 ? ? metalc4 metalc ? ? G MG . MG ? ? ? 1_555 K HOH . O ? ? C MG 102 C HOH 206 1_555 ? ? ? ? ? ? ? 1.835 ? ? metalc5 metalc ? ? G MG . MG ? ? ? 1_555 K HOH . O ? ? C MG 102 C HOH 214 1_555 ? ? ? ? ? ? ? 2.054 ? ? metalc6 metalc ? ? H NA . NA ? ? ? 1_555 K HOH . O ? ? C NA 103 C HOH 216 1_555 ? ? ? ? ? ? ? 2.328 ? ? metalc7 metalc ? ? H NA . NA ? ? ? 1_555 K HOH . O ? ? C NA 103 C HOH 217 1_555 ? ? ? ? ? ? ? 2.757 ? ? hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 C G 24 N1 ? ? A C 2 C G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 C G 24 O6 ? ? A C 2 C G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 C G 24 N2 ? ? A C 2 C G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 3 N1 ? ? ? 1_555 C U 23 N3 ? ? A A 3 C U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 3 N6 ? ? ? 1_555 C U 23 O4 ? ? A A 3 C U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 4 N3 ? ? ? 1_555 C G 22 N1 ? ? A C 4 C G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N4 ? ? ? 1_555 C G 22 O6 ? ? A C 4 C G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 O2 ? ? ? 1_555 C G 22 N2 ? ? A C 4 C G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 5 N3 ? ? ? 1_555 C A 21 N1 ? ? A U 5 C A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 O4 ? ? ? 1_555 C A 21 N6 ? ? A U 5 C A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 6 N1 ? ? ? 1_555 C C 20 N3 ? ? A G 6 C C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 N2 ? ? ? 1_555 C C 20 O2 ? ? A G 6 C C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 O6 ? ? ? 1_555 C C 20 N4 ? ? A G 6 C C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 8 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 8 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 8 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 9 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 9 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 10 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 10 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 10 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 11 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 11 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 11 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 4 N1 ? ? A U 12 B A 4 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog26 hydrog ? ? A U 13 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 13 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 13 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 13 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 14 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 14 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 14 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 14 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 14 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 14 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B U 9 N3 ? ? ? 1_555 C A 10 N7 ? ? B U 9 C A 34 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog32 hydrog ? ? B U 9 O2 ? ? ? 1_555 C A 10 N6 ? ? B U 9 C A 34 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog33 hydrog ? ? B A 11 N6 ? ? ? 1_555 C A 19 N3 ? ? B A 11 C A 43 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog34 hydrog ? ? B C 13 N3 ? ? ? 1_555 C G 14 N1 ? ? B C 13 C G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B C 13 N4 ? ? ? 1_555 C G 14 O6 ? ? B C 13 C G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B C 13 O2 ? ? ? 1_555 C G 14 N2 ? ? B C 13 C G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B C 13 O2 ? ? ? 1_555 C A 17 N6 ? ? B C 13 C A 41 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog38 hydrog ? ? B G 14 N1 ? ? ? 1_555 C C 11 N3 ? ? B G 14 C C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B G 14 N2 ? ? ? 1_555 C C 11 O2 ? ? B G 14 C C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B G 14 O6 ? ? ? 1_555 C C 11 N4 ? ? B G 14 C C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B C 17 N4 ? ? ? 1_555 C A 7 N1 ? ? B C 17 C A 31 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog42 hydrog ? ? B C 18 N3 ? ? ? 1_555 C G 6 N1 ? ? B C 18 C G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B C 18 N4 ? ? ? 1_555 C G 6 O6 ? ? B C 18 C G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B C 18 O2 ? ? ? 1_555 C G 6 N2 ? ? B C 18 C G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? B C 19 N3 ? ? ? 1_555 C G 5 N1 ? ? B C 19 C G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? B C 19 N4 ? ? ? 1_555 C G 5 O6 ? ? B C 19 C G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? B C 19 O2 ? ? ? 1_555 C G 5 N2 ? ? B C 19 C G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? B C 20 N3 ? ? ? 1_555 C G 4 N1 ? ? B C 20 C G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? B C 20 N4 ? ? ? 1_555 C G 4 O6 ? ? B C 20 C G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? B C 20 O2 ? ? ? 1_555 C G 4 N2 ? ? B C 20 C G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? B A 21 N1 ? ? ? 1_555 C U 3 N3 ? ? B A 21 C U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? B A 21 N6 ? ? ? 1_555 C U 3 O4 ? ? B A 21 C U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? B G 22 N1 ? ? ? 1_555 C C 2 N3 ? ? B G 22 C C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? B G 22 N2 ? ? ? 1_555 C C 2 O2 ? ? B G 22 C C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? B G 22 O6 ? ? ? 1_555 C C 2 N4 ? ? B G 22 C C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? B C 23 N3 ? ? ? 1_555 C G 1 N1 ? ? B C 23 C G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? B C 23 N4 ? ? ? 1_555 C G 1 O6 ? ? B C 23 C G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? B C 23 O2 ? ? ? 1_555 C G 1 N2 ? ? B C 23 C G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP1 ? B G 14 ? B G 14 ? 1_555 NA ? E NA . ? B NA 102 ? 1_555 OP1 ? B A 15 ? B A 15 ? 1_555 95.6 ? 2 O ? K HOH . ? C HOH 206 ? 1_555 MG ? G MG . ? C MG 102 ? 1_555 O ? K HOH . ? C HOH 214 ? 1_555 93.7 ? 3 O ? K HOH . ? C HOH 216 ? 1_555 NA ? H NA . ? C NA 103 ? 1_555 O ? K HOH . ? C HOH 217 ? 1_555 71.3 ? # _pdbx_entry_details.entry_id 9S1D _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y+1/2,x+1/2,z+1/4 3 y+1/2,-x+1/2,z+3/4 4 x+1/2,-y+1/2,-z+3/4 5 -x+1/2,y+1/2,-z+1/4 6 -x,-y,z+1/2 7 y,x,-z 8 -y,-x,-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 29.1686159186 -16.3828363238 -2.89113323894 0.318956045333 ? -0.0748165062825 ? -0.0151336575123 ? 0.202307585073 ? -0.0636490272973 ? 0.247837939685 ? 1.59641992244 ? 1.67545769664 ? 0.960491729552 ? 3.56451931584 ? 1.17173173259 ? 0.745535722809 ? 0.118455355664 ? 0.260724882017 ? -0.311627276199 ? -0.237731743779 ? 0.0356448061689 ? -0.0883943066826 ? 0.29230064591 ? -0.0900963833593 ? 0.110018429331 ? 2 'X-RAY DIFFRACTION' ? refined 15.0520399238 -17.4411765283 1.45283493938 0.553361452507 ? -0.126562964573 ? -0.032074454871 ? 0.536193803645 ? -0.289637092522 ? 0.469805690827 ? 0.674185521993 ? 0.367696363715 ? 0.632705689816 ? 1.08691547608 ? -0.154536526321 ? 0.876515924261 ? 0.117291887635 ? -0.451943558784 ? 0.295051160313 ? 0.313676254785 ? -0.126534852287 ? 0.157439083876 ? -0.151977470763 ? -0.386544328762 ? 0.390229171506 ? 3 'X-RAY DIFFRACTION' ? refined 28.7370251761 -6.79153644328 3.31715974388 0.174227088256 ? -0.0680527587317 ? -0.031195707718 ? 0.227114154838 ? -0.0377052645627 ? 0.196796169293 ? 1.62817918264 ? 0.582923080757 ? -0.371157349545 ? 1.57762007181 ? 0.292217436049 ? 1.32555973958 ? 0.380601500117 ? -0.196016634593 ? 0.15810558664 ? 0.145792293277 ? -0.332395111635 ? 0.200929723535 ? -0.0927214020278 ? -0.350010406366 ? 0.313191919824 ? # 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 C ? C 25 ? C ? C 48 ? ? ;(chain 'C' and resid 25 through 101) ; 2 'X-RAY DIFFRACTION' 2 A ? A 1 ? A ? A 14 ? ? ;(chain 'A' and resid 1 through 14) ; 3 'X-RAY DIFFRACTION' 3 B ? B 1 ? B ? B 24 ? ? ;(chain 'B' and resid 1 through 24) ; # 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 1MA P P N N 1 1MA OP1 O N N 2 1MA OP2 O N N 3 1MA OP3 O N N 4 1MA "O5'" O N N 5 1MA "C5'" C N N 6 1MA "C4'" C N R 7 1MA "O4'" O N N 8 1MA "C3'" C N S 9 1MA "O3'" O N N 10 1MA "C2'" C N R 11 1MA "O2'" O N N 12 1MA "C1'" C N R 13 1MA N9 N Y N 14 1MA C8 C Y N 15 1MA N7 N Y N 16 1MA C5 C Y N 17 1MA C6 C N N 18 1MA N6 N N N 19 1MA N1 N N N 20 1MA CM1 C N N 21 1MA C2 C N N 22 1MA N3 N N N 23 1MA C4 C Y N 24 1MA HOP2 H N N 25 1MA HOP3 H N N 26 1MA "H5'" H N N 27 1MA "H5''" H N N 28 1MA "H4'" H N N 29 1MA "H3'" H N N 30 1MA "HO3'" H N N 31 1MA "H2'" H N N 32 1MA "HO2'" H N N 33 1MA "H1'" H N N 34 1MA H8 H N N 35 1MA HN61 H N N 36 1MA HM11 H N N 37 1MA HM12 H N N 38 1MA HM13 H N N 39 1MA H2 H N N 40 A OP3 O N N 41 A P P N N 42 A OP1 O N N 43 A OP2 O N N 44 A "O5'" O N N 45 A "C5'" C N N 46 A "C4'" C N R 47 A "O4'" O N N 48 A "C3'" C N S 49 A "O3'" O N N 50 A "C2'" C N R 51 A "O2'" O N N 52 A "C1'" C N R 53 A N9 N Y N 54 A C8 C Y N 55 A N7 N Y N 56 A C5 C Y N 57 A C6 C Y N 58 A N6 N N N 59 A N1 N Y N 60 A C2 C Y N 61 A N3 N Y N 62 A C4 C Y N 63 A HOP3 H N N 64 A HOP2 H N N 65 A "H5'" H N N 66 A "H5''" H N N 67 A "H4'" H N N 68 A "H3'" H N N 69 A "HO3'" H N N 70 A "H2'" H N N 71 A "HO2'" H N N 72 A "H1'" H N N 73 A H8 H N N 74 A H61 H N N 75 A H62 H N N 76 A H2 H N N 77 C OP3 O N N 78 C P P N N 79 C OP1 O N N 80 C OP2 O N N 81 C "O5'" O N N 82 C "C5'" C N N 83 C "C4'" C N R 84 C "O4'" O N N 85 C "C3'" C N S 86 C "O3'" O N N 87 C "C2'" C N R 88 C "O2'" O N N 89 C "C1'" C N R 90 C N1 N N N 91 C C2 C N N 92 C O2 O N N 93 C N3 N N N 94 C C4 C N N 95 C N4 N N N 96 C C5 C N N 97 C C6 C N N 98 C HOP3 H N N 99 C HOP2 H N N 100 C "H5'" H N N 101 C "H5''" H N N 102 C "H4'" H N N 103 C "H3'" H N N 104 C "HO3'" H N N 105 C "H2'" H N N 106 C "HO2'" H N N 107 C "H1'" H N N 108 C H41 H N N 109 C H42 H N N 110 C H5 H N N 111 C H6 H N N 112 G OP3 O N N 113 G P P N N 114 G OP1 O N N 115 G OP2 O N N 116 G "O5'" O N N 117 G "C5'" C N N 118 G "C4'" C N R 119 G "O4'" O N N 120 G "C3'" C N S 121 G "O3'" O N N 122 G "C2'" C N R 123 G "O2'" O N N 124 G "C1'" C N R 125 G N9 N Y N 126 G C8 C Y N 127 G N7 N Y N 128 G C5 C Y N 129 G C6 C N N 130 G O6 O N N 131 G N1 N N N 132 G C2 C N N 133 G N2 N N N 134 G N3 N N N 135 G C4 C Y N 136 G HOP3 H N N 137 G HOP2 H N N 138 G "H5'" H N N 139 G "H5''" H N N 140 G "H4'" H N N 141 G "H3'" H N N 142 G "HO3'" H N N 143 G "H2'" H N N 144 G "HO2'" H N N 145 G "H1'" H N N 146 G H8 H N N 147 G H1 H N N 148 G H21 H N N 149 G H22 H N N 150 GUN N9 N Y N 151 GUN C8 C Y N 152 GUN N7 N Y N 153 GUN C5 C Y N 154 GUN C6 C N N 155 GUN O6 O N N 156 GUN N1 N N N 157 GUN C2 C N N 158 GUN N2 N N N 159 GUN N3 N N N 160 GUN C4 C Y N 161 GUN HN9 H N N 162 GUN H8 H N N 163 GUN HN1 H N N 164 GUN HN21 H N N 165 GUN HN22 H N N 166 HOH O O N N 167 HOH H1 H N N 168 HOH H2 H N N 169 MG MG MG N N 170 NA NA NA N N 171 OMC N1 N N N 172 OMC C2 C N N 173 OMC N3 N N N 174 OMC C4 C N N 175 OMC C5 C N N 176 OMC C6 C N N 177 OMC O2 O N N 178 OMC N4 N N N 179 OMC "C1'" C N R 180 OMC "C2'" C N R 181 OMC "O2'" O N N 182 OMC CM2 C N N 183 OMC "C3'" C N R 184 OMC "C4'" C N R 185 OMC "O4'" O N N 186 OMC "O3'" O N N 187 OMC "C5'" C N N 188 OMC "O5'" O N N 189 OMC P P N N 190 OMC OP1 O N N 191 OMC OP2 O N N 192 OMC OP3 O N N 193 OMC H5 H N N 194 OMC H6 H N N 195 OMC HN41 H N N 196 OMC HN42 H N N 197 OMC "H1'" H N N 198 OMC "H2'" H N N 199 OMC HM21 H N N 200 OMC HM22 H N N 201 OMC HM23 H N N 202 OMC "H3'" H N N 203 OMC "H4'" H N N 204 OMC "HO3'" H N N 205 OMC "H5'" H N N 206 OMC "H5''" H N N 207 OMC HOP2 H N N 208 OMC HOP3 H N N 209 OMU N1 N N N 210 OMU C2 C N N 211 OMU N3 N N N 212 OMU C4 C N N 213 OMU C5 C N N 214 OMU C6 C N N 215 OMU O2 O N N 216 OMU O4 O N N 217 OMU "C1'" C N R 218 OMU "C2'" C N R 219 OMU "O2'" O N N 220 OMU CM2 C N N 221 OMU "C3'" C N R 222 OMU "C4'" C N R 223 OMU "O3'" O N N 224 OMU "O4'" O N N 225 OMU "C5'" C N N 226 OMU "O5'" O N N 227 OMU P P N N 228 OMU OP1 O N N 229 OMU OP2 O N N 230 OMU OP3 O N N 231 OMU HN3 H N N 232 OMU H5 H N N 233 OMU H6 H N N 234 OMU "H1'" H N N 235 OMU "H2'" H N N 236 OMU HM21 H N N 237 OMU HM22 H N N 238 OMU HM23 H N N 239 OMU "H3'" H N N 240 OMU "H4'" H N N 241 OMU "HO3'" H N N 242 OMU "H5'" H N N 243 OMU "H5''" H N N 244 OMU HOP2 H N N 245 OMU HOP3 H N N 246 U OP3 O N N 247 U P P N N 248 U OP1 O N N 249 U OP2 O N N 250 U "O5'" O N N 251 U "C5'" C N N 252 U "C4'" C N R 253 U "O4'" O N N 254 U "C3'" C N S 255 U "O3'" O N N 256 U "C2'" C N R 257 U "O2'" O N N 258 U "C1'" C N R 259 U N1 N N N 260 U C2 C N N 261 U O2 O N N 262 U N3 N N N 263 U C4 C N N 264 U O4 O N N 265 U C5 C N N 266 U C6 C N N 267 U HOP3 H N N 268 U HOP2 H N N 269 U "H5'" H N N 270 U "H5''" H N N 271 U "H4'" H N N 272 U "H3'" H N N 273 U "HO3'" H N N 274 U "H2'" H N N 275 U "HO2'" H N N 276 U "H1'" H N N 277 U H3 H N N 278 U H5 H N N 279 U H6 H N N 280 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 1MA P OP1 doub N N 1 1MA P OP2 sing N N 2 1MA P OP3 sing N N 3 1MA P "O5'" sing N N 4 1MA OP2 HOP2 sing N N 5 1MA OP3 HOP3 sing N N 6 1MA "O5'" "C5'" sing N N 7 1MA "C5'" "C4'" sing N N 8 1MA "C5'" "H5'" sing N N 9 1MA "C5'" "H5''" sing N N 10 1MA "C4'" "O4'" sing N N 11 1MA "C4'" "C3'" sing N N 12 1MA "C4'" "H4'" sing N N 13 1MA "O4'" "C1'" sing N N 14 1MA "C3'" "O3'" sing N N 15 1MA "C3'" "C2'" sing N N 16 1MA "C3'" "H3'" sing N N 17 1MA "O3'" "HO3'" sing N N 18 1MA "C2'" "O2'" sing N N 19 1MA "C2'" "C1'" sing N N 20 1MA "C2'" "H2'" sing N N 21 1MA "O2'" "HO2'" sing N N 22 1MA "C1'" N9 sing N N 23 1MA "C1'" "H1'" sing N N 24 1MA N9 C8 sing Y N 25 1MA N9 C4 sing Y N 26 1MA C8 N7 doub Y N 27 1MA C8 H8 sing N N 28 1MA N7 C5 sing Y N 29 1MA C5 C6 sing N N 30 1MA C5 C4 doub Y N 31 1MA C6 N6 doub N N 32 1MA C6 N1 sing N N 33 1MA N6 HN61 sing N N 34 1MA N1 CM1 sing N N 35 1MA N1 C2 sing N N 36 1MA CM1 HM11 sing N N 37 1MA CM1 HM12 sing N N 38 1MA CM1 HM13 sing N N 39 1MA C2 N3 doub N N 40 1MA C2 H2 sing N N 41 1MA N3 C4 sing N N 42 A OP3 P sing N N 43 A OP3 HOP3 sing N N 44 A P OP1 doub N N 45 A P OP2 sing N N 46 A P "O5'" sing N N 47 A OP2 HOP2 sing N N 48 A "O5'" "C5'" sing N N 49 A "C5'" "C4'" sing N N 50 A "C5'" "H5'" sing N N 51 A "C5'" "H5''" sing N N 52 A "C4'" "O4'" sing N N 53 A "C4'" "C3'" sing N N 54 A "C4'" "H4'" sing N N 55 A "O4'" "C1'" sing N N 56 A "C3'" "O3'" sing N N 57 A "C3'" "C2'" sing N N 58 A "C3'" "H3'" sing N N 59 A "O3'" "HO3'" sing N N 60 A "C2'" "O2'" sing N N 61 A "C2'" "C1'" sing N N 62 A "C2'" "H2'" sing N N 63 A "O2'" "HO2'" sing N N 64 A "C1'" N9 sing N N 65 A "C1'" "H1'" sing N N 66 A N9 C8 sing Y N 67 A N9 C4 sing Y N 68 A C8 N7 doub Y N 69 A C8 H8 sing N N 70 A N7 C5 sing Y N 71 A C5 C6 sing Y N 72 A C5 C4 doub Y N 73 A C6 N6 sing N N 74 A C6 N1 doub Y N 75 A N6 H61 sing N N 76 A N6 H62 sing N N 77 A N1 C2 sing Y N 78 A C2 N3 doub Y N 79 A C2 H2 sing N N 80 A N3 C4 sing Y N 81 C OP3 P sing N N 82 C OP3 HOP3 sing N N 83 C P OP1 doub N N 84 C P OP2 sing N N 85 C P "O5'" sing N N 86 C OP2 HOP2 sing N N 87 C "O5'" "C5'" sing N N 88 C "C5'" "C4'" sing N N 89 C "C5'" "H5'" sing N N 90 C "C5'" "H5''" sing N N 91 C "C4'" "O4'" sing N N 92 C "C4'" "C3'" sing N N 93 C "C4'" "H4'" sing N N 94 C "O4'" "C1'" sing N N 95 C "C3'" "O3'" sing N N 96 C "C3'" "C2'" sing N N 97 C "C3'" "H3'" sing N N 98 C "O3'" "HO3'" sing N N 99 C "C2'" "O2'" sing N N 100 C "C2'" "C1'" sing N N 101 C "C2'" "H2'" sing N N 102 C "O2'" "HO2'" sing N N 103 C "C1'" N1 sing N N 104 C "C1'" "H1'" sing N N 105 C N1 C2 sing N N 106 C N1 C6 sing N N 107 C C2 O2 doub N N 108 C C2 N3 sing N N 109 C N3 C4 doub N N 110 C C4 N4 sing N N 111 C C4 C5 sing N N 112 C N4 H41 sing N N 113 C N4 H42 sing N N 114 C C5 C6 doub N N 115 C C5 H5 sing N N 116 C C6 H6 sing N N 117 G OP3 P sing N N 118 G OP3 HOP3 sing N N 119 G P OP1 doub N N 120 G P OP2 sing N N 121 G P "O5'" sing N N 122 G OP2 HOP2 sing N N 123 G "O5'" "C5'" sing N N 124 G "C5'" "C4'" sing N N 125 G "C5'" "H5'" sing N N 126 G "C5'" "H5''" sing N N 127 G "C4'" "O4'" sing N N 128 G "C4'" "C3'" sing N N 129 G "C4'" "H4'" sing N N 130 G "O4'" "C1'" sing N N 131 G "C3'" "O3'" sing N N 132 G "C3'" "C2'" sing N N 133 G "C3'" "H3'" sing N N 134 G "O3'" "HO3'" sing N N 135 G "C2'" "O2'" sing N N 136 G "C2'" "C1'" sing N N 137 G "C2'" "H2'" sing N N 138 G "O2'" "HO2'" sing N N 139 G "C1'" N9 sing N N 140 G "C1'" "H1'" sing N N 141 G N9 C8 sing Y N 142 G N9 C4 sing Y N 143 G C8 N7 doub Y N 144 G C8 H8 sing N N 145 G N7 C5 sing Y N 146 G C5 C6 sing N N 147 G C5 C4 doub Y N 148 G C6 O6 doub N N 149 G C6 N1 sing N N 150 G N1 C2 sing N N 151 G N1 H1 sing N N 152 G C2 N2 sing N N 153 G C2 N3 doub N N 154 G N2 H21 sing N N 155 G N2 H22 sing N N 156 G N3 C4 sing N N 157 GUN N9 C8 sing Y N 158 GUN N9 C4 sing Y N 159 GUN N9 HN9 sing N N 160 GUN C8 N7 doub Y N 161 GUN C8 H8 sing N N 162 GUN N7 C5 sing Y N 163 GUN C5 C6 sing N N 164 GUN C5 C4 doub Y N 165 GUN C6 O6 doub N N 166 GUN C6 N1 sing N N 167 GUN N1 C2 sing N N 168 GUN N1 HN1 sing N N 169 GUN C2 N2 sing N N 170 GUN C2 N3 doub N N 171 GUN N2 HN21 sing N N 172 GUN N2 HN22 sing N N 173 GUN N3 C4 sing N N 174 HOH O H1 sing N N 175 HOH O H2 sing N N 176 OMC N1 C2 sing N N 177 OMC N1 C6 sing N N 178 OMC N1 "C1'" sing N N 179 OMC C2 N3 sing N N 180 OMC C2 O2 doub N N 181 OMC N3 C4 doub N N 182 OMC C4 C5 sing N N 183 OMC C4 N4 sing N N 184 OMC C5 C6 doub N N 185 OMC C5 H5 sing N N 186 OMC C6 H6 sing N N 187 OMC N4 HN41 sing N N 188 OMC N4 HN42 sing N N 189 OMC "C1'" "C2'" sing N N 190 OMC "C1'" "O4'" sing N N 191 OMC "C1'" "H1'" sing N N 192 OMC "C2'" "O2'" sing N N 193 OMC "C2'" "C3'" sing N N 194 OMC "C2'" "H2'" sing N N 195 OMC "O2'" CM2 sing N N 196 OMC CM2 HM21 sing N N 197 OMC CM2 HM22 sing N N 198 OMC CM2 HM23 sing N N 199 OMC "C3'" "C4'" sing N N 200 OMC "C3'" "O3'" sing N N 201 OMC "C3'" "H3'" sing N N 202 OMC "C4'" "O4'" sing N N 203 OMC "C4'" "C5'" sing N N 204 OMC "C4'" "H4'" sing N N 205 OMC "O3'" "HO3'" sing N N 206 OMC "C5'" "O5'" sing N N 207 OMC "C5'" "H5'" sing N N 208 OMC "C5'" "H5''" sing N N 209 OMC "O5'" P sing N N 210 OMC P OP1 doub N N 211 OMC P OP2 sing N N 212 OMC P OP3 sing N N 213 OMC OP2 HOP2 sing N N 214 OMC OP3 HOP3 sing N N 215 OMU N1 C2 sing N N 216 OMU N1 C6 sing N N 217 OMU N1 "C1'" sing N N 218 OMU C2 N3 sing N N 219 OMU C2 O2 doub N N 220 OMU N3 C4 sing N N 221 OMU N3 HN3 sing N N 222 OMU C4 C5 sing N N 223 OMU C4 O4 doub N N 224 OMU C5 C6 doub N N 225 OMU C5 H5 sing N N 226 OMU C6 H6 sing N N 227 OMU "C1'" "C2'" sing N N 228 OMU "C1'" "O4'" sing N N 229 OMU "C1'" "H1'" sing N N 230 OMU "C2'" "O2'" sing N N 231 OMU "C2'" "C3'" sing N N 232 OMU "C2'" "H2'" sing N N 233 OMU "O2'" CM2 sing N N 234 OMU CM2 HM21 sing N N 235 OMU CM2 HM22 sing N N 236 OMU CM2 HM23 sing N N 237 OMU "C3'" "C4'" sing N N 238 OMU "C3'" "O3'" sing N N 239 OMU "C3'" "H3'" sing N N 240 OMU "C4'" "O4'" sing N N 241 OMU "C4'" "C5'" sing N N 242 OMU "C4'" "H4'" sing N N 243 OMU "O3'" "HO3'" sing N N 244 OMU "C5'" "O5'" sing N N 245 OMU "C5'" "H5'" sing N N 246 OMU "C5'" "H5''" sing N N 247 OMU "O5'" P sing N N 248 OMU P OP1 doub N N 249 OMU P OP2 sing N N 250 OMU P OP3 sing N N 251 OMU OP2 HOP2 sing N N 252 OMU OP3 HOP3 sing N N 253 U OP3 P sing N N 254 U OP3 HOP3 sing N N 255 U P OP1 doub N N 256 U P OP2 sing N N 257 U P "O5'" sing N N 258 U OP2 HOP2 sing N N 259 U "O5'" "C5'" sing N N 260 U "C5'" "C4'" sing N N 261 U "C5'" "H5'" sing N N 262 U "C5'" "H5''" sing N N 263 U "C4'" "O4'" sing N N 264 U "C4'" "C3'" sing N N 265 U "C4'" "H4'" sing N N 266 U "O4'" "C1'" sing N N 267 U "C3'" "O3'" sing N N 268 U "C3'" "C2'" sing N N 269 U "C3'" "H3'" sing N N 270 U "O3'" "HO3'" sing N N 271 U "C2'" "O2'" sing N N 272 U "C2'" "C1'" sing N N 273 U "C2'" "H2'" sing N N 274 U "O2'" "HO2'" sing N N 275 U "C1'" N1 sing N N 276 U "C1'" "H1'" sing N N 277 U N1 C2 sing N N 278 U N1 C6 sing N N 279 U C2 O2 doub N N 280 U C2 N3 sing N N 281 U N3 C4 sing N N 282 U N3 H3 sing N N 283 U C4 O4 doub N N 284 U C4 C5 sing N N 285 U C5 C6 doub N N 286 U C5 H5 sing N N 287 U C6 H6 sing N N 288 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9S1D 'double helix' 9S1D '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 C 2 1_555 C G 24 1_555 -0.498 0.163 0.259 -1.792 -1.920 1.797 1 A_C2:G48_C A 2 ? C 48 ? 19 1 1 A A 3 1_555 C U 23 1_555 -0.270 -0.038 0.470 7.302 -7.876 3.551 2 A_A3:U47_C A 3 ? C 47 ? 20 1 1 A C 4 1_555 C G 22 1_555 -0.267 0.173 0.114 5.386 -12.837 5.360 3 A_C4:G46_C A 4 ? C 46 ? 19 1 1 A U 5 1_555 C A 21 1_555 0.122 0.146 0.096 1.323 -13.219 9.829 4 A_U5:A45_C A 5 ? C 45 ? 20 1 1 A G 6 1_555 C C 20 1_555 -0.344 0.017 -0.026 -5.164 -14.522 3.117 5 A_G6:C44_C A 6 ? C 44 ? 19 1 1 B A 11 1_555 C A 19 1_555 -6.286 -0.474 -0.392 26.640 9.512 58.885 6 B_A11:A43_C B 11 ? C 43 ? ? 5 1 B C 13 1_555 C G 14 1_555 -0.160 0.090 0.398 -10.499 -2.323 -1.604 7 B_C13:G38_C B 13 ? C 38 ? 19 1 1 B G 14 1_555 C C 11 1_555 -0.147 -0.009 -0.605 -11.478 -3.877 1.102 8 B_G14:C35_C B 14 ? C 35 ? 19 1 1 B G 2 1_555 A C 14 1_555 0.266 0.124 0.116 -3.434 -10.358 -4.175 9 B_G2:C14_A B 2 ? A 14 ? 19 1 1 B A 3 1_555 A U 13 1_555 -0.437 0.083 -0.391 -0.894 -17.598 5.798 10 B_A3:U13_A B 3 ? A 13 ? 20 1 1 B A 4 1_555 A U 12 1_555 -0.082 0.236 0.633 10.036 -19.638 14.093 11 B_A4:U12_A B 4 ? A 12 ? ? 1 1 B G 5 1_555 A C 11 1_555 0.314 0.066 -0.444 -13.740 -24.354 4.648 12 B_G5:C11_A B 5 ? A 11 ? 19 1 1 B C 6 1_555 A G 10 1_555 1.613 -0.522 -0.213 -0.754 -16.147 -8.112 13 B_C6:G10_A B 6 ? A 10 ? 19 1 1 B U 7 1_555 A A 9 1_555 0.473 0.182 -0.188 -3.185 -14.272 1.384 14 B_U7:A9_A B 7 ? A 9 ? 20 1 1 B C 8 1_555 A G 8 1_555 1.195 -0.078 0.050 0.294 -9.661 1.631 15 B_C8:G8_A B 8 ? A 8 ? 19 1 1 B U 9 1_555 C A 10 1_555 4.565 -2.369 -0.700 -11.605 -5.642 -102.518 16 B_U9:A34_C B 9 ? C 34 ? 24 4 1 B C 17 1_555 C A 7 1_555 -2.889 0.682 -1.393 44.584 -24.169 -5.247 17 B_C17:A31_C B 17 ? C 31 ? ? ? 1 B C 18 1_555 C G 6 1_555 0.247 0.038 -0.329 16.276 -17.651 2.758 18 B_C18:G30_C B 18 ? C 30 ? 19 1 1 B C 19 1_555 C G 5 1_555 -0.035 0.017 -0.312 8.090 -12.172 1.106 19 B_C19:G29_C B 19 ? C 29 ? 19 1 1 B C 20 1_555 C G 4 1_555 -0.050 -0.029 -0.163 4.273 -6.565 4.968 20 B_C20:G28_C B 20 ? C 28 ? 19 1 1 B A 21 1_555 C U 3 1_555 -0.220 -0.037 -0.039 -6.584 -15.836 8.261 21 B_A21:U27_C B 21 ? C 27 ? 20 1 1 B G 22 1_555 C C 2 1_555 0.685 0.024 -0.067 -7.863 -21.209 7.243 22 B_G22:C26_C B 22 ? C 26 ? 19 1 1 B C 23 1_555 C G 1 1_555 0.803 -0.385 0.306 -6.358 -7.624 -3.866 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 C 2 1_555 C G 24 1_555 A A 3 1_555 C U 23 1_555 -0.339 -1.602 2.741 -3.813 10.798 31.187 -4.194 0.104 2.111 19.288 6.811 33.174 1 AA_C2A3:U47G48_CC A 2 ? C 48 ? A 3 ? C 47 ? 1 A A 3 1_555 C U 23 1_555 A C 4 1_555 C G 22 1_555 -0.092 -1.355 3.316 2.471 8.366 31.618 -3.787 0.572 2.858 15.001 -4.430 32.770 2 AA_A3C4:G46U47_CC A 3 ? C 47 ? A 4 ? C 46 ? 1 A C 4 1_555 C G 22 1_555 A U 5 1_555 C A 21 1_555 0.457 -1.671 3.316 -0.659 7.994 31.856 -4.263 -0.916 2.815 14.284 1.178 32.826 3 AA_C4U5:A45G46_CC A 4 ? C 46 ? A 5 ? C 45 ? 1 A U 5 1_555 C A 21 1_555 A G 6 1_555 C C 20 1_555 -0.265 -1.634 3.270 1.380 11.002 31.540 -4.518 0.671 2.558 19.501 -2.445 33.386 4 AA_U5G6:C44A45_CC A 5 ? C 45 ? A 6 ? C 44 ? 1 A G 6 1_555 C C 20 1_555 B A 11 1_555 C A 19 1_555 -3.620 -3.557 3.334 15.298 17.490 63.378 -3.753 3.743 1.600 16.089 -14.072 67.085 5 AB_G6A11:A43C44_CC A 6 ? C 44 ? B 11 ? C 43 ? 1 B A 11 1_555 C A 19 1_555 B C 13 1_555 C G 14 1_555 1.733 -1.535 6.764 -13.054 10.301 122.716 -1.056 -1.219 6.561 5.857 7.422 123.372 6 BB_A11C13:G38A43_CC B 11 ? C 43 ? B 13 ? C 38 ? 1 B C 13 1_555 C G 14 1_555 B G 14 1_555 C C 11 1_555 -0.482 -1.826 3.336 7.452 6.033 23.341 -5.826 3.134 2.521 14.169 -17.501 25.209 7 BB_C13G14:C35G38_CC B 13 ? C 38 ? B 14 ? C 35 ? 1 B G 2 1_555 A C 14 1_555 B A 3 1_555 A U 13 1_555 0.100 -1.143 3.163 3.223 12.833 29.223 -4.158 0.343 2.455 23.948 -6.014 32.019 8 BB_G2A3:U13C14_AA B 2 ? A 14 ? B 3 ? A 13 ? 1 B A 3 1_555 A U 13 1_555 B A 4 1_555 A U 12 1_555 0.464 -0.897 2.876 -5.776 9.568 32.382 -2.781 -1.547 2.407 16.553 9.992 34.207 9 BB_A3A4:U12U13_AA B 3 ? A 13 ? B 4 ? A 12 ? 1 B A 4 1_555 A U 12 1_555 B G 5 1_555 A C 11 1_555 -0.068 -1.415 3.577 8.457 19.806 38.277 -3.798 0.902 2.520 27.698 -11.827 43.721 10 BB_A4G5:C11U12_AA B 4 ? A 12 ? B 5 ? A 11 ? 1 B G 5 1_555 A C 11 1_555 B C 6 1_555 A G 10 1_555 -0.753 -1.046 3.048 -4.723 4.402 36.341 -2.207 0.597 2.977 6.990 7.500 36.891 11 BB_G5C6:G10C11_AA B 5 ? A 11 ? B 6 ? A 10 ? 1 B C 6 1_555 A G 10 1_555 B U 7 1_555 A A 9 1_555 0.007 -1.879 3.188 2.657 9.831 23.310 -6.715 0.643 2.212 22.977 -6.210 25.410 12 BB_C6U7:A9G10_AA B 6 ? A 10 ? B 7 ? A 9 ? 1 B U 7 1_555 A A 9 1_555 B C 8 1_555 A G 8 1_555 0.412 -1.667 3.228 -0.419 3.143 32.589 -3.478 -0.800 3.053 5.585 0.744 32.739 13 BB_U7C8:G8A9_AA B 7 ? A 9 ? B 8 ? A 8 ? 1 B C 8 1_555 A G 8 1_555 B U 9 1_555 C A 10 1_555 -3.221 -2.012 3.387 9.376 0.702 78.960 -1.593 2.769 3.038 0.550 -7.349 79.427 14 BB_C8U9:A34G8_CA B 8 ? A 8 ? B 9 ? C 34 ? 1 B C 17 1_555 C A 7 1_555 B C 18 1_555 C G 6 1_555 -0.011 -1.347 4.350 -9.889 16.156 45.752 -3.150 -0.926 3.637 19.810 12.126 49.323 15 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 -0.162 -1.943 3.403 -0.510 8.986 31.664 -4.908 0.202 2.765 16.066 0.913 32.887 16 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 -0.419 -1.909 3.395 -1.515 11.706 26.681 -6.159 0.528 2.383 23.934 3.098 29.132 17 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 0.409 -1.634 3.411 -0.694 15.741 28.772 -5.405 -0.836 2.230 29.086 1.282 32.724 18 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 0.102 -1.360 3.255 1.247 9.043 38.898 -2.984 -0.012 2.882 13.357 -1.842 39.915 19 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 -0.287 -1.464 3.143 -3.045 1.105 31.757 -2.854 -0.007 3.105 2.012 5.547 31.917 20 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 'German Research Foundation (DFG)' Germany ? 1 'European Research Council (ERC)' 'European Union' ? 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 'search for 1 copy' # _space_group.name_H-M_alt 'P 41 21 2' _space_group.name_Hall 'P 4abw 2nw' _space_group.IT_number 92 _space_group.crystal_system tetragonal _space_group.id 1 # _atom_sites.entry_id 9S1D _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] 0.014021 _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] 0.014021 _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] 0.011974 _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. ; ? H ? ? 0.51345 0.48472 ? ? 24.73122 6.32584 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? MG ? ? 9.41153 2.53737 ? ? 2.59044 63.03566 ? ? 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 ? ? 9.38062 1.54875 ? ? 3.38349 72.32734 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 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_ #