data_3GCA # _entry.id 3GCA # _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 3GCA pdb_00003gca 10.2210/pdb3gca/pdb NDB UR0186 ? ? RCSB RCSB051685 ? ? WWPDB D_1000051685 ? ? # 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 2009-03-03 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_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_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3GCA _pdbx_database_status.recvd_initial_deposition_date 2009-02-21 _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_ _audit_author.name _audit_author.pdbx_ordinal 'Spitale, R.C.' 1 'Wedekind, J.E.' 2 # _citation.id primary _citation.title 'The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain.' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 284 _citation.page_first 11012 _citation.page_last 11016 _citation.year 2009 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19261617 _citation.pdbx_database_id_DOI 10.1074/jbc.C900024200 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Spitale, R.C.' 1 ? primary 'Torelli, A.T.' 2 ? primary 'Krucinska, J.' 3 ? primary 'Bandarian, V.' 4 ? primary 'Wedekind, J.E.' 5 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'PreQ1 riboswitch' 10599.417 1 ? ? ? ? 2 non-polymer syn '2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE' 175.147 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG _entity_poly.pdbx_seq_one_letter_code_can CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE' PQ0 3 'SULFATE ION' SO4 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 U n 1 3 G n 1 4 G n 1 5 G n 1 6 U n 1 7 C n 1 8 G n 1 9 C n 1 10 A n 1 11 G n 1 12 U n 1 13 A n 1 14 A n 1 15 C n 1 16 C n 1 17 C n 1 18 C n 1 19 A n 1 20 G n 1 21 U n 1 22 U n 1 23 A n 1 24 A n 1 25 C n 1 26 A n 1 27 A n 1 28 A n 1 29 A n 1 30 C n 1 31 A n 1 32 A n 1 33 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details ;The RNA strand was chemically synthesized based on the sequence of Class I, Type I PreQ1 riboswitch aptamer domain from T. tengcongensis ; # 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 PQ0 non-polymer . '2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE' 7-DEAZA-7-CYANO-GUANINE 'C7 H5 N5 O' 175.147 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 C 1 1 1 C C A . n A 1 2 U 2 2 2 U U A . n A 1 3 G 3 3 3 G G A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G 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 G 11 11 11 G G A . n A 1 12 U 12 12 12 U U A . n A 1 13 A 13 13 13 A A A . n A 1 14 A 14 14 14 A A A . n A 1 15 C 15 15 15 C C A . n A 1 16 C 16 16 16 C C A . n A 1 17 C 17 17 17 C C A . n A 1 18 C 18 18 18 C C 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 U 21 21 21 U U A . n A 1 22 U 22 22 22 U U A . n A 1 23 A 23 23 23 A A A . n A 1 24 A 24 24 24 A A A . n A 1 25 C 25 25 25 C C A . n A 1 26 A 26 26 26 A A A . n A 1 27 A 27 27 27 A A A . n A 1 28 A 28 28 28 A A A . n A 1 29 A 29 29 29 A A A . n A 1 30 C 30 30 30 C C A . n A 1 31 A 31 31 31 A A A . n A 1 32 A 32 32 32 A A A . n A 1 33 G 33 33 33 G G A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 PQ0 1 34 1 PQ0 PQ0 A . C 3 SO4 1 102 102 SO4 SO4 A . D 3 SO4 1 103 103 SO4 SO4 A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 PHENIX 'model building' . ? 2 CNS refinement 1.2 ? 3 DENZO 'data reduction' . ? 4 SCALEPACK 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 3GCA _cell.length_a 110.5 _cell.length_b 110.5 _cell.length_c 59.31 _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 3GCA _symmetry.space_group_name_H-M 'P 63 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3GCA _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.93 _exptl_crystal.density_percent_sol 75.05 _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 6.0 _exptl_crystal_grow.pdbx_details ;1.8 M Li2SO4, 0.10 M Na-cacodylate pH 6.0, 0.01 M Mg(SO4)2-, 5% (v/v) 1,3-propanediol and 2 mM spermine., 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 Li2SO4 ? ? ? 1 2 1 Na-cacodylate ? ? ? 1 3 1 'Mg(SO4)2' ? ? ? 1 4 1 1,3-Propanediol ? ? ? 1 5 1 Spermine ? ? ? 1 6 2 Li2SO4 ? ? ? 1 7 2 Na-cacodylate ? ? ? 1 8 2 'Mg(SO4)2' ? ? ? 1 9 2 1,3-Propanediol ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'Quantum 315 CCD detector' _diffrn_detector.pdbx_collection_date 2009-01-29 _diffrn_detector.details 'Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.1395 1.0 2 1.1407 1.0 3 0.97622 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL7-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL7-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '1.1395, 1.1407, 0.97622, 1.1395' # _reflns.entry_id 3GCA _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50.00 _reflns.d_resolution_high 2.75 _reflns.number_obs 5990 _reflns.number_all ? _reflns.percent_possible_obs 97.6 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.056 _reflns.pdbx_netI_over_sigmaI 36.47 _reflns.B_iso_Wilson_estimate 75 _reflns.pdbx_redundancy 16.6 _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 98.5 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.36 _reflns_shell.meanI_over_sigI_obs 6.5 _reflns_shell.pdbx_redundancy 15.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 579 _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 3GCA _refine.ls_number_reflns_obs 5990 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 303382.60 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 28.33 _refine.ls_d_res_high 2.75 _refine.ls_percent_reflns_obs 93.4 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.245 _refine.ls_R_factor_R_free 0.272 _refine.ls_R_factor_R_free_error 0.013 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 8.0 _refine.ls_number_reflns_R_free 441 _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 76 _refine.aniso_B[1][1] -21 _refine.aniso_B[2][2] -21 _refine.aniso_B[3][3] 42 _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.2 _refine.solvent_model_param_bsol 51.0924 _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 MAD _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'CNS 1.2' _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 3GCA _refine_analyze.Luzzati_coordinate_error_obs 0.44 _refine_analyze.Luzzati_sigma_a_obs 0.52 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.49 _refine_analyze.Luzzati_sigma_a_free 0.53 _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 702 _refine_hist.pdbx_number_atoms_ligand 23 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 725 _refine_hist.d_res_high 2.75 _refine_hist.d_res_low 28.33 # 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 0.008 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.5 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 20.3 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.99 ? ? ? '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 2.92 _refine_ls_shell.number_reflns_R_work 728 _refine_ls_shell.R_factor_R_work 0.438 _refine_ls_shell.percent_reflns_obs 83.0 _refine_ls_shell.R_factor_R_free 0.487 _refine_ls_shell.R_factor_R_free_error 0.060 _refine_ls_shell.percent_reflns_R_free 8.2 _refine_ls_shell.number_reflns_R_free 65 _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 dna-rnaATT 'X-RAY DIFFRACTION' 2 pq pq 'X-RAY DIFFRACTION' 4 to ? 'X-RAY DIFFRACTION' 3 ? ion.top 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3GCA _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 3GCA _struct.title 'The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3GCA _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'PreQ1, PreQ0, riboswitch, RNA, ribosomal binding site, amptamer, metabolite' # 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 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3GCA _struct_ref.pdbx_db_accession 3GCA _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3GCA _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 33 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3GCA _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 33 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 33 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 1 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 1 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 1 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 A A 19 N1 ? ? A U 2 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 A A 19 N6 ? ? A U 2 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 3 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 3 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 3 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 4 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 17 O2 ? ? A G 4 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 17 N4 ? ? A G 4 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 5 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 5 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 5 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 5 N2 ? ? ? 1_555 A A 27 N1 ? ? A G 5 A A 27 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog16 hydrog ? ? A G 5 N3 ? ? ? 1_555 A A 27 N6 ? ? A G 5 A A 27 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog17 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 28 N7 ? ? A U 6 A A 28 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog18 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 6 A A 28 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog19 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 29 N6 ? ? A U 6 A A 29 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog20 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 11 N7 ? ? A C 7 A G 11 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog21 hydrog ? ? A C 7 O2 ? ? ? 1_555 A C 30 N4 ? ? A C 7 A C 30 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog22 hydrog ? ? A G 8 N2 ? ? ? 1_555 A A 31 N1 ? ? A G 8 A A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog23 hydrog ? ? A G 8 N3 ? ? ? 1_555 A A 31 N6 ? ? A G 8 A A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog24 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 9 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 9 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 9 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A A 10 N3 ? ? ? 1_555 A A 32 N6 ? ? A A 10 A A 32 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog28 hydrog ? ? A G 11 N2 ? ? ? 1_555 A A 14 N1 ? ? A G 11 A A 14 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog29 hydrog ? ? A G 11 N3 ? ? ? 1_555 A A 14 N6 ? ? A G 11 A A 14 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog30 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 11 A C 15 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog31 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A A 13 N6 ? ? ? 1_555 A A 31 N3 ? ? A A 13 A A 31 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog35 hydrog ? ? A C 17 O2 ? ? ? 1_555 A A 26 N6 ? ? A C 17 A A 26 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog36 hydrog ? ? A G 20 N2 ? ? ? 1_555 A U 21 O4 ? ? A G 20 A U 21 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 PQ0 34 ? 7 'BINDING SITE FOR RESIDUE PQ0 A 34' AC2 Software A SO4 102 ? 3 'BINDING SITE FOR RESIDUE SO4 A 102' AC3 Software A SO4 103 ? 3 'BINDING SITE FOR RESIDUE SO4 A 103' # 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 7 G A 5 ? G A 5 . ? 1_555 ? 2 AC1 7 U A 6 ? U A 6 . ? 1_555 ? 3 AC1 7 C A 7 ? C A 7 . ? 1_555 ? 4 AC1 7 G A 11 ? G A 11 . ? 1_555 ? 5 AC1 7 C A 15 ? C A 15 . ? 1_555 ? 6 AC1 7 C A 16 ? C A 16 . ? 1_555 ? 7 AC1 7 A A 29 ? A A 29 . ? 1_555 ? 8 AC2 3 C A 15 ? C A 15 . ? 1_555 ? 9 AC2 3 C A 16 ? C A 16 . ? 1_555 ? 10 AC2 3 C A 17 ? C A 17 . ? 1_555 ? 11 AC3 3 U A 2 ? U A 2 . ? 1_555 ? 12 AC3 3 C A 18 ? C A 18 . ? 1_555 ? 13 AC3 3 A A 19 ? A A 19 . ? 1_555 ? # 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 "C2'" A G 8 ? ? "C3'" A G 8 ? ? "O3'" A G 8 ? ? 126.52 113.70 12.82 1.60 N 2 1 "C4'" A G 8 ? ? "C3'" A G 8 ? ? "C2'" A G 8 ? ? 109.26 102.60 6.66 1.00 N 3 1 N9 A G 8 ? ? "C1'" A G 8 ? ? "C2'" A G 8 ? ? 104.94 112.00 -7.06 1.10 N 4 1 "O4'" A G 20 ? ? "C1'" A G 20 ? ? N9 A G 20 ? ? 113.46 108.50 4.96 0.70 N # _pdbx_validate_chiral.id 1 _pdbx_validate_chiral.PDB_model_num 1 _pdbx_validate_chiral.auth_atom_id "C3'" _pdbx_validate_chiral.label_alt_id ? _pdbx_validate_chiral.auth_asym_id A _pdbx_validate_chiral.auth_comp_id G _pdbx_validate_chiral.auth_seq_id 8 _pdbx_validate_chiral.PDB_ins_code ? _pdbx_validate_chiral.details PLANAR _pdbx_validate_chiral.omega . # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 U A 22 ? ? 0.090 'SIDE CHAIN' 2 1 A A 31 ? ? 0.065 'SIDE CHAIN' # 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 PQ0 N1 N Y N 111 PQ0 C2 C Y N 112 PQ0 N3 N Y N 113 PQ0 C4 C Y N 114 PQ0 C5 C Y N 115 PQ0 C6 C Y N 116 PQ0 O6 O N N 117 PQ0 C7 C Y N 118 PQ0 C10 C N N 119 PQ0 N11 N N N 120 PQ0 C8 C Y N 121 PQ0 N9 N Y N 122 PQ0 N2 N N N 123 PQ0 HN1 H N N 124 PQ0 H8 H N N 125 PQ0 HN9 H N N 126 PQ0 HN21 H N N 127 PQ0 HN22 H N N 128 SO4 S S N N 129 SO4 O1 O N N 130 SO4 O2 O N N 131 SO4 O3 O N N 132 SO4 O4 O N N 133 U OP3 O N N 134 U P P N N 135 U OP1 O N N 136 U OP2 O N N 137 U "O5'" O N N 138 U "C5'" C N N 139 U "C4'" C N R 140 U "O4'" O N N 141 U "C3'" C N S 142 U "O3'" O N N 143 U "C2'" C N R 144 U "O2'" O N N 145 U "C1'" C N R 146 U N1 N N N 147 U C2 C N N 148 U O2 O N N 149 U N3 N N N 150 U C4 C N N 151 U O4 O N N 152 U C5 C N N 153 U C6 C N N 154 U HOP3 H N N 155 U HOP2 H N N 156 U "H5'" H N N 157 U "H5''" H N N 158 U "H4'" H N N 159 U "H3'" H N N 160 U "HO3'" H N N 161 U "H2'" H N N 162 U "HO2'" H N N 163 U "H1'" H N N 164 U H3 H N N 165 U H5 H N N 166 U H6 H N N 167 # 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 PQ0 N1 C2 sing Y N 116 PQ0 N1 C6 sing Y N 117 PQ0 N1 HN1 sing N N 118 PQ0 C2 N3 doub Y N 119 PQ0 C2 N2 sing N N 120 PQ0 N3 C4 sing Y N 121 PQ0 C4 C5 doub Y N 122 PQ0 C4 N9 sing Y N 123 PQ0 C5 C6 sing Y N 124 PQ0 C5 C7 sing Y N 125 PQ0 C6 O6 doub N N 126 PQ0 C7 C10 sing N N 127 PQ0 C7 C8 doub Y N 128 PQ0 C10 N11 trip N N 129 PQ0 C8 N9 sing Y N 130 PQ0 C8 H8 sing N N 131 PQ0 N9 HN9 sing N N 132 PQ0 N2 HN21 sing N N 133 PQ0 N2 HN22 sing N N 134 SO4 S O1 doub N N 135 SO4 S O2 doub N N 136 SO4 S O3 sing N N 137 SO4 S O4 sing N N 138 U OP3 P sing N N 139 U OP3 HOP3 sing N N 140 U P OP1 doub N N 141 U P OP2 sing N N 142 U P "O5'" sing N N 143 U OP2 HOP2 sing N N 144 U "O5'" "C5'" sing N N 145 U "C5'" "C4'" sing N N 146 U "C5'" "H5'" sing N N 147 U "C5'" "H5''" sing N N 148 U "C4'" "O4'" sing N N 149 U "C4'" "C3'" sing N N 150 U "C4'" "H4'" sing N N 151 U "O4'" "C1'" sing N N 152 U "C3'" "O3'" sing N N 153 U "C3'" "C2'" sing N N 154 U "C3'" "H3'" sing N N 155 U "O3'" "HO3'" sing N N 156 U "C2'" "O2'" sing N N 157 U "C2'" "C1'" sing N N 158 U "C2'" "H2'" sing N N 159 U "O2'" "HO2'" sing N N 160 U "C1'" N1 sing N N 161 U "C1'" "H1'" sing N N 162 U N1 C2 sing N N 163 U N1 C6 sing N N 164 U C2 O2 doub N N 165 U C2 N3 sing N N 166 U N3 C4 sing N N 167 U N3 H3 sing N N 168 U C4 O4 doub N N 169 U C4 C5 sing N N 170 U C5 C6 doub N N 171 U C5 H5 sing N N 172 U C6 H6 sing N N 173 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3GCA 'double helix' 3GCA 'a-form double helix' 3GCA 'bulge loop' 3GCA 'quadruple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 1 1_555 A G 20 1_555 0.313 -0.317 -0.186 -1.009 -1.016 -2.852 1 A_C1:G20_A A 1 ? A 20 ? 19 1 1 A U 2 1_555 A A 19 1_555 0.327 -0.403 0.079 -3.776 -9.379 -1.038 2 A_U2:A19_A A 2 ? A 19 ? 20 1 1 A G 3 1_555 A C 18 1_555 0.049 -0.502 0.318 -3.814 -10.619 -2.756 3 A_G3:C18_A A 3 ? A 18 ? 19 1 1 A G 4 1_555 A C 17 1_555 -0.025 -0.302 0.345 -4.583 -11.931 -1.807 4 A_G4:C17_A A 4 ? A 17 ? 19 1 1 A G 5 1_555 A C 16 1_555 0.166 -0.147 -0.032 -9.634 -11.244 -2.467 5 A_G5:C16_A A 5 ? A 16 ? 19 1 1 A U 6 1_555 A A 28 1_555 -0.223 2.393 1.135 -31.696 -1.751 -78.965 6 A_U6:A28_A A 6 ? A 28 ? 23 3 1 A C 30 1_555 A G 11 1_555 0.075 -0.473 0.418 10.403 -16.977 -1.457 7 A_C30:G11_A A 30 ? A 11 ? 19 1 1 A A 31 1_555 A G 8 1_555 -3.402 3.409 0.609 -14.812 -9.930 74.796 8 A_A31:G8_A A 31 ? A 8 ? 10 6 1 A A 32 1_555 A A 10 1_555 -6.474 -3.193 -0.051 10.932 -28.024 -12.131 9 A_A32:A10_A A 32 ? A 10 ? ? 6 1 A G 33 1_555 A C 9 1_555 0.379 -0.415 0.087 -5.870 -3.632 -10.372 10 A_G33:C9_A A 33 ? A 9 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 A G 20 1_555 A U 2 1_555 A A 19 1_555 0.557 -1.810 3.118 0.483 8.492 33.297 -4.246 -0.876 2.599 14.526 -0.826 34.337 1 AA_C1U2:A19G20_AA A 1 ? A 20 ? A 2 ? A 19 ? 1 A U 2 1_555 A A 19 1_555 A G 3 1_555 A C 18 1_555 -0.405 -1.732 2.905 1.722 8.666 30.633 -4.443 0.994 2.315 15.990 -3.177 31.853 2 AA_U2G3:C18A19_AA A 2 ? A 19 ? A 3 ? A 18 ? 1 A G 3 1_555 A C 18 1_555 A G 4 1_555 A C 17 1_555 0.760 -1.716 3.012 1.809 7.005 28.150 -4.754 -1.171 2.562 14.110 -3.645 29.047 3 AA_G3G4:C17C18_AA A 3 ? A 18 ? A 4 ? A 17 ? 1 A G 4 1_555 A C 17 1_555 A G 5 1_555 A C 16 1_555 0.248 -1.828 3.303 5.388 6.598 36.115 -3.730 0.309 2.941 10.464 -8.546 37.073 4 AA_G4G5:C16C17_AA A 4 ? A 17 ? A 5 ? A 16 ? 1 A G 5 1_555 A C 16 1_555 A U 6 1_555 A A 28 1_555 -6.107 0.007 1.831 11.386 -0.225 32.544 0.021 10.764 -0.231 -0.387 -19.585 34.428 5 AA_G5U6:A28C16_AA A 5 ? A 16 ? A 6 ? A 28 ? 1 A U 6 1_555 A A 28 1_555 A C 30 1_555 A G 11 1_555 0.337 -3.293 4.990 5.694 4.485 103.755 -2.187 -0.092 4.896 2.848 -3.616 103.935 6 AA_U6C30:G11A28_AA A 6 ? A 28 ? A 30 ? A 11 ? 1 A C 30 1_555 A G 11 1_555 A A 31 1_555 A G 8 1_555 1.174 -3.578 3.192 3.857 8.805 -6.411 0.025 13.611 4.107 -51.641 22.618 -11.550 7 AA_C30A31:G8G11_AA A 30 ? A 11 ? A 31 ? A 8 ? 1 A A 31 1_555 A G 8 1_555 A A 32 1_555 A A 10 1_555 -3.766 3.074 3.102 -7.270 -3.028 42.937 4.431 4.363 3.450 -4.095 9.833 43.620 8 AA_A31A32:A10G8_AA A 31 ? A 8 ? A 32 ? A 10 ? 1 A A 32 1_555 A A 10 1_555 A G 33 1_555 A C 9 1_555 1.135 -1.181 3.996 -4.052 9.905 57.532 -1.824 -1.414 3.685 10.194 4.170 58.435 9 AA_A32G33:C9A10_AA A 32 ? A 10 ? A 33 ? A 9 ? # _atom_sites.entry_id 3GCA _atom_sites.fract_transf_matrix[1][1] 0.009050 _atom_sites.fract_transf_matrix[1][2] 0.005225 _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] 0.010450 _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] 0.016861 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P S # loop_