data_3GS8 # _entry.id 3GS8 # _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 3GS8 pdb_00003gs8 10.2210/pdb3gs8/pdb NDB UR0195 ? ? RCSB RCSB052246 ? ? WWPDB D_1000052246 ? ? # 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 2009-04-21 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' struct_conn 5 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' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3GS8 _pdbx_database_status.recvd_initial_deposition_date 2009-03-26 _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 3GS1 . unspecified PDB 3GS5 . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Spitale, R.C.' 1 'Volpini, R.' 2 'Heller, M.G.' 3 'Krucinska, J.' 4 'Cristalli, G.' 5 'Wedekind, J.E.' 6 # _citation.id primary _citation.title 'Identification of an imino group indispensable for cleavage by a small ribozyme.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 131 _citation.page_first 6093 _citation.page_last 6095 _citation.year 2009 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19354216 _citation.pdbx_database_id_DOI 10.1021/ja900450h # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Spitale, R.C.' 1 ? primary 'Volpini, R.' 2 ? primary 'Heller, M.G.' 3 ? primary 'Krucinska, J.' 4 ? primary 'Cristalli, G.' 5 ? primary 'Wedekind, J.E.' 6 ? # 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(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3') ; 4358.636 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3') ; 3970.448 1 ? ? ? ? 3 polymer syn ;RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3') ; 5535.445 1 ? ? ? ? 4 polymer syn ;RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3') ; 5991.568 1 ? ? ? ? 5 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 6 non-polymer syn '2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE' 230.153 1 ? ? ? ? 7 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? # 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 no UCCCAGUCCACCGU UCCCAGUCCACCGU A ? 2 polyribonucleotide no no CGGUGAGAAGGG CGGUGAGAAGGG B ? 3 polyribonucleotide no no GGCAGAGAAACACACGA GGCAGAGAAACACACGA C ? 4 polyribonucleotide no no UCGUGGUACAUUACCUGCC UCGUGGUACAUUACCUGCC D ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 5 'SULFATE ION' SO4 6 '2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE' S9L 7 'COBALT HEXAMMINE(III)' NCO # 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 C n 1 3 C n 1 4 C n 1 5 A n 1 6 G n 1 7 U n 1 8 C n 1 9 C n 1 10 A n 1 11 C n 1 12 C n 1 13 G n 1 14 U n 2 1 C n 2 2 G n 2 3 G n 2 4 U n 2 5 G n 2 6 A n 2 7 G n 2 8 A n 2 9 A n 2 10 G n 2 11 G n 2 12 G n 3 1 G n 3 2 G n 3 3 C n 3 4 A n 3 5 G n 3 6 A n 3 7 G n 3 8 A n 3 9 A n 3 10 A n 3 11 C n 3 12 A n 3 13 C n 3 14 A n 3 15 C n 3 16 G n 3 17 A n 4 1 U n 4 2 C n 4 3 G n 4 4 U n 4 5 G n 4 6 G n 4 7 U n 4 8 A n 4 9 C n 4 10 A n 4 11 U n 4 12 U n 4 13 A n 4 14 C n 4 15 C n 4 16 U n 4 17 G n 4 18 C n 4 19 C n # 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 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 S9L non-polymer . '2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE' ? 'C6 H15 O7 P' 230.153 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 U 1 1 1 U U A . n A 1 2 C 2 2 2 C C A . n A 1 3 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 A 5 5 5 A A A . n A 1 6 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 C 8 8 8 C C A . n A 1 9 C 9 9 9 C C A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 G 13 13 13 G G A . n A 1 14 U 14 14 ? ? ? A . n B 2 1 C 1 2 2 C C B . n B 2 2 G 2 3 3 G G B . n B 2 3 G 3 4 4 G G B . n B 2 4 U 4 5 5 U U B . n B 2 5 G 5 6 6 G G B . n B 2 6 A 6 7 7 A A B . n B 2 7 G 7 8 8 G G B . n B 2 8 A 8 9 9 A A B . n B 2 9 A 9 10 10 A A B . n B 2 10 G 10 11 11 G G B . n B 2 11 G 11 12 12 G G B . n B 2 12 G 12 13 13 G G B . n C 3 1 G 1 15 15 G G C . n C 3 2 G 2 16 16 G G C . n C 3 3 C 3 17 17 C C C . n C 3 4 A 4 18 18 A A C . n C 3 5 G 5 19 19 G G C . n C 3 6 A 6 20 20 A A C . n C 3 7 G 7 21 21 G G C . n C 3 8 A 8 22 22 A A C . n C 3 9 A 9 23 23 A A C . n C 3 10 A 10 24 24 A A C . n C 3 11 C 11 25 25 C C C . n C 3 12 A 12 26 26 A A C . n C 3 13 C 13 27 27 C C C . n C 3 14 A 14 28 28 A A C . n C 3 15 C 15 29 29 C C C . n C 3 16 G 16 30 30 G G C . n C 3 17 A 17 31 31 A A C . n D 4 1 U 1 31 31 U U D . n D 4 2 C 2 32 32 C C D . n D 4 3 G 3 33 33 G G D . n D 4 4 U 4 34 34 U U D . n D 4 5 G 5 35 35 G G D . n D 4 6 G 6 36 36 G G D . n D 4 7 U 7 37 37 U U D . n D 4 8 A 8 38 38 A A D . n D 4 9 C 9 39 39 C C D . n D 4 10 A 10 40 40 A A D . n D 4 11 U 11 41 41 U U D . n D 4 12 U 12 42 42 U U D . n D 4 13 A 13 43 43 A A D . n D 4 14 C 14 44 44 C C D . n D 4 15 C 15 45 45 C C D . n D 4 16 U 16 46 46 U U D . n D 4 17 G 17 47 47 G G D . n D 4 18 C 18 48 48 C C D . n D 4 19 C 19 49 49 C C D . 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 E 5 SO4 1 15 3 SO4 SO4 A . F 6 S9L 1 14 14 S9L S9L B . G 7 NCO 1 15 2 NCO NCO B . H 7 NCO 1 1 1 NCO NCO C . # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag Y _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id A _pdbx_unobs_or_zero_occ_atoms.auth_comp_id A _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 5 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id "O3'" _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id A _pdbx_unobs_or_zero_occ_atoms.label_comp_id A _pdbx_unobs_or_zero_occ_atoms.label_seq_id 5 _pdbx_unobs_or_zero_occ_atoms.label_atom_id "O3'" # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CrystalClear 'data collection' . ? 1 CNS refinement . ? 2 CrystalClear 'data reduction' . ? 3 CrystalClear 'data scaling' . ? 4 CNS phasing . ? 5 # _cell.entry_id 3GS8 _cell.length_a 93.820 _cell.length_b 93.820 _cell.length_c 134.760 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3GS8 _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3GS8 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.31 _exptl_crystal.density_percent_sol 71.47 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;20.5% (w/v) PEG 2K MME, 0.10 M Na-Cacodylate, 0.25 M Li2SO4, 2.5 mM Co(NH3)6Cl3, 2 mM spermidine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _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 'PEG 2K MME' ? ? ? 1 2 1 Na-Cacodylate ? ? ? 1 3 1 Li2SO4 ? ? ? 1 4 1 'Co(NH3)6Cl3' ? ? ? 1 5 1 spermidine-HCl ? ? ? 1 6 2 'PEG 2K MME' ? ? ? 1 7 2 Na-Cacodylate ? ? ? 1 8 2 Li2SO4 ? ? ? 1 9 2 'Co(NH3)6Cl3' ? ? ? 1 10 2 spermidine-HCl ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2008-09-08 _diffrn_detector.details 'VariMax optics (Rigaku)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator '0.3 x 3 mm focusing cup operated at 4.8 kW' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RUH2R' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.54 # _reflns.entry_id 3GS8 _reflns.observed_criterion_sigma_I 12.2 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 38.5 _reflns.d_resolution_high 2.85 _reflns.number_obs 8407 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs 0.060 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 12.2 _reflns.B_iso_Wilson_estimate 1.2 _reflns.pdbx_redundancy 3.81 _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 2.85 _reflns_shell.d_res_low 2.95 _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs 0.508 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.2 _reflns_shell.pdbx_redundancy 4.10 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 830 _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 3GS8 _refine.ls_number_reflns_obs 8402 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 79272.77 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 27.37 _refine.ls_d_res_high 2.85 _refine.ls_percent_reflns_obs 96.8 _refine.ls_R_factor_obs 0.220 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.220 _refine.ls_R_factor_R_free 0.254 _refine.ls_R_factor_R_free_error 0.010 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.7 _refine.ls_number_reflns_R_free 649 _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 96.9 _refine.aniso_B[1][1] -15.21 _refine.aniso_B[2][2] -15.21 _refine.aniso_B[3][3] 30.43 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.3 _refine.solvent_model_param_bsol 61.382 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'BULK SOLVENT MODEL USED' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_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 3GS8 _refine_analyze.Luzzati_coordinate_error_obs 0.49 _refine_analyze.Luzzati_sigma_a_obs 1.17 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.42 _refine_analyze.Luzzati_sigma_a_free 1.12 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _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 1313 _refine_hist.pdbx_number_atoms_ligand 32 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1345 _refine_hist.d_res_high 2.85 _refine_hist.d_res_low 27.37 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.007 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.3 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 16.7 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 2.25 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.85 _refine_ls_shell.d_res_low 2.95 _refine_ls_shell.number_reflns_R_work 1284 _refine_ls_shell.R_factor_R_work 0.525 _refine_ls_shell.percent_reflns_obs 99.1 _refine_ls_shell.R_factor_R_free 0.548 _refine_ls_shell.R_factor_R_free_error 0.052 _refine_ls_shell.percent_reflns_R_free 7.9 _refine_ls_shell.number_reflns_R_free 110 _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 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 dna-rnaATT protein.top 'X-RAY DIFFRACTION' 2 cobalt.par ? 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3GS8 _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 3GS8 _struct.title 'An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3GS8 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'hairpin ribozyme, RNA ribozyme, N1-deazaadenosine, 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 5 ? F N N 6 ? G N N 7 ? H N N 7 ? # 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 3GS8 3GS8 1 ? ? ? 2 PDB 3GS8 3GS8 2 ? ? ? 3 PDB 3GS8 3GS8 3 ? ? ? 4 PDB 3GS8 3GS8 4 ? ? ? # 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 3GS8 A 1 ? 14 ? 3GS8 1 ? 14 ? 1 14 2 2 3GS8 B 1 ? 12 ? 3GS8 2 ? 13 ? 2 13 3 3 3GS8 C 1 ? 17 ? 3GS8 15 ? 31 ? 15 31 4 4 3GS8 D 1 ? 19 ? 3GS8 31 ? 49 ? 31 49 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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 ? B G 12 "O3'" ? ? ? 1_555 F S9L . P ? ? B G 13 B S9L 14 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale2 covale both ? F S9L . "O3'" ? ? ? 1_555 C G 1 P ? ? B S9L 14 C G 15 1_555 ? ? ? ? ? ? ? 1.613 ? ? hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 5 N3 ? ? ? 1_555 B A 8 N6 ? ? A A 5 B A 9 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog11 hydrog ? ? A A 5 N3 ? ? ? 1_555 B A 9 N6 ? ? A A 5 B A 10 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog12 hydrog ? ? A G 6 N1 ? ? ? 1_555 C C 11 N3 ? ? A G 6 C C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 N2 ? ? ? 1_555 C C 11 O2 ? ? A G 6 C C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 O6 ? ? ? 1_555 C C 11 N4 ? ? A G 6 C C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 7 O4 ? ? ? 1_555 B G 7 N2 ? ? A U 7 B G 8 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog16 hydrog ? ? A C 8 N4 ? ? ? 1_555 B A 6 N1 ? ? A C 8 B A 7 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog17 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 9 B G 6 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog18 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 10 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 10 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog21 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 13 B C 2 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog25 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 19 N3 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 19 O2 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 19 N4 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 18 N3 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C G 2 N2 ? ? ? 1_555 D C 18 O2 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C G 2 O6 ? ? ? 1_555 D C 18 N4 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C C 3 N3 ? ? ? 1_555 D G 17 N1 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C C 3 N4 ? ? ? 1_555 D G 17 O6 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C C 3 O2 ? ? ? 1_555 D G 17 N2 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C A 4 N1 ? ? ? 1_555 D U 16 N3 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C A 4 N6 ? ? ? 1_555 D U 16 O4 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C G 5 N1 ? ? ? 1_555 D C 15 N3 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C G 5 N2 ? ? ? 1_555 D C 15 O2 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C G 5 O6 ? ? ? 1_555 D C 15 N4 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C A 6 N1 ? ? ? 1_555 D C 14 N4 ? ? C A 20 D C 44 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog40 hydrog ? ? C G 7 N2 ? ? ? 1_555 D A 13 N7 ? ? C G 21 D A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog41 hydrog ? ? C G 7 N3 ? ? ? 1_555 D A 13 N6 ? ? C G 21 D A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog42 hydrog ? ? C A 8 N6 ? ? ? 1_555 D U 11 O2 ? ? C A 22 D U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog43 hydrog ? ? C A 8 N7 ? ? ? 1_555 D U 11 N3 ? ? C A 22 D U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog44 hydrog ? ? C A 9 N6 ? ? ? 1_555 D A 10 N1 ? ? C A 23 D A 40 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog45 hydrog ? ? C A 10 N1 ? ? ? 1_555 D A 8 N6 ? ? C A 24 D A 38 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog46 hydrog ? ? C A 10 N6 ? ? ? 1_555 D A 8 N7 ? ? C A 24 D A 38 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog47 hydrog ? ? C A 12 N1 ? ? ? 1_555 D G 6 N1 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog48 hydrog ? ? C A 12 N6 ? ? ? 1_555 D G 6 O6 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog49 hydrog ? ? C C 13 N3 ? ? ? 1_555 D G 5 N1 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C C 13 N4 ? ? ? 1_555 D G 5 O6 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C C 13 O2 ? ? ? 1_555 D G 5 N2 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C A 14 N1 ? ? ? 1_555 D U 4 N3 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C A 14 N6 ? ? ? 1_555 D U 4 O4 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C C 15 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C C 15 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C C 15 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C G 16 N1 ? ? ? 1_555 D C 2 N3 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C G 16 N2 ? ? ? 1_555 D C 2 O2 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C G 16 O6 ? ? ? 1_555 D C 2 N4 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C A 17 N1 ? ? ? 1_555 D U 1 N3 ? ? C A 31 D U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C A 17 N6 ? ? ? 1_555 D U 1 O4 ? ? C A 31 D U 31 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 B S9L 14 ? 4 'BINDING SITE FOR RESIDUE S9L B 14' AC2 Software C NCO 1 ? 4 'BINDING SITE FOR RESIDUE NCO C 1' AC3 Software B NCO 15 ? 5 'BINDING SITE FOR RESIDUE NCO B 15' AC4 Software A SO4 15 ? 2 'BINDING SITE FOR RESIDUE SO4 A 15' # 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 4 U A 1 ? U A 1 . ? 10_665 ? 2 AC1 4 G B 12 ? G B 13 . ? 1_555 ? 3 AC1 4 G C 1 ? G C 15 . ? 1_555 ? 4 AC1 4 A C 17 ? A C 31 . ? 9_665 ? 5 AC2 4 A C 6 ? A C 20 . ? 1_555 ? 6 AC2 4 G C 7 ? G C 21 . ? 1_555 ? 7 AC2 4 A D 10 ? A D 40 . ? 1_555 ? 8 AC2 4 U D 11 ? U D 41 . ? 1_555 ? 9 AC3 5 C A 2 ? C A 2 . ? 1_555 ? 10 AC3 5 SO4 E . ? SO4 A 15 . ? 1_555 ? 11 AC3 5 G B 10 ? G B 11 . ? 1_555 ? 12 AC3 5 G B 11 ? G B 12 . ? 1_555 ? 13 AC3 5 G B 12 ? G B 13 . ? 1_555 ? 14 AC4 2 C A 2 ? C A 2 . ? 1_555 ? 15 AC4 2 NCO G . ? NCO B 15 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 "O2'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 A _pdbx_validate_close_contact.auth_seq_id_1 5 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 P _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 G _pdbx_validate_close_contact.auth_seq_id_2 6 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.62 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 "O3'" _pdbx_validate_symm_contact.auth_asym_id_1 C _pdbx_validate_symm_contact.auth_comp_id_1 A _pdbx_validate_symm_contact.auth_seq_id_1 31 _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 "O3'" _pdbx_validate_symm_contact.auth_asym_id_2 C _pdbx_validate_symm_contact.auth_comp_id_2 A _pdbx_validate_symm_contact.auth_seq_id_2 31 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 11_655 _pdbx_validate_symm_contact.dist 2.12 # 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 6 ? ? "C1'" A G 6 ? ? "C2'" A G 6 ? ? 122.19 114.00 8.19 1.30 N 2 1 "C1'" D A 38 ? ? "O4'" D A 38 ? ? "C4'" D A 38 ? ? 104.49 109.70 -5.21 0.70 N 3 1 N9 D A 38 ? ? "C1'" D A 38 ? ? "C2'" D A 38 ? ? 126.01 114.00 12.01 1.30 N 4 1 "O4'" D A 38 ? ? "C1'" D A 38 ? ? N9 D A 38 ? ? 114.17 108.50 5.67 0.70 N 5 1 "C5'" D U 42 ? ? "C4'" D U 42 ? ? "C3'" D U 42 ? ? 105.90 115.20 -9.30 1.40 N # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id U _pdbx_unobs_or_zero_occ_residues.auth_seq_id 14 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id U _pdbx_unobs_or_zero_occ_residues.label_seq_id 14 # 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 NCO CO CO N N 111 NCO N1 N N N 112 NCO N2 N N N 113 NCO N3 N N N 114 NCO N4 N N N 115 NCO N5 N N N 116 NCO N6 N N N 117 NCO HN11 H N N 118 NCO HN12 H N N 119 NCO HN13 H N N 120 NCO HN21 H N N 121 NCO HN22 H N N 122 NCO HN23 H N N 123 NCO HN31 H N N 124 NCO HN32 H N N 125 NCO HN33 H N N 126 NCO HN41 H N N 127 NCO HN42 H N N 128 NCO HN43 H N N 129 NCO HN51 H N N 130 NCO HN52 H N N 131 NCO HN53 H N N 132 NCO HN61 H N N 133 NCO HN62 H N N 134 NCO HN63 H N N 135 S9L O3P O N N 136 S9L P P N N 137 S9L O1P O N N 138 S9L O2P O N N 139 S9L "O5'" O N N 140 S9L C12 C N N 141 S9L C22 C N N 142 S9L OH3 O N N 143 S9L C13 C N N 144 S9L C23 C N N 145 S9L OH4 O N N 146 S9L C14 C N N 147 S9L C24 C N N 148 S9L "O3'" O N N 149 S9L HO3P H N N 150 S9L HO1P H N N 151 S9L H121 H N N 152 S9L H122 H N N 153 S9L H221 H N N 154 S9L H222 H N N 155 S9L H131 H N N 156 S9L H132 H N N 157 S9L H231 H N N 158 S9L H232 H N N 159 S9L H141 H N N 160 S9L H142 H N N 161 S9L H241 H N N 162 S9L H242 H N N 163 S9L "HO3'" H N N 164 SO4 S S N N 165 SO4 O1 O N N 166 SO4 O2 O N N 167 SO4 O3 O N N 168 SO4 O4 O N N 169 U OP3 O N N 170 U P P N N 171 U OP1 O N N 172 U OP2 O N N 173 U "O5'" O N N 174 U "C5'" C N N 175 U "C4'" C N R 176 U "O4'" O N N 177 U "C3'" C N S 178 U "O3'" O N N 179 U "C2'" C N R 180 U "O2'" O N N 181 U "C1'" C N R 182 U N1 N N N 183 U C2 C N N 184 U O2 O N N 185 U N3 N N N 186 U C4 C N N 187 U O4 O N N 188 U C5 C N N 189 U C6 C N N 190 U HOP3 H N N 191 U HOP2 H N N 192 U "H5'" H N N 193 U "H5''" H N N 194 U "H4'" H N N 195 U "H3'" H N N 196 U "HO3'" H N N 197 U "H2'" H N N 198 U "HO2'" H N N 199 U "H1'" H N N 200 U H3 H N N 201 U H5 H N N 202 U H6 H N N 203 # 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 NCO CO N1 sing N N 116 NCO CO N2 sing N N 117 NCO CO N3 sing N N 118 NCO CO N4 sing N N 119 NCO CO N5 sing N N 120 NCO CO N6 sing N N 121 NCO N1 HN11 sing N N 122 NCO N1 HN12 sing N N 123 NCO N1 HN13 sing N N 124 NCO N2 HN21 sing N N 125 NCO N2 HN22 sing N N 126 NCO N2 HN23 sing N N 127 NCO N3 HN31 sing N N 128 NCO N3 HN32 sing N N 129 NCO N3 HN33 sing N N 130 NCO N4 HN41 sing N N 131 NCO N4 HN42 sing N N 132 NCO N4 HN43 sing N N 133 NCO N5 HN51 sing N N 134 NCO N5 HN52 sing N N 135 NCO N5 HN53 sing N N 136 NCO N6 HN61 sing N N 137 NCO N6 HN62 sing N N 138 NCO N6 HN63 sing N N 139 S9L O3P P sing N N 140 S9L O3P HO3P sing N N 141 S9L P O2P doub N N 142 S9L P O1P sing N N 143 S9L P "O5'" sing N N 144 S9L O1P HO1P sing N N 145 S9L "O5'" C12 sing N N 146 S9L C12 C22 sing N N 147 S9L C12 H121 sing N N 148 S9L C12 H122 sing N N 149 S9L C22 OH3 sing N N 150 S9L C22 H221 sing N N 151 S9L C22 H222 sing N N 152 S9L OH3 C23 sing N N 153 S9L C13 C23 sing N N 154 S9L C13 OH4 sing N N 155 S9L C13 H131 sing N N 156 S9L C13 H132 sing N N 157 S9L C23 H231 sing N N 158 S9L C23 H232 sing N N 159 S9L OH4 C24 sing N N 160 S9L C14 C24 sing N N 161 S9L C14 "O3'" sing N N 162 S9L C14 H141 sing N N 163 S9L C14 H142 sing N N 164 S9L C24 H241 sing N N 165 S9L C24 H242 sing N N 166 S9L "O3'" "HO3'" sing N N 167 SO4 S O1 doub N N 168 SO4 S O2 doub N N 169 SO4 S O3 sing N N 170 SO4 S O4 sing N N 171 U OP3 P sing N N 172 U OP3 HOP3 sing N N 173 U P OP1 doub N N 174 U P OP2 sing N N 175 U P "O5'" sing N N 176 U OP2 HOP2 sing N N 177 U "O5'" "C5'" sing N N 178 U "C5'" "C4'" sing N N 179 U "C5'" "H5'" sing N N 180 U "C5'" "H5''" sing N N 181 U "C4'" "O4'" sing N N 182 U "C4'" "C3'" sing N N 183 U "C4'" "H4'" sing N N 184 U "O4'" "C1'" sing N N 185 U "C3'" "O3'" sing N N 186 U "C3'" "C2'" sing N N 187 U "C3'" "H3'" sing N N 188 U "O3'" "HO3'" sing N N 189 U "C2'" "O2'" sing N N 190 U "C2'" "C1'" sing N N 191 U "C2'" "H2'" sing N N 192 U "O2'" "HO2'" sing N N 193 U "C1'" N1 sing N N 194 U "C1'" "H1'" sing N N 195 U N1 C2 sing N N 196 U N1 C6 sing N N 197 U C2 O2 doub N N 198 U C2 N3 sing N N 199 U N3 C4 sing N N 200 U N3 H3 sing N N 201 U C4 O4 doub N N 202 U C4 C5 sing N N 203 U C5 C6 doub N N 204 U C5 H5 sing N N 205 U C6 H6 sing N N 206 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3GS8 'double helix' 3GS8 'a-form double helix' 3GS8 'bulge loop' 3GS8 'mismatched base pair' 3GS8 'internal loop' # 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 12 1_555 0.160 0.031 -0.178 5.112 -20.569 7.350 1 A_C2:G13_B A 2 ? B 13 ? 19 1 1 A C 3 1_555 B G 11 1_555 0.047 -0.124 -0.073 -1.637 -7.736 -0.466 2 A_C3:G12_B A 3 ? B 12 ? 19 1 1 A C 4 1_555 B G 10 1_555 0.485 0.014 0.078 1.249 2.149 8.020 3 A_C4:G11_B A 4 ? B 11 ? 19 1 1 A A 5 1_555 B A 8 1_555 6.598 -3.415 -0.601 4.171 -7.117 -29.453 4 A_A5:A9_B A 5 ? B 9 ? ? ? 1 A U 7 1_555 B G 7 1_555 -7.802 -3.099 -0.344 0.362 15.304 -16.121 5 A_U7:G8_B A 7 ? B 8 ? ? ? 1 A C 8 1_555 B A 6 1_555 -2.137 0.424 -1.028 21.590 -11.581 7.827 6 A_C8:A7_B A 8 ? B 7 ? ? ? 1 A C 9 1_555 B G 5 1_555 -0.217 0.311 -0.647 17.666 -11.367 10.513 7 A_C9:G6_B A 9 ? B 6 ? ? 1 1 A A 10 1_555 B U 4 1_555 0.577 0.186 0.208 4.663 -6.352 -3.973 8 A_A10:U5_B A 10 ? B 5 ? 20 1 1 A C 11 1_555 B G 3 1_555 0.710 0.248 0.513 0.793 -13.215 9.201 9 A_C11:G4_B A 11 ? B 4 ? ? 1 1 A C 12 1_555 B G 2 1_555 0.395 -0.452 0.503 0.201 -11.795 0.006 10 A_C12:G3_B A 12 ? B 3 ? 19 1 1 A G 13 1_555 B C 1 1_555 -0.260 0.464 0.201 -2.544 -15.660 12.733 11 A_G13:C2_B A 13 ? B 2 ? ? 1 1 C G 1 1_555 D C 19 1_555 -0.240 0.014 0.903 7.442 2.665 0.958 12 C_G15:C49_D C 15 ? D 49 ? 19 1 1 C G 2 1_555 D C 18 1_555 -0.281 0.027 0.389 11.730 -6.695 -2.018 13 C_G16:C48_D C 16 ? D 48 ? 19 1 1 C C 3 1_555 D G 17 1_555 -0.055 -0.047 -0.162 9.986 -12.937 4.841 14 C_C17:G47_D C 17 ? D 47 ? 19 1 1 C A 4 1_555 D U 16 1_555 -0.138 -0.109 -0.070 -3.592 -6.624 6.082 15 C_A18:U46_D C 18 ? D 46 ? 20 1 1 C G 5 1_555 D C 15 1_555 -0.359 -0.136 -0.437 -7.660 -2.917 6.051 16 C_G19:C45_D C 19 ? D 45 ? 19 1 1 C A 6 1_555 D C 14 1_555 2.236 0.288 -0.361 -9.630 -3.842 18.155 17 C_A20:C44_D C 20 ? D 44 ? ? 1 1 C G 7 1_555 D A 13 1_555 6.770 -4.454 -0.020 -8.017 2.609 -10.435 18 C_G21:A43_D C 21 ? D 43 ? 11 10 1 C A 8 1_555 D U 11 1_555 -4.110 -1.797 -0.230 -6.032 -8.932 -100.387 19 C_A22:U41_D C 22 ? D 41 ? 24 4 1 C A 9 1_555 D A 10 1_555 -4.420 0.826 -0.017 0.188 -13.195 -93.423 20 C_A23:A40_D C 23 ? D 40 ? ? ? 1 C A 10 1_555 D A 8 1_555 4.335 1.962 -0.210 2.659 -20.832 -124.874 21 C_A24:A38_D C 24 ? D 38 ? 5 4 1 C C 11 1_555 A G 6 1_555 0.267 -0.192 0.095 12.421 -13.102 1.359 22 C_C25:G6_A C 25 ? A 6 ? 19 1 1 C A 12 1_555 D G 6 1_555 0.057 1.289 -0.309 -7.668 -18.931 -12.039 23 C_A26:G36_D C 26 ? D 36 ? 8 1 1 C C 13 1_555 D G 5 1_555 0.420 -0.202 0.135 10.720 -18.975 0.958 24 C_C27:G35_D C 27 ? D 35 ? 19 1 1 C A 14 1_555 D U 4 1_555 0.295 -0.022 0.507 13.127 -14.965 -2.599 25 C_A28:U34_D C 28 ? D 34 ? 20 1 1 C C 15 1_555 D G 3 1_555 -0.177 0.033 0.126 4.884 -11.123 2.875 26 C_C29:G33_D C 29 ? D 33 ? 19 1 1 C G 16 1_555 D C 2 1_555 -0.121 -0.082 0.420 -2.523 -9.880 -3.979 27 C_G30:C32_D C 30 ? D 32 ? 19 1 1 C A 17 1_555 D U 1 1_555 0.542 -0.095 0.662 0.167 2.695 -1.315 28 C_A31:U31_D C 31 ? D 31 ? 20 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 12 1_555 A C 3 1_555 B G 11 1_555 -0.744 -1.598 3.511 -2.640 7.801 34.066 -3.864 0.827 3.127 13.079 4.426 35.018 1 AA_C2C3:G12G13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A C 3 1_555 B G 11 1_555 A C 4 1_555 B G 10 1_555 0.823 -1.639 3.413 0.966 9.386 28.837 -4.973 -1.385 2.779 18.240 -1.877 30.310 2 AA_C3C4:G11G12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A C 4 1_555 B G 10 1_555 A A 5 1_555 B A 8 1_555 -0.196 -0.918 5.343 -0.100 22.456 71.711 -1.877 0.157 4.920 18.722 0.084 74.692 3 AA_C4A5:A9G11_BB A 4 ? B 11 ? A 5 ? B 9 ? 1 A A 5 1_555 B A 8 1_555 A U 7 1_555 B G 7 1_555 -1.181 0.091 3.418 13.495 6.787 11.906 -2.816 9.678 1.330 23.349 -46.425 19.212 4 AA_A5U7:G8A9_BB A 5 ? B 9 ? A 7 ? B 8 ? 1 A U 7 1_555 B G 7 1_555 A C 8 1_555 B A 6 1_555 0.965 -0.827 2.954 -4.057 9.528 50.310 -1.526 -1.358 2.686 11.073 4.715 51.297 5 AA_U7C8:A7G8_BB A 7 ? B 8 ? A 8 ? B 7 ? 1 A C 8 1_555 B A 6 1_555 A C 9 1_555 B G 5 1_555 -0.052 -1.288 3.577 -2.259 7.834 34.582 -3.318 -0.262 3.215 12.955 3.736 35.502 6 AA_C8C9:G6A7_BB A 8 ? B 7 ? A 9 ? B 6 ? 1 A C 9 1_555 B G 5 1_555 A A 10 1_555 B U 4 1_555 -0.890 -1.791 3.442 -6.566 15.472 37.170 -4.251 0.570 2.639 22.893 9.716 40.671 7 AA_C9A10:U5G6_BB A 9 ? B 6 ? A 10 ? B 5 ? 1 A A 10 1_555 B U 4 1_555 A C 11 1_555 B G 3 1_555 0.335 -1.666 3.459 -1.023 2.207 28.814 -3.845 -0.906 3.311 4.425 2.051 28.914 8 AA_A10C11:G4U5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A C 11 1_555 B G 3 1_555 A C 12 1_555 B G 2 1_555 -0.124 -2.039 2.921 0.033 8.337 32.148 -4.713 0.222 2.333 14.747 -0.058 33.184 9 AA_C11C12:G3G4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A C 12 1_555 B G 2 1_555 A G 13 1_555 B C 1 1_555 0.665 -1.693 3.092 4.955 7.824 29.990 -4.455 -0.393 2.651 14.685 -9.300 31.356 10 AA_C12G13:C2G3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 C G 1 1_555 D C 19 1_555 C G 2 1_555 D C 18 1_555 -0.756 -1.188 3.015 -0.071 9.034 33.892 -3.163 1.247 2.624 15.164 0.120 35.042 11 CC_G15G16:C48C49_DD C 15 ? D 49 ? C 16 ? D 48 ? 1 C G 2 1_555 D C 18 1_555 C C 3 1_555 D G 17 1_555 0.540 -1.377 3.245 4.506 9.845 34.134 -3.586 -0.265 2.800 16.272 -7.447 35.762 12 CC_G16C17:G47C48_DD C 16 ? D 48 ? C 17 ? D 47 ? 1 C C 3 1_555 D G 17 1_555 C A 4 1_555 D U 16 1_555 0.309 -1.719 3.410 -4.360 13.912 31.267 -4.926 -1.156 2.390 24.230 7.593 34.422 13 CC_C17A18:U46G47_DD C 17 ? D 47 ? C 18 ? D 46 ? 1 C A 4 1_555 D U 16 1_555 C G 5 1_555 D C 15 1_555 -0.030 -1.747 3.438 -0.648 3.966 30.013 -4.160 -0.076 3.186 7.615 1.245 30.274 14 CC_A18G19:C45U46_DD C 18 ? D 46 ? C 19 ? D 45 ? 1 C G 5 1_555 D C 15 1_555 C A 6 1_555 D C 14 1_555 0.749 -1.486 3.339 2.861 5.735 39.907 -2.795 -0.763 3.149 8.337 -4.159 40.398 15 CC_G19A20:C44C45_DD C 19 ? D 45 ? C 20 ? D 44 ? 1 C A 6 1_555 D C 14 1_555 C G 7 1_555 D A 13 1_555 -0.947 -1.157 3.288 6.559 5.834 56.184 -1.531 1.350 3.045 6.153 -6.917 56.810 16 CC_A20G21:A43C44_DD C 20 ? D 44 ? C 21 ? D 43 ? 1 C G 7 1_555 D A 13 1_555 C A 8 1_555 D U 11 1_555 -2.058 -0.546 3.420 3.498 -0.081 14.072 -2.093 11.172 2.829 -0.323 -13.997 14.498 17 CC_G21A22:U41A43_DD C 21 ? D 43 ? C 22 ? D 41 ? 1 C A 8 1_555 D U 11 1_555 C A 9 1_555 D A 10 1_555 0.024 -2.151 3.397 -11.222 4.143 44.999 -3.079 -0.988 3.108 5.302 14.365 46.482 18 CC_A22A23:A40U41_DD C 22 ? D 41 ? C 23 ? D 40 ? 1 C A 9 1_555 D A 10 1_555 C A 10 1_555 D A 8 1_555 -2.919 -2.399 3.599 -6.500 2.522 66.142 -2.302 2.372 3.755 2.305 5.938 66.467 19 CC_A23A24:A38A40_DD C 23 ? D 40 ? C 24 ? D 38 ? 1 C A 10 1_555 D A 8 1_555 C C 11 1_555 A G 6 1_555 1.578 -0.425 3.020 3.457 2.239 -24.603 0.384 4.581 2.802 -5.208 8.041 -24.940 20 CC_A24C25:G6A38_AD C 24 ? D 38 ? C 25 ? A 6 ? 1 C C 11 1_555 A G 6 1_555 C A 12 1_555 D G 6 1_555 0.587 -2.074 3.697 4.182 4.024 45.887 -3.023 -0.351 3.550 5.136 -5.338 46.233 21 CC_C25A26:G36G6_DA C 25 ? A 6 ? C 26 ? D 36 ? 1 C A 12 1_555 D G 6 1_555 C C 13 1_555 D G 5 1_555 1.082 -0.571 2.829 -4.631 1.993 31.904 -1.322 -2.632 2.611 3.597 8.359 32.289 22 CC_A26C27:G35G36_DD C 26 ? D 36 ? C 27 ? D 35 ? 1 C C 13 1_555 D G 5 1_555 C A 14 1_555 D U 4 1_555 -0.265 -1.452 3.077 -1.785 7.055 34.742 -3.314 0.199 2.748 11.656 2.949 35.473 23 CC_C27A28:U34G35_DD C 27 ? D 35 ? C 28 ? D 34 ? 1 C A 14 1_555 D U 4 1_555 C C 15 1_555 D G 3 1_555 0.614 -1.344 3.351 5.035 2.535 31.301 -2.929 -0.177 3.291 4.652 -9.239 31.792 24 CC_A28C29:G33U34_DD C 28 ? D 34 ? C 29 ? D 33 ? 1 C C 15 1_555 D G 3 1_555 C G 16 1_555 D C 2 1_555 0.119 -1.661 3.197 0.783 9.837 36.971 -3.670 -0.092 2.686 15.182 -1.209 38.221 25 CC_C29G30:C32G33_DD C 29 ? D 33 ? C 30 ? D 32 ? 1 C G 16 1_555 D C 2 1_555 C A 17 1_555 D U 1 1_555 0.775 -2.004 3.069 1.817 1.678 33.201 -3.757 -1.071 3.004 2.931 -3.175 33.291 26 CC_G30A31:U31C32_DD C 30 ? D 32 ? C 31 ? D 31 ? # _atom_sites.entry_id 3GS8 _atom_sites.fract_transf_matrix[1][1] 0.010659 _atom_sites.fract_transf_matrix[1][2] 0.006154 _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] 0.012308 _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] 0.007421 _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 CO N O P S # loop_