data_364D # _entry.id 364D # _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 364D pdb_0000364d 10.2210/pdb364d/pdb RCSB URL069 ? ? WWPDB D_1000178834 ? ? # 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 1998-01-02 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_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.pdb_id 364D _pdbx_database_PDB_obs_spr.replace_pdb_id 356D _pdbx_database_PDB_obs_spr.date 1998-01-02 _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 364D _pdbx_database_status.recvd_initial_deposition_date 1997-12-08 _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 (5'-R(*UP*GP*)-D(*(1SC)P*)-R(*CP*UP*GP*GP*CP*GP*GP*C)-3') ; 3530.195 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 12 ? ? ? ? 5 water nat water 18.015 4 ? ? ? ? # 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(1SC)UGGCGGC' 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 water HOH # 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 1SC n 1 5 U 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 1SC 'RNA linking' n "5'-O-THIOPHOSPHONOCYTIDINE" ? 'C9 H14 N3 O7 P S' 339.262 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 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 1SC 4 4 4 1SC +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 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 1 207 207 MG MG A . E 4 MG 1 210 210 MG MG A . F 4 MG 1 201 201 MG MG B . G 4 MG 1 214 214 MG MG B . H 4 MG 1 202 202 MG MG C . I 4 MG 1 204 204 MG MG C . J 4 MG 1 205 205 MG MG C . K 4 MG 1 208 208 MG MG C . L 4 MG 1 209 209 MG MG C . M 4 MG 1 211 211 MG MG C . N 4 MG 1 213 213 MG MG C . O 4 MG 1 216 216 MG MG C . P 5 HOH 1 301 301 HOH HOH B . Q 5 HOH 1 302 302 HOH HOH C . Q 5 HOH 2 303 303 HOH HOH C . Q 5 HOH 3 304 304 HOH HOH 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 0 A C 3 ? "O2'" ? A C 3 "O2'" 2 1 Y 1 C U 120 ? "C5'" ? C U 31 "C5'" 3 1 Y 1 C U 120 ? "C4'" ? C U 31 "C4'" 4 1 Y 1 C U 120 ? "O4'" ? C U 31 "O4'" 5 1 Y 1 C U 120 ? "C3'" ? C U 31 "C3'" 6 1 Y 1 C U 120 ? "O3'" ? C U 31 "O3'" 7 1 Y 1 C U 120 ? "C2'" ? C U 31 "C2'" 8 1 Y 1 C U 120 ? "O2'" ? C U 31 "O2'" 9 1 Y 1 C U 120 ? "C1'" ? C U 31 "C1'" 10 1 Y 1 C U 120 ? N1 ? C U 31 N1 11 1 Y 1 C U 120 ? C2 ? C U 31 C2 12 1 Y 1 C U 120 ? O2 ? C U 31 O2 13 1 Y 1 C U 120 ? N3 ? C U 31 N3 14 1 Y 1 C U 120 ? C4 ? C U 31 C4 15 1 Y 1 C U 120 ? O4 ? C U 31 O4 16 1 Y 1 C U 120 ? C5 ? C U 31 C5 17 1 Y 1 C U 120 ? C6 ? C U 31 C6 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 CNS refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 X-PLOR phasing . ? 5 # _cell.entry_id 364D _cell.length_a 59.030 _cell.length_b 59.030 _cell.length_c 254.070 _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 364D _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 364D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.24 _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 CCD _diffrn_detector.type 'PRINCETON 2K' _diffrn_detector.pdbx_collection_date 1995-03-28 _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 ? _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 'CHESS BEAMLINE A1' _diffrn_source.pdbx_synchrotron_site CHESS _diffrn_source.pdbx_synchrotron_beamline A1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 364D _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F -3.000 _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 2.980 _reflns.number_obs 4950 _reflns.number_all ? _reflns.percent_possible_obs 82.500 _reflns.pdbx_Rmerge_I_obs 0.047 _reflns.pdbx_Rsym_value 0.047 _reflns.pdbx_netI_over_sigmaI 10.400 _reflns.B_iso_Wilson_estimate 87.70 _reflns.pdbx_redundancy 3.900 _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 2.980 _reflns_shell.d_res_low 3.090 _reflns_shell.percent_possible_all 47.50 _reflns_shell.Rmerge_I_obs 0.372 _reflns_shell.pdbx_Rsym_value 0.37 _reflns_shell.meanI_over_sigI_obs 2.000 _reflns_shell.pdbx_redundancy 2.000 _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 364D _refine.ls_number_reflns_obs 4668 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF 525997.650 _refine.pdbx_data_cutoff_low_absF 0.0000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.000 _refine.ls_d_res_high 3.000 _refine.ls_percent_reflns_obs 80.100 _refine.ls_R_factor_obs 0.272 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.272 _refine.ls_R_factor_R_free 0.324 _refine.ls_R_factor_R_free_error 0.015 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.90 _refine.ls_number_reflns_R_free 510 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 83.50 _refine.aniso_B[1][1] 10.540 _refine.aniso_B[2][2] 10.540 _refine.aniso_B[3][3] -21.10 _refine.aniso_B[1][2] 18.910 _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 MLF: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _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_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 364D _refine_analyze.Luzzati_coordinate_error_obs 0.54 _refine_analyze.Luzzati_sigma_a_obs 0.52 _refine_analyze.Luzzati_d_res_low_obs 20.0 _refine_analyze.Luzzati_coordinate_error_free 0.74 _refine_analyze.Luzzati_sigma_a_free 0.8 _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 1295 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 4 _refine_hist.number_atoms_total 1313 _refine_hist.d_res_high 3.000 _refine_hist.d_res_low 20.000 # 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 0.007 ? ? ? '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 1.10 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 29.7 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 2.24 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.930 1.500 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 3.180 2.000 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 1.920 2.000 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 3.210 2.500 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 3.00 _refine_ls_shell.d_res_low 3.19 _refine_ls_shell.number_reflns_R_work 392 _refine_ls_shell.R_factor_R_work 0.402 _refine_ls_shell.percent_reflns_obs 47.60 _refine_ls_shell.R_factor_R_free 0.502 _refine_ls_shell.R_factor_R_free_error 0.07 _refine_ls_shell.percent_reflns_R_free 5.10 _refine_ls_shell.number_reflns_R_free 47 _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? # 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 364D _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 364D _struct.title '3.0 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 364D _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 4 ? H N N 4 ? I N N 4 ? J N N 4 ? K N N 4 ? L N N 4 ? M N N 4 ? N N N 4 ? O N N 4 ? P N N 5 ? Q N N 5 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 1 PDB 364D 364D ? ? ? 2 2 PDB 364D 364D ? ? ? 3 3 PDB 364D 364D ? ? ? # 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 364D A 1 ? 11 ? 364D 1 ? 11 ? 1 11 2 2 364D B 1 ? 19 ? 364D 70 ? 88 ? 70 88 3 3 364D C 1 ? 31 ? 364D 90 ? 120 ? 90 120 # _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 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q # _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.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 C 3 "O3'" ? ? ? 1_555 A 1SC 4 P ? ? A C 3 A 1SC 4 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale2 covale one ? A 1SC 4 "O3'" ? ? ? 1_555 A U 5 P ? ? A 1SC 4 A U 5 1_555 ? ? ? ? ? ? ? 1.600 ? ? metalc1 metalc ? ? B U 5 OP1 ? ? ? 1_555 H MG . MG ? ? B U 74 C MG 202 1_555 ? ? ? ? ? ? ? 2.198 ? ? metalc2 metalc ? ? B G 6 OP2 ? ? ? 1_555 F MG . MG ? ? B G 75 B MG 201 1_555 ? ? ? ? ? ? ? 2.100 ? ? metalc3 metalc ? ? F MG . MG ? ? ? 1_555 C A 10 OP2 ? ? B MG 201 C A 99 1_555 ? ? ? ? ? ? ? 2.325 ? ? metalc4 metalc ? ? G MG . MG ? ? ? 1_555 O MG . MG ? ? B MG 214 C MG 216 1_555 ? ? ? ? ? ? ? 3.009 ? ? metalc5 metalc ? ? C U 6 OP2 ? ? ? 1_555 N MG . MG ? ? C U 95 C MG 213 1_555 ? ? ? ? ? ? ? 2.059 ? ? metalc6 metalc ? ? C G 9 O6 ? ? ? 1_555 J MG . MG ? ? C G 98 C MG 205 1_555 ? ? ? ? ? ? ? 2.430 ? ? metalc7 metalc ? ? C A 10 OP1 ? ? ? 1_555 H MG . MG ? ? C A 99 C MG 202 1_555 ? ? ? ? ? ? ? 2.918 ? ? metalc8 metalc ? ? C G 11 OP2 ? ? ? 1_555 I MG . MG ? ? C G 100 C MG 204 1_555 ? ? ? ? ? ? ? 2.473 ? ? metalc9 metalc ? ? C G 17 N7 ? ? ? 1_555 L MG . MG ? ? C G 106 C MG 209 1_555 ? ? ? ? ? ? ? 3.108 ? ? 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 1SC 4 N3 ? ? ? 1_555 C G 27 N1 ? ? A 1SC 4 C G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 1SC 4 N4 ? ? ? 1_555 C G 27 O6 ? ? A 1SC 4 C G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A 1SC 4 O2 ? ? ? 1_555 C G 27 N2 ? ? A 1SC 4 C G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 5 N3 ? ? ? 1_555 C A 26 N1 ? ? A U 5 C A 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 5 O4 ? ? ? 1_555 C A 26 N6 ? ? A U 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 O6 ? ? ? 1_555 C A 20 N6 ? ? A G 10 C A 109 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog26 hydrog ? ? A G 10 N1 ? ? ? 1_555 C C 21 N3 ? ? A G 10 C C 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 10 N2 ? ? ? 1_555 C C 21 O2 ? ? A G 10 C C 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 10 O6 ? ? ? 1_555 C C 21 N4 ? ? A G 10 C C 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 11 O2 ? ? ? 1_555 C A 20 N6 ? ? A C 11 C A 109 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog30 hydrog ? ? B C 1 N3 ? ? ? 1_555 C G 17 N1 ? ? B C 70 C G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 1 N4 ? ? ? 1_555 C G 17 O6 ? ? B C 70 C G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B C 1 O2 ? ? ? 1_555 C G 17 N2 ? ? B C 70 C G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B C 2 N3 ? ? ? 1_555 C G 16 N1 ? ? B C 71 C G 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B C 2 N4 ? ? ? 1_555 C G 16 O6 ? ? B C 71 C G 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B C 2 O2 ? ? ? 1_555 C G 16 N2 ? ? B C 71 C G 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B G 3 N2 ? ? ? 1_555 C A 15 N7 ? ? B G 72 C A 104 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog37 hydrog ? ? B G 3 N3 ? ? ? 1_555 C A 15 N6 ? ? B G 72 C A 104 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog38 hydrog ? ? B A 4 N6 ? ? ? 1_555 C U 14 O2 ? ? B A 73 C U 103 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog39 hydrog ? ? B A 4 N7 ? ? ? 1_555 C U 14 N3 ? ? B A 73 C U 103 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog40 hydrog ? ? B U 5 O4 ? ? ? 1_555 C G 13 N1 ? ? B U 74 C G 102 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog41 hydrog ? ? B U 5 O4 ? ? ? 1_555 C U 14 N3 ? ? B U 74 C U 103 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog42 hydrog ? ? B G 6 O6 ? ? ? 1_555 C A 12 N6 ? ? B G 75 C A 101 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog43 hydrog ? ? B G 7 N1 ? ? ? 1_555 C G 11 O6 ? ? B G 76 C G 100 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog44 hydrog ? ? B G 7 N2 ? ? ? 1_555 C A 12 N1 ? ? B G 76 C A 101 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog45 hydrog ? ? B U 8 O4 ? ? ? 1_555 C G 9 N2 ? ? B U 77 C G 98 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog46 hydrog ? ? B U 8 N3 ? ? ? 1_555 C A 10 N7 ? ? B U 77 C A 99 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog47 hydrog ? ? B U 8 O2 ? ? ? 1_555 C A 10 N6 ? ? B U 77 C A 99 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog48 hydrog ? ? B A 9 N6 ? ? ? 1_555 C G 9 N3 ? ? B A 78 C G 98 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog49 hydrog ? ? B A 9 N7 ? ? ? 1_555 C G 9 N2 ? ? B A 78 C G 98 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog50 hydrog ? ? B G 10 N1 ? ? ? 1_555 C C 8 N3 ? ? B G 79 C C 97 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? B G 10 N2 ? ? ? 1_555 C C 8 O2 ? ? B G 79 C C 97 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? B G 10 O6 ? ? ? 1_555 C C 8 N4 ? ? B G 79 C C 97 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? B G 10 O6 ? ? ? 1_555 C G 9 N1 ? ? B G 79 C G 98 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog54 hydrog ? ? B U 11 N3 ? ? ? 1_555 C G 7 O6 ? ? B U 80 C G 96 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog55 hydrog ? ? B G 12 N1 ? ? ? 1_555 C U 6 O2 ? ? B G 81 C U 95 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog56 hydrog ? ? B G 12 O6 ? ? ? 1_555 C U 6 N3 ? ? B G 81 C U 95 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog57 hydrog ? ? B U 13 N3 ? ? ? 1_555 C A 5 N1 ? ? B U 82 C A 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? B U 13 O4 ? ? ? 1_555 C A 5 N6 ? ? B U 82 C A 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? B G 14 N1 ? ? ? 1_555 C C 4 N3 ? ? B G 83 C C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? B G 14 N2 ? ? ? 1_555 C C 4 O2 ? ? B G 83 C C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? B G 14 O6 ? ? ? 1_555 C C 4 N4 ? ? B G 83 C C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? B G 15 N1 ? ? ? 1_555 C C 3 N3 ? ? B G 84 C C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? B G 15 N2 ? ? ? 1_555 C C 3 O2 ? ? B G 84 C C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? B G 15 O6 ? ? ? 1_555 C C 3 N4 ? ? B G 84 C C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? B G 16 N1 ? ? ? 1_555 C C 2 N3 ? ? B G 85 C C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? B G 16 N2 ? ? ? 1_555 C C 2 O2 ? ? B G 85 C C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? B G 16 O6 ? ? ? 1_555 C C 2 N4 ? ? B G 85 C C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? B G 17 N1 ? ? ? 1_555 C C 1 N3 ? ? B G 86 C C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? B G 17 N2 ? ? ? 1_555 C C 1 O2 ? ? B G 86 C C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 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_ _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 U 5 ? B U 74 ? 1_555 MG ? H MG . ? C MG 202 ? 1_555 OP1 ? C A 10 ? C A 99 ? 1_555 58.8 ? 2 OP2 ? B G 6 ? B G 75 ? 1_555 MG ? F MG . ? B MG 201 ? 1_555 OP2 ? C A 10 ? C A 99 ? 1_555 90.4 ? # 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 201 ? 2 'BINDING SITE FOR RESIDUE MG B 201' AC2 Software C MG 202 ? 1 'BINDING SITE FOR RESIDUE MG C 202' AC3 Software C MG 204 ? 1 'BINDING SITE FOR RESIDUE MG C 204' AC4 Software C MG 205 ? 1 'BINDING SITE FOR RESIDUE MG C 205' BC1 Software C MG 213 ? 1 'BINDING SITE FOR RESIDUE MG C 213' # 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 1 U B 5 ? U B 74 . ? 1_555 ? 4 AC3 1 G C 11 ? G C 100 . ? 1_555 ? 5 AC4 1 G C 9 ? G C 98 . ? 1_555 ? 6 BC1 1 U C 6 ? U C 95 . ? 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 N1 B U 77 ? ? "C1'" B U 77 ? ? "C2'" B U 77 ? ? 104.94 112.00 -7.06 1.10 N 2 1 "O4'" C G 116 ? ? "C1'" C G 116 ? ? N9 C G 116 ? ? 102.67 108.20 -5.53 0.80 N # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id 1SC _pdbx_struct_mod_residue.label_seq_id 4 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id 1SC _pdbx_struct_mod_residue.auth_seq_id 4 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id C _pdbx_struct_mod_residue.details "5'-O-THIOPHOSPHONOCYTIDINE" # 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 1SC O3P O N N 1 1SC P P N S 2 1SC O1P O N N 3 1SC "O5'" O N N 4 1SC "C5'" C N N 5 1SC "C4'" C N R 6 1SC "O4'" O N N 7 1SC "C3'" C N S 8 1SC "O3'" O N N 9 1SC "C2'" C N R 10 1SC "O2'" O N N 11 1SC "C1'" C N R 12 1SC N1 N N N 13 1SC C2 C N N 14 1SC O2 O N N 15 1SC N3 N N N 16 1SC C4 C N N 17 1SC N4 N N N 18 1SC C5 C N N 19 1SC C6 C N N 20 1SC S S N N 21 1SC HO3P H N N 22 1SC "H5'1" H N N 23 1SC "H5'2" H N N 24 1SC "H4'" H N N 25 1SC "H3'" H N N 26 1SC "HO3'" H N N 27 1SC "H2'" H N N 28 1SC "HO2'" H N N 29 1SC "H1'" H N N 30 1SC HN41 H N N 31 1SC HN42 H N N 32 1SC H5 H N N 33 1SC H6 H N N 34 1SC HS H N N 35 A OP3 O N N 36 A P P N N 37 A OP1 O N N 38 A OP2 O N N 39 A "O5'" O N N 40 A "C5'" C N N 41 A "C4'" C N R 42 A "O4'" O N N 43 A "C3'" C N S 44 A "O3'" O N N 45 A "C2'" C N R 46 A "O2'" O N N 47 A "C1'" C N R 48 A N9 N Y N 49 A C8 C Y N 50 A N7 N Y N 51 A C5 C Y N 52 A C6 C Y N 53 A N6 N N N 54 A N1 N Y N 55 A C2 C Y N 56 A N3 N Y N 57 A C4 C Y N 58 A HOP3 H N N 59 A HOP2 H N N 60 A "H5'" H N N 61 A "H5''" H N N 62 A "H4'" H N N 63 A "H3'" H N N 64 A "HO3'" H N N 65 A "H2'" H N N 66 A "HO2'" H N N 67 A "H1'" H N N 68 A H8 H N N 69 A H61 H N N 70 A H62 H N N 71 A H2 H N N 72 C OP3 O N N 73 C P P N N 74 C OP1 O N N 75 C OP2 O N N 76 C "O5'" O N N 77 C "C5'" C N N 78 C "C4'" C N R 79 C "O4'" O N N 80 C "C3'" C N S 81 C "O3'" O N N 82 C "C2'" C N R 83 C "O2'" O N N 84 C "C1'" C N R 85 C N1 N N N 86 C C2 C N N 87 C O2 O N N 88 C N3 N N N 89 C C4 C N N 90 C N4 N N N 91 C C5 C N N 92 C C6 C N N 93 C HOP3 H N N 94 C HOP2 H N N 95 C "H5'" H N N 96 C "H5''" H N N 97 C "H4'" H N N 98 C "H3'" H N N 99 C "HO3'" H N N 100 C "H2'" H N N 101 C "HO2'" H N N 102 C "H1'" H N N 103 C H41 H N N 104 C H42 H N N 105 C H5 H N N 106 C H6 H N N 107 G OP3 O N N 108 G P P N N 109 G OP1 O N N 110 G OP2 O N N 111 G "O5'" O N N 112 G "C5'" C N N 113 G "C4'" C N R 114 G "O4'" O N N 115 G "C3'" C N S 116 G "O3'" O N N 117 G "C2'" C N R 118 G "O2'" O N N 119 G "C1'" C N R 120 G N9 N Y N 121 G C8 C Y N 122 G N7 N Y N 123 G C5 C Y N 124 G C6 C N N 125 G O6 O N N 126 G N1 N N N 127 G C2 C N N 128 G N2 N N N 129 G N3 N N N 130 G C4 C Y N 131 G HOP3 H N N 132 G HOP2 H N N 133 G "H5'" H N N 134 G "H5''" H N N 135 G "H4'" H N N 136 G "H3'" H N N 137 G "HO3'" H N N 138 G "H2'" H N N 139 G "HO2'" H N N 140 G "H1'" H N N 141 G H8 H N N 142 G H1 H N N 143 G H21 H N N 144 G H22 H N N 145 HOH O O N N 146 HOH H1 H N N 147 HOH H2 H N N 148 MG MG MG N N 149 U OP3 O N N 150 U P P N N 151 U OP1 O N N 152 U OP2 O N N 153 U "O5'" O N N 154 U "C5'" C N N 155 U "C4'" C N R 156 U "O4'" O N N 157 U "C3'" C N S 158 U "O3'" O N N 159 U "C2'" C N R 160 U "O2'" O N N 161 U "C1'" C N R 162 U N1 N N N 163 U C2 C N N 164 U O2 O N N 165 U N3 N N N 166 U C4 C N N 167 U O4 O N N 168 U C5 C N N 169 U C6 C N N 170 U HOP3 H N N 171 U HOP2 H N N 172 U "H5'" H N N 173 U "H5''" H N N 174 U "H4'" H N N 175 U "H3'" H N N 176 U "HO3'" H N N 177 U "H2'" H N N 178 U "HO2'" H N N 179 U "H1'" H N N 180 U H3 H N N 181 U H5 H N N 182 U H6 H N N 183 # 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 1SC O3P P sing N N 1 1SC O3P HO3P sing N N 2 1SC P O1P doub N N 3 1SC P "O5'" sing N N 4 1SC P S sing N N 5 1SC "O5'" "C5'" sing N N 6 1SC "C5'" "C4'" sing N N 7 1SC "C5'" "H5'1" sing N N 8 1SC "C5'" "H5'2" sing N N 9 1SC "C4'" "O4'" sing N N 10 1SC "C4'" "C3'" sing N N 11 1SC "C4'" "H4'" sing N N 12 1SC "O4'" "C1'" sing N N 13 1SC "C3'" "O3'" sing N N 14 1SC "C3'" "C2'" sing N N 15 1SC "C3'" "H3'" sing N N 16 1SC "O3'" "HO3'" sing N N 17 1SC "C2'" "O2'" sing N N 18 1SC "C2'" "C1'" sing N N 19 1SC "C2'" "H2'" sing N N 20 1SC "O2'" "HO2'" sing N N 21 1SC "C1'" N1 sing N N 22 1SC "C1'" "H1'" sing N N 23 1SC N1 C2 sing N N 24 1SC N1 C6 sing N N 25 1SC C2 O2 doub N N 26 1SC C2 N3 sing N N 27 1SC N3 C4 doub N N 28 1SC C4 N4 sing N N 29 1SC C4 C5 sing N N 30 1SC N4 HN41 sing N N 31 1SC N4 HN42 sing N N 32 1SC C5 C6 doub N N 33 1SC C5 H5 sing N N 34 1SC C6 H6 sing N N 35 1SC S HS sing N N 36 A OP3 P sing N N 37 A OP3 HOP3 sing N N 38 A P OP1 doub N N 39 A P OP2 sing N N 40 A P "O5'" sing N N 41 A OP2 HOP2 sing N N 42 A "O5'" "C5'" sing N N 43 A "C5'" "C4'" sing N N 44 A "C5'" "H5'" sing N N 45 A "C5'" "H5''" sing N N 46 A "C4'" "O4'" sing N N 47 A "C4'" "C3'" sing N N 48 A "C4'" "H4'" sing N N 49 A "O4'" "C1'" sing N N 50 A "C3'" "O3'" sing N N 51 A "C3'" "C2'" sing N N 52 A "C3'" "H3'" sing N N 53 A "O3'" "HO3'" sing N N 54 A "C2'" "O2'" sing N N 55 A "C2'" "C1'" sing N N 56 A "C2'" "H2'" sing N N 57 A "O2'" "HO2'" sing N N 58 A "C1'" N9 sing N N 59 A "C1'" "H1'" sing N N 60 A N9 C8 sing Y N 61 A N9 C4 sing Y N 62 A C8 N7 doub Y N 63 A C8 H8 sing N N 64 A N7 C5 sing Y N 65 A C5 C6 sing Y N 66 A C5 C4 doub Y N 67 A C6 N6 sing N N 68 A C6 N1 doub Y N 69 A N6 H61 sing N N 70 A N6 H62 sing N N 71 A N1 C2 sing Y N 72 A C2 N3 doub Y N 73 A C2 H2 sing N N 74 A N3 C4 sing Y N 75 C OP3 P sing N N 76 C OP3 HOP3 sing N N 77 C P OP1 doub N N 78 C P OP2 sing N N 79 C P "O5'" sing N N 80 C OP2 HOP2 sing N N 81 C "O5'" "C5'" sing N N 82 C "C5'" "C4'" sing N N 83 C "C5'" "H5'" sing N N 84 C "C5'" "H5''" sing N N 85 C "C4'" "O4'" sing N N 86 C "C4'" "C3'" sing N N 87 C "C4'" "H4'" sing N N 88 C "O4'" "C1'" sing N N 89 C "C3'" "O3'" sing N N 90 C "C3'" "C2'" sing N N 91 C "C3'" "H3'" sing N N 92 C "O3'" "HO3'" sing N N 93 C "C2'" "O2'" sing N N 94 C "C2'" "C1'" sing N N 95 C "C2'" "H2'" sing N N 96 C "O2'" "HO2'" sing N N 97 C "C1'" N1 sing N N 98 C "C1'" "H1'" sing N N 99 C N1 C2 sing N N 100 C N1 C6 sing N N 101 C C2 O2 doub N N 102 C C2 N3 sing N N 103 C N3 C4 doub N N 104 C C4 N4 sing N N 105 C C4 C5 sing N N 106 C N4 H41 sing N N 107 C N4 H42 sing N N 108 C C5 C6 doub N N 109 C C5 H5 sing N N 110 C C6 H6 sing N N 111 G OP3 P sing N N 112 G OP3 HOP3 sing N N 113 G P OP1 doub N N 114 G P OP2 sing N N 115 G P "O5'" sing N N 116 G OP2 HOP2 sing N N 117 G "O5'" "C5'" sing N N 118 G "C5'" "C4'" sing N N 119 G "C5'" "H5'" sing N N 120 G "C5'" "H5''" sing N N 121 G "C4'" "O4'" sing N N 122 G "C4'" "C3'" sing N N 123 G "C4'" "H4'" sing N N 124 G "O4'" "C1'" sing N N 125 G "C3'" "O3'" sing N N 126 G "C3'" "C2'" sing N N 127 G "C3'" "H3'" sing N N 128 G "O3'" "HO3'" sing N N 129 G "C2'" "O2'" sing N N 130 G "C2'" "C1'" sing N N 131 G "C2'" "H2'" sing N N 132 G "O2'" "HO2'" sing N N 133 G "C1'" N9 sing N N 134 G "C1'" "H1'" sing N N 135 G N9 C8 sing Y N 136 G N9 C4 sing Y N 137 G C8 N7 doub Y N 138 G C8 H8 sing N N 139 G N7 C5 sing Y N 140 G C5 C6 sing N N 141 G C5 C4 doub Y N 142 G C6 O6 doub N N 143 G C6 N1 sing N N 144 G N1 C2 sing N N 145 G N1 H1 sing N N 146 G C2 N2 sing N N 147 G C2 N3 doub N N 148 G N2 H21 sing N N 149 G N2 H22 sing N N 150 G N3 C4 sing N N 151 HOH O H1 sing N N 152 HOH O H2 sing N N 153 U OP3 P sing N N 154 U OP3 HOP3 sing N N 155 U P OP1 doub N N 156 U P OP2 sing N N 157 U P "O5'" sing N N 158 U OP2 HOP2 sing N N 159 U "O5'" "C5'" sing N N 160 U "C5'" "C4'" sing N N 161 U "C5'" "H5'" sing N N 162 U "C5'" "H5''" sing N N 163 U "C4'" "O4'" sing N N 164 U "C4'" "C3'" sing N N 165 U "C4'" "H4'" sing N N 166 U "O4'" "C1'" sing N N 167 U "C3'" "O3'" sing N N 168 U "C3'" "C2'" sing N N 169 U "C3'" "H3'" sing N N 170 U "O3'" "HO3'" sing N N 171 U "C2'" "O2'" sing N N 172 U "C2'" "C1'" sing N N 173 U "C2'" "H2'" sing N N 174 U "O2'" "HO2'" sing N N 175 U "C1'" N1 sing N N 176 U "C1'" "H1'" sing N N 177 U N1 C2 sing N N 178 U N1 C6 sing N N 179 U C2 O2 doub N N 180 U C2 N3 sing N N 181 U N3 C4 sing N N 182 U N3 H3 sing N N 183 U C4 O4 doub N N 184 U C4 C5 sing N N 185 U C5 C6 doub N N 186 U C5 H5 sing N N 187 U C6 H6 sing N N 188 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 364D 'double helix' 364D 'a-form double helix' 364D '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 -0.472 -0.086 0.379 7.014 -24.843 0.190 1 A_U1:A119_C A 1 ? C 119 ? 20 1 1 A G 2 1_555 C C 29 1_555 0.269 -0.277 -0.606 6.430 18.266 -0.650 2 A_G2:C118_C A 2 ? C 118 ? 19 1 1 A C 3 1_555 C G 28 1_555 -0.243 -0.288 -0.679 8.438 -4.214 4.091 3 A_C3:G117_C A 3 ? C 117 ? 19 1 1 A 1SC 4 1_555 C G 27 1_555 0.463 -0.482 -0.859 13.323 -25.745 9.225 4 A_1SC4:G116_C A 4 ? C 116 ? 19 1 1 A U 5 1_555 C A 26 1_555 0.203 -0.090 0.007 -3.110 -16.909 10.391 5 A_U5:A115_C A 5 ? C 115 ? 20 1 1 A G 6 1_555 C C 25 1_555 0.114 0.147 0.150 -4.843 -8.710 4.939 6 A_G6:C114_C A 6 ? C 114 ? 19 1 1 A G 7 1_555 C C 24 1_555 -0.359 -0.172 0.131 6.538 5.174 -1.275 7 A_G7:C113_C A 7 ? C 113 ? 19 1 1 A C 8 1_555 C G 23 1_555 0.671 -0.671 -0.433 0.576 3.672 -10.159 8 A_C8:G112_C A 8 ? C 112 ? 19 1 1 A G 9 1_555 C U 22 1_555 -1.939 -0.824 0.106 2.413 -1.574 0.995 9 A_G9:U111_C A 9 ? C 111 ? 28 1 1 A G 10 1_555 C C 21 1_555 -0.180 -0.305 0.216 -16.435 -11.116 -1.067 10 A_G10:C110_C A 10 ? C 110 ? 19 1 1 A C 11 1_555 C A 20 1_555 2.265 0.285 0.635 -16.251 -3.539 -79.445 11 A_C11:A109_C A 11 ? C 109 ? ? 1 1 B C 1 1_555 C G 17 1_555 -0.089 -0.457 -0.878 4.652 -7.333 -1.319 12 B_C70:G106_C B 70 ? C 106 ? 19 1 1 B C 2 1_555 C G 16 1_555 0.294 -0.019 -0.042 -5.440 5.293 2.508 13 B_C71:G105_C B 71 ? C 105 ? 19 1 1 B G 3 1_555 C A 15 1_555 6.931 -3.923 0.484 -14.254 1.134 -8.371 14 B_G72:A104_C B 72 ? C 104 ? 11 10 1 B A 4 1_555 C U 14 1_555 -3.855 -1.530 -1.528 1.315 -19.311 -100.660 15 B_A73:U103_C B 73 ? C 103 ? 24 4 1 B U 5 1_555 C G 13 1_555 -5.196 0.008 -0.969 4.235 0.597 -79.745 16 B_U74:G102_C B 74 ? C 102 ? ? 2 1 B G 6 1_555 C A 12 1_555 -0.951 2.996 -0.922 10.666 9.108 -66.156 17 B_G75:A101_C B 75 ? C 101 ? ? ? 1 B G 7 1_555 C G 11 1_555 4.131 0.651 -0.866 9.100 -8.371 -70.584 18 B_G76:G100_C B 76 ? C 100 ? ? ? 1 B U 8 1_555 C A 10 1_555 3.850 -1.903 -2.402 4.531 -44.988 -97.451 19 B_U77:A99_C B 77 ? C 99 ? 24 4 1 B A 9 1_555 C G 9 1_555 -6.749 -3.750 0.325 -3.534 29.620 1.959 20 B_A78:G98_C B 78 ? C 98 ? 11 9 1 B G 10 1_555 C C 8 1_555 -0.040 -0.306 -0.017 9.648 42.054 5.129 21 B_G79:C97_C B 79 ? C 97 ? 19 1 1 B U 11 1_555 C G 7 1_555 3.411 -1.029 1.197 -13.849 27.721 -16.990 22 B_U80:G96_C B 80 ? C 96 ? ? ? 1 B G 12 1_555 C U 6 1_555 -3.191 -0.735 -0.103 -4.096 -5.086 5.926 23 B_G81:U95_C B 81 ? C 95 ? 28 ? 1 B U 13 1_555 C A 5 1_555 -0.238 -0.052 0.279 1.814 -18.225 0.286 24 B_U82:A94_C B 82 ? C 94 ? 20 1 1 B G 14 1_555 C C 4 1_555 -0.407 -0.334 0.250 -1.143 -5.378 -11.957 25 B_G83:C93_C B 83 ? C 93 ? 19 1 1 B G 15 1_555 C C 3 1_555 0.449 -0.154 0.326 4.924 -17.153 -6.332 26 B_G84:C92_C B 84 ? C 92 ? 19 1 1 B G 16 1_555 C C 2 1_555 -0.046 -0.192 -0.521 -9.666 -17.412 -2.088 27 B_G85:C91_C B 85 ? C 91 ? 19 1 1 B G 17 1_555 C C 1 1_555 0.361 -0.013 0.566 -1.181 -0.796 0.531 28 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 0.165 -2.292 3.530 -5.457 4.272 27.264 -5.742 -1.649 3.052 8.882 11.346 28.115 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 -0.593 -1.974 3.123 -2.112 4.894 19.373 -7.675 0.830 2.598 14.198 6.127 20.086 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 1SC 4 1_555 C G 27 1_555 -0.968 -1.528 3.489 4.321 3.109 33.789 -3.103 2.348 3.195 5.308 -7.376 34.194 3 AA_C31SC4:G116G117_CC A 3 ? C 117 ? A 4 ? C 116 ? 1 A 1SC 4 1_555 C G 27 1_555 A U 5 1_555 C A 26 1_555 0.257 -1.598 3.899 -5.685 14.491 31.173 -5.081 -1.375 2.817 25.100 9.847 34.757 4 AA_1SC4U5:A115G116_CC A 4 ? C 116 ? A 5 ? C 115 ? 1 A U 5 1_555 C A 26 1_555 A G 6 1_555 C C 25 1_555 -0.131 -1.038 3.043 0.811 15.931 31.810 -3.712 0.317 2.279 27.045 -1.376 35.494 5 AA_U5G6: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 -0.259 -1.475 2.639 -4.490 12.599 28.825 -4.375 -0.123 1.866 23.761 8.468 31.718 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 -0.074 -2.091 3.423 2.660 3.848 38.613 -3.615 0.439 3.196 5.794 -4.005 38.884 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 0.130 -2.950 3.180 -2.435 -1.877 9.553 -13.187 -5.512 3.547 -10.904 14.149 10.035 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 -0.537 -2.183 3.803 -0.487 4.878 40.700 -3.717 0.708 3.535 6.983 0.696 40.982 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 2.220 -2.510 2.740 7.672 -0.208 92.746 -1.727 -1.407 2.880 -0.144 -5.292 92.990 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 0.153 -2.375 3.719 -6.584 4.971 28.073 -5.860 -1.833 3.145 9.978 13.216 29.237 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 -0.984 -1.044 3.372 5.307 12.547 60.138 -1.605 1.209 3.033 12.350 -5.224 61.521 12 BB_C71G72:A104G105_CC B 71 ? C 105 ? B 72 ? C 104 ? 1 B G 3 1_555 C A 15 1_555 B A 4 1_555 C U 14 1_555 -6.014 -1.216 2.767 2.831 1.600 -4.557 -1.101 -37.590 5.640 -17.478 30.929 -5.598 13 BB_G72A73:U103A104_CC B 72 ? C 104 ? B 73 ? C 103 ? 1 B A 4 1_555 C U 14 1_555 B U 5 1_555 C G 13 1_555 0.225 -1.524 2.850 1.945 -4.712 34.783 -1.887 -0.110 3.032 -7.830 -3.232 35.143 14 BB_A73U74:G102U103_CC B 73 ? C 103 ? B 74 ? C 102 ? 1 B U 5 1_555 C G 13 1_555 B G 6 1_555 C A 12 1_555 1.332 -2.580 3.704 -0.947 3.655 51.666 -3.225 -1.595 3.503 4.187 1.085 51.795 15 BB_U74G75:A101G102_CC B 74 ? C 102 ? B 75 ? C 101 ? 1 B G 6 1_555 C A 12 1_555 B G 7 1_555 C G 11 1_555 0.076 -2.401 3.591 2.651 9.832 50.746 -3.442 0.098 3.107 11.341 -3.058 51.691 16 BB_G75G76:G100A101_CC B 75 ? C 101 ? B 76 ? C 100 ? 1 B G 7 1_555 C G 11 1_555 B U 8 1_555 C A 10 1_555 -0.325 -1.675 2.993 10.914 4.582 50.842 -2.177 1.013 2.724 5.255 -12.518 52.112 17 BB_G76U77:A99G100_CC B 76 ? C 100 ? B 77 ? C 99 ? 1 B U 8 1_555 C A 10 1_555 B A 9 1_555 C G 9 1_555 5.267 -1.876 3.339 -6.129 1.325 -12.464 5.913 13.308 5.469 -5.658 -26.169 -13.947 18 BB_U77A78:G98A99_CC B 77 ? C 99 ? B 78 ? C 98 ? 1 B A 9 1_555 C G 9 1_555 B G 10 1_555 C C 8 1_555 0.334 -1.792 2.524 -0.961 0.401 59.663 -1.817 -0.372 2.508 0.403 0.966 59.671 19 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 -1.037 -2.750 3.799 -3.632 3.083 43.274 -4.049 0.997 3.675 4.165 4.908 43.523 20 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 0.177 -3.735 2.558 8.144 -4.221 5.163 -12.380 14.443 2.890 -27.926 -53.882 10.523 21 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 -0.431 -1.492 3.292 -3.467 5.425 38.892 -2.843 0.236 3.090 8.080 5.163 39.401 22 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 -0.895 -1.966 3.285 -2.970 2.846 27.869 -4.697 1.152 3.149 5.868 6.124 28.165 23 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 0.681 -1.168 3.044 1.535 3.539 37.900 -2.202 -0.865 2.951 5.431 -2.356 38.088 24 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 -0.066 -2.346 3.849 7.957 1.304 17.853 -7.631 4.646 3.332 3.952 -24.107 19.576 25 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 1.117 -1.887 2.748 1.293 7.614 43.799 -3.056 -1.382 2.434 10.113 -1.718 44.441 26 BB_G85G86:C90C91_CC B 85 ? C 91 ? B 86 ? C 90 ? # _atom_sites.entry_id 364D _atom_sites.fract_transf_matrix[1][1] 0.016941 _atom_sites.fract_transf_matrix[1][2] 0.009781 _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] 0.019561 _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] 0.003936 _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 MG N O P S # loop_