data_3GS5 # _entry.id 3GS5 # _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 3GS5 pdb_00003gs5 10.2210/pdb3gs5/pdb NDB UR0194 ? ? RCSB RCSB052243 ? ? WWPDB D_1000052243 ? ? # 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 3GS5 _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 3GS8 . 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 (25-MER)' 8067.876 1 ? ? ? ? 2 polymer syn 'RNA (36-MER)' 11571.971 1 ? ? ? ? 3 non-polymer syn '2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE' 230.153 1 ? ? ? ? 4 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 5 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? # 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 UCCCAGUCCACCGCGGUGAGAAGGG UCCCAGUCCACCGCGGUGAGAAGGG A ? 2 polyribonucleotide no no GGCAGAGAAACACACGAUCGUGGUACAUUACCUGCC GGCAGAGAAACACACGAUCGUGGUACAUUACCUGCC C ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 '2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE' S9L 4 'COBALT HEXAMMINE(III)' NCO 5 'SULFATE ION' SO4 # 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 C n 1 15 G n 1 16 G n 1 17 U n 1 18 G n 1 19 A n 1 20 G n 1 21 A n 1 22 A n 1 23 G n 1 24 G n 1 25 G n 2 1 G n 2 2 G n 2 3 C n 2 4 A n 2 5 G n 2 6 A n 2 7 G n 2 8 A n 2 9 A n 2 10 A n 2 11 C n 2 12 A n 2 13 C n 2 14 A n 2 15 C n 2 16 G n 2 17 A n 2 18 U n 2 19 C n 2 20 G n 2 21 U n 2 22 G n 2 23 G n 2 24 U n 2 25 A n 2 26 C n 2 27 A n 2 28 U n 2 29 U n 2 30 A n 2 31 C n 2 32 C n 2 33 U n 2 34 G n 2 35 C n 2 36 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 C 14 14 14 C C A . n A 1 15 G 15 15 15 G G A . n A 1 16 G 16 16 16 G G A . n A 1 17 U 17 17 17 U U A . n A 1 18 G 18 18 18 G G A . n A 1 19 A 19 19 19 A A A . n A 1 20 G 20 20 20 G G A . n A 1 21 A 21 21 21 A A A . n A 1 22 A 22 22 22 A A A . n A 1 23 G 23 23 23 G G A . n A 1 24 G 24 24 24 G G A . n A 1 25 G 25 25 25 G G A . n B 2 1 G 1 27 27 G G C . n B 2 2 G 2 28 28 G G C . n B 2 3 C 3 29 29 C C C . n B 2 4 A 4 30 30 A A C . n B 2 5 G 5 31 31 G G C . n B 2 6 A 6 32 32 A A C . n B 2 7 G 7 33 33 G G C . n B 2 8 A 8 34 34 A A C . n B 2 9 A 9 35 35 A A C . n B 2 10 A 10 36 36 A A C . n B 2 11 C 11 37 37 C C C . n B 2 12 A 12 38 38 A A C . n B 2 13 C 13 39 39 C C C . n B 2 14 A 14 40 40 A A C . n B 2 15 C 15 41 41 C C C . n B 2 16 G 16 42 42 G G C . n B 2 17 A 17 43 43 A A C . n B 2 18 U 18 44 44 U U C . n B 2 19 C 19 45 45 C C C . n B 2 20 G 20 46 46 G G C . n B 2 21 U 21 47 47 U U C . n B 2 22 G 22 48 48 G G C . n B 2 23 G 23 49 49 G G C . n B 2 24 U 24 50 50 U U C . n B 2 25 A 25 51 51 A A C . n B 2 26 C 26 52 52 C C C . n B 2 27 A 27 53 53 A A C . n B 2 28 U 28 54 54 U U C . n B 2 29 U 29 55 55 U U C . n B 2 30 A 30 56 56 A A C . n B 2 31 C 31 57 57 C C C . n B 2 32 C 32 58 58 C C C . n B 2 33 U 33 59 59 U U C . n B 2 34 G 34 60 60 G G C . n B 2 35 C 35 61 61 C C C . n B 2 36 C 36 62 62 C C C . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 S9L 1 26 26 S9L S9L A . D 4 NCO 1 27 2 NCO NCO A . E 5 SO4 1 28 23 SO4 SO4 A . F 4 NCO 1 1 1 NCO NCO C . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A G 6 ? P ? A G 6 P 2 1 Y 1 A G 6 ? OP1 ? A G 6 OP1 3 1 Y 1 A G 6 ? OP2 ? A G 6 OP2 4 1 Y 1 A C 14 ? P ? A C 14 P 5 1 Y 1 A C 14 ? OP1 ? A C 14 OP1 6 1 Y 1 A C 14 ? OP2 ? A C 14 OP2 7 1 Y 1 C U 44 ? P ? B U 18 P 8 1 Y 1 C U 44 ? OP1 ? B U 18 OP1 9 1 Y 1 C U 44 ? OP2 ? B U 18 OP2 # 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 3GS5 _cell.length_a 93.830 _cell.length_b 93.830 _cell.length_c 132.090 _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 3GS5 _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 3GS5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.27 _exptl_crystal.density_percent_sol 71.22 _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' _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 3GS5 _reflns.observed_criterion_sigma_I 2.3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 29.91 _reflns.d_resolution_high 2.75 _reflns.number_obs 9256 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs 0.488 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 24.4 _reflns.B_iso_Wilson_estimate 64.4 _reflns.pdbx_redundancy 4.75 _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 2.75 _reflns_shell.d_res_low 2.85 _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs 0.488 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.3 _reflns_shell.pdbx_redundancy 4.75 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 894 _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 3GS5 _refine.ls_number_reflns_obs 9221 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 54013.67 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 27.85 _refine.ls_d_res_high 2.75 _refine.ls_percent_reflns_obs 97.6 _refine.ls_R_factor_obs 0.218 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.218 _refine.ls_R_factor_R_free 0.243 _refine.ls_R_factor_R_free_error 0.009 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.5 _refine.ls_number_reflns_R_free 694 _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 74.8 _refine.aniso_B[1][1] -11.57 _refine.aniso_B[2][2] -11.57 _refine.aniso_B[3][3] 23.14 _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 0.35 _refine.solvent_model_param_bsol 54.6298 _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 3GS5 _refine_analyze.Luzzati_coordinate_error_obs 0.51 _refine_analyze.Luzzati_sigma_a_obs 0.72 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.48 _refine_analyze.Luzzati_sigma_a_free 0.68 _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 1334 _refine_hist.pdbx_number_atoms_ligand 32 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1366 _refine_hist.d_res_high 2.75 _refine_hist.d_res_low 27.85 # 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 17.2 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.73 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.75 _refine_ls_shell.d_res_low 2.85 _refine_ls_shell.number_reflns_R_work 1394 _refine_ls_shell.R_factor_R_work 0.527 _refine_ls_shell.percent_reflns_obs 98.8 _refine_ls_shell.R_factor_R_free 0.521 _refine_ls_shell.R_factor_R_free_error 0.050 _refine_ls_shell.percent_reflns_R_free 7.1 _refine_ls_shell.number_reflns_R_free 107 _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 3GS5 _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 3GS5 _struct.title 'An all-RNA hairpin ribozyme A38N1dA variant with a product mimic substrate strand' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3GS5 _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 4 ? # 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 3GS5 3GS5 1 ? ? ? 2 PDB 3GS5 3GS5 2 ? ? ? # 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 3GS5 A 1 ? 25 ? 3GS5 1 ? 25 ? 1 25 2 2 3GS5 C 1 ? 36 ? 3GS5 27 ? 62 ? 27 62 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # _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 25 "O3'" ? ? ? 1_555 C S9L . P ? ? A G 25 A S9L 26 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale2 covale both ? C S9L . "O3'" ? ? ? 1_555 B G 1 P ? ? A S9L 26 C G 27 1_555 ? ? ? ? ? ? ? 1.608 ? ? hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 2 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 2 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 2 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 24 N1 ? ? A C 3 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 24 O6 ? ? A C 3 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 24 N2 ? ? A C 3 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 4 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 4 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 4 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 5 N3 ? ? ? 1_555 A A 21 N6 ? ? A A 5 A A 21 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog11 hydrog ? ? A A 5 N3 ? ? ? 1_555 A A 22 N6 ? ? A A 5 A A 22 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog12 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 6 C C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 6 C C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 6 C C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 7 O4 ? ? ? 1_555 A G 20 N2 A ? A U 7 A G 20 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog16 hydrog ? ? A C 8 N4 ? ? ? 1_555 A A 19 N1 ? ? A C 8 A A 19 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog17 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 18 N1 ? ? A C 9 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 18 O6 ? ? A C 9 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 18 N2 ? ? A C 9 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 17 N3 ? ? A A 10 A U 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 17 O4 ? ? A A 10 A U 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 11 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 11 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 11 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 12 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 12 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 12 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 13 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 13 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 13 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B G 1 N1 ? ? ? 1_555 B C 36 N3 ? ? C G 27 C C 62 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B G 1 N2 ? ? ? 1_555 B C 36 O2 ? ? C G 27 C C 62 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B G 1 O6 ? ? ? 1_555 B C 36 N4 ? ? C G 27 C C 62 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B G 2 N1 ? ? ? 1_555 B C 35 N3 ? ? C G 28 C C 61 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 2 N2 ? ? ? 1_555 B C 35 O2 ? ? C G 28 C C 61 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B G 2 O6 ? ? ? 1_555 B C 35 N4 ? ? C G 28 C C 61 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B C 3 N3 ? ? ? 1_555 B G 34 N1 ? ? C C 29 C G 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B C 3 N4 ? ? ? 1_555 B G 34 O6 ? ? C C 29 C G 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B C 3 O2 ? ? ? 1_555 B G 34 N2 ? ? C C 29 C G 60 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B A 4 N1 ? ? ? 1_555 B U 33 N3 ? ? C A 30 C U 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B A 4 N6 ? ? ? 1_555 B U 33 O4 ? ? C A 30 C U 59 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B G 5 N1 ? ? ? 1_555 B C 32 N3 ? ? C G 31 C C 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B G 5 N2 ? ? ? 1_555 B C 32 O2 ? ? C G 31 C C 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B G 5 O6 ? ? ? 1_555 B C 32 N4 ? ? C G 31 C C 58 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? B A 6 N1 ? ? ? 1_555 B C 31 N4 ? ? C A 32 C C 57 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog46 hydrog ? ? B G 7 N2 ? ? ? 1_555 B A 30 N7 ? ? C G 33 C A 56 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog47 hydrog ? ? B G 7 N3 ? ? ? 1_555 B A 30 N6 ? ? C G 33 C A 56 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog48 hydrog ? ? B A 8 N6 ? ? ? 1_555 B U 28 O2 ? ? C A 34 C U 54 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog49 hydrog ? ? B A 8 N7 ? ? ? 1_555 B U 28 N3 ? ? C A 34 C U 54 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog50 hydrog ? ? B A 9 N6 ? ? ? 1_555 B A 27 N1 ? ? C A 35 C A 53 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog51 hydrog ? ? B A 10 N6 ? ? ? 1_555 B A 25 N7 ? ? C A 36 C A 51 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog52 hydrog ? ? B A 12 N1 ? ? ? 1_555 B G 23 N1 ? ? C A 38 C G 49 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog53 hydrog ? ? B A 12 N6 ? ? ? 1_555 B G 23 O6 ? ? C A 38 C G 49 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog54 hydrog ? ? B C 13 N3 ? ? ? 1_555 B G 22 N1 ? ? C C 39 C G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? B C 13 N4 ? ? ? 1_555 B G 22 O6 ? ? C C 39 C G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? B C 13 O2 ? ? ? 1_555 B G 22 N2 ? ? C C 39 C G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? B A 14 N1 ? ? ? 1_555 B U 21 N3 ? ? C A 40 C U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? B A 14 N6 ? ? ? 1_555 B U 21 O4 ? ? C A 40 C U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? B C 15 N3 ? ? ? 1_555 B G 20 N1 ? ? C C 41 C G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? B C 15 N4 ? ? ? 1_555 B G 20 O6 ? ? C C 41 C G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? B C 15 O2 ? ? ? 1_555 B G 20 N2 ? ? C C 41 C G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? B G 16 N1 ? ? ? 1_555 B C 19 N3 ? ? C G 42 C C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? B G 16 N2 ? ? ? 1_555 B C 19 O2 ? ? C G 42 C C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? B G 16 O6 ? ? ? 1_555 B C 19 N4 ? ? C G 42 C C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? B A 17 N1 ? ? ? 1_555 B U 18 N3 ? ? C A 43 C U 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? B A 17 N6 ? ? ? 1_555 B U 18 O4 ? ? C A 43 C U 44 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 S9L 26 ? 4 'BINDING SITE FOR RESIDUE S9L A 26' AC2 Software C NCO 1 ? 4 'BINDING SITE FOR RESIDUE NCO C 1' AC3 Software A NCO 27 ? 6 'BINDING SITE FOR RESIDUE NCO A 27' AC4 Software A SO4 28 ? 3 'BINDING SITE FOR RESIDUE SO4 A 28' # 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 A 25 ? G A 25 . ? 1_555 ? 3 AC1 4 G B 1 ? G C 27 . ? 1_555 ? 4 AC1 4 A B 17 ? A C 43 . ? 9_665 ? 5 AC2 4 A B 6 ? A C 32 . ? 1_555 ? 6 AC2 4 G B 7 ? G C 33 . ? 1_555 ? 7 AC2 4 A B 27 ? A C 53 . ? 1_555 ? 8 AC2 4 U B 28 ? U C 54 . ? 1_555 ? 9 AC3 6 C A 2 ? C A 2 . ? 1_555 ? 10 AC3 6 C A 3 ? C A 3 . ? 1_555 ? 11 AC3 6 G A 23 ? G A 23 . ? 1_555 ? 12 AC3 6 G A 24 ? G A 24 . ? 1_555 ? 13 AC3 6 G A 25 ? G A 25 . ? 1_555 ? 14 AC3 6 SO4 E . ? SO4 A 28 . ? 1_555 ? 15 AC4 3 U A 1 ? U A 1 . ? 1_555 ? 16 AC4 3 C A 2 ? C A 2 . ? 1_555 ? 17 AC4 3 NCO D . ? NCO A 27 . ? 1_555 ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 P _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 G _pdbx_validate_rmsd_bond.auth_seq_id_1 20 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 A _pdbx_validate_rmsd_bond.auth_atom_id_2 OP2 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 G _pdbx_validate_rmsd_bond.auth_seq_id_2 20 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 A _pdbx_validate_rmsd_bond.bond_value 1.383 _pdbx_validate_rmsd_bond.bond_target_value 1.485 _pdbx_validate_rmsd_bond.bond_deviation -0.102 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.017 _pdbx_validate_rmsd_bond.linker_flag N # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 N9 _pdbx_validate_rmsd_angle.auth_asym_id_1 C _pdbx_validate_rmsd_angle.auth_comp_id_1 A _pdbx_validate_rmsd_angle.auth_seq_id_1 51 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 C _pdbx_validate_rmsd_angle.auth_comp_id_2 A _pdbx_validate_rmsd_angle.auth_seq_id_2 51 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 "C2'" _pdbx_validate_rmsd_angle.auth_asym_id_3 C _pdbx_validate_rmsd_angle.auth_comp_id_3 A _pdbx_validate_rmsd_angle.auth_seq_id_3 51 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 122.81 _pdbx_validate_rmsd_angle.angle_target_value 114.00 _pdbx_validate_rmsd_angle.angle_deviation 8.81 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.30 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 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 3GS5 'double helix' 3GS5 'a-form double helix' 3GS5 'bulge loop' 3GS5 'mismatched base pair' 3GS5 '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 A G 25 1_555 0.187 -0.016 -0.186 4.621 -18.683 8.016 1 A_C2:G25_A A 2 ? A 25 ? 19 1 1 A C 3 1_555 A G 24 1_555 0.355 -0.150 0.094 -5.570 -5.567 2.755 2 A_C3:G24_A A 3 ? A 24 ? 19 1 1 A C 4 1_555 A G 23 1_555 0.575 -0.126 0.242 1.103 6.271 6.198 3 A_C4:G23_A A 4 ? A 23 ? 19 1 1 A A 5 1_555 A A 21 1_555 6.669 -4.170 -0.427 13.455 2.032 -28.142 4 A_A5:A21_A A 5 ? A 21 ? ? 10 1 A U 7 1_555 A G 20 1_555 -7.695 -2.169 0.005 8.032 10.338 0.899 5 A_U7:G20_A A 7 ? A 20 ? ? ? 1 A C 8 1_555 A A 19 1_555 -2.183 0.463 -0.880 23.520 -18.162 4.842 6 A_C8:A19_A A 8 ? A 19 ? ? ? 1 A C 9 1_555 A G 18 1_555 -0.071 0.196 0.182 8.099 -9.248 7.589 7 A_C9:G18_A A 9 ? A 18 ? 19 1 1 A A 10 1_555 A U 17 1_555 0.248 -0.172 0.172 7.090 -12.178 -2.033 8 A_A10:U17_A A 10 ? A 17 ? 20 1 1 A C 11 1_555 A G 16 1_555 0.188 0.053 0.174 3.012 -12.303 5.583 9 A_C11:G16_A A 11 ? A 16 ? 19 1 1 A C 12 1_555 A G 15 1_555 0.501 -0.209 0.581 -0.893 -15.349 8.588 10 A_C12:G15_A A 12 ? A 15 ? 19 1 1 A G 13 1_555 A C 14 1_555 -0.351 0.070 0.149 -1.270 -10.309 8.728 11 A_G13:C14_A A 13 ? A 14 ? 19 1 1 B G 1 1_555 B C 36 1_555 -0.461 -0.247 0.715 4.572 -9.088 -1.004 12 C_G27:C62_C C 27 ? C 62 ? 19 1 1 B G 2 1_555 B C 35 1_555 -0.678 -0.128 0.435 9.960 -11.165 2.578 13 C_G28:C61_C C 28 ? C 61 ? 19 1 1 B C 3 1_555 B G 34 1_555 -0.149 0.034 0.040 7.573 -14.338 3.100 14 C_C29:G60_C C 29 ? C 60 ? 19 1 1 B A 4 1_555 B U 33 1_555 -0.275 0.030 -0.122 -2.866 -10.854 8.992 15 C_A30:U59_C C 30 ? C 59 ? 20 1 1 B G 5 1_555 B C 32 1_555 -0.554 -0.300 -0.407 -8.315 -5.320 5.420 16 C_G31:C58_C C 31 ? C 58 ? 19 1 1 B A 6 1_555 B C 31 1_555 1.967 0.160 -0.418 -15.836 -5.857 16.377 17 C_A32:C57_C C 32 ? C 57 ? ? 1 1 B G 7 1_555 B A 30 1_555 6.855 -4.396 -0.236 -7.620 2.728 -6.079 18 C_G33:A56_C C 33 ? C 56 ? 11 10 1 B A 8 1_555 B U 28 1_555 -4.222 -2.087 -0.071 -4.817 -9.914 -98.316 19 C_A34:U54_C C 34 ? C 54 ? 24 4 1 B A 9 1_555 B A 27 1_555 -4.748 0.458 0.019 -0.650 -14.683 -88.473 20 C_A35:A53_C C 35 ? C 53 ? ? ? 1 B A 10 1_555 B A 25 1_555 4.564 2.651 -0.225 4.893 -16.049 -137.669 21 C_A36:A51_C C 36 ? C 51 ? ? ? 1 B C 11 1_555 A G 6 1_555 0.516 -0.267 0.150 18.547 -12.670 -0.507 22 C_C37:G6_A C 37 ? A 6 ? 19 1 1 B A 12 1_555 B G 23 1_555 0.321 1.286 -0.448 -13.792 -15.400 -16.623 23 C_A38:G49_C C 38 ? C 49 ? 8 ? 1 B C 13 1_555 B G 22 1_555 0.246 -0.194 0.091 4.143 -21.417 2.666 24 C_C39:G48_C C 39 ? C 48 ? 19 1 1 B A 14 1_555 B U 21 1_555 -0.031 -0.224 0.274 5.105 -18.266 1.636 25 C_A40:U47_C C 40 ? C 47 ? 20 1 1 B C 15 1_555 B G 20 1_555 0.203 -0.090 0.169 5.100 -12.253 4.880 26 C_C41:G46_C C 41 ? C 46 ? 19 1 1 B G 16 1_555 B C 19 1_555 -0.304 -0.186 0.187 -6.042 -13.729 -1.643 27 C_G42:C45_C C 42 ? C 45 ? 19 1 1 B A 17 1_555 B U 18 1_555 0.462 -0.090 0.323 -2.828 -4.484 2.770 28 C_A43:U44_C C 43 ? C 44 ? 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 A G 25 1_555 A C 3 1_555 A G 24 1_555 -0.729 -1.772 3.493 -3.340 11.664 34.538 -4.427 0.705 2.823 18.936 5.422 36.546 1 AA_C2C3:G24G25_AA A 2 ? A 25 ? A 3 ? A 24 ? 1 A C 3 1_555 A G 24 1_555 A C 4 1_555 A G 23 1_555 0.586 -1.656 3.258 -0.891 6.329 28.005 -4.676 -1.370 2.804 12.866 1.811 28.711 2 AA_C3C4:G23G24_AA A 3 ? A 24 ? A 4 ? A 23 ? 1 A C 4 1_555 A G 23 1_555 A A 5 1_555 A A 21 1_555 -0.280 -0.969 5.127 -0.896 25.614 73.892 -1.899 0.184 4.647 20.716 0.725 77.607 3 AA_C4A5:A21G23_AA A 4 ? A 23 ? A 5 ? A 21 ? 1 A A 5 1_555 A A 21 1_555 A U 7 1_555 A G 20 1_555 -0.587 0.690 3.459 8.605 0.935 11.273 1.917 10.398 2.438 4.064 -37.394 14.204 4 AA_A5U7:G20A21_AA A 5 ? A 21 ? A 7 ? A 20 ? 1 A U 7 1_555 A G 20 1_555 A C 8 1_555 A A 19 1_555 -0.042 -0.750 2.867 -1.413 11.320 50.119 -1.530 -0.035 2.651 13.167 1.644 51.319 5 AA_U7C8:A19G20_AA A 7 ? A 20 ? A 8 ? A 19 ? 1 A C 8 1_555 A A 19 1_555 A C 9 1_555 A G 18 1_555 0.209 -1.405 3.843 -8.502 7.050 38.296 -2.991 -1.424 3.421 10.483 12.642 39.800 6 AA_C8C9:G18A19_AA A 8 ? A 19 ? A 9 ? A 18 ? 1 A C 9 1_555 A G 18 1_555 A A 10 1_555 A U 17 1_555 -0.763 -1.623 3.065 -0.507 9.849 36.586 -3.611 1.119 2.568 15.349 0.790 37.848 7 AA_C9A10:U17G18_AA A 9 ? A 18 ? A 10 ? A 17 ? 1 A A 10 1_555 A U 17 1_555 A C 11 1_555 A G 16 1_555 0.040 -1.695 3.354 0.688 5.924 27.153 -4.913 0.077 2.925 12.428 -1.444 27.788 8 AA_A10C11:G16U17_AA A 10 ? A 17 ? A 11 ? A 16 ? 1 A C 11 1_555 A G 16 1_555 A C 12 1_555 A G 15 1_555 0.245 -1.981 3.127 -1.764 7.944 33.940 -4.375 -0.646 2.596 13.371 2.969 34.874 9 AA_C11C12:G15G16_AA A 11 ? A 16 ? A 12 ? A 15 ? 1 A C 12 1_555 A G 15 1_555 A G 13 1_555 A C 14 1_555 -0.038 -1.769 3.010 2.947 8.510 26.861 -5.271 0.650 2.334 17.699 -6.129 28.304 10 AA_C12G13:C14G15_AA A 12 ? A 15 ? A 13 ? A 14 ? 1 B G 1 1_555 B C 36 1_555 B G 2 1_555 B C 35 1_555 -0.526 -1.118 3.039 -1.822 5.798 33.447 -2.753 0.637 2.835 9.973 3.133 33.979 11 CC_G27G28:C61C62_CC C 27 ? C 62 ? C 28 ? C 61 ? 1 B G 2 1_555 B C 35 1_555 B C 3 1_555 B G 34 1_555 0.315 -1.277 3.339 2.416 6.234 35.117 -2.974 -0.168 3.088 10.218 -3.959 35.728 12 CC_G28C29:G60C61_CC C 28 ? C 61 ? C 29 ? C 60 ? 1 B C 3 1_555 B G 34 1_555 B A 4 1_555 B U 33 1_555 0.552 -1.657 3.323 0.461 13.852 31.232 -4.841 -0.873 2.402 24.287 -0.809 34.099 13 CC_C29A30:U59G60_CC C 29 ? C 60 ? C 30 ? C 59 ? 1 B A 4 1_555 B U 33 1_555 B G 5 1_555 B C 32 1_555 0.078 -1.901 3.461 -0.357 6.078 27.831 -5.251 -0.239 2.985 12.448 0.730 28.476 14 CC_A30G31:C58U59_CC C 30 ? C 59 ? C 31 ? C 58 ? 1 B G 5 1_555 B C 32 1_555 B A 6 1_555 B C 31 1_555 1.010 -1.200 3.441 3.134 9.293 40.663 -2.682 -1.078 3.170 13.143 -4.432 41.780 15 CC_G31A32:C57C58_CC C 31 ? C 58 ? C 32 ? C 57 ? 1 B A 6 1_555 B C 31 1_555 B G 7 1_555 B A 30 1_555 -0.590 -0.872 3.147 4.836 3.592 57.173 -1.092 0.862 3.037 3.742 -5.038 57.463 16 CC_A32G33:A56C57_CC C 32 ? C 57 ? C 33 ? C 56 ? 1 B G 7 1_555 B A 30 1_555 B A 8 1_555 B U 28 1_555 -2.226 -0.559 3.416 2.339 -0.015 13.000 -2.416 12.145 2.971 -0.065 -10.220 13.208 17 CC_G33A34:U54A56_CC C 33 ? C 56 ? C 34 ? C 54 ? 1 B A 8 1_555 B U 28 1_555 B A 9 1_555 B A 27 1_555 0.239 -2.222 3.363 -8.405 2.979 44.391 -3.155 -1.062 3.123 3.896 10.993 45.233 18 CC_A34A35:A53U54_CC C 34 ? C 54 ? C 35 ? C 53 ? 1 B A 9 1_555 B A 27 1_555 B A 10 1_555 B A 25 1_555 -3.047 -2.851 3.497 -5.254 2.451 72.404 -2.495 2.386 3.596 2.072 4.441 72.604 19 CC_A35A36:A51A53_CC C 35 ? C 53 ? C 36 ? C 51 ? 1 B A 10 1_555 B A 25 1_555 B C 11 1_555 A G 6 1_555 1.910 -0.545 2.913 0.593 1.968 -24.709 0.738 4.607 2.901 -4.589 1.384 -24.793 20 CC_A36C37:G6A51_AC C 36 ? C 51 ? C 37 ? A 6 ? 1 B C 11 1_555 A G 6 1_555 B A 12 1_555 B G 23 1_555 0.024 -2.186 3.916 5.851 6.286 44.542 -3.481 0.569 3.567 8.203 -7.635 45.321 21 CC_C37A38:G49G6_CA C 37 ? A 6 ? C 38 ? C 49 ? 1 B A 12 1_555 B G 23 1_555 B C 13 1_555 B G 22 1_555 1.105 -0.675 2.884 -4.959 1.502 29.450 -1.572 -3.015 2.630 2.927 9.661 29.893 22 CC_A38C39:G48G49_CC C 38 ? C 49 ? C 39 ? C 48 ? 1 B C 13 1_555 B G 22 1_555 B A 14 1_555 B U 21 1_555 0.107 -1.079 3.179 -0.656 7.905 33.236 -3.009 -0.279 2.852 13.581 1.127 34.143 23 CC_C39A40:U47G48_CC C 39 ? C 48 ? C 40 ? C 47 ? 1 B A 14 1_555 B U 21 1_555 B C 15 1_555 B G 20 1_555 0.529 -1.049 3.245 2.075 1.041 34.987 -1.897 -0.568 3.239 1.729 -3.447 35.062 24 CC_A40C41:G46U47_CC C 40 ? C 47 ? C 41 ? C 46 ? 1 B C 15 1_555 B G 20 1_555 B G 16 1_555 B C 19 1_555 0.078 -1.544 3.326 1.739 10.428 33.374 -4.064 0.119 2.735 17.616 -2.939 34.963 25 CC_C41G42:C45G46_CC C 41 ? C 46 ? C 42 ? C 45 ? 1 B G 16 1_555 B C 19 1_555 B A 17 1_555 B U 18 1_555 0.809 -1.735 3.075 3.428 3.388 32.515 -3.604 -0.886 2.952 6.010 -6.081 32.861 26 CC_G42A43:U44C45_CC C 42 ? C 45 ? C 43 ? C 44 ? # _atom_sites.entry_id 3GS5 _atom_sites.fract_transf_matrix[1][1] 0.010658 _atom_sites.fract_transf_matrix[1][2] 0.006153 _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] 0.012306 _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] 0.007571 _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_