data_3CGP # _entry.id 3CGP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 3CGP pdb_00003cgp 10.2210/pdb3cgp/pdb NDB AR0093 ? ? RCSB RCSB046755 ? ? WWPDB D_1000046755 ? ? # 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 2008-07-01 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 4 'Structure model' 1 3 2024-04-03 # _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' 5 4 'Structure model' 'Refinement description' # 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' struct_conn 5 3 'Structure model' struct_ref_seq 6 3 'Structure model' struct_site 7 4 'Structure model' pdbx_initial_refinement_model # 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' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_ref_seq.db_align_beg' 5 3 'Structure model' '_struct_ref_seq.db_align_end' 6 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 7 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 8 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3CGP _pdbx_database_status.recvd_initial_deposition_date 2008-03-06 _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.pdb_format_compatible Y _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 3CGQ . unspecified PDB 3CGR . unspecified PDB 3CGS . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Lin, Y.' 1 'Kielkopf, C.L.' 2 # _citation.id primary _citation.title 'X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines.' _citation.journal_abbrev Biochemistry _citation.journal_volume 47 _citation.page_first 5503 _citation.page_last 5514 _citation.year 2008 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18435545 _citation.pdbx_database_id_DOI 10.1021/bi7022392 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lin, Y.' 1 ? primary 'Kielkopf, C.L.' 2 ? # 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(*GP*CP*GP*CP*GP*(PSU)P*AP*GP*UP*AP*GP*C)-3') ; 3867.360 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*CP*GP*CP*UP*AP*CP*UP*AP*AP*CP*GP*CP*G)-3') ; 4116.518 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 4 non-polymer syn 'IODIDE ION' 126.904 3 ? ? ? ? 5 water nat water 18.015 158 ? ? ? ? # 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 'GCGCG(PSU)AGUAGC' GCGCGUAGUAGC A ? 2 polyribonucleotide no no CGCUACUAACGCG CGCUACUAACGCG B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'SULFATE ION' SO4 4 'IODIDE ION' IOD 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 G n 1 4 C n 1 5 G n 1 6 PSU n 1 7 A n 1 8 G n 1 9 U n 1 10 A n 1 11 G n 1 12 C n 2 1 C n 2 2 G n 2 3 C n 2 4 U n 2 5 A n 2 6 C n 2 7 U n 2 8 A n 2 9 A n 2 10 C n 2 11 G n 2 12 C n 2 13 G n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? 'Central nucleotides of this sequence are highly conserved in yeast U2 snRNA' 2 1 sample ? ? ? ? ? 'Central nucleotides of this sequence are highly conserved in yeast pre-mRNAs' # 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 IOD non-polymer . 'IODIDE ION' ? 'I -1' 126.904 PSU 'RNA linking' n "PSEUDOURIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 G 1 1 1 G G A . n A 1 2 C 2 2 2 C C A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 PSU 6 6 6 PSU PSU A . n A 1 7 A 7 7 7 A A A . n A 1 8 G 8 8 8 G G A . n A 1 9 U 9 9 9 U U A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 C 12 12 12 C C A . n B 2 1 C 1 13 13 C C B . n B 2 2 G 2 14 14 G G B . n B 2 3 C 3 15 15 C C B . n B 2 4 U 4 16 16 U U B . n B 2 5 A 5 17 17 A A B . n B 2 6 C 6 18 18 C C B . n B 2 7 U 7 19 19 U U B . n B 2 8 A 8 20 20 A A B . n B 2 9 A 9 21 21 A A B . n B 2 10 C 10 22 22 C C B . n B 2 11 G 11 23 23 G G B . n B 2 12 C 12 24 24 C C B . n B 2 13 G 13 25 25 G G B . 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 C 3 SO4 1 13 1 SO4 SO4 A . D 4 IOD 1 14 1 IOD IOD A . E 4 IOD 1 15 3 IOD IOD A . F 4 IOD 1 2 2 IOD IOD B . G 5 HOH 1 16 2 HOH HOH A . G 5 HOH 2 17 9 HOH HOH A . G 5 HOH 3 18 10 HOH HOH A . G 5 HOH 4 19 11 HOH HOH A . G 5 HOH 5 20 13 HOH HOH A . G 5 HOH 6 21 15 HOH HOH A . G 5 HOH 7 22 17 HOH HOH A . G 5 HOH 8 23 19 HOH HOH A . G 5 HOH 9 24 20 HOH HOH A . G 5 HOH 10 25 21 HOH HOH A . G 5 HOH 11 26 24 HOH HOH A . G 5 HOH 12 27 26 HOH HOH A . G 5 HOH 13 28 29 HOH HOH A . G 5 HOH 14 29 32 HOH HOH A . G 5 HOH 15 30 34 HOH HOH A . G 5 HOH 16 31 35 HOH HOH A . G 5 HOH 17 32 38 HOH HOH A . G 5 HOH 18 33 39 HOH HOH A . G 5 HOH 19 34 46 HOH HOH A . G 5 HOH 20 35 49 HOH HOH A . G 5 HOH 21 36 51 HOH HOH A . G 5 HOH 22 37 52 HOH HOH A . G 5 HOH 23 38 57 HOH HOH A . G 5 HOH 24 39 63 HOH HOH A . G 5 HOH 25 40 65 HOH HOH A . G 5 HOH 26 41 66 HOH HOH A . G 5 HOH 27 42 67 HOH HOH A . G 5 HOH 28 43 68 HOH HOH A . G 5 HOH 29 44 71 HOH HOH A . G 5 HOH 30 45 72 HOH HOH A . G 5 HOH 31 46 74 HOH HOH A . G 5 HOH 32 47 75 HOH HOH A . G 5 HOH 33 48 77 HOH HOH A . G 5 HOH 34 49 81 HOH HOH A . G 5 HOH 35 50 84 HOH HOH A . G 5 HOH 36 51 85 HOH HOH A . G 5 HOH 37 52 87 HOH HOH A . G 5 HOH 38 53 88 HOH HOH A . G 5 HOH 39 54 96 HOH HOH A . G 5 HOH 40 55 98 HOH HOH A . G 5 HOH 41 56 101 HOH HOH A . G 5 HOH 42 57 102 HOH HOH A . G 5 HOH 43 58 103 HOH HOH A . G 5 HOH 44 59 106 HOH HOH A . G 5 HOH 45 60 108 HOH HOH A . G 5 HOH 46 61 109 HOH HOH A . G 5 HOH 47 62 111 HOH HOH A . G 5 HOH 48 63 114 HOH HOH A . G 5 HOH 49 64 118 HOH HOH A . G 5 HOH 50 65 119 HOH HOH A . G 5 HOH 51 66 125 HOH HOH A . G 5 HOH 52 67 127 HOH HOH A . G 5 HOH 53 68 128 HOH HOH A . G 5 HOH 54 69 129 HOH HOH A . G 5 HOH 55 70 132 HOH HOH A . G 5 HOH 56 71 137 HOH HOH A . G 5 HOH 57 72 138 HOH HOH A . G 5 HOH 58 73 139 HOH HOH A . G 5 HOH 59 74 146 HOH HOH A . G 5 HOH 60 75 147 HOH HOH A . G 5 HOH 61 76 148 HOH HOH A . G 5 HOH 62 77 149 HOH HOH A . G 5 HOH 63 78 154 HOH HOH A . G 5 HOH 64 79 155 HOH HOH A . G 5 HOH 65 80 157 HOH HOH A . G 5 HOH 66 81 158 HOH HOH A . H 5 HOH 1 26 1 HOH HOH B . H 5 HOH 2 27 3 HOH HOH B . H 5 HOH 3 28 4 HOH HOH B . H 5 HOH 4 29 5 HOH HOH B . H 5 HOH 5 30 6 HOH HOH B . H 5 HOH 6 31 7 HOH HOH B . H 5 HOH 7 32 8 HOH HOH B . H 5 HOH 8 33 12 HOH HOH B . H 5 HOH 9 34 14 HOH HOH B . H 5 HOH 10 35 16 HOH HOH B . H 5 HOH 11 36 18 HOH HOH B . H 5 HOH 12 37 22 HOH HOH B . H 5 HOH 13 38 23 HOH HOH B . H 5 HOH 14 39 25 HOH HOH B . H 5 HOH 15 40 27 HOH HOH B . H 5 HOH 16 41 28 HOH HOH B . H 5 HOH 17 42 30 HOH HOH B . H 5 HOH 18 43 31 HOH HOH B . H 5 HOH 19 44 33 HOH HOH B . H 5 HOH 20 45 36 HOH HOH B . H 5 HOH 21 46 37 HOH HOH B . H 5 HOH 22 47 40 HOH HOH B . H 5 HOH 23 48 41 HOH HOH B . H 5 HOH 24 49 42 HOH HOH B . H 5 HOH 25 50 43 HOH HOH B . H 5 HOH 26 51 44 HOH HOH B . H 5 HOH 27 52 45 HOH HOH B . H 5 HOH 28 53 47 HOH HOH B . H 5 HOH 29 54 48 HOH HOH B . H 5 HOH 30 55 50 HOH HOH B . H 5 HOH 31 56 53 HOH HOH B . H 5 HOH 32 57 54 HOH HOH B . H 5 HOH 33 58 55 HOH HOH B . H 5 HOH 34 59 56 HOH HOH B . H 5 HOH 35 60 58 HOH HOH B . H 5 HOH 36 61 59 HOH HOH B . H 5 HOH 37 62 60 HOH HOH B . H 5 HOH 38 63 61 HOH HOH B . H 5 HOH 39 64 62 HOH HOH B . H 5 HOH 40 65 64 HOH HOH B . H 5 HOH 41 66 69 HOH HOH B . H 5 HOH 42 67 70 HOH HOH B . H 5 HOH 43 68 73 HOH HOH B . H 5 HOH 44 69 76 HOH HOH B . H 5 HOH 45 70 78 HOH HOH B . H 5 HOH 46 71 79 HOH HOH B . H 5 HOH 47 72 80 HOH HOH B . H 5 HOH 48 73 82 HOH HOH B . H 5 HOH 49 74 83 HOH HOH B . H 5 HOH 50 75 86 HOH HOH B . H 5 HOH 51 76 89 HOH HOH B . H 5 HOH 52 77 90 HOH HOH B . H 5 HOH 53 78 91 HOH HOH B . H 5 HOH 54 79 92 HOH HOH B . H 5 HOH 55 80 93 HOH HOH B . H 5 HOH 56 81 94 HOH HOH B . H 5 HOH 57 82 95 HOH HOH B . H 5 HOH 58 83 97 HOH HOH B . H 5 HOH 59 84 99 HOH HOH B . H 5 HOH 60 85 100 HOH HOH B . H 5 HOH 61 86 104 HOH HOH B . H 5 HOH 62 87 105 HOH HOH B . H 5 HOH 63 88 107 HOH HOH B . H 5 HOH 64 89 110 HOH HOH B . H 5 HOH 65 90 112 HOH HOH B . H 5 HOH 66 91 113 HOH HOH B . H 5 HOH 67 92 115 HOH HOH B . H 5 HOH 68 93 116 HOH HOH B . H 5 HOH 69 94 117 HOH HOH B . H 5 HOH 70 95 120 HOH HOH B . H 5 HOH 71 96 121 HOH HOH B . H 5 HOH 72 97 122 HOH HOH B . H 5 HOH 73 98 123 HOH HOH B . H 5 HOH 74 99 124 HOH HOH B . H 5 HOH 75 100 126 HOH HOH B . H 5 HOH 76 101 130 HOH HOH B . H 5 HOH 77 102 131 HOH HOH B . H 5 HOH 78 103 133 HOH HOH B . H 5 HOH 79 104 134 HOH HOH B . H 5 HOH 80 105 135 HOH HOH B . H 5 HOH 81 106 136 HOH HOH B . H 5 HOH 82 107 140 HOH HOH B . H 5 HOH 83 108 141 HOH HOH B . H 5 HOH 84 109 142 HOH HOH B . H 5 HOH 85 110 143 HOH HOH B . H 5 HOH 86 111 144 HOH HOH B . H 5 HOH 87 112 145 HOH HOH B . H 5 HOH 88 113 150 HOH HOH B . H 5 HOH 89 114 151 HOH HOH B . H 5 HOH 90 115 152 HOH HOH B . H 5 HOH 91 116 153 HOH HOH B . H 5 HOH 92 117 156 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 CNS refinement . ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 CNS phasing . ? 5 # _cell.entry_id 3CGP _cell.length_a 68.30 _cell.length_b 40.79 _cell.length_c 32.55 _cell.angle_alpha 90.00 _cell.angle_beta 94.93 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 3CGP _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3CGP _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.83 _exptl_crystal.density_percent_sol 56.52 _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 298.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details '1M ammonium sulfate, 0.2M sodium iodide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K' _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 'sodium iodide' ? ? ? 1 3 2 'ammonium sulfate' ? ? ? 1 4 2 'sodium iodide' ? ? ? # _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 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2005-04-04 _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 1.10 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X8C' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X8C _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.10 # _reflns.entry_id 3CGP _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 1.57 _reflns.d_resolution_low 20.0 _reflns.number_all 12574 _reflns.number_obs 12181 _reflns.percent_possible_obs 96.5 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.043 _reflns.pdbx_netI_over_sigmaI 24.3 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.3 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.57 _reflns_shell.d_res_low 1.63 _reflns_shell.percent_possible_all 92.5 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.122 _reflns_shell.meanI_over_sigI_obs 9.7 _reflns_shell.pdbx_redundancy 3.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3CGP _refine.ls_d_res_high 1.57 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 0 _refine.pdbx_ls_sigma_I 0 _refine.ls_number_reflns_all 12181 _refine.ls_number_reflns_obs 11922 _refine.ls_number_reflns_R_free 857 _refine.ls_percent_reflns_obs 95.4 _refine.ls_R_factor_all 0.2024 _refine.ls_R_factor_obs 0.2024 _refine.ls_R_factor_R_work 0.2012 _refine.ls_R_factor_R_free 0.2276 _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 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'our previously solved RNA duplex' _refine.pdbx_ls_cross_valid_method THROUGHOUT _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 21.4 _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_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _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 ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3CGP _refine_analyze.Luzzati_coordinate_error_obs 0.18 _refine_analyze.Luzzati_sigma_a_obs 0.09 _refine_analyze.Luzzati_d_res_low_obs 5.0 _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 528 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 158 _refine_hist.number_atoms_total 694 _refine_hist.d_res_high 1.57 _refine_hist.d_res_low 20.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.003 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.85 ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 3CGP _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 3CGP _struct.title 'X-ray structure of a pseudouridine-containing yeast spliceosomal U2 snRNA-intron branch site duplex bound to iodide ions' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3CGP _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA double helix, Branchpoint sequence, BPS, U2 snRNA, pseudouridine, pre-mRNA splicing, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 4 ? G N N 5 ? H N N 5 ? # loop_ _struct_ref.entity_id _struct_ref.pdbx_db_accession _struct_ref.db_code _struct_ref.db_name _struct_ref.id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 3CGP 3CGP PDB 1 1 GCGCGUAGUAGC ? 2 3CGP 3CGP PDB 2 1 CGCUACUAACGCG ? # 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 3CGP A 1 ? 12 ? 3CGP 1 ? 12 ? 1 12 2 2 3CGP B 1 ? 13 ? 3CGP 13 ? 25 ? 13 25 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2050 ? 1 MORE -4.3 ? 1 'SSA (A^2)' 4950 ? # _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 # _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 G 5 "O3'" ? ? ? 1_555 A PSU 6 P ? ? A G 5 A PSU 6 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale both ? A PSU 6 "O3'" ? ? ? 1_555 A A 7 P ? ? A PSU 6 A A 7 1_555 ? ? ? ? ? ? ? 1.609 ? ? hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 2 B G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 2 B G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 2 B G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 3 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 3 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 3 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 4 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 4 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 4 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 5 B C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 5 B C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 5 B C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A PSU 6 N3 ? ? ? 1_555 B A 9 N1 ? ? A PSU 6 B A 21 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog14 hydrog ? ? A PSU 6 O2 ? ? ? 1_555 B A 9 N6 ? ? A PSU 6 B A 21 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog15 hydrog ? ? A A 7 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 7 B U 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 7 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 7 B U 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 8 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 8 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 8 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 8 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 9 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 9 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 9 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 9 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 10 B U 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 10 B U 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 11 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 11 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 11 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 12 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 12 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 12 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SO4 13 ? 3 'BINDING SITE FOR RESIDUE SO4 A 13' AC2 Software A IOD 14 ? 1 'BINDING SITE FOR RESIDUE IOD A 14' # 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 HOH G . ? HOH A 39 . ? 1_555 ? 2 AC1 3 HOH H . ? HOH B 45 . ? 1_556 ? 3 AC1 3 HOH H . ? HOH B 65 . ? 1_556 ? 4 AC2 1 HOH H . ? HOH B 38 . ? 1_555 ? # _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_1 100 _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 B _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 100 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 2_555 _pdbx_validate_symm_contact.dist 1.32 # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id PSU _pdbx_struct_mod_residue.label_seq_id 6 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id PSU _pdbx_struct_mod_residue.auth_seq_id 6 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id U _pdbx_struct_mod_residue.details "PSEUDOURIDINE-5'-MONOPHOSPHATE" # 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 IOD I I N N 114 PSU N1 N N N 115 PSU C2 C N N 116 PSU N3 N N N 117 PSU C4 C N N 118 PSU C5 C N N 119 PSU C6 C N N 120 PSU O2 O N N 121 PSU O4 O N N 122 PSU "C1'" C N S 123 PSU "C2'" C N R 124 PSU "O2'" O N N 125 PSU "C3'" C N S 126 PSU "C4'" C N R 127 PSU "O3'" O N N 128 PSU "O4'" O N N 129 PSU "C5'" C N N 130 PSU "O5'" O N N 131 PSU P P N N 132 PSU OP1 O N N 133 PSU OP2 O N N 134 PSU OP3 O N N 135 PSU HN1 H N N 136 PSU HN3 H N N 137 PSU H6 H N N 138 PSU "H1'" H N N 139 PSU "H2'" H N N 140 PSU "HO2'" H N N 141 PSU "H3'" H N N 142 PSU "H4'" H N N 143 PSU "HO3'" H N N 144 PSU "H5'" H N N 145 PSU "H5''" H N N 146 PSU HOP2 H N N 147 PSU HOP3 H N N 148 SO4 S S N N 149 SO4 O1 O N N 150 SO4 O2 O N N 151 SO4 O3 O N N 152 SO4 O4 O N N 153 U OP3 O N N 154 U P P N N 155 U OP1 O N N 156 U OP2 O N N 157 U "O5'" O N N 158 U "C5'" C N N 159 U "C4'" C N R 160 U "O4'" O N N 161 U "C3'" C N S 162 U "O3'" O N N 163 U "C2'" C N R 164 U "O2'" O N N 165 U "C1'" C N R 166 U N1 N N N 167 U C2 C N N 168 U O2 O N N 169 U N3 N N N 170 U C4 C N N 171 U O4 O N N 172 U C5 C N N 173 U C6 C N N 174 U HOP3 H N N 175 U HOP2 H N N 176 U "H5'" H N N 177 U "H5''" H N N 178 U "H4'" H N N 179 U "H3'" H N N 180 U "HO3'" H N N 181 U "H2'" H N N 182 U "HO2'" H N N 183 U "H1'" H N N 184 U H3 H N N 185 U H5 H N N 186 U H6 H N N 187 # 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 PSU N1 C2 sing N N 118 PSU N1 C6 sing N N 119 PSU N1 HN1 sing N N 120 PSU C2 N3 sing N N 121 PSU C2 O2 doub N N 122 PSU N3 C4 sing N N 123 PSU N3 HN3 sing N N 124 PSU C4 C5 sing N N 125 PSU C4 O4 doub N N 126 PSU C5 C6 doub N N 127 PSU C5 "C1'" sing N N 128 PSU C6 H6 sing N N 129 PSU "C1'" "C2'" sing N N 130 PSU "C1'" "O4'" sing N N 131 PSU "C1'" "H1'" sing N N 132 PSU "C2'" "O2'" sing N N 133 PSU "C2'" "C3'" sing N N 134 PSU "C2'" "H2'" sing N N 135 PSU "O2'" "HO2'" sing N N 136 PSU "C3'" "C4'" sing N N 137 PSU "C3'" "O3'" sing N N 138 PSU "C3'" "H3'" sing N N 139 PSU "C4'" "O4'" sing N N 140 PSU "C4'" "C5'" sing N N 141 PSU "C4'" "H4'" sing N N 142 PSU "O3'" "HO3'" sing N N 143 PSU "C5'" "O5'" sing N N 144 PSU "C5'" "H5'" sing N N 145 PSU "C5'" "H5''" sing N N 146 PSU "O5'" P sing N N 147 PSU P OP1 doub N N 148 PSU P OP2 sing N N 149 PSU P OP3 sing N N 150 PSU OP2 HOP2 sing N N 151 PSU OP3 HOP3 sing N N 152 SO4 S O1 doub N N 153 SO4 S O2 doub N N 154 SO4 S O3 sing N N 155 SO4 S O4 sing N N 156 U OP3 P sing N N 157 U OP3 HOP3 sing N N 158 U P OP1 doub N N 159 U P OP2 sing N N 160 U P "O5'" sing N N 161 U OP2 HOP2 sing N N 162 U "O5'" "C5'" sing N N 163 U "C5'" "C4'" sing N N 164 U "C5'" "H5'" sing N N 165 U "C5'" "H5''" sing N N 166 U "C4'" "O4'" sing N N 167 U "C4'" "C3'" sing N N 168 U "C4'" "H4'" sing N N 169 U "O4'" "C1'" sing N N 170 U "C3'" "O3'" sing N N 171 U "C3'" "C2'" sing N N 172 U "C3'" "H3'" sing N N 173 U "O3'" "HO3'" sing N N 174 U "C2'" "O2'" sing N N 175 U "C2'" "C1'" sing N N 176 U "C2'" "H2'" sing N N 177 U "O2'" "HO2'" sing N N 178 U "C1'" N1 sing N N 179 U "C1'" "H1'" sing N N 180 U N1 C2 sing N N 181 U N1 C6 sing N N 182 U C2 O2 doub N N 183 U C2 N3 sing N N 184 U N3 C4 sing N N 185 U N3 H3 sing N N 186 U C4 O4 doub N N 187 U C4 C5 sing N N 188 U C5 C6 doub N N 189 U C5 H5 sing N N 190 U C6 H6 sing N N 191 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3CGP 'bulge loop' 3CGP '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 2 1_555 B G 13 1_555 -0.025 -0.075 0.040 6.330 -7.049 -0.508 1 A_C2:G25_B A 2 ? B 25 ? 19 1 1 A G 3 1_555 B C 12 1_555 -0.281 -0.127 0.149 2.223 -13.353 3.028 2 A_G3:C24_B A 3 ? B 24 ? 19 1 1 A C 4 1_555 B G 11 1_555 0.099 -0.115 0.042 1.325 -11.143 0.287 3 A_C4:G23_B A 4 ? B 23 ? 19 1 1 A G 5 1_555 B C 10 1_555 -0.279 -0.076 0.101 -3.764 -16.188 3.657 4 A_G5:C22_B A 5 ? B 22 ? 19 1 1 A PSU 6 1_555 B A 9 1_555 -0.361 -0.082 0.074 -3.275 -8.956 -2.788 5 A_PSU6:A21_B A 6 ? B 21 ? 21 1 1 A A 7 1_555 B U 7 1_555 0.121 -0.157 0.354 2.367 -11.682 -2.580 6 A_A7:U19_B A 7 ? B 19 ? 20 1 1 A G 8 1_555 B C 6 1_555 -0.277 -0.181 0.013 -10.000 -22.183 0.793 7 A_G8:C18_B A 8 ? B 18 ? 19 1 1 A U 9 1_555 B A 5 1_555 0.065 -0.103 0.172 -7.966 -14.810 1.109 8 A_U9:A17_B A 9 ? B 17 ? 20 1 1 A A 10 1_555 B U 4 1_555 0.150 -0.093 0.094 -3.069 -6.425 -1.118 9 A_A10:U16_B A 10 ? B 16 ? 20 1 1 A G 11 1_555 B C 3 1_555 -0.224 -0.137 0.175 0.625 -14.662 2.777 10 A_G11:C15_B A 11 ? B 15 ? 19 1 1 A C 12 1_555 B G 2 1_555 0.417 -0.052 -0.037 1.565 -11.190 2.160 11 A_C12:G14_B A 12 ? B 14 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 2 1_555 B G 13 1_555 A G 3 1_555 B C 12 1_555 0.110 -1.900 3.231 -3.028 8.848 31.565 -4.733 -0.665 2.596 15.836 5.419 32.888 1 AA_C2G3:C24G25_BB A 2 ? B 25 ? A 3 ? B 24 ? 1 A G 3 1_555 B C 12 1_555 A C 4 1_555 B G 11 1_555 -0.461 -1.889 3.229 -1.070 2.131 32.530 -3.722 0.640 3.116 3.798 1.906 32.615 2 AA_G3C4:G23C24_BB A 3 ? B 24 ? A 4 ? B 23 ? 1 A C 4 1_555 B G 11 1_555 A G 5 1_555 B C 10 1_555 0.146 -1.803 3.161 -0.486 13.327 27.514 -5.667 -0.360 2.082 26.162 0.955 30.519 3 AA_C4G5:C22G23_BB A 4 ? B 23 ? A 5 ? B 22 ? 1 A G 5 1_555 B C 10 1_555 A PSU 6 1_555 B A 9 1_555 -0.771 -1.677 3.139 -3.277 4.362 33.226 -3.564 0.831 2.962 7.564 5.682 33.658 4 AA_G5PSU6:A21C22_BB A 5 ? B 22 ? A 6 ? B 21 ? 1 A PSU 6 1_555 B A 9 1_555 A A 7 1_555 B U 7 1_555 1.020 -1.442 2.938 -1.298 7.498 38.513 -2.911 -1.652 2.589 11.233 1.945 39.229 5 AA_PSU6A7:U19A21_BB A 6 ? B 21 ? A 7 ? B 19 ? 1 A A 7 1_555 B U 7 1_555 A G 8 1_555 B C 6 1_555 0.155 -1.592 3.451 3.015 8.972 35.264 -3.786 0.170 2.974 14.490 -4.869 36.473 6 AA_A7G8:C18U19_BB A 7 ? B 19 ? A 8 ? B 18 ? 1 A G 8 1_555 B C 6 1_555 A U 9 1_555 B A 5 1_555 0.146 -1.253 3.187 0.251 4.409 32.615 -2.927 -0.218 2.997 7.807 -0.444 32.905 7 AA_G8U9:A17C18_BB A 8 ? B 18 ? A 9 ? B 17 ? 1 A U 9 1_555 B A 5 1_555 A A 10 1_555 B U 4 1_555 0.228 -1.342 3.032 1.336 8.324 32.518 -3.524 -0.202 2.625 14.562 -2.337 33.565 8 AA_U9A10:U16A17_BB A 9 ? B 17 ? A 10 ? B 16 ? 1 A A 10 1_555 B U 4 1_555 A G 11 1_555 B C 3 1_555 0.664 -1.914 3.095 0.479 8.476 25.654 -5.950 -1.317 2.364 18.455 -1.044 27.000 9 AA_A10G11:C15U16_BB A 10 ? B 16 ? A 11 ? B 15 ? 1 A G 11 1_555 B C 3 1_555 A C 12 1_555 B G 2 1_555 -0.150 -1.639 3.124 1.673 4.382 38.453 -2.970 0.416 2.919 6.623 -2.528 38.727 10 AA_G11C12:G14C15_BB A 11 ? B 15 ? A 12 ? B 14 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'our previously solved RNA duplex' # _atom_sites.entry_id 3CGP _atom_sites.fract_transf_matrix[1][1] 0.014641 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.001263 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.024516 _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] 0.030832 _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 I N O P S # loop_