data_3P59 # _entry.id 3P59 # _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 3P59 pdb_00003p59 10.2210/pdb3p59/pdb NDB NA0813 ? ? RCSB RCSB061972 ? ? WWPDB D_1000061972 ? ? # 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 2011-04-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.value' 10 3 'Structure model' '_struct_conn.pdbx_dist_value' 11 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 13 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 15 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 18 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 19 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3P59 _pdbx_database_status.recvd_initial_deposition_date 2010-10-08 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Dibrov, S.' 1 'Hermann, T.' 2 'McLean, J.' 3 'Parsons, J.' 4 # _citation.id primary _citation.title 'Self-assembling RNA square.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 108 _citation.page_first 6405 _citation.page_last 6408 _citation.year 2011 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21464284 _citation.pdbx_database_id_DOI 10.1073/pnas.1017999108 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dibrov, S.M.' 1 ? primary 'McLean, J.' 2 ? primary 'Parsons, J.' 3 ? primary 'Hermann, T.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU)P*G)-3') ; 4909.849 4 ? ? ? ? 2 polymer syn ;RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3') ; 3151.940 4 ? ? ? ? 3 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 10 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 5 water nat water 18.015 118 ? ? ? ? # 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 'CCGGAGGAACUAC(5BU)G' CCGGAGGAACUACUG A,C,E,G ? 2 polyribonucleotide no no CCGGCAGCCU CCGGCAGCCU B,D,F,H ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'COBALT HEXAMMINE(III)' NCO 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 C n 1 2 C n 1 3 G n 1 4 G n 1 5 A n 1 6 G n 1 7 G n 1 8 A n 1 9 A n 1 10 C n 1 11 U n 1 12 A n 1 13 C n 1 14 5BU n 1 15 G n 2 1 C n 2 2 C n 2 3 G n 2 4 G n 2 5 C n 2 6 A n 2 7 G n 2 8 C n 2 9 C n 2 10 U n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? 'Chemically Synthesized' 2 1 sample ? ? ? ? ? 'Chemically Synthesized' # 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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 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 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 46 46 C C A . n A 1 2 C 2 47 47 C C A . n A 1 3 G 3 48 48 G G A . n A 1 4 G 4 49 49 G G A . n A 1 5 A 5 50 50 A A A . n A 1 6 G 6 51 51 G G A . n A 1 7 G 7 52 52 G G A . n A 1 8 A 8 53 53 A A A . n A 1 9 A 9 54 54 A A A . n A 1 10 C 10 55 55 C C A . n A 1 11 U 11 56 56 U U A . n A 1 12 A 12 57 57 A A A . n A 1 13 C 13 58 58 C C A . n A 1 14 5BU 14 59 59 5BU 5BU A . n A 1 15 G 15 60 60 G G A . n B 2 1 C 1 104 104 C C B . n B 2 2 C 2 105 105 C C B . n B 2 3 G 3 106 106 G G B . n B 2 4 G 4 107 107 G G B . n B 2 5 C 5 108 108 C C B . n B 2 6 A 6 109 109 A A B . n B 2 7 G 7 110 110 G G B . n B 2 8 C 8 111 111 C C B . n B 2 9 C 9 112 112 C C B . n B 2 10 U 10 113 113 U U B . n C 1 1 C 1 46 46 C C C . n C 1 2 C 2 47 47 C C C . n C 1 3 G 3 48 48 G G C . n C 1 4 G 4 49 49 G G C . n C 1 5 A 5 50 50 A A C . n C 1 6 G 6 51 51 G G C . n C 1 7 G 7 52 52 G G C . n C 1 8 A 8 53 53 A A C . n C 1 9 A 9 54 54 A A C . n C 1 10 C 10 55 55 C C C . n C 1 11 U 11 56 56 U U C . n C 1 12 A 12 57 57 A A C . n C 1 13 C 13 58 58 C C C . n C 1 14 5BU 14 59 59 5BU 5BU C . n C 1 15 G 15 60 60 G G C . n D 2 1 C 1 104 104 C C D . n D 2 2 C 2 105 105 C C D . n D 2 3 G 3 106 106 G G D . n D 2 4 G 4 107 107 G G D . n D 2 5 C 5 108 108 C C D . n D 2 6 A 6 109 109 A A D . n D 2 7 G 7 110 110 G G D . n D 2 8 C 8 111 111 C C D . n D 2 9 C 9 112 112 C C D . n D 2 10 U 10 113 113 U U D . n E 1 1 C 1 46 46 C C E . n E 1 2 C 2 47 47 C C E . n E 1 3 G 3 48 48 G G E . n E 1 4 G 4 49 49 G G E . n E 1 5 A 5 50 50 A A E . n E 1 6 G 6 51 51 G G E . n E 1 7 G 7 52 52 G G E . n E 1 8 A 8 53 53 A A E . n E 1 9 A 9 54 54 A A E . n E 1 10 C 10 55 55 C C E . n E 1 11 U 11 56 56 U U E . n E 1 12 A 12 57 57 A A E . n E 1 13 C 13 58 58 C C E . n E 1 14 5BU 14 59 59 5BU 5BU E . n E 1 15 G 15 60 60 G G E . n F 2 1 C 1 104 104 C C F . n F 2 2 C 2 105 105 C C F . n F 2 3 G 3 106 106 G G F . n F 2 4 G 4 107 107 G G F . n F 2 5 C 5 108 108 C C F . n F 2 6 A 6 109 109 A A F . n F 2 7 G 7 110 110 G G F . n F 2 8 C 8 111 111 C C F . n F 2 9 C 9 112 112 C C F . n F 2 10 U 10 113 113 U U F . n G 1 1 C 1 46 46 C C G . n G 1 2 C 2 47 47 C C G . n G 1 3 G 3 48 48 G G G . n G 1 4 G 4 49 49 G G G . n G 1 5 A 5 50 50 A A G . n G 1 6 G 6 51 51 G G G . n G 1 7 G 7 52 52 G G G . n G 1 8 A 8 53 53 A A G . n G 1 9 A 9 54 54 A A G . n G 1 10 C 10 55 55 C C G . n G 1 11 U 11 56 ? ? ? G . n G 1 12 A 12 57 ? ? ? G . n G 1 13 C 13 58 58 C C G . n G 1 14 5BU 14 59 59 5BU 5BU G . n G 1 15 G 15 60 60 G G G . n H 2 1 C 1 104 104 C C H . n H 2 2 C 2 105 105 C C H . n H 2 3 G 3 106 106 G G H . n H 2 4 G 4 107 107 G G H . n H 2 5 C 5 108 108 C C H . n H 2 6 A 6 109 109 A A H . n H 2 7 G 7 110 110 G G H . n H 2 8 C 8 111 111 C C H . n H 2 9 C 9 112 112 C C H . n H 2 10 U 10 113 113 U U H . 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 I 3 NCO 1 1 1 NCO NCO A . J 4 MG 1 61 1 MG MG A . K 3 NCO 1 1 1 NCO NCO B . L 3 NCO 1 1 1 NCO NCO C . M 3 NCO 1 61 1 NCO NCO C . N 3 NCO 1 1 1 NCO NCO D . O 3 NCO 1 1 1 NCO NCO E . P 4 MG 1 61 1 MG MG E . Q 3 NCO 1 1 1 NCO NCO F . R 3 NCO 1 1 1 NCO NCO G . S 3 NCO 1 61 1 NCO NCO G . T 3 NCO 1 1 1 NCO NCO H . U 5 HOH 1 6 6 HOH HOH A . U 5 HOH 2 8 8 HOH HOH A . U 5 HOH 3 9 9 HOH HOH A . U 5 HOH 4 10 10 HOH HOH A . U 5 HOH 5 29 29 HOH HOH A . U 5 HOH 6 30 30 HOH HOH A . U 5 HOH 7 31 31 HOH HOH A . U 5 HOH 8 33 33 HOH HOH A . U 5 HOH 9 35 35 HOH HOH A . U 5 HOH 10 62 1 HOH HOH A . U 5 HOH 11 63 47 HOH HOH A . U 5 HOH 12 64 48 HOH HOH A . U 5 HOH 13 65 54 HOH HOH A . U 5 HOH 14 66 55 HOH HOH A . U 5 HOH 15 67 57 HOH HOH A . U 5 HOH 16 68 59 HOH HOH A . U 5 HOH 17 78 78 HOH HOH A . U 5 HOH 18 94 94 HOH HOH A . U 5 HOH 19 96 96 HOH HOH A . U 5 HOH 20 99 99 HOH HOH A . U 5 HOH 21 102 102 HOH HOH A . U 5 HOH 22 108 108 HOH HOH A . V 5 HOH 1 5 5 HOH HOH B . V 5 HOH 2 19 19 HOH HOH B . V 5 HOH 3 22 22 HOH HOH B . V 5 HOH 4 23 23 HOH HOH B . V 5 HOH 5 25 25 HOH HOH B . V 5 HOH 6 27 27 HOH HOH B . V 5 HOH 7 37 37 HOH HOH B . V 5 HOH 8 43 43 HOH HOH B . V 5 HOH 9 46 46 HOH HOH B . V 5 HOH 10 53 53 HOH HOH B . V 5 HOH 11 62 62 HOH HOH B . V 5 HOH 12 64 64 HOH HOH B . V 5 HOH 13 67 67 HOH HOH B . V 5 HOH 14 79 79 HOH HOH B . V 5 HOH 15 81 81 HOH HOH B . V 5 HOH 16 85 85 HOH HOH B . V 5 HOH 17 91 91 HOH HOH B . V 5 HOH 18 114 110 HOH HOH B . V 5 HOH 19 118 118 HOH HOH B . W 5 HOH 1 2 2 HOH HOH C . W 5 HOH 2 11 11 HOH HOH C . W 5 HOH 3 14 14 HOH HOH C . W 5 HOH 4 17 17 HOH HOH C . W 5 HOH 5 20 20 HOH HOH C . W 5 HOH 6 40 40 HOH HOH C . W 5 HOH 7 42 42 HOH HOH C . W 5 HOH 8 62 52 HOH HOH C . W 5 HOH 9 63 58 HOH HOH C . W 5 HOH 10 64 61 HOH HOH C . W 5 HOH 11 71 71 HOH HOH C . W 5 HOH 12 74 74 HOH HOH C . W 5 HOH 13 75 75 HOH HOH C . W 5 HOH 14 76 76 HOH HOH C . W 5 HOH 15 87 87 HOH HOH C . W 5 HOH 16 92 92 HOH HOH C . W 5 HOH 17 95 95 HOH HOH C . W 5 HOH 18 98 98 HOH HOH C . W 5 HOH 19 104 104 HOH HOH C . X 5 HOH 1 15 15 HOH HOH D . X 5 HOH 2 16 16 HOH HOH D . X 5 HOH 3 26 26 HOH HOH D . X 5 HOH 4 32 32 HOH HOH D . X 5 HOH 5 36 36 HOH HOH D . X 5 HOH 6 41 41 HOH HOH D . X 5 HOH 7 65 65 HOH HOH D . X 5 HOH 8 66 66 HOH HOH D . X 5 HOH 9 68 68 HOH HOH D . X 5 HOH 10 114 113 HOH HOH D . X 5 HOH 11 115 115 HOH HOH D . Y 5 HOH 1 4 4 HOH HOH E . Y 5 HOH 2 7 7 HOH HOH E . Y 5 HOH 3 18 18 HOH HOH E . Y 5 HOH 4 21 21 HOH HOH E . Y 5 HOH 5 45 45 HOH HOH E . Y 5 HOH 6 62 50 HOH HOH E . Y 5 HOH 7 63 51 HOH HOH E . Y 5 HOH 8 64 56 HOH HOH E . Y 5 HOH 9 80 80 HOH HOH E . Y 5 HOH 10 82 82 HOH HOH E . Y 5 HOH 11 86 86 HOH HOH E . Y 5 HOH 12 88 88 HOH HOH E . Y 5 HOH 13 89 89 HOH HOH E . Y 5 HOH 14 90 90 HOH HOH E . Y 5 HOH 15 97 97 HOH HOH E . Y 5 HOH 16 109 109 HOH HOH E . Y 5 HOH 17 111 111 HOH HOH E . Y 5 HOH 18 112 112 HOH HOH E . Y 5 HOH 19 114 114 HOH HOH E . Y 5 HOH 20 117 117 HOH HOH E . Z 5 HOH 1 12 12 HOH HOH F . Z 5 HOH 2 13 13 HOH HOH F . Z 5 HOH 3 28 28 HOH HOH F . Z 5 HOH 4 39 39 HOH HOH F . Z 5 HOH 5 69 69 HOH HOH F . Z 5 HOH 6 70 70 HOH HOH F . Z 5 HOH 7 77 77 HOH HOH F . Z 5 HOH 8 83 83 HOH HOH F . Z 5 HOH 9 84 84 HOH HOH F . Z 5 HOH 10 93 93 HOH HOH F . Z 5 HOH 11 100 100 HOH HOH F . Z 5 HOH 12 114 106 HOH HOH F . AA 5 HOH 1 3 3 HOH HOH G . AA 5 HOH 2 34 34 HOH HOH G . AA 5 HOH 3 38 38 HOH HOH G . AA 5 HOH 4 62 49 HOH HOH G . AA 5 HOH 5 63 63 HOH HOH G . AA 5 HOH 6 72 72 HOH HOH G . AA 5 HOH 7 107 107 HOH HOH G . AA 5 HOH 8 116 116 HOH HOH G . BA 5 HOH 1 24 24 HOH HOH H . BA 5 HOH 2 44 44 HOH HOH H . BA 5 HOH 3 60 60 HOH HOH H . BA 5 HOH 4 73 73 HOH HOH H . BA 5 HOH 5 101 101 HOH HOH H . BA 5 HOH 6 103 103 HOH HOH H . BA 5 HOH 7 114 105 HOH HOH H . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 PHENIX 'model building' . ? 2 PHENIX refinement '(phenix.refine: 1.6.1_357)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 3P59 _cell.length_a 62.378 _cell.length_b 62.378 _cell.length_c 126.268 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 24 _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 3P59 _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3P59 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.20 _exptl_crystal.density_percent_sol 44.07 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 289 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details ;150 mM magnesium chloride, 50 mM sodium cacodylate, 10mM hexamminecobalt (III) chloride, 50 mM KCl, 17% PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 173.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2010-04-23 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si 111' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9202752 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 17-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 17-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9202752 # _reflns.entry_id 3P59 _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 25.06 _reflns.d_resolution_high 2.157 _reflns.number_obs 25640 _reflns.number_all ? _reflns.percent_possible_obs 86.7 _reflns.pdbx_Rmerge_I_obs 0.065 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 49.5 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 30.2 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.157 _reflns_shell.d_res_low 2.27 _reflns_shell.percent_possible_all 30 _reflns_shell.Rmerge_I_obs 0.33 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.0 _reflns_shell.pdbx_redundancy 2.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 946 _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 3P59 _refine.ls_number_reflns_obs 25640 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.99 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 25.059 _refine.ls_d_res_high 2.1793 _refine.ls_percent_reflns_obs 86.70 _refine.ls_R_factor_obs 0.1570 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1556 _refine.ls_R_factor_R_free 0.1920 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.05 _refine.ls_number_reflns_R_free 1295 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 0.0000 _refine.aniso_B[2][2] 0.0000 _refine.aniso_B[3][3] 0.0000 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.361 _refine.solvent_model_param_bsol 34.400 _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values TWIN_LSQ_F _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML . _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_phase_error 20.61 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _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_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 2074 _refine_hist.pdbx_number_atoms_ligand 72 _refine_hist.number_atoms_solvent 118 _refine_hist.number_atoms_total 2264 _refine_hist.d_res_high 2.1793 _refine_hist.d_res_low 25.059 # 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 f_bond_d 0.008 ? ? 2372 'X-RAY DIFFRACTION' ? f_angle_d 1.114 ? ? 3741 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 21.687 ? ? 1141 'X-RAY DIFFRACTION' ? f_chiral_restr 0.058 ? ? 478 'X-RAY DIFFRACTION' ? f_plane_restr 0.009 ? ? 98 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id . 2.1793 2.2665 946 0.2730 30.00 0.2808 . . 66 . . . . 'X-RAY DIFFRACTION' . 2.2665 2.3695 2158 0.2683 67.00 0.3079 . . 116 . . . . 'X-RAY DIFFRACTION' . 2.3695 2.4944 3019 0.2408 94.00 0.2582 . . 151 . . . . 'X-RAY DIFFRACTION' . 2.4944 2.6505 3002 0.2413 95.00 0.3194 . . 151 . . . . 'X-RAY DIFFRACTION' . 2.6505 2.8549 2993 0.2255 94.00 0.2841 . . 203 . . . . 'X-RAY DIFFRACTION' . 2.8549 3.1416 3040 0.1717 95.00 0.1777 . . 141 . . . . 'X-RAY DIFFRACTION' . 3.1416 3.5951 3043 0.1394 95.00 0.1561 . . 149 . . . . 'X-RAY DIFFRACTION' . 3.5951 4.5249 3039 0.1152 95.00 0.1642 . . 145 . . . . 'X-RAY DIFFRACTION' . 4.5249 24.8348 3042 0.1186 95.00 0.1645 . . 146 . . . . 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3P59 _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 3P59 _struct.title 'First Crystal Structure of a RNA Nanosquare' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3P59 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA square, 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 1 ? D N N 2 ? E N N 1 ? F N N 2 ? G N N 1 ? H N N 2 ? I N N 3 ? J N N 4 ? K N N 3 ? L N N 3 ? M N N 3 ? N N N 3 ? O N N 3 ? P N N 4 ? Q N N 3 ? R N N 3 ? S N N 3 ? T N N 3 ? U N N 5 ? V N N 5 ? W N N 5 ? X N N 5 ? Y N N 5 ? Z N N 5 ? AA N N 5 ? BA N N 5 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 3P59 3P59 1 1 CCGGAGGAACUACUG ? 2 PDB 3P59 3P59 2 1 CCGGCAGCCU ? # 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 3P59 A 1 ? 15 ? 3P59 46 ? 60 ? 46 60 2 1 3P59 C 1 ? 15 ? 3P59 46 ? 60 ? 46 60 3 1 3P59 E 1 ? 15 ? 3P59 46 ? 60 ? 46 60 4 1 3P59 G 1 ? 15 ? 3P59 46 ? 60 ? 46 60 5 2 3P59 B 1 ? 10 ? 3P59 104 ? 113 ? 104 113 6 2 3P59 D 1 ? 10 ? 3P59 104 ? 113 ? 104 113 7 2 3P59 F 1 ? 10 ? 3P59 104 ? 113 ? 104 113 8 2 3P59 H 1 ? 10 ? 3P59 104 ? 113 ? 104 113 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 # _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,R,S,T,U,V,W,X,Y,Z,AA,BA # _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 13 "O3'" ? ? ? 1_555 A 5BU 14 P ? ? A C 58 A 5BU 59 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale2 covale both ? A 5BU 14 "O3'" ? ? ? 1_555 A G 15 P ? ? A 5BU 59 A G 60 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale3 covale both ? C C 13 "O3'" ? ? ? 1_555 C 5BU 14 P ? ? C C 58 C 5BU 59 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale4 covale both ? C 5BU 14 "O3'" ? ? ? 1_555 C G 15 P ? ? C 5BU 59 C G 60 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale5 covale both ? E C 13 "O3'" ? ? ? 1_555 E 5BU 14 P ? ? E C 58 E 5BU 59 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale6 covale both ? E 5BU 14 "O3'" ? ? ? 1_555 E G 15 P ? ? E 5BU 59 E G 60 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale7 covale both ? G C 13 "O3'" ? ? ? 1_555 G 5BU 14 P ? ? G C 58 G 5BU 59 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale8 covale both ? G 5BU 14 "O3'" ? ? ? 1_555 G G 15 P ? ? G 5BU 59 G G 60 1_555 ? ? ? ? ? ? ? 1.612 ? ? metalc1 metalc ? ? A C 10 O2 ? ? ? 1_555 J MG . MG ? ? A C 55 A MG 61 1_555 ? ? ? ? ? ? ? 2.372 ? ? metalc2 metalc ? ? J MG . MG ? ? ? 1_555 U HOH . O ? ? A MG 61 A HOH 63 1_555 ? ? ? ? ? ? ? 2.162 ? ? metalc3 metalc ? ? J MG . MG ? ? ? 1_555 U HOH . O ? ? A MG 61 A HOH 96 1_555 ? ? ? ? ? ? ? 2.961 ? ? metalc4 metalc ? ? J MG . MG ? ? ? 1_555 V HOH . O ? ? A MG 61 B HOH 46 1_555 ? ? ? ? ? ? ? 2.069 ? ? metalc5 metalc ? ? P MG . MG ? ? ? 1_555 Y HOH . O ? ? E MG 61 E HOH 64 1_555 ? ? ? ? ? ? ? 2.966 ? ? metalc6 metalc ? ? P MG . MG ? ? ? 1_555 Y HOH . O ? ? E MG 61 E HOH 109 1_555 ? ? ? ? ? ? ? 2.367 ? ? hydrog1 hydrog ? ? A C 1 O2 ? ? ? 1_555 D G 4 N1 ? ? A C 46 D G 107 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog2 hydrog ? ? A C 2 N3 ? ? ? 1_555 D G 3 N1 ? ? A C 47 D G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 N4 ? ? ? 1_555 D G 3 O6 ? ? A C 47 D G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 O2 ? ? ? 1_555 D G 3 N2 ? ? A C 47 D G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 3 N1 ? ? ? 1_555 D C 2 N3 ? ? A G 48 D C 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N2 ? ? ? 1_555 D C 2 O2 ? ? A G 48 D C 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 O6 ? ? ? 1_555 D C 2 N4 ? ? A G 48 D C 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 D C 1 N3 ? ? A G 49 D C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 D C 1 O2 ? ? A G 49 D C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 D C 1 N4 ? ? A G 49 D C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 10 N3 ? ? A A 50 B U 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 10 O4 ? ? A A 50 B U 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 51 B C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 51 B C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 51 B C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 52 B C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 52 B C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 52 B C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 58 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 58 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 58 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A 5BU 14 N3 ? ? ? 1_555 B A 6 N1 ? ? A 5BU 59 B A 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A 5BU 14 O4 ? ? ? 1_555 B A 6 N6 ? ? A 5BU 59 B A 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 60 B C 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 60 B C 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 60 B C 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B C 1 N3 ? ? ? 1_555 G G 4 N1 ? ? B C 104 G G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B C 1 N4 ? ? ? 1_555 G G 4 O6 ? ? B C 104 G G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B C 1 O2 ? ? ? 1_555 G G 4 N2 ? ? B C 104 G G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B C 2 N3 ? ? ? 1_555 G G 3 N1 ? ? B C 105 G G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 2 N4 ? ? ? 1_555 G G 3 O6 ? ? B C 105 G G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B C 2 O2 ? ? ? 1_555 G G 3 N2 ? ? B C 105 G G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B G 3 N1 ? ? ? 1_555 G C 2 N3 ? ? B G 106 G C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B G 3 N2 ? ? ? 1_555 G C 2 O2 ? ? B G 106 G C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 3 O6 ? ? ? 1_555 G C 2 N4 ? ? B G 106 G C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B G 4 N1 ? ? ? 1_555 G C 1 N3 ? ? B G 107 G C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B G 4 N2 ? ? ? 1_555 G C 1 O2 ? ? B G 107 G C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B G 4 O6 ? ? ? 1_555 G C 1 N4 ? ? B G 107 G C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C C 1 N3 ? ? ? 1_555 F G 4 N1 ? ? C C 46 F G 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C C 1 N4 ? ? ? 1_555 F G 4 O6 ? ? C C 46 F G 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C C 1 O2 ? ? ? 1_555 F G 4 N2 ? ? C C 46 F G 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C C 2 N3 ? ? ? 1_555 F G 3 N1 ? ? C C 47 F G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C C 2 N4 ? ? ? 1_555 F G 3 O6 ? ? C C 47 F G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C C 2 O2 ? ? ? 1_555 F G 3 N2 ? ? C C 47 F G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C G 3 N1 ? ? ? 1_555 F C 2 N3 ? ? C G 48 F C 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C G 3 N2 ? ? ? 1_555 F C 2 O2 ? ? C G 48 F C 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C G 3 O6 ? ? ? 1_555 F C 2 N4 ? ? C G 48 F C 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C G 4 N1 ? ? ? 1_555 F C 1 N3 ? ? C G 49 F C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C G 4 N2 ? ? ? 1_555 F C 1 O2 ? ? C G 49 F C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C G 4 O6 ? ? ? 1_555 F C 1 N4 ? ? C G 49 F C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C A 5 N1 ? ? ? 1_555 D U 10 N3 ? ? C A 50 D U 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C A 5 N6 ? ? ? 1_555 D U 10 O4 ? ? C A 50 D U 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C G 6 N1 ? ? ? 1_555 D C 9 N3 ? ? C G 51 D C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C G 6 N2 ? ? ? 1_555 D C 9 O2 ? ? C G 51 D C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C G 6 O6 ? ? ? 1_555 D C 9 N4 ? ? C G 51 D C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C G 7 N1 ? ? ? 1_555 D C 8 N3 ? ? C G 52 D C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C G 7 N2 ? ? ? 1_555 D C 8 O2 ? ? C G 52 D C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C G 7 O6 ? ? ? 1_555 D C 8 N4 ? ? C G 52 D C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C C 13 N4 ? ? ? 1_555 D G 7 O6 ? ? C C 58 D G 110 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog60 hydrog ? ? E C 1 O2 ? ? ? 1_555 H G 4 N2 ? ? E C 46 H G 107 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog61 hydrog ? ? E C 2 N3 ? ? ? 1_555 H G 3 N1 ? ? E C 47 H G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? E C 2 N4 ? ? ? 1_555 H G 3 O6 ? ? E C 47 H G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? E C 2 O2 ? ? ? 1_555 H G 3 N2 ? ? E C 47 H G 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? E G 3 N1 ? ? ? 1_555 H C 2 N3 ? ? E G 48 H C 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? E G 3 N2 ? ? ? 1_555 H C 2 O2 ? ? E G 48 H C 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? E G 3 O6 ? ? ? 1_555 H C 2 N4 ? ? E G 48 H C 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? E G 4 N1 ? ? ? 1_555 H C 1 N3 ? ? E G 49 H C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? E G 4 N2 ? ? ? 1_555 H C 1 O2 ? ? E G 49 H C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? E G 4 O6 ? ? ? 1_555 H C 1 N4 ? ? E G 49 H C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? E A 5 N1 ? ? ? 1_555 F U 10 N3 ? ? E A 50 F U 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? E A 5 N6 ? ? ? 1_555 F U 10 O4 ? ? E A 50 F U 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? E G 6 N1 ? ? ? 1_555 F C 9 O2 ? ? E G 51 F C 112 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog73 hydrog ? ? E C 10 O2 ? ? ? 1_555 E C 13 N4 ? ? E C 55 E C 58 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog74 hydrog ? ? E C 10 N4 ? ? ? 1_555 F G 7 N7 ? ? E C 55 F G 110 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog75 hydrog ? ? E A 12 N6 ? ? ? 1_555 F C 8 N3 ? ? E A 57 F C 111 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog76 hydrog ? ? E C 13 N3 ? ? ? 1_555 F G 7 N1 ? ? E C 58 F G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? E C 13 N4 ? ? ? 1_555 F G 7 O6 ? ? E C 58 F G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? E C 13 O2 ? ? ? 1_555 F G 7 N2 ? ? E C 58 F G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? E 5BU 14 N3 ? ? ? 1_555 F A 6 N1 ? ? E 5BU 59 F A 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? E 5BU 14 O4 ? ? ? 1_555 F A 6 N6 ? ? E 5BU 59 F A 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? E G 15 N1 ? ? ? 1_555 F C 5 N3 ? ? E G 60 F C 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? E G 15 N2 ? ? ? 1_555 F C 5 O2 ? ? E G 60 F C 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? E G 15 O6 ? ? ? 1_555 F C 5 N4 ? ? E G 60 F C 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? G A 5 N1 ? ? ? 1_555 H U 10 N3 ? ? G A 50 H U 113 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog85 hydrog ? ? G G 6 N1 ? ? ? 1_555 H C 9 N3 ? ? G G 51 H C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? G G 6 N2 ? ? ? 1_555 H C 9 O2 ? ? G G 51 H C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? G G 6 O6 ? ? ? 1_555 H C 9 N4 ? ? G G 51 H C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? G G 7 N1 ? ? ? 1_555 H C 8 N3 ? ? G G 52 H C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? G G 7 N2 ? ? ? 1_555 H C 8 O2 ? ? G G 52 H C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? G G 7 O6 ? ? ? 1_555 H C 8 N4 ? ? G G 52 H C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? G C 13 N3 ? ? ? 1_555 H G 7 N1 ? ? G C 58 H G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog92 hydrog ? ? G C 13 N4 ? ? ? 1_555 H G 7 O6 ? ? G C 58 H G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog93 hydrog ? ? G C 13 O2 ? ? ? 1_555 H G 7 N2 ? ? G C 58 H G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog94 hydrog ? ? G 5BU 14 N3 ? ? ? 1_555 H A 6 N1 ? ? G 5BU 59 H A 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog95 hydrog ? ? G 5BU 14 O4 ? ? ? 1_555 H A 6 N6 ? ? G 5BU 59 H A 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog96 hydrog ? ? G G 15 N1 ? ? ? 1_555 H C 5 O2 ? ? G G 60 H C 108 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? # 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 O2 ? A C 10 ? A C 55 ? 1_555 MG ? J MG . ? A MG 61 ? 1_555 O ? U HOH . ? A HOH 63 ? 1_555 76.1 ? 2 O2 ? A C 10 ? A C 55 ? 1_555 MG ? J MG . ? A MG 61 ? 1_555 O ? U HOH . ? A HOH 96 ? 1_555 72.1 ? 3 O ? U HOH . ? A HOH 63 ? 1_555 MG ? J MG . ? A MG 61 ? 1_555 O ? U HOH . ? A HOH 96 ? 1_555 142.4 ? 4 O2 ? A C 10 ? A C 55 ? 1_555 MG ? J MG . ? A MG 61 ? 1_555 O ? V HOH . ? B HOH 46 ? 1_555 109.3 ? 5 O ? U HOH . ? A HOH 63 ? 1_555 MG ? J MG . ? A MG 61 ? 1_555 O ? V HOH . ? B HOH 46 ? 1_555 114.7 ? 6 O ? U HOH . ? A HOH 96 ? 1_555 MG ? J MG . ? A MG 61 ? 1_555 O ? V HOH . ? B HOH 46 ? 1_555 94.6 ? 7 O ? Y HOH . ? E HOH 64 ? 1_555 MG ? P MG . ? E MG 61 ? 1_555 O ? Y HOH . ? E HOH 109 ? 1_555 48.4 ? # 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 A NCO 1 ? 3 'BINDING SITE FOR RESIDUE NCO A 1' AC2 Software A MG 61 ? 5 'BINDING SITE FOR RESIDUE MG A 61' AC3 Software B NCO 1 ? 11 'BINDING SITE FOR RESIDUE NCO B 1' AC4 Software C NCO 1 ? 6 'BINDING SITE FOR RESIDUE NCO C 1' AC5 Software C NCO 61 ? 3 'BINDING SITE FOR RESIDUE NCO C 61' AC6 Software D NCO 1 ? 5 'BINDING SITE FOR RESIDUE NCO D 1' AC7 Software E NCO 1 ? 3 'BINDING SITE FOR RESIDUE NCO E 1' AC8 Software E MG 61 ? 3 'BINDING SITE FOR RESIDUE MG E 61' AC9 Software F NCO 1 ? 6 'BINDING SITE FOR RESIDUE NCO F 1' BC1 Software G NCO 1 ? 3 'BINDING SITE FOR RESIDUE NCO G 1' BC2 Software G NCO 61 ? 4 'BINDING SITE FOR RESIDUE NCO G 61' BC3 Software H NCO 1 ? 5 'BINDING SITE FOR RESIDUE NCO H 1' # 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 3 C A 2 ? C A 47 . ? 1_555 ? 2 AC1 3 G A 3 ? G A 48 . ? 1_555 ? 3 AC1 3 G A 4 ? G A 49 . ? 1_555 ? 4 AC2 5 C A 10 ? C A 55 . ? 1_555 ? 5 AC2 5 HOH U . ? HOH A 62 . ? 1_555 ? 6 AC2 5 HOH U . ? HOH A 63 . ? 1_555 ? 7 AC2 5 HOH U . ? HOH A 96 . ? 1_555 ? 8 AC2 5 HOH V . ? HOH B 46 . ? 1_555 ? 9 AC3 11 5BU A 14 ? 5BU A 59 . ? 1_555 ? 10 AC3 11 G A 15 ? G A 60 . ? 1_555 ? 11 AC3 11 HOH V . ? HOH B 19 . ? 1_555 ? 12 AC3 11 HOH V . ? HOH B 25 . ? 1_555 ? 13 AC3 11 HOH V . ? HOH B 62 . ? 1_555 ? 14 AC3 11 HOH V . ? HOH B 79 . ? 1_555 ? 15 AC3 11 C B 2 ? C B 105 . ? 1_555 ? 16 AC3 11 G B 3 ? G B 106 . ? 1_555 ? 17 AC3 11 G B 4 ? G B 107 . ? 1_555 ? 18 AC3 11 C B 5 ? C B 108 . ? 1_555 ? 19 AC3 11 C G 1 ? C G 46 . ? 1_555 ? 20 AC4 6 HOH W . ? HOH C 11 . ? 1_555 ? 21 AC4 6 C C 2 ? C C 47 . ? 1_555 ? 22 AC4 6 G C 3 ? G C 48 . ? 1_555 ? 23 AC4 6 G C 4 ? G C 49 . ? 1_555 ? 24 AC4 6 HOH W . ? HOH C 75 . ? 1_555 ? 25 AC4 6 HOH W . ? HOH C 95 . ? 1_555 ? 26 AC5 3 A C 8 ? A C 53 . ? 1_555 ? 27 AC5 3 A C 9 ? A C 54 . ? 1_555 ? 28 AC5 3 HOH W . ? HOH C 62 . ? 1_555 ? 29 AC6 5 HOH X . ? HOH D 66 . ? 1_555 ? 30 AC6 5 C D 2 ? C D 105 . ? 1_555 ? 31 AC6 5 G D 3 ? G D 106 . ? 1_555 ? 32 AC6 5 G D 4 ? G D 107 . ? 1_555 ? 33 AC6 5 C D 5 ? C D 108 . ? 1_555 ? 34 AC7 3 C E 2 ? C E 47 . ? 1_555 ? 35 AC7 3 G E 3 ? G E 48 . ? 1_555 ? 36 AC7 3 G E 4 ? G E 49 . ? 1_555 ? 37 AC8 3 G E 6 ? G E 51 . ? 1_555 ? 38 AC8 3 HOH Y . ? HOH E 64 . ? 1_555 ? 39 AC8 3 HOH Y . ? HOH E 109 . ? 1_555 ? 40 AC9 6 C C 1 ? C C 46 . ? 1_555 ? 41 AC9 6 5BU E 14 ? 5BU E 59 . ? 1_555 ? 42 AC9 6 G E 15 ? G E 60 . ? 1_555 ? 43 AC9 6 C F 2 ? C F 105 . ? 1_555 ? 44 AC9 6 G F 3 ? G F 106 . ? 1_555 ? 45 AC9 6 G F 4 ? G F 107 . ? 1_555 ? 46 BC1 3 C G 2 ? C G 47 . ? 1_555 ? 47 BC1 3 G G 3 ? G G 48 . ? 1_555 ? 48 BC1 3 G G 4 ? G G 49 . ? 1_555 ? 49 BC2 4 HOH AA . ? HOH G 34 . ? 1_555 ? 50 BC2 4 G G 6 ? G G 51 . ? 1_555 ? 51 BC2 4 G G 7 ? G G 52 . ? 1_555 ? 52 BC2 4 A H 6 ? A H 109 . ? 1_555 ? 53 BC3 5 C E 2 ? C E 47 . ? 1_555 ? 54 BC3 5 G G 15 ? G G 60 . ? 1_555 ? 55 BC3 5 C H 2 ? C H 105 . ? 1_555 ? 56 BC3 5 G H 3 ? G H 106 . ? 1_555 ? 57 BC3 5 G H 4 ? G H 107 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 OP1 A A 57 ? ? O A HOH 64 ? ? 1.85 2 1 O A HOH 10 ? ? O B HOH 53 ? ? 1.93 3 1 O B HOH 27 ? ? O B HOH 62 ? ? 1.95 4 1 N7 A G 52 ? ? O A HOH 9 ? ? 1.95 5 1 O F HOH 77 ? ? O F HOH 83 ? ? 2.05 6 1 N4 B C 108 ? ? O B HOH 25 ? ? 2.11 7 1 N2 E G 51 ? ? O2 F C 112 ? ? 2.12 8 1 "O2'" D C 105 ? ? O D HOH 15 ? ? 2.13 9 1 OP1 D G 107 ? ? O D HOH 32 ? ? 2.18 10 1 OP2 A A 54 ? ? O A HOH 30 ? ? 2.19 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 B _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 85 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 C _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 87 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 1_445 _pdbx_validate_symm_contact.dist 1.83 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N3 A G 51 ? ? C4 A G 51 ? ? N9 A G 51 ? ? 121.46 126.00 -4.54 0.60 N 2 1 C5 B C 105 ? ? C6 B C 105 ? ? N1 B C 105 ? ? 124.71 121.00 3.71 0.50 N 3 1 C8 B G 106 ? ? N9 B G 106 ? ? C4 B G 106 ? ? 110.44 106.40 4.04 0.40 N 4 1 N9 B G 106 ? ? C4 B G 106 ? ? C5 B G 106 ? ? 102.35 105.40 -3.05 0.40 N 5 1 C5 B C 108 ? ? C6 B C 108 ? ? N1 B C 108 ? ? 124.30 121.00 3.30 0.50 N 6 1 N3 C G 48 ? ? C4 C G 48 ? ? C5 C G 48 ? ? 131.82 128.60 3.22 0.50 N 7 1 C8 C G 48 ? ? N9 C G 48 ? ? C4 C G 48 ? ? 109.21 106.40 2.81 0.40 N 8 1 N3 E G 52 ? ? C4 E G 52 ? ? N9 E G 52 ? ? 121.68 126.00 -4.32 0.60 N 9 1 N9 F G 110 ? ? C4 F G 110 ? ? C5 F G 110 ? ? 108.38 105.40 2.98 0.40 N 10 1 N3 F G 110 ? ? C4 F G 110 ? ? N9 F G 110 ? ? 121.07 126.00 -4.93 0.60 N 11 1 C5 F G 110 ? ? C6 F G 110 ? ? O6 F G 110 ? ? 133.81 128.60 5.21 0.60 N 12 1 N1 F C 111 ? ? C2 F C 111 ? ? O2 F C 111 ? ? 122.74 118.90 3.84 0.60 N 13 1 C6 G G 49 ? ? C5 G G 49 ? ? N7 G G 49 ? ? 134.02 130.40 3.62 0.60 N 14 1 C4 G G 49 ? ? N9 G G 49 ? ? "C1'" G G 49 ? ? 118.55 126.50 -7.95 1.30 N 15 1 C6 H C 112 ? ? N1 H C 112 ? ? C2 H C 112 ? ? 117.77 120.30 -2.53 0.40 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 5BU 14 A 5BU 59 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 2 C 5BU 14 C 5BU 59 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 3 E 5BU 14 E 5BU 59 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 4 G 5BU 14 G 5BU 59 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id H _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 24 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id BA _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 17.6206 _pdbx_refine_tls.origin_y -26.3046 _pdbx_refine_tls.origin_z 10.6335 _pdbx_refine_tls.T[1][1] 0.1072 _pdbx_refine_tls.T[2][2] 0.1453 _pdbx_refine_tls.T[3][3] 0.0085 _pdbx_refine_tls.T[1][2] -0.0039 _pdbx_refine_tls.T[1][3] -0.0231 _pdbx_refine_tls.T[2][3] -0.0400 _pdbx_refine_tls.L[1][1] 0.3323 _pdbx_refine_tls.L[2][2] 0.4423 _pdbx_refine_tls.L[3][3] -0.4430 _pdbx_refine_tls.L[1][2] 0.2191 _pdbx_refine_tls.L[1][3] 0.0498 _pdbx_refine_tls.L[2][3] 0.1218 _pdbx_refine_tls.S[1][1] 0.0279 _pdbx_refine_tls.S[1][2] 0.0525 _pdbx_refine_tls.S[1][3] 0.0085 _pdbx_refine_tls.S[2][1] -0.0279 _pdbx_refine_tls.S[2][2] 0.1192 _pdbx_refine_tls.S[2][3] -0.0171 _pdbx_refine_tls.S[3][1] 0.0807 _pdbx_refine_tls.S[3][2] -0.0062 _pdbx_refine_tls.S[3][3] 0.1480 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id ? _pdbx_refine_tls_group.beg_auth_seq_id ? _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id ? _pdbx_refine_tls_group.end_auth_seq_id ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details all # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 G U 56 ? G U 11 2 1 Y 1 G A 57 ? G A 12 # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C 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 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 MG MG MG N N 148 NCO CO CO N N 149 NCO N1 N N N 150 NCO N2 N N N 151 NCO N3 N N N 152 NCO N4 N N N 153 NCO N5 N N N 154 NCO N6 N N N 155 NCO HN11 H N N 156 NCO HN12 H N N 157 NCO HN13 H N N 158 NCO HN21 H N N 159 NCO HN22 H N N 160 NCO HN23 H N N 161 NCO HN31 H N N 162 NCO HN32 H N N 163 NCO HN33 H N N 164 NCO HN41 H N N 165 NCO HN42 H N N 166 NCO HN43 H N N 167 NCO HN51 H N N 168 NCO HN52 H N N 169 NCO HN53 H N N 170 NCO HN61 H N N 171 NCO HN62 H N N 172 NCO HN63 H N N 173 U OP3 O N N 174 U P P N N 175 U OP1 O N N 176 U OP2 O N N 177 U "O5'" O N N 178 U "C5'" C N N 179 U "C4'" C N R 180 U "O4'" O N N 181 U "C3'" C N S 182 U "O3'" O N N 183 U "C2'" C N R 184 U "O2'" O N N 185 U "C1'" C N R 186 U N1 N N N 187 U C2 C N N 188 U O2 O N N 189 U N3 N N N 190 U C4 C N N 191 U O4 O N N 192 U C5 C N N 193 U C6 C N N 194 U HOP3 H N N 195 U HOP2 H N N 196 U "H5'" H N N 197 U "H5''" H N N 198 U "H4'" H N N 199 U "H3'" H N N 200 U "HO3'" H N N 201 U "H2'" H N N 202 U "HO2'" H N N 203 U "H1'" H N N 204 U H3 H N N 205 U H5 H N N 206 U H6 H N N 207 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C 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 HOH O H1 sing N N 151 HOH O H2 sing N N 152 NCO CO N1 sing N N 153 NCO CO N2 sing N N 154 NCO CO N3 sing N N 155 NCO CO N4 sing N N 156 NCO CO N5 sing N N 157 NCO CO N6 sing N N 158 NCO N1 HN11 sing N N 159 NCO N1 HN12 sing N N 160 NCO N1 HN13 sing N N 161 NCO N2 HN21 sing N N 162 NCO N2 HN22 sing N N 163 NCO N2 HN23 sing N N 164 NCO N3 HN31 sing N N 165 NCO N3 HN32 sing N N 166 NCO N3 HN33 sing N N 167 NCO N4 HN41 sing N N 168 NCO N4 HN42 sing N N 169 NCO N4 HN43 sing N N 170 NCO N5 HN51 sing N N 171 NCO N5 HN52 sing N N 172 NCO N5 HN53 sing N N 173 NCO N6 HN61 sing N N 174 NCO N6 HN62 sing N N 175 NCO N6 HN63 sing N N 176 U OP3 P sing N N 177 U OP3 HOP3 sing N N 178 U P OP1 doub N N 179 U P OP2 sing N N 180 U P "O5'" sing N N 181 U OP2 HOP2 sing N N 182 U "O5'" "C5'" sing N N 183 U "C5'" "C4'" sing N N 184 U "C5'" "H5'" sing N N 185 U "C5'" "H5''" sing N N 186 U "C4'" "O4'" sing N N 187 U "C4'" "C3'" sing N N 188 U "C4'" "H4'" sing N N 189 U "O4'" "C1'" sing N N 190 U "C3'" "O3'" sing N N 191 U "C3'" "C2'" sing N N 192 U "C3'" "H3'" sing N N 193 U "O3'" "HO3'" sing N N 194 U "C2'" "O2'" sing N N 195 U "C2'" "C1'" sing N N 196 U "C2'" "H2'" sing N N 197 U "O2'" "HO2'" sing N N 198 U "C1'" N1 sing N N 199 U "C1'" "H1'" sing N N 200 U N1 C2 sing N N 201 U N1 C6 sing N N 202 U C2 O2 doub N N 203 U C2 N3 sing N N 204 U N3 C4 sing N N 205 U N3 H3 sing N N 206 U C4 O4 doub N N 207 U C4 C5 sing N N 208 U C5 C6 doub N N 209 U C5 H5 sing N N 210 U C6 H6 sing N N 211 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3P59 'double helix' 3P59 'a-form double helix' 3P59 'bulge loop' 3P59 '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 C 1 1_555 D G 4 1_555 1.766 -0.049 -0.123 13.301 -20.031 27.928 1 A_C46:G107_D A 46 ? D 107 ? ? 1 1 A C 2 1_555 D G 3 1_555 -0.250 0.073 0.424 -6.187 0.102 -1.733 2 A_C47:G106_D A 47 ? D 106 ? 19 1 1 A G 3 1_555 D C 2 1_555 0.687 -0.448 0.680 6.698 -12.964 0.005 3 A_G48:C105_D A 48 ? D 105 ? 19 1 1 A G 4 1_555 D C 1 1_555 0.260 -0.350 -0.081 -6.355 -27.217 -3.470 4 A_G49:C104_D A 49 ? D 104 ? 19 1 1 A A 5 1_555 B U 10 1_555 0.259 -0.069 0.196 -1.546 -20.937 0.296 5 A_A50:U113_B A 50 ? B 113 ? 20 1 1 A G 6 1_555 B C 9 1_555 0.112 -0.100 0.528 7.974 -12.261 -1.596 6 A_G51:C112_B A 51 ? B 112 ? 19 1 1 A G 7 1_555 B C 8 1_555 -0.585 -0.254 0.101 15.724 -12.501 -6.472 7 A_G52:C111_B A 52 ? B 111 ? 19 1 1 A C 13 1_555 B G 7 1_555 0.702 -0.160 -0.241 9.562 -8.702 3.284 8 A_C58:G110_B A 58 ? B 110 ? 19 1 1 A 5BU 14 1_555 B A 6 1_555 0.469 -0.520 -0.137 10.807 -13.704 1.982 9 A_5BU59:A109_B A 59 ? B 109 ? 20 1 1 A G 15 1_555 B C 5 1_555 -0.461 0.110 0.299 5.212 -15.738 4.271 10 A_G60:C108_B A 60 ? B 108 ? 19 1 1 G C 1 1_555 B G 4 1_555 0.197 -0.434 -0.162 1.591 -14.832 -5.990 11 G_C46:G107_B G 46 ? B 107 ? 19 1 1 G C 2 1_555 B G 3 1_555 1.351 -0.456 -0.184 2.359 -6.101 7.466 12 G_C47:G106_B G 47 ? B 106 ? 19 1 1 G G 3 1_555 B C 2 1_555 -0.299 0.049 -0.290 -7.546 -8.422 4.723 13 G_G48:C105_B G 48 ? B 105 ? 19 1 1 G G 4 1_555 B C 1 1_555 -0.695 0.157 -0.123 -4.729 -10.238 -0.551 14 G_G49:C104_B G 49 ? B 104 ? 19 1 1 G A 5 1_555 H U 10 1_555 1.368 0.213 -0.861 -0.086 -4.357 6.156 15 G_A50:U113_H G 50 ? H 113 ? ? ? 1 G G 6 1_555 H C 9 1_555 -0.251 -0.230 -1.149 -14.993 -5.348 4.319 16 G_G51:C112_H G 51 ? H 112 ? 19 1 1 G G 7 1_555 H C 8 1_555 -0.392 -0.203 0.212 2.412 3.268 0.262 17 G_G52:C111_H G 52 ? H 111 ? 19 1 1 D C 8 1_555 C G 7 1_555 0.664 -0.090 -0.687 13.440 -21.189 3.806 18 D_C111:G52_C D 111 ? C 52 ? 19 1 1 D C 9 1_555 C G 6 1_555 -0.194 -0.255 0.131 -2.687 -15.320 -0.335 19 D_C112:G51_C D 112 ? C 51 ? 19 1 1 D U 10 1_555 C A 5 1_555 -0.143 0.094 -0.180 0.041 -8.662 4.356 20 D_U113:A50_C D 113 ? C 50 ? 20 1 1 F C 1 1_555 C G 4 1_555 0.483 0.100 -0.029 2.571 -17.414 5.995 21 F_C104:G49_C F 104 ? C 49 ? 19 1 1 F C 2 1_555 C G 3 1_555 0.665 0.057 -0.552 11.805 -15.081 4.780 22 F_C105:G48_C F 105 ? C 48 ? 19 1 1 F G 3 1_555 C C 2 1_555 -0.247 -0.138 0.126 -1.305 -12.777 -1.175 23 F_G106:C47_C F 106 ? C 47 ? 19 1 1 F G 4 1_555 C C 1 1_555 -0.416 -0.185 -0.236 -1.115 -18.314 4.047 24 F_G107:C46_C F 107 ? C 46 ? 19 1 1 F C 5 1_555 E G 15 1_555 0.121 0.068 0.031 1.526 -16.953 1.426 25 F_C108:G60_E F 108 ? E 60 ? 19 1 1 F A 6 1_555 E 5BU 14 1_555 0.121 0.006 0.023 -6.538 -20.054 7.388 26 F_A109:5BU59_E F 109 ? E 59 ? 20 1 1 F G 7 1_555 E C 13 1_555 -0.714 0.092 -0.236 -9.573 -19.032 3.436 27 F_G110:C58_E F 110 ? E 58 ? 19 1 1 F C 8 1_555 E A 12 1_555 2.521 -0.156 0.300 -10.886 -20.943 12.029 28 F_C111:A57_E F 111 ? E 57 ? ? 1 1 C C 13 1_555 D G 7 1_555 -1.847 -0.475 1.544 14.630 10.134 -25.419 29 C_C58:G110_D C 58 ? D 110 ? ? 1 1 F C 9 1_555 E G 6 1_555 1.339 0.027 0.521 -9.024 -7.042 23.612 30 F_C112:G51_E F 112 ? E 51 ? ? 1 1 F U 10 1_555 E A 5 1_555 1.270 -0.593 -0.469 -5.087 -3.014 4.325 31 F_U113:A50_E F 113 ? E 50 ? 20 1 1 H C 1 1_555 E G 4 1_555 -0.386 -0.142 0.387 -0.258 -4.643 8.664 32 H_C104:G49_E H 104 ? E 49 ? 19 1 1 H C 2 1_555 E G 3 1_555 1.257 -1.064 0.121 -2.492 -2.398 -0.778 33 H_C105:G48_E H 105 ? E 48 ? 19 1 1 H G 3 1_555 E C 2 1_555 -0.375 -0.511 0.182 -3.907 -11.971 -6.251 34 H_G106:C47_E H 106 ? E 47 ? 19 1 1 H G 4 1_555 E C 1 1_555 -0.870 0.616 0.186 -5.299 -9.601 5.502 35 H_G107:C46_E H 107 ? E 46 ? ? ? 1 H C 5 1_555 G G 15 1_555 1.465 -0.080 -0.098 -4.163 -10.859 6.618 36 H_C108:G60_G H 108 ? G 60 ? ? 1 1 H A 6 1_555 G 5BU 14 1_555 0.195 0.010 0.427 5.313 -24.431 -2.440 37 H_A109:5BU59_G H 109 ? G 59 ? 20 1 1 H G 7 1_555 G C 13 1_555 -0.111 -0.333 -0.752 -0.433 10.393 -14.469 38 H_G110:C58_G H 110 ? G 58 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 D G 4 1_555 A C 2 1_555 D G 3 1_555 -1.846 -2.207 3.549 -5.999 15.385 23.779 -7.711 2.420 2.151 32.756 12.773 28.882 1 AA_C46C47:G106G107_DD A 46 ? D 107 ? A 47 ? D 106 ? 1 A C 2 1_555 D G 3 1_555 A G 3 1_555 D C 2 1_555 0.275 -2.539 2.648 -1.491 10.709 38.559 -4.583 -0.523 1.893 15.840 2.205 39.991 2 AA_C47G48:C105G106_DD A 47 ? D 106 ? A 48 ? D 105 ? 1 A G 3 1_555 D C 2 1_555 A G 4 1_555 D C 1 1_555 0.424 -1.821 3.795 9.940 3.569 23.918 -5.148 2.174 3.394 8.124 -22.624 26.115 3 AA_G48G49:C104C105_DD A 48 ? D 105 ? A 49 ? D 104 ? 1 A G 4 1_555 D C 1 1_555 A A 5 1_555 B U 10 1_555 -0.624 -2.341 2.822 -2.181 12.621 31.702 -5.465 0.807 1.822 22.013 3.804 34.130 4 AA_G49A50:U113C104_BD A 49 ? D 104 ? A 50 ? B 113 ? 1 A A 5 1_555 B U 10 1_555 A G 6 1_555 B C 9 1_555 -0.680 -1.789 2.982 -3.551 4.292 21.243 -6.151 0.583 2.650 11.392 9.426 21.953 5 AA_A50G51:C112U113_BB A 50 ? B 113 ? A 51 ? B 112 ? 1 A G 6 1_555 B C 9 1_555 A G 7 1_555 B C 8 1_555 -0.218 -2.370 2.988 3.227 2.992 27.536 -5.541 1.125 2.678 6.235 -6.725 27.879 6 AA_G51G52:C111C112_BB A 51 ? B 112 ? A 52 ? B 111 ? 1 A C 13 1_555 B G 7 1_555 A 5BU 14 1_555 B A 6 1_555 -0.956 -1.536 3.478 -2.822 10.586 26.997 -5.361 1.290 2.774 21.581 5.754 29.097 7 AA_C585BU59:A109G110_BB A 58 ? B 110 ? A 59 ? B 109 ? 1 A 5BU 14 1_555 B A 6 1_555 A G 15 1_555 B C 5 1_555 -0.338 -1.671 3.278 -4.349 14.873 25.241 -6.050 -0.148 2.030 30.628 8.955 29.552 8 AA_5BU59G60:C108A109_BB A 59 ? B 109 ? A 60 ? B 108 ? 1 A G 15 1_555 B C 5 1_555 G C 1 1_555 B G 4 1_555 -1.104 -0.936 3.279 -1.631 3.802 42.859 -1.650 1.344 3.226 5.189 2.226 43.049 9 AG_G60C46:G107C108_BB A 60 ? B 108 ? G 46 ? B 107 ? 1 G C 1 1_555 B G 4 1_555 G C 2 1_555 B G 3 1_555 -0.098 -1.617 3.332 2.070 7.794 37.770 -3.380 0.397 2.944 11.875 -3.153 38.591 10 GG_C46C47:G106G107_BB G 46 ? B 107 ? G 47 ? B 106 ? 1 G C 2 1_555 B G 3 1_555 G G 3 1_555 B C 2 1_555 0.462 -2.061 3.230 4.173 18.417 23.272 -7.017 -0.212 1.338 38.529 -8.731 29.887 11 GG_C47G48:C105G106_BB G 47 ? B 106 ? G 48 ? B 105 ? 1 G G 3 1_555 B C 2 1_555 G G 4 1_555 B C 1 1_555 0.612 -1.934 2.957 -0.344 10.985 25.373 -6.149 -1.347 1.957 23.644 0.740 27.615 12 GG_G48G49:C104C105_BB G 48 ? B 105 ? G 49 ? B 104 ? 1 G G 4 1_555 B C 1 1_555 G A 5 1_555 H U 10 1_555 -1.584 -2.284 3.284 4.423 7.718 34.808 -4.702 3.141 2.523 12.648 -7.249 35.892 13 GG_G49A50:U113C104_HB G 49 ? B 104 ? G 50 ? H 113 ? 1 G A 5 1_555 H U 10 1_555 G G 6 1_555 H C 9 1_555 0.213 -1.623 3.933 2.971 16.879 16.467 -9.571 0.472 1.620 45.754 -8.055 23.725 14 GG_A50G51:C112U113_HH G 50 ? H 113 ? G 51 ? H 112 ? 1 G G 6 1_555 H C 9 1_555 G G 7 1_555 H C 8 1_555 0.696 -1.924 3.010 -9.643 -0.641 31.078 -3.337 -2.755 2.716 -1.161 17.476 32.511 15 GG_G51G52:C111C112_HH G 51 ? H 112 ? G 52 ? H 111 ? 1 D C 8 1_555 C G 7 1_555 D C 9 1_555 C G 6 1_555 -0.873 -1.702 3.716 -9.129 10.425 27.670 -5.405 -0.295 3.027 20.266 17.748 30.886 16 DD_C111C112:G51G52_CC D 111 ? C 52 ? D 112 ? C 51 ? 1 D C 9 1_555 C G 6 1_555 D U 10 1_555 C A 5 1_555 0.032 -1.832 3.165 -1.309 5.914 30.597 -4.441 -0.289 2.767 11.071 2.451 31.177 17 DD_C112U113:A50G51_CC D 112 ? C 51 ? D 113 ? C 50 ? 1 D U 10 1_555 C A 5 1_555 F C 1 1_555 C G 4 1_555 1.892 -1.942 3.320 5.974 10.453 20.654 -7.961 -2.707 2.505 26.450 -15.117 23.874 18 DF_U113C104:G49A50_CC D 113 ? C 50 ? F 104 ? C 49 ? 1 F C 1 1_555 C G 4 1_555 F C 2 1_555 C G 3 1_555 -0.906 -1.472 3.031 1.513 7.883 30.896 -3.921 1.888 2.541 14.493 -2.782 31.898 19 FF_C104C105:G48G49_CC F 104 ? C 49 ? F 105 ? C 48 ? 1 F C 2 1_555 C G 3 1_555 F G 3 1_555 C C 2 1_555 -0.577 -1.722 3.592 -7.487 13.848 23.517 -6.720 -0.542 2.319 30.043 16.243 28.238 20 FF_C105G106:C47G48_CC F 105 ? C 48 ? F 106 ? C 47 ? 1 F G 3 1_555 C C 2 1_555 F G 4 1_555 C C 1 1_555 -0.310 -1.267 3.211 0.773 8.716 35.631 -3.133 0.592 2.827 13.984 -1.240 36.656 21 FF_G106G107:C46C47_CC F 106 ? C 47 ? F 107 ? C 46 ? 1 F G 4 1_555 C C 1 1_555 F C 5 1_555 E G 15 1_555 0.874 -1.141 3.194 -1.092 2.755 36.148 -2.203 -1.551 3.075 4.431 1.756 36.266 22 FF_G107C108:G60C46_EC F 107 ? C 46 ? F 108 ? E 60 ? 1 F C 5 1_555 E G 15 1_555 F A 6 1_555 E 5BU 14 1_555 0.861 -1.118 3.280 -0.169 13.585 37.108 -3.178 -1.295 2.718 20.523 0.255 39.435 23 FF_C108A109:5BU59G60_EE F 108 ? E 60 ? F 109 ? E 59 ? 1 F A 6 1_555 E 5BU 14 1_555 F G 7 1_555 E C 13 1_555 -0.851 -2.074 3.203 -1.535 10.485 21.442 -7.901 1.633 2.033 26.218 3.837 23.890 24 FF_A109G110:C585BU59_EE F 109 ? E 59 ? F 110 ? E 58 ? 1 F G 7 1_555 E C 13 1_555 F C 8 1_555 E A 12 1_555 0.079 -0.864 3.367 1.045 11.077 46.568 -1.950 -0.015 3.097 13.781 -1.300 47.806 25 FF_G110C111:A57C58_EE F 110 ? E 58 ? F 111 ? E 57 ? 1 F C 9 1_555 E G 6 1_555 F U 10 1_555 E A 5 1_555 -0.795 -2.058 3.242 7.061 -1.209 27.737 -3.894 3.167 3.036 -2.469 -14.425 28.629 26 FF_C112U113:A50G51_EE F 112 ? E 51 ? F 113 ? E 50 ? 1 F U 10 1_555 E A 5 1_555 H C 1 1_555 E G 4 1_555 1.091 -1.812 3.112 -4.451 9.577 24.000 -6.127 -3.396 2.020 21.733 10.100 26.189 27 FH_U113C104:G49A50_EE F 113 ? E 50 ? H 104 ? E 49 ? 1 H C 1 1_555 E G 4 1_555 H C 2 1_555 E G 3 1_555 -0.867 -1.582 3.108 -1.582 1.971 43.154 -2.329 1.031 3.064 2.678 2.149 43.225 28 HH_C104C105:G48G49_EE H 104 ? E 49 ? H 105 ? E 48 ? 1 H C 2 1_555 E G 3 1_555 H G 3 1_555 E C 2 1_555 -0.548 -1.775 3.275 1.520 -1.183 21.649 -4.237 2.059 3.320 -3.143 -4.038 21.734 29 HH_C105G106:C47G48_EE H 105 ? E 48 ? H 106 ? E 47 ? 1 H G 3 1_555 E C 2 1_555 H G 4 1_555 E C 1 1_555 0.167 -2.730 2.963 -1.481 19.385 31.512 -6.100 -0.400 1.138 32.152 2.457 36.897 30 HH_G106G107:C46C47_EE H 106 ? E 47 ? H 107 ? E 46 ? 1 H G 4 1_555 E C 1 1_555 H C 5 1_555 G G 15 1_555 0.438 -1.042 3.238 1.899 -0.343 46.079 -1.301 -0.398 3.260 -0.438 -2.425 46.117 31 HH_G107C108:G60C46_GE H 107 ? E 46 ? H 108 ? G 60 ? 1 H C 5 1_555 G G 15 1_555 H A 6 1_555 G 5BU 14 1_555 -0.154 -1.903 2.834 -5.179 18.479 26.114 -5.699 -0.362 1.256 35.442 9.933 32.309 32 HH_C108A109:5BU59G60_GG H 108 ? G 60 ? H 109 ? G 59 ? 1 H A 6 1_555 G 5BU 14 1_555 H G 7 1_555 G C 13 1_555 0.084 -1.990 3.646 7.722 3.826 31.564 -4.253 1.298 3.316 6.875 -13.875 32.690 33 HH_A109G110:C585BU59_GG H 109 ? G 59 ? H 110 ? G 58 ? # _atom_sites.entry_id 3P59 _atom_sites.fract_transf_matrix[1][1] 0.016031 _atom_sites.fract_transf_matrix[1][2] 0.009256 _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] 0.018511 _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] 0.007920 _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 BR C CO MG N O P # loop_