data_357D # _entry.id 357D # _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 357D pdb_0000357d 10.2210/pdb357d/pdb RCSB URL066 ? ? WWPDB D_1000178826 ? ? # 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 1997-12-01 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-21 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_conn_type 6 4 'Structure model' struct_site # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.conn_type_id' 4 4 'Structure model' '_struct_conn.id' 5 4 'Structure model' '_struct_conn.pdbx_dist_value' 6 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 14 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 15 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 16 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 19 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 20 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 21 4 'Structure model' '_struct_conn_type.id' 22 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 23 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 24 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 357D _pdbx_database_status.recvd_initial_deposition_date 1997-10-09 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Correll, C.C.' 1 'Freeborn, B.' 2 'Moore, P.B.' 3 'Steitz, T.A.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.' 'Cell(Cambridge,Mass.)' 91 705 712 1997 CELLB5 US 0092-8674 0998 ? 9393863 '10.1016/S0092-8674(00)80457-2' 1 ;Use of Chemically Modified Nucleotides to Determine a 62-Nucleotide RNA Crystal Structure: A Survey of Phosphorothioates, Br, Pt, and Hg ; J.Biomol.Struct.Dyn. 15 165 172 1997 JBSDD6 US 0739-1102 0646 ? ? ? 2 'The Solution Structure of the Loop E/Loop D Region of E. Coli 5S rRNA' 'To be Published' ? ? ? ? ? ? ? 0353 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Correll, C.C.' 1 ? primary 'Freeborn, B.' 2 ? primary 'Moore, P.B.' 3 ? primary 'Steitz, T.A.' 4 ? 1 'Correll, C.C.' 5 ? 1 'Freeborn, B.' 6 ? 1 'Moore, P.B.' 7 ? 1 'Steitz, T.A.' 8 ? 2 'Dallas, A.' 9 ? 2 'Moore, P.B.' 10 ? # 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 man ;RNA-DNA (5'-R(*UP*GP*DCP)-D(*CP(S)*)-R(*UP*GP*GP*CP*GP*GP*C)-3') ; 3514.196 1 ? ? ? ? 2 polymer man ;RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G*UP*C)-3') ; 6166.682 1 ? ? ? ? 3 polymer man ;RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G P*GP*AP*AP*CP*UP* GP*CP*CP*AP*GP*GP*CP*AP*U)-3') ; 10012.047 1 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 8 ? ? ? ? 5 non-polymer syn 'MERCURY (II) ION' 200.590 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes 'UGC(DC)(SSU)GGCGGC' UGCCUGGCGGC A ? 2 polyribonucleotide no no CCGAUGGUAGUGUGGGGUC CCGAUGGUAGUGUGGGGUC B ? 3 polyribonucleotide no no CCCCAUGCGAGAGUAGGGAACUGCCAGGCAU CCCCAUGCGAGAGUAGGGAACUGCCAGGCAU C ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'MAGNESIUM ION' MG 5 'MERCURY (II) ION' HG # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 G n 1 3 C n 1 4 DC n 1 5 SSU n 1 6 G n 1 7 G n 1 8 C n 1 9 G n 1 10 G n 1 11 C n 2 1 C n 2 2 C n 2 3 G n 2 4 A n 2 5 U n 2 6 G n 2 7 G n 2 8 U n 2 9 A n 2 10 G n 2 11 U n 2 12 G n 2 13 U n 2 14 G n 2 15 G n 2 16 G n 2 17 G n 2 18 U n 2 19 C n 3 1 C n 3 2 C n 3 3 C n 3 4 C n 3 5 A n 3 6 U n 3 7 G n 3 8 C n 3 9 G n 3 10 A n 3 11 G n 3 12 A n 3 13 G n 3 14 U n 3 15 A n 3 16 G n 3 17 G n 3 18 G n 3 19 A n 3 20 A n 3 21 C n 3 22 U n 3 23 G n 3 24 C n 3 25 C n 3 26 A n 3 27 G n 3 28 G n 3 29 C n 3 30 A n 3 31 U n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample ? ? ? ? Escherichia ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 Escherichia ? ? ? ? ? ? ? ? ? ? ? CYTOSOL ? ? ? ? ? ? ? ? 2 1 sample ? ? ? ? Escherichia ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 Escherichia ? ? ? ? ? HB101 ? ? ? ? ? CYTOSOL ? ? ? ? ? 'PKK5-1 RRNB 5S CISTRON' ? ? 3 1 sample ? ? ? ? Escherichia ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 Escherichia ? ? ? ? ? HB101 ? ? ? ? ? CYTOSOL ? ? ? ? ? 'PKK5-1 RRNB 5S CISTRON' ? ? # 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 HG non-polymer . 'MERCURY (II) ION' ? 'Hg 2' 200.590 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SSU 'RNA linking' n "URIDINE-5'-PHOSPHOROTHIOATE" 'SP-SULFUR-SUBSTITUTED URIDINE' 'C9 H13 N2 O8 P S' 340.247 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 U 1 1 1 U U A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 SSU 5 5 5 SSU SSU A . n A 1 6 G 6 6 6 G G A . n A 1 7 G 7 7 7 G G A . n A 1 8 C 8 8 8 C C A . n A 1 9 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . n B 2 1 C 1 70 70 C C B . n B 2 2 C 2 71 71 C C B . n B 2 3 G 3 72 72 G G B . n B 2 4 A 4 73 73 A A B . n B 2 5 U 5 74 74 U U B . n B 2 6 G 6 75 75 G G B . n B 2 7 G 7 76 76 G G B . n B 2 8 U 8 77 77 U U B . n B 2 9 A 9 78 78 A A B . n B 2 10 G 10 79 79 G G B . n B 2 11 U 11 80 80 U U B . n B 2 12 G 12 81 81 G G B . n B 2 13 U 13 82 82 U U B . n B 2 14 G 14 83 83 G G B . n B 2 15 G 15 84 84 G G B . n B 2 16 G 16 85 85 G G B . n B 2 17 G 17 86 86 G G B . n B 2 18 U 18 87 87 U U B . n B 2 19 C 19 88 88 C C B . n C 3 1 C 1 90 90 C C C . n C 3 2 C 2 91 91 C C C . n C 3 3 C 3 92 92 C C C . n C 3 4 C 4 93 93 C C C . n C 3 5 A 5 94 94 A A C . n C 3 6 U 6 95 95 U U C . n C 3 7 G 7 96 96 G G C . n C 3 8 C 8 97 97 C C C . n C 3 9 G 9 98 98 G G C . n C 3 10 A 10 99 99 A A C . n C 3 11 G 11 100 100 G G C . n C 3 12 A 12 101 101 A A C . n C 3 13 G 13 102 102 G G C . n C 3 14 U 14 103 103 U U C . n C 3 15 A 15 104 104 A A C . n C 3 16 G 16 105 105 G G C . n C 3 17 G 17 106 106 G G C . n C 3 18 G 18 107 107 G G C . n C 3 19 A 19 108 108 A A C . n C 3 20 A 20 109 109 A A C . n C 3 21 C 21 110 110 C C C . n C 3 22 U 22 111 111 U U C . n C 3 23 G 23 112 112 G G C . n C 3 24 C 24 113 113 C C C . n C 3 25 C 25 114 114 C C C . n C 3 26 A 26 115 115 A A C . n C 3 27 G 27 116 116 G G C . n C 3 28 G 28 117 117 G G C . n C 3 29 C 29 118 118 C C C . n C 3 30 A 30 119 119 A A C . n C 3 31 U 31 120 120 U U C . 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 D 4 MG 1 69 69 MG MG A . E 4 MG 1 62 62 MG MG B . F 4 MG 1 66 66 MG MG B . G 5 HG 1 89 89 HG HG B . H 4 MG 1 63 63 MG MG C . I 4 MG 1 64 64 MG MG C . J 4 MG 1 65 65 MG MG C . K 4 MG 1 67 67 MG MG C . L 4 MG 1 68 68 MG MG C . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 C U 120 ? "C5'" ? C U 31 "C5'" 2 1 Y 1 C U 120 ? "C4'" ? C U 31 "C4'" 3 1 Y 1 C U 120 ? "O4'" ? C U 31 "O4'" 4 1 Y 1 C U 120 ? "C3'" ? C U 31 "C3'" 5 1 Y 1 C U 120 ? "O3'" ? C U 31 "O3'" 6 1 Y 1 C U 120 ? "C2'" ? C U 31 "C2'" 7 1 Y 1 C U 120 ? "O2'" ? C U 31 "O2'" 8 1 Y 1 C U 120 ? "C1'" ? C U 31 "C1'" 9 1 Y 1 C U 120 ? N1 ? C U 31 N1 10 1 Y 1 C U 120 ? C2 ? C U 31 C2 11 1 Y 1 C U 120 ? O2 ? C U 31 O2 12 1 Y 1 C U 120 ? N3 ? C U 31 N3 13 1 Y 1 C U 120 ? C4 ? C U 31 C4 14 1 Y 1 C U 120 ? O4 ? C U 31 O4 15 1 Y 1 C U 120 ? C5 ? C U 31 C5 16 1 Y 1 C U 120 ? C6 ? C U 31 C6 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CCP4 'model building' . ? 1 X-PLOR/CNS 'model building' . ? 2 CNS refinement . ? 3 DENZO 'data reduction' . ? 4 SCALEPACK 'data scaling' . ? 5 CCP4 phasing . ? 6 X-PLOR phasing . ? 7 CNS phasing . ? 8 # _cell.entry_id 357D _cell.length_a 58.670 _cell.length_b 58.670 _cell.length_c 248.840 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 357D _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? # _exptl.entry_id 357D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.14 _exptl_crystal.density_percent_sol 59.0000 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.40 _exptl_crystal_grow.pdbx_details 'pH 6.40, VAPOR DIFFUSION' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MGCL2 ? ? ? 1 3 1 'NA MES' ? ? ? 1 4 1 'MG SULFATE' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type FUJI _diffrn_detector.pdbx_collection_date 1996-04-30 _diffrn_detector.details 'SILICON 111 BENDING MIRROR' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X4A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X4A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 357D _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F -3.000 _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 3.500 _reflns.number_obs 6037 _reflns.number_all ? _reflns.percent_possible_obs 99.100 _reflns.pdbx_Rmerge_I_obs 0.057 _reflns.pdbx_Rsym_value 0.057 _reflns.pdbx_netI_over_sigmaI 11.300 _reflns.B_iso_Wilson_estimate 56.60 _reflns.pdbx_redundancy 4.900 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 3.500 _reflns_shell.d_res_low 3.620 _reflns_shell.percent_possible_all 95.10 _reflns_shell.Rmerge_I_obs 0.291 _reflns_shell.pdbx_Rsym_value 0.291 _reflns_shell.meanI_over_sigI_obs 3.700 _reflns_shell.pdbx_redundancy 4.500 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 357D _refine.ls_number_reflns_obs 3374 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF 18352194.500 _refine.pdbx_data_cutoff_low_absF 0.0000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 3.500 _refine.ls_percent_reflns_obs 97.400 _refine.ls_R_factor_obs 0.312 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.312 _refine.ls_R_factor_R_free 0.265 _refine.ls_R_factor_R_free_error 0.017 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 11.00 _refine.ls_number_reflns_R_free 372 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 98.60 _refine.aniso_B[1][1] 6.0500 _refine.aniso_B[2][2] 6.0500 _refine.aniso_B[3][3] -12.00 _refine.aniso_B[1][2] 32.870 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;TARGET FOR REFINEMENT WAS MLHL: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES AND PHASE PROBABILITY DISTRIBUTION FROM THE COMBINED PHASES DESCRIBED BELOW. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ;MAD PHASES FROM A BROMINE WERE COMBINED WITH MAD AND SIRAS PHASES FROM A MERCURY DERIVIATIVE. MLPHARE WAS USED TO CALCULATE THE PHASES WHILE SIGMAA WAS USED TO COMBINE THE THREE PHASES SETS. ; _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_phase_error ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 357D _refine_analyze.Luzzati_coordinate_error_obs 0.54 _refine_analyze.Luzzati_sigma_a_obs 0.55 _refine_analyze.Luzzati_d_res_low_obs 6.00 _refine_analyze.Luzzati_coordinate_error_free 0.64 _refine_analyze.Luzzati_sigma_a_free 0.7 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 1294 _refine_hist.pdbx_number_atoms_ligand 9 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1303 _refine_hist.d_res_high 3.500 _refine_hist.d_res_low 10.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.50 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 29.9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 2.63 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.350 1.500 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 2.340 2.000 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 0.980 2.000 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 1.640 2.500 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 3.50 _refine_ls_shell.d_res_low 3.71 _refine_ls_shell.number_reflns_R_work 442 _refine_ls_shell.R_factor_R_work 0.354 _refine_ls_shell.percent_reflns_obs 91.70 _refine_ls_shell.R_factor_R_free 0.418 _refine_ls_shell.R_factor_R_free_error 0.05 _refine_ls_shell.percent_reflns_R_free 13.20 _refine_ls_shell.number_reflns_R_free 67 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 DNA-RNA-MULTI-ENDO.PARAM DNA-RNA-MULTI-ENDO.TOP 'X-RAY DIFFRACTION' 2 MG.PARAM MG.PARAM 'X-RAY DIFFRACTION' 3 PATCH.PAR PATCH.PAR 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 357D _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 357D _struct.title '3.5 A structure of fragment I from E. coli 5S RRNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 357D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'U-RNA, DOUBLE HELIX, KINKED, INTERNAL LOOP, OVERHANGING BASE, MODIFIED, MISMATCHED, 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 4 ? F N N 4 ? G N N 5 ? H N N 4 ? I N N 4 ? J N N 4 ? K N N 4 ? L N N 4 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 357D 357D ? ? ? 2 2 PDB 357D 357D ? ? ? 3 3 PDB 357D 357D ? ? ? # 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 357D A 1 ? 11 ? 357D 1 ? 11 ? 1 11 2 2 357D B 1 ? 19 ? 357D 70 ? 88 ? 70 88 3 3 357D C 1 ? 31 ? 357D 90 ? 120 ? 90 120 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 4980 ? 1 MORE -93.5 ? 1 'SSA (A^2)' 10800 ? # _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 # _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 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # 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 DC 4 "O3'" ? ? ? 1_555 A SSU 5 P ? ? A DC 4 A SSU 5 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale2 covale both ? A SSU 5 "O3'" ? ? ? 1_555 A G 6 P ? ? A SSU 5 A G 6 1_555 ? ? ? ? ? ? ? 1.603 ? ? metalc1 metalc ? ? E MG . MG ? ? ? 1_555 B G 6 OP2 ? ? B MG 62 B G 75 1_555 ? ? ? ? ? ? ? 2.151 ? ? metalc2 metalc ? ? F MG . MG ? ? ? 1_555 B A 9 OP2 ? ? B MG 66 B A 78 1_555 ? ? ? ? ? ? ? 2.269 ? ? metalc3 metalc ? ? B U 5 OP1 ? ? ? 1_555 H MG . MG ? ? B U 74 C MG 63 1_555 ? ? ? ? ? ? ? 2.212 ? ? metalc4 metalc ? ? I MG . MG ? ? ? 1_555 C G 11 OP2 ? ? C MG 64 C G 100 1_555 ? ? ? ? ? ? ? 2.425 ? ? metalc5 metalc ? ? L MG . MG ? ? ? 1_555 C A 30 OP2 ? ? C MG 68 C A 119 1_555 ? ? ? ? ? ? ? 2.404 ? ? hydrog1 hydrog ? ? A U 1 N3 ? ? ? 1_555 C A 30 N1 ? ? A U 1 C A 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A U 1 O4 ? ? ? 1_555 C A 30 N6 ? ? A U 1 C A 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N1 ? ? ? 1_555 C C 29 N3 ? ? A G 2 C C 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N2 ? ? ? 1_555 C C 29 O2 ? ? A G 2 C C 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 C C 29 N4 ? ? A G 2 C C 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 N3 ? ? ? 1_555 C G 28 N1 ? ? A C 3 C G 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N4 ? ? ? 1_555 C G 28 O6 ? ? A C 3 C G 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 O2 ? ? ? 1_555 C G 28 N2 ? ? A C 3 C G 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 N3 ? ? ? 1_555 C G 27 N1 ? ? A DC 4 C G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C G 27 O6 ? ? A DC 4 C G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 O2 ? ? ? 1_555 C G 27 N2 ? ? A DC 4 C G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A SSU 5 N3 ? ? ? 1_555 C A 26 N1 ? ? A SSU 5 C A 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A SSU 5 O4 ? ? ? 1_555 C A 26 N6 ? ? A SSU 5 C A 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 N1 ? ? ? 1_555 C C 25 N3 ? ? A G 6 C C 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N2 ? ? ? 1_555 C C 25 O2 ? ? A G 6 C C 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 O6 ? ? ? 1_555 C C 25 N4 ? ? A G 6 C C 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N1 ? ? ? 1_555 C C 24 N3 ? ? A G 7 C C 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 N2 ? ? ? 1_555 C C 24 O2 ? ? A G 7 C C 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 7 O6 ? ? ? 1_555 C C 24 N4 ? ? A G 7 C C 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 N3 ? ? ? 1_555 C G 23 N1 ? ? A C 8 C G 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 8 N4 ? ? ? 1_555 C G 23 O6 ? ? A C 8 C G 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 8 O2 ? ? ? 1_555 C G 23 N2 ? ? A C 8 C G 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N1 ? ? ? 1_555 C U 22 O2 ? ? A G 9 C U 111 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog24 hydrog ? ? A G 9 O6 ? ? ? 1_555 C U 22 N3 ? ? A G 9 C U 111 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog25 hydrog ? ? A G 10 N1 ? ? ? 1_555 C C 21 N3 ? ? A G 10 C C 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 10 N2 ? ? ? 1_555 C C 21 O2 ? ? A G 10 C C 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 10 O6 ? ? ? 1_555 C C 21 N4 ? ? A G 10 C C 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 11 O2 ? ? ? 1_555 C A 20 N6 ? ? A C 11 C A 109 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog29 hydrog ? ? B C 1 N3 ? ? ? 1_555 C G 17 N1 ? ? B C 70 C G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B C 1 N4 ? ? ? 1_555 C G 17 O6 ? ? B C 70 C G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 1 O2 ? ? ? 1_555 C G 17 N2 ? ? B C 70 C G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B C 2 N3 ? ? ? 1_555 C G 16 N1 ? ? B C 71 C G 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B C 2 N4 ? ? ? 1_555 C G 16 O6 ? ? B C 71 C G 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B C 2 O2 ? ? ? 1_555 C G 16 N2 ? ? B C 71 C G 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 3 N2 ? ? ? 1_555 C A 15 N7 ? ? B G 72 C A 104 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog36 hydrog ? ? B G 3 N3 ? ? ? 1_555 C A 15 N6 ? ? B G 72 C A 104 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog37 hydrog ? ? B U 5 O4 ? ? ? 1_555 C G 13 N1 ? ? B U 74 C G 102 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog38 hydrog ? ? B U 5 O4 ? ? ? 1_555 C U 14 N3 ? ? B U 74 C U 103 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog39 hydrog ? ? B G 6 O6 ? ? ? 1_555 C G 13 N1 ? ? B G 75 C G 102 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog40 hydrog ? ? B G 7 N2 ? ? ? 1_555 C A 12 N1 ? ? B G 76 C A 101 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog41 hydrog ? ? B U 8 O4 ? ? ? 1_555 C G 9 N2 ? ? B U 77 C G 98 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog42 hydrog ? ? B U 8 N3 ? ? ? 1_555 C G 11 O6 ? ? B U 77 C G 100 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog43 hydrog ? ? B A 9 N6 ? ? ? 1_555 C G 9 N3 ? ? B A 78 C G 98 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog44 hydrog ? ? B A 9 N7 ? ? ? 1_555 C G 9 N2 ? ? B A 78 C G 98 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog45 hydrog ? ? B G 10 N1 ? ? ? 1_555 C C 8 N3 ? ? B G 79 C C 97 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? B G 10 N2 ? ? ? 1_555 C C 8 O2 ? ? B G 79 C C 97 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? B G 10 O6 ? ? ? 1_555 C C 8 N4 ? ? B G 79 C C 97 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? B G 10 O6 ? ? ? 1_555 C G 9 N1 ? ? B G 79 C G 98 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog49 hydrog ? ? B U 11 N3 ? ? ? 1_555 C G 7 O6 ? ? B U 80 C G 96 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog50 hydrog ? ? B U 11 O2 ? ? ? 1_555 C G 7 N1 ? ? B U 80 C G 96 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog51 hydrog ? ? B G 12 N1 ? ? ? 1_555 C U 6 O2 ? ? B G 81 C U 95 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog52 hydrog ? ? B G 12 O6 ? ? ? 1_555 C U 6 N3 ? ? B G 81 C U 95 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog53 hydrog ? ? B U 13 N3 ? ? ? 1_555 C A 5 N1 ? ? B U 82 C A 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? B U 13 O4 ? ? ? 1_555 C A 5 N6 ? ? B U 82 C A 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? B G 14 N1 ? ? ? 1_555 C C 4 N3 ? ? B G 83 C C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? B G 14 N2 ? ? ? 1_555 C C 4 O2 ? ? B G 83 C C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? B G 14 O6 ? ? ? 1_555 C C 4 N4 ? ? B G 83 C C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? B G 15 N1 ? ? ? 1_555 C C 3 N3 ? ? B G 84 C C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? B G 15 N2 ? ? ? 1_555 C C 3 O2 ? ? B G 84 C C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? B G 15 O6 ? ? ? 1_555 C C 3 N4 ? ? B G 84 C C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? B G 15 N1 ? ? ? 1_555 C C 4 N3 ? ? B G 84 C C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? B G 15 N2 ? ? ? 1_555 C C 4 O2 ? ? B G 84 C C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? B G 15 O6 ? ? ? 1_555 C C 4 N4 ? ? B G 84 C C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? B G 16 N1 ? ? ? 1_555 C C 2 N3 ? ? B G 85 C C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? B G 16 N2 ? ? ? 1_555 C C 2 O2 ? ? B G 85 C C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? B G 16 O6 ? ? ? 1_555 C C 2 N4 ? ? B G 85 C C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? B G 17 N1 ? ? ? 1_555 C C 1 N3 ? ? B G 86 C C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? B G 17 N2 ? ? ? 1_555 C C 1 O2 ? ? B G 86 C C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? B G 17 O6 ? ? ? 1_555 C C 1 N4 ? ? B G 86 C C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # 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 B MG 62 ? 2 'BINDING SITE FOR RESIDUE MG B 62' AC2 Software C MG 63 ? 2 'BINDING SITE FOR RESIDUE MG C 63' AC3 Software C MG 64 ? 1 'BINDING SITE FOR RESIDUE MG C 64' AC4 Software C MG 65 ? 1 'BINDING SITE FOR RESIDUE MG C 65' AC5 Software B MG 66 ? 2 'BINDING SITE FOR RESIDUE MG B 66' AC6 Software C MG 68 ? 1 'BINDING SITE FOR RESIDUE MG C 68' AC7 Software B HG 89 ? 2 'BINDING SITE FOR RESIDUE HG B 89' # 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 B 6 ? G B 75 . ? 1_555 ? 2 AC1 2 A C 10 ? A C 99 . ? 1_555 ? 3 AC2 2 U B 5 ? U B 74 . ? 1_555 ? 4 AC2 2 A C 10 ? A C 99 . ? 1_555 ? 5 AC3 1 G C 11 ? G C 100 . ? 1_555 ? 6 AC4 1 G C 9 ? G C 98 . ? 1_555 ? 7 AC5 2 A B 9 ? A B 78 . ? 1_555 ? 8 AC5 2 G B 10 ? G B 79 . ? 1_555 ? 9 AC6 1 A C 30 ? A C 119 . ? 1_555 ? 10 AC7 2 A B 4 ? A B 73 . ? 1_555 ? 11 AC7 2 U B 5 ? U B 74 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 110.64 108.30 2.34 0.30 N 2 1 "C2'" B C 88 ? ? "C3'" B C 88 ? ? "O3'" B C 88 ? ? 123.86 113.70 10.16 1.60 N 3 1 N1 B C 88 ? ? "C1'" B C 88 ? ? "C2'" B C 88 ? ? 124.45 114.00 10.45 1.30 N # _pdbx_validate_chiral.id 1 _pdbx_validate_chiral.PDB_model_num 1 _pdbx_validate_chiral.auth_atom_id "C2'" _pdbx_validate_chiral.label_alt_id ? _pdbx_validate_chiral.auth_asym_id C _pdbx_validate_chiral.auth_comp_id A _pdbx_validate_chiral.auth_seq_id 119 _pdbx_validate_chiral.PDB_ins_code ? _pdbx_validate_chiral.details PLANAR _pdbx_validate_chiral.omega . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id SSU _pdbx_struct_mod_residue.label_seq_id 5 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id SSU _pdbx_struct_mod_residue.auth_seq_id 5 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id U _pdbx_struct_mod_residue.details "URIDINE-5'-PHOSPHOROTHIOATE" # 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 HG HG HG N N 145 MG MG MG N N 146 SSU "O2'" O N N 147 SSU "C2'" C N R 148 SSU "C1'" C N R 149 SSU "O4'" O N N 150 SSU "C4'" C N R 151 SSU "C5'" C N N 152 SSU "O5'" O N N 153 SSU P P N N 154 SSU S1P S N N 155 SSU OP2 O N N 156 SSU OP3 O N N 157 SSU "C3'" C N S 158 SSU "O3'" O N N 159 SSU N1 N N N 160 SSU C6 C N N 161 SSU C5 C N N 162 SSU C4 C N N 163 SSU O4 O N N 164 SSU N3 N N N 165 SSU C2 C N N 166 SSU O2 O N N 167 SSU "HO2'" H N N 168 SSU "H2'" H N N 169 SSU "H1'" H N N 170 SSU "H4'" H N N 171 SSU "H5'" H N N 172 SSU "H5''" H N N 173 SSU H2P H N N 174 SSU H3P H N N 175 SSU "H3'" H N N 176 SSU "HO3'" H N N 177 SSU H6 H N N 178 SSU H5 H N N 179 SSU H3 H N N 180 U OP3 O N N 181 U P P N N 182 U OP1 O N N 183 U OP2 O N N 184 U "O5'" O N N 185 U "C5'" C N N 186 U "C4'" C N R 187 U "O4'" O N N 188 U "C3'" C N S 189 U "O3'" O N N 190 U "C2'" C N R 191 U "O2'" O N N 192 U "C1'" C N R 193 U N1 N N N 194 U C2 C N N 195 U O2 O N N 196 U N3 N N N 197 U C4 C N N 198 U O4 O N N 199 U C5 C N N 200 U C6 C N N 201 U HOP3 H N N 202 U HOP2 H N N 203 U "H5'" H N N 204 U "H5''" H N N 205 U "H4'" H N N 206 U "H3'" H N N 207 U "HO3'" H N N 208 U "H2'" H N N 209 U "HO2'" H N N 210 U "H1'" H N N 211 U H3 H N N 212 U H5 H N N 213 U H6 H N N 214 # 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 SSU "O2'" "C2'" sing N N 151 SSU "O2'" "HO2'" sing N N 152 SSU "C2'" "C1'" sing N N 153 SSU "C2'" "C3'" sing N N 154 SSU "C2'" "H2'" sing N N 155 SSU "C1'" "O4'" sing N N 156 SSU "C1'" N1 sing N N 157 SSU "C1'" "H1'" sing N N 158 SSU "O4'" "C4'" sing N N 159 SSU "C4'" "C5'" sing N N 160 SSU "C4'" "C3'" sing N N 161 SSU "C4'" "H4'" sing N N 162 SSU "C5'" "O5'" sing N N 163 SSU "C5'" "H5'" sing N N 164 SSU "C5'" "H5''" sing N N 165 SSU "O5'" P sing N N 166 SSU P S1P doub N N 167 SSU P OP2 sing N N 168 SSU P OP3 sing N N 169 SSU OP2 H2P sing N N 170 SSU OP3 H3P sing N N 171 SSU "C3'" "O3'" sing N N 172 SSU "C3'" "H3'" sing N N 173 SSU "O3'" "HO3'" sing N N 174 SSU N1 C6 sing N N 175 SSU N1 C2 sing N N 176 SSU C6 C5 doub N N 177 SSU C6 H6 sing N N 178 SSU C5 C4 sing N N 179 SSU C5 H5 sing N N 180 SSU C4 O4 doub N N 181 SSU C4 N3 sing N N 182 SSU N3 C2 sing N N 183 SSU N3 H3 sing N N 184 SSU C2 O2 doub N N 185 U OP3 P sing N N 186 U OP3 HOP3 sing N N 187 U P OP1 doub N N 188 U P OP2 sing N N 189 U P "O5'" sing N N 190 U OP2 HOP2 sing N N 191 U "O5'" "C5'" sing N N 192 U "C5'" "C4'" sing N N 193 U "C5'" "H5'" sing N N 194 U "C5'" "H5''" sing N N 195 U "C4'" "O4'" sing N N 196 U "C4'" "C3'" sing N N 197 U "C4'" "H4'" sing N N 198 U "O4'" "C1'" sing N N 199 U "C3'" "O3'" sing N N 200 U "C3'" "C2'" sing N N 201 U "C3'" "H3'" sing N N 202 U "O3'" "HO3'" sing N N 203 U "C2'" "O2'" sing N N 204 U "C2'" "C1'" sing N N 205 U "C2'" "H2'" sing N N 206 U "O2'" "HO2'" sing N N 207 U "C1'" N1 sing N N 208 U "C1'" "H1'" sing N N 209 U N1 C2 sing N N 210 U N1 C6 sing N N 211 U C2 O2 doub N N 212 U C2 N3 sing N N 213 U N3 C4 sing N N 214 U N3 H3 sing N N 215 U C4 O4 doub N N 216 U C4 C5 sing N N 217 U C5 C6 doub N N 218 U C5 H5 sing N N 219 U C6 H6 sing N N 220 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 357D 'double helix' 357D 'a-form double helix' 357D 'bulge loop' 357D '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 1 1_555 C A 30 1_555 -0.424 -0.280 -0.564 -9.419 -15.173 10.276 1 A_U1:A119_C A 1 ? C 119 ? 20 1 1 A G 2 1_555 C C 29 1_555 0.359 -0.142 -0.160 5.929 7.742 0.526 2 A_G2:C118_C A 2 ? C 118 ? 19 1 1 A C 3 1_555 C G 28 1_555 0.329 -0.419 -0.584 16.218 -11.404 -3.280 3 A_C3:G117_C A 3 ? C 117 ? 19 1 1 A DC 4 1_555 C G 27 1_555 0.190 -0.068 0.137 -3.936 11.959 5.739 4 A_DC4:G116_C A 4 ? C 116 ? 19 1 1 A SSU 5 1_555 C A 26 1_555 0.028 -0.059 -0.740 8.022 -28.098 7.951 5 A_SSU5:A115_C A 5 ? C 115 ? 20 1 1 A G 6 1_555 C C 25 1_555 0.205 -0.059 -0.328 -3.066 -13.431 -0.815 6 A_G6:C114_C A 6 ? C 114 ? 19 1 1 A G 7 1_555 C C 24 1_555 -0.536 -0.050 -0.152 4.079 13.606 5.153 7 A_G7:C113_C A 7 ? C 113 ? 19 1 1 A C 8 1_555 C G 23 1_555 -0.041 -0.347 -1.169 0.586 8.787 -8.732 8 A_C8:G112_C A 8 ? C 112 ? 19 1 1 A G 9 1_555 C U 22 1_555 -1.858 -0.516 1.127 4.771 1.253 -18.562 9 A_G9:U111_C A 9 ? C 111 ? 28 ? 1 A G 10 1_555 C C 21 1_555 -0.135 -0.154 0.334 -4.021 -16.698 -3.115 10 A_G10:C110_C A 10 ? C 110 ? 19 1 1 A C 11 1_555 C A 20 1_555 2.689 -3.272 1.224 -20.556 2.289 -95.474 11 A_C11:A109_C A 11 ? C 109 ? ? ? 1 B C 1 1_555 C G 17 1_555 0.340 -0.043 0.398 -4.289 3.101 -2.990 12 B_C70:G106_C B 70 ? C 106 ? 19 1 1 B C 2 1_555 C G 16 1_555 0.271 -0.242 0.242 -3.242 3.594 1.446 13 B_C71:G105_C B 71 ? C 105 ? 19 1 1 B G 3 1_555 C A 15 1_555 7.049 -4.307 -0.487 -6.572 -6.558 -4.881 14 B_G72:A104_C B 72 ? C 104 ? 11 10 1 B U 5 1_555 C G 13 1_555 -3.390 1.313 -0.845 -2.323 24.874 -86.588 15 B_U74:G102_C B 74 ? C 102 ? ? ? 1 B G 7 1_555 C A 12 1_555 2.328 0.999 1.173 20.226 16.292 -21.710 16 B_G76:A101_C B 76 ? C 101 ? ? ? 1 B U 8 1_555 C G 11 1_555 3.809 -1.310 -0.687 32.387 -19.859 -38.363 17 B_U77:G100_C B 77 ? C 100 ? ? ? 1 B A 9 1_555 C G 9 1_555 -6.548 -3.895 0.655 -0.610 15.403 -5.768 18 B_A78:G98_C B 78 ? C 98 ? 11 10 1 B G 10 1_555 C C 8 1_555 0.099 -0.344 0.143 7.400 34.735 5.401 19 B_G79:C97_C B 79 ? C 97 ? 19 1 1 B U 11 1_555 C G 7 1_555 3.233 -0.714 -0.042 4.993 22.876 4.730 20 B_U80:G96_C B 80 ? C 96 ? 28 ? 1 B G 12 1_555 C U 6 1_555 -1.671 -0.334 -0.041 -3.406 -2.996 -0.418 21 B_G81:U95_C B 81 ? C 95 ? 28 1 1 B U 13 1_555 C A 5 1_555 -0.342 0.019 -0.583 5.307 -13.162 8.134 22 B_U82:A94_C B 82 ? C 94 ? 20 1 1 B G 14 1_555 C C 4 1_555 -0.510 -0.402 -0.879 -12.183 -16.178 -1.082 23 B_G83:C93_C B 83 ? C 93 ? 19 1 1 B G 15 1_555 C C 3 1_555 -0.559 -0.294 -0.261 6.098 4.174 -5.300 24 B_G84:C92_C B 84 ? C 92 ? 19 1 1 B G 16 1_555 C C 2 1_555 -0.510 -0.198 0.415 7.792 -8.519 -5.575 25 B_G85:C91_C B 85 ? C 91 ? 19 1 1 B G 17 1_555 C C 1 1_555 0.091 0.178 -0.432 -9.693 -7.692 3.611 26 B_G86:C90_C B 86 ? C 90 ? 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 U 1 1_555 C A 30 1_555 A G 2 1_555 C C 29 1_555 -0.174 -1.882 3.534 -11.693 -6.697 18.635 -1.908 -4.487 3.507 -17.949 31.340 22.962 1 AA_U1G2:C118A119_CC A 1 ? C 119 ? A 2 ? C 118 ? 1 A G 2 1_555 C C 29 1_555 A C 3 1_555 C G 28 1_555 -1.245 -2.271 2.872 1.204 1.195 28.651 -4.813 2.744 2.724 2.413 -2.430 28.701 2 AA_G2C3:G117C118_CC A 2 ? C 118 ? A 3 ? C 117 ? 1 A C 3 1_555 C G 28 1_555 A DC 4 1_555 C G 27 1_555 -0.320 -2.628 3.653 -9.336 14.740 29.832 -6.631 -0.849 2.161 26.020 16.481 34.460 3 AA_C3DC4:G116G117_CC A 3 ? C 117 ? A 4 ? C 116 ? 1 A DC 4 1_555 C G 27 1_555 A SSU 5 1_555 C A 26 1_555 -0.168 -1.292 2.877 11.360 9.267 34.520 -3.021 1.496 2.302 14.817 -18.163 37.417 4 AA_DC4SSU5:A115G116_CC A 4 ? C 116 ? A 5 ? C 115 ? 1 A SSU 5 1_555 C A 26 1_555 A G 6 1_555 C C 25 1_555 -0.286 -0.848 3.631 -5.516 14.164 32.729 -3.529 -0.378 3.029 23.613 9.197 35.999 5 AA_SSU5G6:C114A115_CC A 5 ? C 115 ? A 6 ? C 114 ? 1 A G 6 1_555 C C 25 1_555 A G 7 1_555 C C 24 1_555 0.067 -1.682 2.812 -5.185 10.535 24.901 -5.502 -1.107 1.905 22.878 11.260 27.491 6 AA_G6G7:C113C114_CC A 6 ? C 114 ? A 7 ? C 113 ? 1 A G 7 1_555 C C 24 1_555 A C 8 1_555 C G 23 1_555 -0.092 -2.088 3.431 8.011 5.059 34.784 -4.099 1.291 3.014 8.274 -13.101 36.013 7 AA_G7C8:G112C113_CC A 7 ? C 113 ? A 8 ? C 112 ? 1 A C 8 1_555 C G 23 1_555 A G 9 1_555 C U 22 1_555 0.181 -3.495 3.279 -9.545 -8.277 14.238 -5.214 -6.733 3.884 -27.369 31.558 19.013 8 AA_C8G9:U111G112_CC A 8 ? C 112 ? A 9 ? C 111 ? 1 A G 9 1_555 C U 22 1_555 A G 10 1_555 C C 21 1_555 0.792 -2.209 3.207 4.447 9.821 39.393 -4.161 -0.687 2.674 14.248 -6.452 40.785 9 AA_G9G10:C110U111_CC A 9 ? C 111 ? A 10 ? C 110 ? 1 A G 10 1_555 C C 21 1_555 A C 11 1_555 C A 20 1_555 1.126 -1.257 3.317 8.781 3.097 115.652 -0.775 -0.570 3.346 1.828 -5.183 115.890 10 AA_G10C11:A109C110_CC A 10 ? C 110 ? A 11 ? C 109 ? 1 B C 1 1_555 C G 17 1_555 B C 2 1_555 C G 16 1_555 -0.799 -3.105 2.784 -0.553 1.984 29.734 -6.378 1.459 2.590 3.860 1.075 29.804 11 BB_C70C71:G105G106_CC B 70 ? C 106 ? B 71 ? C 105 ? 1 B C 2 1_555 C G 16 1_555 B G 3 1_555 C A 15 1_555 -0.638 -0.994 3.706 5.462 -1.317 61.102 -0.904 0.916 3.661 -1.293 -5.361 61.335 12 BB_C71G72:A104G105_CC B 71 ? C 105 ? B 72 ? C 104 ? 1 B U 5 1_555 C G 13 1_555 B G 7 1_555 C A 12 1_555 1.351 -2.814 4.948 3.690 -21.092 68.313 -1.221 -0.951 5.566 -18.332 -3.207 71.200 13 BB_U74G76:A101G102_CC B 74 ? C 102 ? B 76 ? C 101 ? 1 B G 7 1_555 C A 12 1_555 B U 8 1_555 C G 11 1_555 0.511 -0.704 2.888 24.396 15.480 37.055 -2.062 1.205 2.349 20.913 -32.957 46.674 14 BB_G76U77:G100A101_CC B 76 ? C 101 ? B 77 ? C 100 ? 1 B A 9 1_555 C G 9 1_555 B G 10 1_555 C C 8 1_555 0.473 -1.424 2.491 -2.750 8.543 58.624 -1.758 -0.580 2.260 8.669 2.790 59.247 15 BB_A78G79:C97G98_CC B 78 ? C 98 ? B 79 ? C 97 ? 1 B G 10 1_555 C C 8 1_555 B U 11 1_555 C G 7 1_555 -0.763 -2.672 3.215 1.600 -0.829 39.765 -3.830 1.304 3.236 -1.218 -2.350 39.804 16 BB_G79U80:G96C97_CC B 79 ? C 97 ? B 80 ? C 96 ? 1 B U 11 1_555 C G 7 1_555 B G 12 1_555 C U 6 1_555 -0.640 -3.435 3.262 1.357 2.727 8.458 -27.090 6.658 1.933 17.753 -8.831 8.989 17 BB_U80G81:U95G96_CC B 80 ? C 96 ? B 81 ? C 95 ? 1 B G 12 1_555 C U 6 1_555 B U 13 1_555 C A 5 1_555 0.247 -1.467 3.237 4.746 4.057 34.788 -2.998 0.274 3.058 6.719 -7.860 35.327 18 BB_G81U82:A94U95_CC B 81 ? C 95 ? B 82 ? C 94 ? 1 B U 13 1_555 C A 5 1_555 B G 14 1_555 C C 4 1_555 -1.030 -1.256 4.086 -0.566 9.226 23.544 -6.050 2.160 3.381 21.574 1.324 25.270 19 BB_U82G83:C93A94_CC B 82 ? C 94 ? B 83 ? C 93 ? 1 B G 14 1_555 C C 4 1_555 B G 15 1_555 C C 3 1_555 0.131 -2.037 2.729 -8.189 8.214 40.974 -3.452 -0.823 2.233 11.460 11.426 42.516 20 BB_G83G84:C92C93_CC B 83 ? C 93 ? B 84 ? C 92 ? 1 B G 15 1_555 C C 3 1_555 B G 16 1_555 C C 2 1_555 0.660 -2.071 3.125 -3.354 -3.811 24.810 -3.631 -2.469 3.284 -8.753 7.704 25.316 21 BB_G84G85:C91C92_CC B 84 ? C 92 ? B 85 ? C 91 ? 1 B G 16 1_555 C C 2 1_555 B G 17 1_555 C C 1 1_555 0.303 -2.536 3.688 15.389 7.266 32.708 -5.086 1.776 2.929 11.947 -25.306 36.763 22 BB_G85G86:C90C91_CC B 85 ? C 91 ? B 86 ? C 90 ? # _atom_sites.entry_id 357D _atom_sites.fract_transf_matrix[1][1] 0.017044 _atom_sites.fract_transf_matrix[1][2] 0.009841 _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] 0.019681 _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] 0.004019 _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 HG MG N O P S # loop_