data_1Q29 # _entry.id 1Q29 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1Q29 pdb_00001q29 10.2210/pdb1q29/pdb NDB UR0032 ? ? RCSB RCSB019824 ? ? WWPDB D_1000019824 ? ? # 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 2004-02-24 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2019-07-24 5 'Structure model' 1 4 2024-02-14 6 'Structure model' 1 5 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' Advisory 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Database references' 9 5 'Structure model' 'Derived calculations' 10 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' pdbx_validate_polymer_linkage 2 4 'Structure model' software 3 4 'Structure model' struct_conn 4 5 'Structure model' chem_comp_atom 5 5 'Structure model' chem_comp_bond 6 5 'Structure model' database_2 7 5 'Structure model' struct_conn 8 5 'Structure model' struct_site 9 6 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.name' 3 4 'Structure model' '_software.version' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 5 'Structure model' '_database_2.pdbx_DOI' 6 5 'Structure model' '_database_2.pdbx_database_accession' 7 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 9 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 11 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 12 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 13 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 14 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 15 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Q29 _pdbx_database_status.recvd_initial_deposition_date 2003-07-23 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1NYI _pdbx_database_related.details 'Crosslinked Hammerhead Ribozyme Initial State' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Dunham, C.M.' 1 'Murray, J.B.' 2 'Scott, W.G.' 3 # _citation.id primary _citation.title 'A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 332 _citation.page_first 327 _citation.page_last 336 _citation.year 2003 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12948485 _citation.pdbx_database_id_DOI '10.1016/S0022-2836(03)00843-X' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dunham, C.M.' 1 ? primary 'Murray, J.B.' 2 ? primary 'Scott, W.G.' 3 ? # 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 "5'-R(*GP*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'" 5515.309 1 ? ? ? ? 2 polymer syn Ribozyme 7674.670 1 ? ? ? ? 3 non-polymer syn 'COBALT (II) ION' 58.933 5 ? ? ? ? # 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 GGUGGUCUGAUGAGGCC GGUGGUCUGAUGAGGCC A ? 2 polyribonucleotide no no GCCGAAACUCGUAAGAGUCACCAC GCCGAAACUCGUAAGAGUCACCAC B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name 'COBALT (II) ION' _pdbx_entity_nonpoly.comp_id CO # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 U n 1 4 G n 1 5 G n 1 6 U n 1 7 C n 1 8 U n 1 9 G n 1 10 A n 1 11 U n 1 12 G n 1 13 A n 1 14 G n 1 15 G n 1 16 C n 1 17 C n 2 1 G n 2 2 C n 2 3 C n 2 4 G n 2 5 A n 2 6 A n 2 7 A n 2 8 C n 2 9 U n 2 10 C n 2 11 G n 2 12 U n 2 13 A n 2 14 A n 2 15 G n 2 16 A n 2 17 G n 2 18 U n 2 19 C n 2 20 A n 2 21 C n 2 22 C n 2 23 A n 2 24 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 CO non-polymer . 'COBALT (II) ION' ? 'Co 2' 58.933 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 10 500 G G A . n A 1 2 G 2 11 11 G G A . n A 1 3 U 3 12 12 U U A . n A 1 4 G 4 13 13 G G A . n A 1 5 G 5 14 14 G G A . n A 1 6 U 6 15 15 U U A . n A 1 7 C 7 16 16 C C A . n A 1 8 U 8 17 17 U U A . n A 1 9 G 9 18 18 G G A . n A 1 10 A 10 19 19 A A A . n A 1 11 U 11 20 20 U U A . n A 1 12 G 12 21 21 G G A . n A 1 13 A 13 22 22 A A A . n A 1 14 G 14 23 23 G G A . n A 1 15 G 15 24 24 G G A . n A 1 16 C 16 25 25 C C A . n A 1 17 C 17 26 26 C C A . n B 2 1 G 1 102 102 G G B . n B 2 2 C 2 103 103 C C B . n B 2 3 C 3 104 104 C C B . n B 2 4 G 4 105 105 G G B . n B 2 5 A 5 106 106 A A B . n B 2 6 A 6 107 107 A A B . n B 2 7 A 7 108 108 A A B . n B 2 8 C 8 109 109 C C B . n B 2 9 U 9 110 110 U U B . n B 2 10 C 10 111 111 C C B . n B 2 11 G 11 112 112 G G B . n B 2 12 U 12 113 113 U U B . n B 2 13 A 13 114 114 A A B . n B 2 14 A 14 115 115 A A B . n B 2 15 G 15 116 116 G G B . n B 2 16 A 16 117 117 A A B . n B 2 17 G 17 118 118 G G B . n B 2 18 U 18 119 119 U U B . n B 2 19 C 19 120 120 C C B . n B 2 20 A 20 121 121 A A B . n B 2 21 C 21 122 122 C C B . n B 2 22 C 22 123 123 C C B . n B 2 23 A 23 124 124 A A B . n B 2 24 C 24 125 125 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 CO 1 1 1 CO CO A . D 3 CO 1 2 2 CO CO A . E 3 CO 1 5 5 CO CO A . F 3 CO 1 3 3 CO CO B . G 3 CO 1 4 4 CO CO B . # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag Y _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id A _pdbx_unobs_or_zero_occ_atoms.auth_comp_id G _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 18 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id N2 _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id A _pdbx_unobs_or_zero_occ_atoms.label_comp_id G _pdbx_unobs_or_zero_occ_atoms.label_seq_id 9 _pdbx_unobs_or_zero_occ_atoms.label_atom_id N2 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1 ? 1 SCALA 'data scaling' . ? 2 CNS refinement . ? 3 MOSFLM 'data reduction' . ? 4 CCP4 'data scaling' '(SCALA)' ? 5 CNS phasing . ? 6 # _cell.entry_id 1Q29 _cell.length_a 66.689 _cell.length_b 66.689 _cell.length_c 140.528 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Q29 _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 # _exptl.entry_id 1Q29 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 6.84 _exptl_crystal.density_percent_sol 82.02 _exptl_crystal.description ? # _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 ? _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 5.0.2' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 5.0.2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _refine.entry_id 1Q29 _refine.ls_number_reflns_obs 6872 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.80 _refine.ls_d_res_high 3.00 _refine.ls_percent_reflns_obs 99.30 _refine.ls_R_factor_obs 0.24559 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.24196 _refine.ls_R_factor_R_free 0.27914 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.8 _refine.ls_number_reflns_R_free 744 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.944 _refine.correlation_coeff_Fo_to_Fc_free 0.924 _refine.B_iso_mean 77.623 _refine.aniso_B[1][1] 0.19 _refine.aniso_B[2][2] 0.19 _refine.aniso_B[3][3] -0.28 _refine.aniso_B[1][2] 0.09 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'NDB entry urx057' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.385 _refine.pdbx_overall_ESU_R_Free 0.310 _refine.overall_SU_ML 0.310 _refine.overall_SU_B 17.927 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 872 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 877 _refine_hist.d_res_high 3.00 _refine_hist.d_res_low 19.80 # 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 r_bond_refined_d 0.011 ? .021 975 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.077 ? 3.0 1512 'X-RAY DIFFRACTION' ? r_chiral_restr 0.092 ? .20 164 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 ? .02 427 'X-RAY DIFFRACTION' ? r_nbd_refined 0.196 ? .20 396 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.212 ? .20 14 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.195 ? .20 25 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.173 ? .20 4 'X-RAY DIFFRACTION' ? r_scbond_it 1.087 ? 3.0 975 'X-RAY DIFFRACTION' ? r_scangle_it 1.728 ? 4.5 1512 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 3.001 _refine_ls_shell.d_res_low 3.077 _refine_ls_shell.number_reflns_R_work 474 _refine_ls_shell.R_factor_R_work 0.438 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.412 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 55 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 1Q29 _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 1Q29 _struct.title ;Hammerhead Ribozyme with 5'-5' G-G linkage: Conformational change experiment ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Q29 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Hammerhead Ribozyme, 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 3 ? E N N 3 ? F N N 3 ? G N N 3 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1Q29 1Q29 ? ? ? 2 2 PDB 1Q29 1Q29 ? ? ? # 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 1Q29 A 1 ? 17 ? 1Q29 10 ? 26 ? 10 26 2 2 1Q29 B 1 ? 24 ? 1Q29 102 ? 125 ? 102 125 # _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,G # _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 ;Hammerhead Ribozyme with 5'-5' G-G linkage at 5' end of enzyme strand ; _struct_biol.pdbx_parent_biol_id ? # 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 one ? A G 1 "O5'" ? ? ? 1_555 A G 2 P ? ? A G 10 A G 11 1_555 ? ? ? ? ? ? ? 1.591 ? ? metalc1 metalc ? ? D CO . CO ? ? ? 1_555 A G 9 N7 ? ? A CO 2 A G 18 1_555 ? ? ? ? ? ? ? 2.560 ? ? metalc2 metalc ? ? E CO . CO ? ? ? 1_555 A A 13 OP2 ? ? A CO 5 A A 22 1_555 ? ? ? ? ? ? ? 2.326 ? ? metalc3 metalc ? ? E CO . CO ? ? ? 1_555 A G 14 N7 ? ? A CO 5 A G 23 1_555 ? ? ? ? ? ? ? 2.348 ? ? metalc4 metalc ? ? F CO . CO ? ? ? 1_555 B G 15 N7 ? ? B CO 3 B G 116 1_555 ? ? ? ? ? ? ? 2.583 ? ? metalc5 metalc ? ? G CO . CO ? ? ? 1_555 B G 17 N7 ? ? B CO 4 B G 118 1_555 ? ? ? ? ? ? ? 1.996 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 10 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 17 O2 ? ? A G 10 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 17 N4 ? ? A G 10 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 24 N3 ? ? A G 11 B C 125 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog5 hydrog ? ? A U 3 N3 ? ? ? 1_555 B A 23 N1 ? ? A U 12 B A 124 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog6 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 22 N3 ? ? A G 13 B C 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 22 O2 ? ? A G 13 B C 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 22 N4 ? ? A G 13 B C 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 14 B C 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 14 B C 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 14 B C 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 20 N1 ? ? A U 15 B A 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 20 N6 ? ? A U 15 B A 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 11 O2 ? ? ? 1_555 B A 6 N6 ? ? A U 20 B A 107 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog15 hydrog ? ? A G 12 N2 ? ? ? 1_555 B A 5 N7 ? ? A G 21 B A 106 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog16 hydrog ? ? A G 12 N3 ? ? ? 1_555 B A 5 N6 ? ? A G 21 B A 106 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A A 13 N6 ? ? ? 1_555 B G 4 N3 ? ? A A 22 B G 105 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog18 hydrog ? ? A A 13 N7 ? ? ? 1_555 B G 4 N2 ? ? A A 22 B G 105 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog19 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 23 B C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 23 B C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 23 B C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 24 B C 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 24 B C 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 24 B C 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 16 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 25 B G 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 16 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 25 B G 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 16 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 25 B G 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B C 8 N3 ? ? ? 1_555 B G 17 N1 ? ? B C 109 B G 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B C 8 N4 ? ? ? 1_555 B G 17 O6 ? ? B C 109 B G 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B C 8 O2 ? ? ? 1_555 B G 17 N2 ? ? B C 109 B G 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B U 9 N3 ? ? ? 1_555 B A 16 N1 ? ? B U 110 B A 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B U 9 O4 ? ? ? 1_555 B A 16 N6 ? ? B U 110 B A 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B C 10 N3 ? ? ? 1_555 B G 15 N1 ? ? B C 111 B G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B C 10 N4 ? ? ? 1_555 B G 15 O6 ? ? B C 111 B G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B C 10 O2 ? ? ? 1_555 B G 15 N2 ? ? B C 111 B G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B G 11 N2 ? ? ? 1_555 B A 14 N7 ? ? B G 112 B A 115 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id OP2 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id A _pdbx_struct_conn_angle.ptnr1_label_comp_id A _pdbx_struct_conn_angle.ptnr1_label_seq_id 13 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id A _pdbx_struct_conn_angle.ptnr1_auth_seq_id 22 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id CO _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id E _pdbx_struct_conn_angle.ptnr2_label_comp_id CO _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id CO _pdbx_struct_conn_angle.ptnr2_auth_seq_id 5 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id N7 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id A _pdbx_struct_conn_angle.ptnr3_label_comp_id G _pdbx_struct_conn_angle.ptnr3_label_seq_id 14 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id A _pdbx_struct_conn_angle.ptnr3_auth_comp_id G _pdbx_struct_conn_angle.ptnr3_auth_seq_id 23 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 84.3 _pdbx_struct_conn_angle.value_esd ? # 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 CO 1 ? 1 'BINDING SITE FOR RESIDUE CO A 1' AC2 Software A CO 2 ? 1 'BINDING SITE FOR RESIDUE CO A 2' AC3 Software B CO 3 ? 1 'BINDING SITE FOR RESIDUE CO B 3' AC4 Software B CO 4 ? 1 'BINDING SITE FOR RESIDUE CO B 4' AC5 Software A CO 5 ? 2 'BINDING SITE FOR RESIDUE CO A 5' # 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 1 G A 5 ? G A 14 . ? 1_555 ? 2 AC2 1 G A 9 ? G A 18 . ? 1_555 ? 3 AC3 1 G B 15 ? G B 116 . ? 1_555 ? 4 AC4 1 G B 17 ? G B 118 . ? 1_555 ? 5 AC5 2 A A 13 ? A A 22 . ? 1_555 ? 6 AC5 2 G A 14 ? G A 23 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 "O2'" _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 C _pdbx_validate_close_contact.auth_seq_id_1 120 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 OP1 _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 A _pdbx_validate_close_contact.auth_seq_id_2 121 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.72 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C5'" A G 11 ? ? "C4'" A G 11 ? ? 1.742 1.509 0.233 0.012 N 2 1 C5 A G 18 ? ? N7 A G 18 ? ? 1.343 1.388 -0.045 0.006 N 3 1 N7 A G 18 ? ? C8 A G 18 ? ? 1.348 1.305 0.043 0.006 N 4 1 "O3'" B C 109 ? ? "C3'" B C 109 ? ? 1.332 1.417 -0.085 0.014 N 5 1 "C4'" B A 121 ? ? "C3'" B A 121 ? ? 1.642 1.527 0.115 0.011 N 6 1 "O4'" B A 121 ? ? "C1'" B A 121 ? ? 1.231 1.412 -0.181 0.013 N # 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 "C5'" A G 11 ? ? "C4'" A G 11 ? ? "O4'" A G 11 ? ? 100.19 109.10 -8.91 1.20 N 2 1 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.10 108.50 4.60 0.70 N 3 1 "C4'" A U 17 ? ? "C3'" A U 17 ? ? "C2'" A U 17 ? ? 93.81 102.60 -8.79 1.00 N 4 1 "O5'" A G 18 ? ? P A G 18 ? ? OP2 A G 18 ? ? 94.78 105.70 -10.92 0.90 N 5 1 C6 A G 18 ? ? N1 A G 18 ? ? C2 A G 18 ? ? 120.81 125.10 -4.29 0.60 N 6 1 C2 A G 18 ? ? N3 A G 18 ? ? C4 A G 18 ? ? 120.37 111.90 8.47 0.50 N 7 1 N3 A G 18 ? ? C4 A G 18 ? ? C5 A G 18 ? ? 120.30 128.60 -8.30 0.50 N 8 1 C5 A G 18 ? ? C6 A G 18 ? ? N1 A G 18 ? ? 119.01 111.50 7.51 0.50 N 9 1 C4 A G 18 ? ? C5 A G 18 ? ? N7 A G 18 ? ? 107.88 110.80 -2.92 0.40 N 10 1 C5 A G 18 ? ? N7 A G 18 ? ? C8 A G 18 ? ? 108.96 104.30 4.66 0.50 N 11 1 N7 A G 18 ? ? C8 A G 18 ? ? N9 A G 18 ? ? 108.80 113.10 -4.30 0.50 N 12 1 N3 A G 18 ? ? C4 A G 18 ? ? N9 A G 18 ? ? 132.87 126.00 6.87 0.60 N 13 1 C5 A G 18 ? ? C6 A G 18 ? ? O6 A G 18 ? ? 120.71 128.60 -7.89 0.60 N 14 1 "O5'" B U 110 ? ? P B U 110 ? ? OP2 B U 110 ? ? 118.92 110.70 8.22 1.20 N 15 1 N9 B A 114 ? ? "C1'" B A 114 ? ? "C2'" B A 114 ? ? 122.03 114.00 8.03 1.30 N 16 1 "O3'" B G 116 ? ? P B A 117 ? ? "O5'" B A 117 ? ? 91.96 104.00 -12.04 1.90 Y 17 1 "O5'" B A 117 ? ? P B A 117 ? ? OP2 B A 117 ? ? 118.61 110.70 7.91 1.20 N 18 1 N1 B G 118 ? ? C6 B G 118 ? ? O6 B G 118 ? ? 115.99 119.90 -3.91 0.60 N 19 1 "C5'" B C 120 ? ? "C4'" B C 120 ? ? "C3'" B C 120 ? ? 128.01 116.00 12.01 1.60 N 20 1 "C1'" B C 120 ? ? "O4'" B C 120 ? ? "C4'" B C 120 ? ? 101.90 109.70 -7.80 0.70 N 21 1 "C2'" B C 120 ? ? "C3'" B C 120 ? ? "O3'" B C 120 ? ? 90.30 109.50 -19.20 2.20 N 22 1 "C4'" B C 120 ? ? "C3'" B C 120 ? ? "C2'" B C 120 ? ? 91.57 102.60 -11.03 1.00 N 23 1 "C4'" B A 121 ? ? "C3'" B A 121 ? ? "C2'" B A 121 ? ? 86.55 102.60 -16.05 1.00 N 24 1 "O4'" B A 121 ? ? "C1'" B A 121 ? ? N9 B A 121 ? ? 118.17 108.50 9.67 0.70 N 25 1 N3 B C 122 ? ? C2 B C 122 ? ? O2 B C 122 ? ? 117.59 121.90 -4.31 0.70 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 CO CO CO N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 U OP3 O N N 112 U P P N N 113 U OP1 O N N 114 U OP2 O N N 115 U "O5'" O N N 116 U "C5'" C N N 117 U "C4'" C N R 118 U "O4'" O N N 119 U "C3'" C N S 120 U "O3'" O N N 121 U "C2'" C N R 122 U "O2'" O N N 123 U "C1'" C N R 124 U N1 N N N 125 U C2 C N N 126 U O2 O N N 127 U N3 N N N 128 U C4 C N N 129 U O4 O N N 130 U C5 C N N 131 U C6 C N N 132 U HOP3 H N N 133 U HOP2 H N N 134 U "H5'" H N N 135 U "H5''" H N N 136 U "H4'" H N N 137 U "H3'" H N N 138 U "HO3'" H N N 139 U "H2'" H N N 140 U "HO2'" H N N 141 U "H1'" H N N 142 U H3 H N N 143 U H5 H N N 144 U H6 H N N 145 # 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 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1Q29 'double helix' 1Q29 'a-form double helix' 1Q29 tetraloop 1Q29 'mismatched base pair' 1Q29 'three-way junction' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 17 1_555 -0.132 0.079 0.299 15.266 -18.011 -2.138 1 A_G10:C26_A A 10 ? A 26 ? 19 1 1 B G 1 1_555 A C 16 1_555 -0.509 0.099 0.433 6.452 -8.451 -4.787 2 B_G102:C25_A B 102 ? A 25 ? 19 1 1 B C 2 1_555 A G 15 1_555 -0.207 -0.112 0.069 3.562 -15.645 -1.864 3 B_C103:G24_A B 103 ? A 24 ? 19 1 1 B C 3 1_555 A G 14 1_555 0.177 0.076 0.064 2.261 -13.455 5.665 4 B_C104:G23_A B 104 ? A 23 ? 19 1 1 B G 4 1_555 A A 13 1_555 6.942 -4.443 -0.075 9.922 -15.934 -5.210 5 B_G105:A22_A B 105 ? A 22 ? 11 10 1 B A 5 1_555 A G 12 1_555 -6.882 -4.357 0.097 -24.878 18.921 1.176 6 B_A106:G21_A B 106 ? A 21 ? 11 10 1 B A 6 1_555 A U 11 1_555 -6.458 -0.645 0.130 14.159 -2.005 45.065 7 B_A107:U20_A B 107 ? A 20 ? ? 5 1 B C 8 1_555 B G 17 1_555 0.664 0.021 0.456 -0.418 -19.246 -5.250 8 B_C109:G118_B B 109 ? B 118 ? 19 1 1 B U 9 1_555 B A 16 1_555 -0.702 0.133 0.226 5.680 -9.031 5.179 9 B_U110:A117_B B 110 ? B 117 ? 20 1 1 B C 10 1_555 B G 15 1_555 0.748 -0.178 -0.224 15.951 -8.879 4.291 10 B_C111:G116_B B 111 ? B 116 ? 19 1 1 B G 11 1_555 B A 14 1_555 7.501 -5.611 0.309 -2.885 -18.874 -43.914 11 B_G112:A115_B B 112 ? B 115 ? ? ? 1 A G 2 1_555 B C 24 1_555 0.350 0.460 0.160 -3.760 -23.123 1.135 12 A_G11:C125_B A 11 ? B 125 ? ? 1 1 A U 3 1_555 B A 23 1_555 0.288 0.424 0.273 4.806 -12.952 5.882 13 A_U12:A124_B A 12 ? B 124 ? ? ? 1 A G 4 1_555 B C 22 1_555 0.249 -0.082 0.369 3.544 -11.667 -0.101 14 A_G13:C123_B A 13 ? B 123 ? 19 1 1 A G 5 1_555 B C 21 1_555 0.192 -0.061 -0.120 -10.734 -17.890 3.641 15 A_G14:C122_B A 14 ? B 122 ? 19 1 1 A U 6 1_555 B A 20 1_555 0.408 -0.009 0.465 -10.552 -8.295 0.429 16 A_U15:A121_B A 15 ? B 121 ? 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 G 1 1_555 A C 17 1_555 B G 1 1_555 A C 16 1_555 0.390 -1.599 3.388 -4.580 12.283 28.236 -5.178 -1.547 2.410 23.634 8.813 31.075 1 AB_G10G102:C25C26_AA A 10 ? A 26 ? B 102 ? A 25 ? 1 B G 1 1_555 A C 16 1_555 B C 2 1_555 A G 15 1_555 0.171 -2.238 3.250 1.611 -0.782 34.962 -3.603 -0.042 3.302 -1.301 -2.679 35.006 2 BB_G102C103:G24C25_AA B 102 ? A 25 ? B 103 ? A 24 ? 1 B C 2 1_555 A G 15 1_555 B C 3 1_555 A G 14 1_555 0.190 -1.980 3.289 -0.622 4.736 29.834 -4.721 -0.486 2.942 9.125 1.199 30.205 3 BB_C103C104:G23G24_AA B 103 ? A 24 ? B 104 ? A 23 ? 1 B C 3 1_555 A G 14 1_555 B G 4 1_555 A A 13 1_555 -0.875 -0.516 3.431 0.389 3.099 58.178 -0.701 0.920 3.396 3.184 -0.400 58.254 4 BB_C104G105:A22G23_AA B 104 ? A 23 ? B 105 ? A 22 ? 1 B G 4 1_555 A A 13 1_555 B A 5 1_555 A G 12 1_555 1.016 -1.192 3.929 4.498 0.185 -9.609 6.098 13.993 3.151 -1.034 25.120 -10.609 5 BB_G105A106:G21A22_AA B 105 ? A 22 ? B 106 ? A 21 ? 1 B A 5 1_555 A G 12 1_555 B A 6 1_555 A U 11 1_555 2.911 -1.073 2.021 -19.873 10.667 30.018 -2.117 -5.367 -0.177 17.781 33.126 37.391 6 BB_A106A107:U20G21_AA B 106 ? A 21 ? B 107 ? A 20 ? 1 B A 6 1_555 A U 11 1_555 B C 8 1_555 B G 17 1_555 -0.177 -1.567 6.694 -13.419 3.798 109.916 -1.047 -0.224 6.648 2.314 8.175 110.509 7 BB_A107C109:G118U20_BA B 107 ? A 20 ? B 109 ? B 118 ? 1 B C 8 1_555 B G 17 1_555 B U 9 1_555 B A 16 1_555 0.236 -1.575 3.190 -3.705 -1.419 26.927 -2.998 -1.415 3.206 -3.027 7.901 27.213 8 BB_C109U110:A117G118_BB B 109 ? B 118 ? B 110 ? B 117 ? 1 B U 9 1_555 B A 16 1_555 B C 10 1_555 B G 15 1_555 0.068 -1.093 2.987 1.659 4.400 42.265 -1.908 0.056 2.865 6.079 -2.293 42.514 9 BB_U110C111:G116A117_BB B 110 ? B 117 ? B 111 ? B 116 ? 1 B C 10 1_555 B G 15 1_555 B G 11 1_555 B A 14 1_555 -4.857 -1.273 4.123 5.981 21.532 48.353 -2.968 5.872 2.785 24.809 -6.892 52.984 10 BB_C111G112:A115G116_BB B 111 ? B 116 ? B 112 ? B 115 ? 1 A G 2 1_555 B C 24 1_555 A U 3 1_555 B A 23 1_555 -0.163 -1.395 2.950 -1.798 4.359 37.042 -2.685 0.046 2.778 6.827 2.817 37.331 11 AA_G11U12:A124C125_BB A 11 ? B 125 ? A 12 ? B 124 ? 1 A U 3 1_555 B A 23 1_555 A G 4 1_555 B C 22 1_555 -0.105 -1.404 3.182 2.643 4.546 33.144 -3.136 0.592 2.952 7.907 -4.597 33.547 12 AA_U12G13:C123A124_BB A 12 ? B 124 ? A 13 ? B 123 ? 1 A G 4 1_555 B C 22 1_555 A G 5 1_555 B C 21 1_555 0.629 -2.362 3.483 4.719 9.710 28.002 -6.498 -0.279 2.606 19.189 -9.326 29.972 13 AA_G13G14:C122C123_BB A 13 ? B 123 ? A 14 ? B 122 ? 1 A G 5 1_555 B C 21 1_555 A U 6 1_555 B A 20 1_555 -0.825 -2.152 3.119 -5.335 1.585 31.311 -4.206 0.569 3.103 2.908 9.788 31.790 14 AA_G14U15:A121C122_BB A 14 ? B 122 ? A 15 ? B 121 ? # _pdbx_initial_refinement_model.accession_code 299D _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details 'NDB entry urx057' # _atom_sites.entry_id 1Q29 _atom_sites.fract_transf_matrix[1][1] 0.014995 _atom_sites.fract_transf_matrix[1][2] 0.008657 _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] 0.017315 _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] 0.007116 _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 # loop_