data_1Q9A # _entry.id 1Q9A # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1Q9A pdb_00001q9a 10.2210/pdb1q9a/pdb NDB UR0035 ? ? RCSB RCSB020077 ? ? WWPDB D_1000020077 ? ? # 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 2003-11-25 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _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' # 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 # 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' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Q9A _pdbx_database_status.recvd_initial_deposition_date 2003-08-22 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1MSY 'Guaa Tetraloop Mutant Of Sarcin/Ricin Domain From E. Coli 23 S Rrna' unspecified PDB 483D 'Crystal Structure Of The Sarcin/Ricin Domain From E. Coli 23 S Rrna' unspecified PDB 1JBS 'Crystal Structure Of Ribotoxin Restrictocin and A 29-Mer Srd RNA Analog' unspecified PDB 1JBR 'Crystal Structure Of The Ribotoxin Restrictocin and A 31- Mer Srd RNA Inhibitor' unspecified PDB 480D 'Crystal Structure Of The Sarcin/Ricin Domain From E. Coli 23 S Rrna' unspecified PDB 1Q93 'Crystal structure of a mutant of the sarcin/ricin domain from rat 28S rRNA' unspecified PDB 1Q96 'Crystal structure of a mutant of the sarcin/ricin domain from rat 28S rRNA' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Correll, C.C.' 1 'Beneken, J.' 2 'Plantinga, M.J.' 3 'Lubbers, M.' 4 'Chan, Y.L.' 5 # _citation.id primary _citation.title 'The common and distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 31 _citation.page_first 6806 _citation.page_last 6818 _citation.year 2003 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 14627814 _citation.pdbx_database_id_DOI 10.1093/nar/gkg908 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Correll, C.C.' 1 ? primary 'Beneken, J.' 2 ? primary 'Plantinga, M.J.' 3 ? primary 'Lubbers, M.' 4 ? primary 'Chan, Y.L.' 5 ? # 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 'Sarcin/ricin 23S rRNA' 8744.255 1 ? ? 'sarcin/ricin domain' ? 2 water nat water 18.015 179 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code UGCUCCUAGUACGAGAGGACCGGAGUG _entity_poly.pdbx_seq_one_letter_code_can UGCUCCUAGUACGAGAGGACCGGAGUG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 U n 1 5 C n 1 6 C n 1 7 U n 1 8 A n 1 9 G n 1 10 U n 1 11 A n 1 12 C n 1 13 G n 1 14 A n 1 15 G n 1 16 A n 1 17 G n 1 18 G n 1 19 A n 1 20 C n 1 21 C n 1 22 G n 1 23 G n 1 24 A n 1 25 G n 1 26 U n 1 27 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _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 ;THE 23S ribosomal RNA WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE 23S ribosomal RNA IS NATURALLY FOUND IN Escherichia coli (bacteria). ; # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 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 2647 2647 U U A . n A 1 2 G 2 2648 2648 G G A . n A 1 3 C 3 2649 2649 C C A . n A 1 4 U 4 2650 2650 U U A . n A 1 5 C 5 2651 2651 C C A . n A 1 6 C 6 2652 2652 C C A . n A 1 7 U 7 2653 2653 U U A . n A 1 8 A 8 2654 2654 A A A . n A 1 9 G 9 2655 2655 G G A . n A 1 10 U 10 2656 2656 U U A . n A 1 11 A 11 2657 2657 A A A . n A 1 12 C 12 2658 2658 C C A . n A 1 13 G 13 2659 2659 G G A . n A 1 14 A 14 2660 2660 A A A . n A 1 15 G 15 2661 2661 G G A . n A 1 16 A 16 2662 2662 A A A . n A 1 17 G 17 2663 2663 G G A . n A 1 18 G 18 2664 2664 G G A . n A 1 19 A 19 2665 2665 A A A . n A 1 20 C 20 2666 2666 C C A . n A 1 21 C 21 2667 2667 C C A . n A 1 22 G 22 2668 2668 G G A . n A 1 23 G 23 2669 2669 G G A . n A 1 24 A 24 2670 2670 A A A . n A 1 25 G 25 2671 2671 G G A . n A 1 26 U 26 2672 2672 U U A . n A 1 27 G 27 2673 2673 G G A . 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 B 2 HOH 1 4001 4001 HOH HOH A . B 2 HOH 2 4002 4002 HOH HOH A . B 2 HOH 3 4003 4003 HOH HOH A . B 2 HOH 4 4004 4004 HOH HOH A . B 2 HOH 5 4005 4005 HOH HOH A . B 2 HOH 6 4006 4006 HOH HOH A . B 2 HOH 7 4007 4007 HOH HOH A . B 2 HOH 8 4008 4008 HOH HOH A . B 2 HOH 9 4009 4009 HOH HOH A . B 2 HOH 10 4010 4010 HOH HOH A . B 2 HOH 11 4011 4011 HOH HOH A . B 2 HOH 12 4012 4012 HOH HOH A . B 2 HOH 13 4013 4013 HOH HOH A . B 2 HOH 14 4014 4014 HOH HOH A . B 2 HOH 15 4015 4015 HOH HOH A . B 2 HOH 16 4016 4016 HOH HOH A . B 2 HOH 17 4017 4017 HOH HOH A . B 2 HOH 18 4018 4018 HOH HOH A . B 2 HOH 19 4019 4019 HOH HOH A . B 2 HOH 20 4020 4020 HOH HOH A . B 2 HOH 21 4021 4021 HOH HOH A . B 2 HOH 22 4022 4022 HOH HOH A . B 2 HOH 23 4023 4023 HOH HOH A . B 2 HOH 24 4024 4024 HOH HOH A . B 2 HOH 25 4025 4025 HOH HOH A . B 2 HOH 26 4026 4026 HOH HOH A . B 2 HOH 27 4027 4027 HOH HOH A . B 2 HOH 28 4028 4028 HOH HOH A . B 2 HOH 29 4029 4029 HOH HOH A . B 2 HOH 30 4030 4030 HOH HOH A . B 2 HOH 31 4031 4031 HOH HOH A . B 2 HOH 32 4032 4032 HOH HOH A . B 2 HOH 33 4033 4033 HOH HOH A . B 2 HOH 34 4034 4034 HOH HOH A . B 2 HOH 35 4035 4035 HOH HOH A . B 2 HOH 36 4036 4036 HOH HOH A . B 2 HOH 37 4037 4037 HOH HOH A . B 2 HOH 38 4038 4038 HOH HOH A . B 2 HOH 39 4039 4039 HOH HOH A . B 2 HOH 40 4040 4040 HOH HOH A . B 2 HOH 41 4041 4041 HOH HOH A . B 2 HOH 42 4042 4042 HOH HOH A . B 2 HOH 43 4043 4043 HOH HOH A . B 2 HOH 44 4044 4044 HOH HOH A . B 2 HOH 45 4045 4045 HOH HOH A . B 2 HOH 46 4046 4046 HOH HOH A . B 2 HOH 47 4047 4047 HOH HOH A . B 2 HOH 48 4048 4048 HOH HOH A . B 2 HOH 49 4049 4049 HOH HOH A . B 2 HOH 50 4050 4050 HOH HOH A . B 2 HOH 51 4051 4051 HOH HOH A . B 2 HOH 52 4052 4052 HOH HOH A . B 2 HOH 53 4053 4053 HOH HOH A . B 2 HOH 54 4054 4054 HOH HOH A . B 2 HOH 55 4055 4055 HOH HOH A . B 2 HOH 56 4056 4056 HOH HOH A . B 2 HOH 57 4057 4057 HOH HOH A . B 2 HOH 58 4058 4058 HOH HOH A . B 2 HOH 59 4059 4059 HOH HOH A . B 2 HOH 60 4060 4060 HOH HOH A . B 2 HOH 61 4061 4061 HOH HOH A . B 2 HOH 62 4062 4062 HOH HOH A . B 2 HOH 63 4063 4063 HOH HOH A . B 2 HOH 64 4064 4064 HOH HOH A . B 2 HOH 65 4065 4065 HOH HOH A . B 2 HOH 66 4066 4066 HOH HOH A . B 2 HOH 67 4067 4067 HOH HOH A . B 2 HOH 68 4068 4068 HOH HOH A . B 2 HOH 69 4069 4069 HOH HOH A . B 2 HOH 70 4070 4070 HOH HOH A . B 2 HOH 71 4071 4071 HOH HOH A . B 2 HOH 72 4072 4072 HOH HOH A . B 2 HOH 73 4073 4073 HOH HOH A . B 2 HOH 74 4074 4074 HOH HOH A . B 2 HOH 75 4075 4075 HOH HOH A . B 2 HOH 76 4076 4076 HOH HOH A . B 2 HOH 77 4077 4077 HOH HOH A . B 2 HOH 78 4078 4078 HOH HOH A . B 2 HOH 79 4079 4079 HOH HOH A . B 2 HOH 80 4080 4080 HOH HOH A . B 2 HOH 81 4081 4081 HOH HOH A . B 2 HOH 82 4082 4082 HOH HOH A . B 2 HOH 83 4083 4083 HOH HOH A . B 2 HOH 84 4084 4084 HOH HOH A . B 2 HOH 85 4085 4085 HOH HOH A . B 2 HOH 86 4086 4086 HOH HOH A . B 2 HOH 87 4087 4087 HOH HOH A . B 2 HOH 88 4088 4088 HOH HOH A . B 2 HOH 89 4089 4089 HOH HOH A . B 2 HOH 90 4090 4090 HOH HOH A . B 2 HOH 91 4091 4091 HOH HOH A . B 2 HOH 92 4092 4092 HOH HOH A . B 2 HOH 93 4093 4093 HOH HOH A . B 2 HOH 94 4094 4094 HOH HOH A . B 2 HOH 95 4095 4095 HOH HOH A . B 2 HOH 96 4096 4096 HOH HOH A . B 2 HOH 97 4097 4097 HOH HOH A . B 2 HOH 98 4098 4098 HOH HOH A . B 2 HOH 99 4099 4099 HOH HOH A . B 2 HOH 100 4100 4100 HOH HOH A . B 2 HOH 101 4101 4101 HOH HOH A . B 2 HOH 102 4102 4102 HOH HOH A . B 2 HOH 103 4103 4103 HOH HOH A . B 2 HOH 104 4104 4104 HOH HOH A . B 2 HOH 105 4105 4105 HOH HOH A . B 2 HOH 106 4106 4106 HOH HOH A . B 2 HOH 107 4107 4107 HOH HOH A . B 2 HOH 108 4108 4108 HOH HOH A . B 2 HOH 109 4109 4109 HOH HOH A . B 2 HOH 110 4110 4110 HOH HOH A . B 2 HOH 111 4111 4111 HOH HOH A . B 2 HOH 112 4112 4112 HOH HOH A . B 2 HOH 113 4113 4113 HOH HOH A . B 2 HOH 114 4114 4114 HOH HOH A . B 2 HOH 115 4115 4115 HOH HOH A . B 2 HOH 116 4116 4116 HOH HOH A . B 2 HOH 117 4117 4117 HOH HOH A . B 2 HOH 118 4118 4118 HOH HOH A . B 2 HOH 119 4119 4119 HOH HOH A . B 2 HOH 120 4120 4120 HOH HOH A . B 2 HOH 121 4121 4121 HOH HOH A . B 2 HOH 122 4122 4122 HOH HOH A . B 2 HOH 123 4123 4123 HOH HOH A . B 2 HOH 124 4124 4124 HOH HOH A . B 2 HOH 125 4125 4125 HOH HOH A . B 2 HOH 126 4126 4126 HOH HOH A . B 2 HOH 127 4127 4127 HOH HOH A . B 2 HOH 128 4128 4128 HOH HOH A . B 2 HOH 129 4129 4129 HOH HOH A . B 2 HOH 130 4130 4130 HOH HOH A . B 2 HOH 131 4131 4131 HOH HOH A . B 2 HOH 132 4132 4132 HOH HOH A . B 2 HOH 133 4133 4133 HOH HOH A . B 2 HOH 134 4134 4134 HOH HOH A . B 2 HOH 135 4135 4135 HOH HOH A . B 2 HOH 136 4136 4136 HOH HOH A . B 2 HOH 137 4137 4137 HOH HOH A . B 2 HOH 138 4138 4138 HOH HOH A . B 2 HOH 139 4139 4139 HOH HOH A . B 2 HOH 140 4140 4140 HOH HOH A . B 2 HOH 141 4141 4141 HOH HOH A . B 2 HOH 142 4142 4142 HOH HOH A . B 2 HOH 143 4143 4143 HOH HOH A . B 2 HOH 144 4144 4144 HOH HOH A . B 2 HOH 145 4145 4145 HOH HOH A . B 2 HOH 146 4146 4146 HOH HOH A . B 2 HOH 147 4147 4147 HOH HOH A . B 2 HOH 148 4148 4148 HOH HOH A . B 2 HOH 149 4149 4149 HOH HOH A . B 2 HOH 150 4150 4150 HOH HOH A . B 2 HOH 151 4151 4151 HOH HOH A . B 2 HOH 152 4152 4152 HOH HOH A . B 2 HOH 153 4153 4153 HOH HOH A . B 2 HOH 154 4154 4154 HOH HOH A . B 2 HOH 155 4155 4155 HOH HOH A . B 2 HOH 156 4156 4156 HOH HOH A . B 2 HOH 157 4157 4157 HOH HOH A . B 2 HOH 158 4158 4158 HOH HOH A . B 2 HOH 159 4159 4159 HOH HOH A . B 2 HOH 160 4160 4160 HOH HOH A . B 2 HOH 161 4161 4161 HOH HOH A . B 2 HOH 162 4162 4162 HOH HOH A . B 2 HOH 163 4163 4163 HOH HOH A . B 2 HOH 164 4164 4164 HOH HOH A . B 2 HOH 165 4165 4165 HOH HOH A . B 2 HOH 166 4166 4166 HOH HOH A . B 2 HOH 167 4167 4167 HOH HOH A . B 2 HOH 168 4168 4168 HOH HOH A . B 2 HOH 169 4169 4169 HOH HOH A . B 2 HOH 170 4170 4170 HOH HOH A . B 2 HOH 171 4171 4171 HOH HOH A . B 2 HOH 172 4172 4172 HOH HOH A . B 2 HOH 173 4173 4173 HOH HOH A . B 2 HOH 174 4174 4174 HOH HOH A . B 2 HOH 175 4175 4175 HOH HOH A . B 2 HOH 176 4176 4176 HOH HOH A . B 2 HOH 177 4177 4177 HOH HOH A . B 2 HOH 178 4178 4178 HOH HOH A . B 2 HOH 179 4179 4179 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 SCALEPACK 'data scaling' . ? 2 SHELXS phasing . ? 3 SHELXL-97 refinement . ? 4 HKL-2000 'data reduction' . ? 5 # _cell.entry_id 1Q9A _cell.length_a 29.529 _cell.length_b 29.529 _cell.length_c 76.574 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Q9A _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 78 _symmetry.cell_setting ? # _exptl.entry_id 1Q9A _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.91 _exptl_crystal.density_percent_sol 35.57 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'ammonium sulfate, K-MOPS, magnesium chloride, manganese chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K' _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 'ammonium sulfate' ? ? ? 1 2 1 K-MOPS ? ? ? 1 3 1 'magnesium chloride' ? ? ? 1 4 1 'manganese chloride' ? ? ? 1 5 1 H2O ? ? ? 1 6 2 'ammonium sulfate' ? ? ? 1 7 2 K-MOPS ? ? ? 1 8 2 'magnesium chloride' ? ? ? 1 9 2 'manganese chloride' ? ? ? 1 10 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type CUSTOM-MADE _diffrn_detector.pdbx_collection_date 2000-07-07 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97764 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97764 # _reflns.entry_id 1Q9A _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 1.04 _reflns.d_resolution_low 40 _reflns.number_all 31452 _reflns.number_obs 29848 _reflns.percent_possible_obs 94.9 _reflns.pdbx_Rmerge_I_obs 0.037 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 55.3 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.1 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.04 _reflns_shell.d_res_low 1.06 _reflns_shell.percent_possible_all 82.5 _reflns_shell.Rmerge_I_obs 0.446 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.0 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1Q9A _refine.ls_d_res_high 1.04 _refine.ls_d_res_low 40 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I 0.0 _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 29814 _refine.ls_number_reflns_R_free 2981 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_all 0.1477 _refine.ls_R_factor_obs 0.1477 _refine.ls_R_factor_R_work 0.1361 _refine.ls_R_factor_R_free 0.1774 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _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.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 708 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 179 _refine_hist.number_atoms_total 887 _refine_hist.d_res_high 1.04 _refine_hist.d_res_low 40 # 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 o_bond_d 0.007 ? ? ? 'X-RAY DIFFRACTION' ? o_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? o_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? o_angle_d 0.023 ? ? ? 'X-RAY DIFFRACTION' ? o_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? o_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? o_angle_deg ? ? ? ? 'X-RAY DIFFRACTION' ? o_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? o_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? o_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? o_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? o_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? o_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? o_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? o_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? o_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? o_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? o_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? o_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1Q9A _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 1Q9A _struct.title 'Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Q9A _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'sarcin/ricin domain, ribonucleic acid, RNA recognition, high resolution, ribosomes, 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 ? # _struct_ref.id 1 _struct_ref.db_name GB _struct_ref.db_code AE016770 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code UGCUCCUAGUACGAGAGGACCGGAGUG _struct_ref.pdbx_align_begin 32034 _struct_ref.pdbx_db_accession 26111017 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1Q9A _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 27 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 26111017 _struct_ref_seq.db_align_beg 32034 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 32060 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2647 _struct_ref_seq.pdbx_auth_seq_align_end 2673 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 2 N1 A ? ? 1_555 A U 26 O2 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A G 2 O6 A ? ? 1_555 A U 26 N3 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A C 3 N3 A ? ? 1_555 A G 25 N1 A ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N4 A ? ? 1_555 A G 25 O6 A ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 O2 A ? ? 1_555 A G 25 N2 A ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 4 N3 A ? ? 1_555 A A 24 N1 ? ? A U 2650 A A 2670 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 4 O4 A ? ? 1_555 A A 24 N6 ? ? A U 2650 A A 2670 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 O2 ? ? ? 1_555 A C 21 N4 ? ? A U 2653 A C 2667 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog15 hydrog ? ? A G 9 N2 ? ? ? 1_555 A U 10 O4 ? ? A G 2655 A U 2656 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog16 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 19 N7 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog17 hydrog ? ? A U 10 O2 ? ? ? 1_555 A A 19 N6 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog18 hydrog ? ? A A 11 N6 ? ? ? 1_555 A G 18 N3 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog19 hydrog ? ? A A 11 N7 ? ? ? 1_555 A G 18 N2 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog20 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 13 N2 ? ? ? 1_555 A A 16 N7 ? ? A G 2659 A A 2662 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 N9 A G 2659 ? ? "C1'" A G 2659 ? ? "C2'" A G 2659 ? ? 104.22 112.00 -7.78 1.10 N 2 1 N9 A G 2663 ? ? "C1'" A G 2663 ? ? "C2'" A G 2663 ? ? 104.99 112.00 -7.01 1.10 N 3 1 C5 A G 2668 ? ? C6 A G 2668 ? ? N1 A G 2668 ? ? 114.59 111.50 3.09 0.50 N 4 1 "C3'" A G 2669 ? ? "C2'" A G 2669 ? ? "C1'" A G 2669 ? ? 96.97 101.30 -4.33 0.70 N 5 1 C5 A G 2673 ? ? C6 A G 2673 ? ? O6 A G 2673 ? ? 124.96 128.60 -3.64 0.60 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 U OP3 O N N 114 U P P N N 115 U OP1 O N N 116 U OP2 O N N 117 U "O5'" O N N 118 U "C5'" C N N 119 U "C4'" C N R 120 U "O4'" O N N 121 U "C3'" C N S 122 U "O3'" O N N 123 U "C2'" C N R 124 U "O2'" O N N 125 U "C1'" C N R 126 U N1 N N N 127 U C2 C N N 128 U O2 O N N 129 U N3 N N N 130 U C4 C N N 131 U O4 O N N 132 U C5 C N N 133 U C6 C N N 134 U HOP3 H N N 135 U HOP2 H N N 136 U "H5'" H N N 137 U "H5''" H N N 138 U "H4'" H N N 139 U "H3'" H N N 140 U "HO3'" H N N 141 U "H2'" H N N 142 U "HO2'" H N N 143 U "H1'" H N N 144 U H3 H N N 145 U H5 H N N 146 U H6 H N N 147 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1Q9A 'double helix' 1Q9A 'a-form double helix' 1Q9A 'mismatched base pair' 1Q9A 'triple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 2 1_555 A U 26 1_555 -2.514 -0.759 0.287 -0.169 -15.910 -0.536 1 A_G2648:U2672_A A 2648 ? A 2672 ? 28 ? 1 A C 3 1_555 A G 25 1_555 0.393 -0.043 0.360 1.421 -10.426 -0.203 2 A_C2649:G2671_A A 2649 ? A 2671 ? 19 1 1 A U 4 1_555 A A 24 1_555 -0.389 -0.179 0.041 6.499 -13.935 -7.001 3 A_U2650:A2670_A A 2650 ? A 2670 ? 20 1 1 A C 5 1_555 A G 23 1_555 0.288 -0.133 0.035 5.553 -17.360 1.888 4 A_C2651:G2669_A A 2651 ? A 2669 ? 19 1 1 A C 6 1_555 A G 22 1_555 0.295 -0.151 0.004 -2.568 -12.508 -1.965 5 A_C2652:G2668_A A 2652 ? A 2668 ? 19 1 1 A U 7 1_555 A C 21 1_555 5.876 -2.201 -0.400 -3.860 -14.603 -13.089 6 A_U2653:C2667_A A 2653 ? A 2667 ? ? ? 1 A U 10 1_555 A A 19 1_555 4.140 -1.870 -0.708 6.717 -18.944 -102.879 7 A_U2656:A2665_A A 2656 ? A 2665 ? 24 4 1 A A 11 1_555 A G 18 1_555 -6.798 -4.307 -0.186 -2.391 4.169 -2.820 8 A_A2657:G2664_A A 2657 ? A 2664 ? 11 9 1 A C 12 1_555 A G 17 1_555 0.167 -0.102 -0.195 7.463 -1.954 0.474 9 A_C2658:G2663_A A 2658 ? A 2663 ? 19 1 1 A G 13 1_555 A A 16 1_555 7.218 -5.231 0.720 18.206 -5.008 -19.003 10 A_G2659:A2662_A A 2659 ? A 2662 ? ? ? # 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 G 2 1_555 A U 26 1_555 A C 3 1_555 A G 25 1_555 -0.544 -1.220 3.293 -4.266 3.556 44.606 -1.917 0.326 3.228 4.664 5.594 44.933 1 AA_G2648C2649:G2671U2672_AA A 2648 ? A 2672 ? A 2649 ? A 2671 ? 1 A C 3 1_555 A G 25 1_555 A U 4 1_555 A A 24 1_555 0.419 -2.424 2.840 3.110 5.287 23.118 -7.219 -0.207 2.272 12.904 -7.591 23.908 2 AA_C2649U2650:A2670G2671_AA A 2649 ? A 2671 ? A 2650 ? A 2670 ? 1 A U 4 1_555 A A 24 1_555 A C 5 1_555 A G 23 1_555 0.852 -1.461 3.170 1.069 5.130 38.248 -2.808 -1.164 2.979 7.784 -1.623 38.592 3 AA_U2650C2651:G2669A2670_AA A 2650 ? A 2670 ? A 2651 ? A 2669 ? 1 A C 5 1_555 A G 23 1_555 A C 6 1_555 A G 22 1_555 -0.708 -1.928 3.344 0.003 8.184 32.012 -4.713 1.246 2.780 14.544 -0.005 33.015 4 AA_C2651C2652:G2668G2669_AA A 2651 ? A 2669 ? A 2652 ? A 2668 ? 1 A C 6 1_555 A G 22 1_555 A U 7 1_555 A C 21 1_555 -0.531 -1.010 3.490 7.636 8.655 54.504 -1.603 1.028 3.213 9.333 -8.234 55.621 5 AA_C2652U2653:C2667G2668_AA A 2652 ? A 2668 ? A 2653 ? A 2667 ? 1 A U 7 1_555 A C 21 1_555 A U 10 1_555 A A 19 1_555 0.639 -1.033 6.275 5.555 -3.014 32.035 -0.818 0.744 6.361 -5.397 -9.945 32.637 6 AA_U2653U2656:A2665C2667_AA A 2653 ? A 2667 ? A 2656 ? A 2665 ? 1 A U 10 1_555 A A 19 1_555 A A 11 1_555 A G 18 1_555 5.029 -1.245 3.585 -1.620 -1.258 -10.944 8.670 23.019 4.113 6.522 -8.397 -11.134 7 AA_U2656A2657:G2664A2665_AA A 2656 ? A 2665 ? A 2657 ? A 2664 ? 1 A A 11 1_555 A G 18 1_555 A C 12 1_555 A G 17 1_555 -0.016 -1.127 3.134 -2.615 3.891 59.567 -1.316 -0.108 3.060 3.910 2.627 59.735 8 AA_A2657C2658:G2663G2664_AA A 2657 ? A 2664 ? A 2658 ? A 2663 ? 1 A C 12 1_555 A G 17 1_555 A G 13 1_555 A A 16 1_555 -2.690 -1.289 3.016 -6.877 6.577 49.978 -1.940 2.676 3.154 7.703 8.055 50.819 9 AA_C2658G2659:A2662G2663_AA A 2658 ? A 2663 ? A 2659 ? A 2662 ? # _atom_sites.entry_id 1Q9A _atom_sites.fract_transf_matrix[1][1] 0.033865 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.033865 _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] 0.013059 _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 N O P # loop_