data_1NYI # _entry.id 1NYI # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.397 _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 1NYI pdb_00001nyi 10.2210/pdb1nyi/pdb NDB UR0029 ? ? RCSB RCSB018351 ? ? WWPDB D_1000018351 ? ? # 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 2018-01-31 5 'Structure model' 1 4 2018-02-28 6 'Structure model' 1 5 2019-07-24 7 'Structure model' 1 6 2024-02-14 8 'Structure model' 1 7 2024-04-03 9 'Structure model' 2 0 2024-10-16 # _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 5 'Structure model' 'Experimental preparation' 5 6 'Structure model' 'Data collection' 6 6 'Structure model' 'Derived calculations' 7 6 'Structure model' 'Refinement description' 8 7 'Structure model' 'Data collection' 9 7 'Structure model' 'Database references' 10 7 'Structure model' 'Derived calculations' 11 8 'Structure model' 'Refinement description' 12 9 'Structure model' Advisory 13 9 'Structure model' 'Atomic model' 14 9 'Structure model' 'Data collection' 15 9 'Structure model' 'Derived calculations' 16 9 'Structure model' 'Non-polymer description' 17 9 'Structure model' 'Source and taxonomy' 18 9 'Structure model' 'Structure summary' # 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_unobs_or_zero_occ_atoms 2 5 'Structure model' exptl_crystal_grow 3 6 'Structure model' software 4 6 'Structure model' struct_conn 5 7 'Structure model' chem_comp_atom 6 7 'Structure model' chem_comp_bond 7 7 'Structure model' database_2 8 7 'Structure model' struct_conn 9 7 'Structure model' struct_site 10 8 'Structure model' pdbx_initial_refinement_model 11 9 'Structure model' atom_site 12 9 'Structure model' chem_comp 13 9 'Structure model' chem_comp_atom 14 9 'Structure model' chem_comp_bond 15 9 'Structure model' ndb_struct_conf_na 16 9 'Structure model' ndb_struct_na_base_pair 17 9 'Structure model' pdbx_entity_nonpoly 18 9 'Structure model' pdbx_entity_src_syn 19 9 'Structure model' pdbx_entry_details 20 9 'Structure model' pdbx_nonpoly_scheme 21 9 'Structure model' pdbx_validate_close_contact 22 9 'Structure model' struct_conn 23 9 '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 5 'Structure model' '_exptl_crystal_grow.temp' 2 6 'Structure model' '_software.classification' 3 6 'Structure model' '_software.name' 4 6 'Structure model' '_software.version' 5 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 7 'Structure model' '_database_2.pdbx_DOI' 7 7 'Structure model' '_database_2.pdbx_database_accession' 8 7 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 7 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 7 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 7 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 7 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 7 'Structure model' '_struct_conn.ptnr1_label_seq_id' 14 7 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 7 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 7 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 7 'Structure model' '_struct_conn.ptnr2_label_atom_id' 18 7 'Structure model' '_struct_conn.ptnr2_label_comp_id' 19 7 'Structure model' '_struct_conn.ptnr2_label_seq_id' 20 7 'Structure model' '_struct_site.pdbx_auth_asym_id' 21 7 'Structure model' '_struct_site.pdbx_auth_comp_id' 22 7 'Structure model' '_struct_site.pdbx_auth_seq_id' 23 9 'Structure model' '_atom_site.auth_comp_id' 24 9 'Structure model' '_atom_site.label_comp_id' 25 9 'Structure model' '_chem_comp.formula' 26 9 'Structure model' '_chem_comp.formula_weight' 27 9 'Structure model' '_chem_comp.id' 28 9 'Structure model' '_chem_comp.mon_nstd_flag' 29 9 'Structure model' '_chem_comp.name' 30 9 'Structure model' '_chem_comp.type' 31 9 'Structure model' '_ndb_struct_na_base_pair.hbond_type_12' 32 9 'Structure model' '_ndb_struct_na_base_pair.propeller' 33 9 'Structure model' '_pdbx_entity_nonpoly.comp_id' 34 9 'Structure model' '_pdbx_nonpoly_scheme.mon_id' 35 9 'Structure model' '_pdbx_nonpoly_scheme.pdb_mon_id' 36 9 'Structure model' '_pdbx_validate_close_contact.auth_comp_id_2' 37 9 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 38 9 'Structure model' '_struct_conn.ptnr2_label_comp_id' 39 9 'Structure model' '_struct_site.details' 40 9 'Structure model' '_struct_site.pdbx_auth_comp_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NYI _pdbx_database_status.recvd_initial_deposition_date 2003-02-12 _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 ? # 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(P*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'" 5170.103 1 ? ? ? ? 2 polymer syn "5'-R(*GP*CP*CP*GP*AP*AP*AP*CP*UP*CP*GP*UP*AP*AP*GP*AP*GP*UP*CP*AP*CP*CP*AP*C)-3'" 7674.670 1 ? ? ? ? 3 non-polymer syn 'COBALT (II) ION' 58.933 4 ? ? ? ? 4 non-polymer syn "GUANOSINE-5'-MONOPHOSPHATE" 363.221 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 GUGGUCUGAUGAGGCC GUGGUCUGAUGAGGCC A ? 2 polyribonucleotide no no GCCGAAACUCGUAAGAGUCACCAC GCCGAAACUCGUAAGAGUCACCAC B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'COBALT (II) ION' CO 4 "GUANOSINE-5'-MONOPHOSPHATE" 5GP # 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 U n 1 3 G n 1 4 G n 1 5 U n 1 6 C n 1 7 U n 1 8 G n 1 9 A n 1 10 U n 1 11 G n 1 12 A n 1 13 G n 1 14 G n 1 15 C n 1 16 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_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? 'synthetic construct' ? 32630 ? 2 1 sample ? ? 'synthetic construct' ? 32630 ? # 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 5GP non-polymer . "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 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 11 11 G GUA A . n A 1 2 U 2 12 12 U URI A . n A 1 3 G 3 13 13 G GUA A . n A 1 4 G 4 14 14 G GUA A . n A 1 5 U 5 15 15 U URI A . n A 1 6 C 6 16 16 C CYT A . n A 1 7 U 7 17 17 U URI A . n A 1 8 G 8 18 18 G GUA A . n A 1 9 A 9 19 19 A ADE A . n A 1 10 U 10 20 20 U URI A . n A 1 11 G 11 21 21 G GUA A . n A 1 12 A 12 22 22 A ADE A . n A 1 13 G 13 23 23 G GUA A . n A 1 14 G 14 24 24 G GUA A . n A 1 15 C 15 25 25 C CYT A . n A 1 16 C 16 26 26 C CYT A . n B 2 1 G 1 102 102 G GUA B . n B 2 2 C 2 103 103 C CYT B . n B 2 3 C 3 104 104 C CYT B . n B 2 4 G 4 105 105 G GUA B . n B 2 5 A 5 106 106 A ADE B . n B 2 6 A 6 107 107 A ADE B . n B 2 7 A 7 108 108 A ADE B . n B 2 8 C 8 109 109 C CYT B . n B 2 9 U 9 110 110 U URI B . n B 2 10 C 10 111 111 C CYT B . n B 2 11 G 11 112 112 G GUA B . n B 2 12 U 12 113 113 U URI B . n B 2 13 A 13 114 114 A ADE B . n B 2 14 A 14 115 115 A ADE B . n B 2 15 G 15 116 116 G GUA B . n B 2 16 A 16 117 117 A ADE B . n B 2 17 G 17 118 118 G GUA B . n B 2 18 U 18 119 119 U URI B . n B 2 19 C 19 120 120 C CYT B . n B 2 20 A 20 121 121 A ADE B . n B 2 21 C 21 122 122 C CYT B . n B 2 22 C 22 123 123 C CYT B . n B 2 23 A 23 124 124 A ADE B . n B 2 24 C 24 125 125 C CYT 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 2 2 CO CO A . D 4 5GP 1 500 500 5GP GUA A . E 3 CO 1 1 1 CO CO B . F 3 CO 1 3 3 CO CO B . G 3 CO 1 4 4 CO CO B . # 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 1NYI _cell.length_a 65.639 _cell.length_b 65.639 _cell.length_c 137.475 _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 1NYI _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 1NYI _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details '1.8 M Lithium sulphate and 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 LiSO4 ? ? ? 1 2 1 'sodium cacodylate' ? ? ? 1 3 2 LiSO4 ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2001-12-01 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.15 _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 1.15 # _reflns.entry_id 1NYI _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 2.85 _reflns.d_resolution_low 19.76 _reflns.number_all 7544 _reflns.number_obs 7544 _reflns.percent_possible_obs 99.53 _reflns.pdbx_Rmerge_I_obs 0.072 _reflns.pdbx_Rsym_value 0.064 _reflns.pdbx_netI_over_sigmaI 13.8 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.2 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.85 _reflns_shell.d_res_low 2.923 _reflns_shell.percent_possible_all 99.3 _reflns_shell.Rmerge_I_obs 0.349 _reflns_shell.pdbx_Rsym_value 0.316 _reflns_shell.meanI_over_sigI_obs 2.2 _reflns_shell.pdbx_redundancy 5.3 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 565 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1NYI _refine.ls_number_reflns_obs 7544 _refine.ls_number_reflns_all 7544 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.76 _refine.ls_d_res_high 2.85 _refine.ls_percent_reflns_obs 99.53 _refine.ls_R_factor_obs 0.20607 _refine.ls_R_factor_all 0.20607 _refine.ls_R_factor_R_work 0.20332 _refine.ls_R_factor_R_free 0.23241 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 840 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.957 _refine.correlation_coeff_Fo_to_Fc_free 0.939 _refine.B_iso_mean 41.892 _refine.aniso_B[1][1] 0.12 _refine.aniso_B[2][2] 0.12 _refine.aniso_B[3][3] -0.18 _refine.aniso_B[1][2] 0.06 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details ? _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 'urx 057' _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R 0.280 _refine.pdbx_overall_ESU_R_Free 0.234 _refine.overall_SU_ML 0.184 _refine.overall_SU_B 10.150 _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_analyze.entry_id 1NYI _refine_analyze.Luzzati_coordinate_error_obs .280 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 873 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 877 _refine_hist.d_res_high 2.85 _refine_hist.d_res_low 19.76 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 976 0.010 0.021 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1515 2.007 3.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 164 0.097 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 428 0.007 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 427 0.203 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 28 0.228 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 39 0.224 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 5 0.152 0.200 ? 'X-RAY DIFFRACTION' ? r_scbond_it 976 1.340 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 1515 2.152 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.850 _refine_ls_shell.d_res_low 2.923 _refine_ls_shell.number_reflns_R_work 514 _refine_ls_shell.R_factor_R_work 0.479 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free ? _refine_ls_shell.R_factor_R_free_error 0.468 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 64 _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 1NYI _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 1NYI _struct.title 'Crosslinked Hammerhead Ribozyme Initial State' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1NYI _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Hammerhead Ribozyme crosslink conformational change, 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 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 1NYI 1NYI ? ? ? 2 2 PDB 1NYI 1NYI ? ? ? # 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 1NYI A 1 ? 16 ? 1NYI 11 ? 26 ? 11 26 2 2 1NYI B 1 ? 24 ? 1NYI 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 # 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 P ? ? ? 1_555 D 5GP . "O5'" ? ? A G 11 A 5GP 500 1_555 ? ? ? ? ? ? ? 1.579 ? ? metalc1 metalc ? ? A U 10 O4 ? ? ? 1_555 G CO . CO ? ? A U 20 B CO 4 1_555 ? ? ? ? ? ? ? 2.229 ? ? metalc2 metalc ? ? G CO . CO ? ? ? 1_555 B U 18 "O2'" ? ? B CO 4 B U 119 1_555 ? ? ? ? ? ? ? 1.784 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 24 N3 ? ? A G 11 B C 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 24 O2 ? ? A G 11 B C 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 24 N4 ? ? A G 11 B C 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 B A 23 N1 ? ? A U 12 B A 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 B A 23 N6 ? ? A U 12 B A 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 22 N3 ? ? A G 13 B C 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 22 O2 ? ? A G 13 B C 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 22 N4 ? ? A G 13 B C 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 14 B C 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 14 B C 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 14 B C 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 5 N3 ? ? ? 1_555 B A 20 N1 ? ? A U 15 B A 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 5 O4 ? ? ? 1_555 B A 20 N6 ? ? A U 15 B A 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N3 ? ? ? 1_555 B C 19 N4 ? ? A C 16 B C 120 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog15 hydrog ? ? A U 10 O2 ? ? ? 1_555 B A 6 N6 ? ? A U 20 B A 107 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog16 hydrog ? ? A G 11 N2 ? ? ? 1_555 B A 5 N7 ? ? A G 21 B A 106 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A G 11 N3 ? ? ? 1_555 B A 5 N6 ? ? A G 21 B A 106 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog18 hydrog ? ? A A 12 N6 ? ? ? 1_555 B G 4 N3 ? ? A A 22 B G 105 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog19 hydrog ? ? A A 12 N7 ? ? ? 1_555 B G 4 N2 ? ? A A 22 B G 105 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog20 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 23 B C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 23 B C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 23 B C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 24 B C 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 24 B C 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 24 B C 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 25 B G 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 25 B G 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 25 B G 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B A 7 N6 ? ? ? 1_555 B U 18 O4 ? ? B A 108 B U 119 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog30 hydrog ? ? B C 8 N3 ? ? ? 1_555 B G 17 N1 ? ? B C 109 B G 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 8 N4 ? ? ? 1_555 B G 17 O6 ? ? B C 109 B G 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B C 8 O2 ? ? ? 1_555 B G 17 N2 ? ? B C 109 B G 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B U 9 N3 ? ? ? 1_555 B A 16 N1 ? ? B U 110 B A 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B U 9 O4 ? ? ? 1_555 B A 16 N6 ? ? B U 110 B A 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B C 10 N3 ? ? ? 1_555 B G 15 N1 ? ? B C 111 B G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B C 10 N4 ? ? ? 1_555 B G 15 O6 ? ? B C 111 B G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B C 10 O2 ? ? ? 1_555 B G 15 N2 ? ? B C 111 B G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 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 O4 _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 U _pdbx_struct_conn_angle.ptnr1_label_seq_id 10 _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 U _pdbx_struct_conn_angle.ptnr1_auth_seq_id 20 _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 G _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 B _pdbx_struct_conn_angle.ptnr2_auth_comp_id CO _pdbx_struct_conn_angle.ptnr2_auth_seq_id 4 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id "O2'" _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id B _pdbx_struct_conn_angle.ptnr3_label_comp_id U _pdbx_struct_conn_angle.ptnr3_label_seq_id 18 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id B _pdbx_struct_conn_angle.ptnr3_auth_comp_id U _pdbx_struct_conn_angle.ptnr3_auth_seq_id 119 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 162.1 _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 B CO 1 ? 1 'BINDING SITE FOR RESIDUE CO B 1' AC2 Software A CO 2 ? 1 'BINDING SITE FOR RESIDUE CO A 2' AC3 Software B CO 3 ? 2 'BINDING SITE FOR RESIDUE CO B 3' AC4 Software B CO 4 ? 2 'BINDING SITE FOR RESIDUE CO B 4' AC5 Software A 5GP 500 ? 4 'BINDING SITE FOR RESIDUE 5GP A 500' # 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 C B 21 ? C B 122 . ? 1_555 ? 2 AC2 1 G A 8 ? G A 18 . ? 1_555 ? 3 AC3 2 G A 4 ? G A 14 . ? 6_655 ? 4 AC3 2 U A 5 ? U A 15 . ? 6_655 ? 5 AC4 2 U A 10 ? U A 20 . ? 1_555 ? 6 AC4 2 U B 18 ? U B 119 . ? 1_555 ? 7 AC5 4 G A 1 ? G A 11 . ? 1_555 ? 8 AC5 4 G A 1 ? G A 11 . ? 5_555 ? 9 AC5 4 C A 16 ? C A 26 . ? 1_555 ? 10 AC5 4 G B 1 ? G B 102 . ? 1_555 ? # _pdbx_entry_details.entry_id 1NYI _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification N # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OP1 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 G _pdbx_validate_close_contact.auth_seq_id_1 11 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 "O5'" _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 5GP _pdbx_validate_close_contact.auth_seq_id_2 500 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.14 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 "O5'" _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 U _pdbx_validate_symm_contact.auth_seq_id_1 15 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 CO _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 CO _pdbx_validate_symm_contact.auth_seq_id_2 3 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 6_665 _pdbx_validate_symm_contact.dist 1.67 # 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 "O4'" A U 15 ? ? "C1'" A U 15 ? ? N1 A U 15 ? ? 113.46 108.50 4.96 0.70 N 2 1 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 113.96 108.50 5.46 0.70 N 3 1 "O4'" A G 21 ? ? "C1'" A G 21 ? ? N9 A G 21 ? ? 115.56 108.50 7.06 0.70 N 4 1 "C3'" A G 21 ? ? "O3'" A G 21 ? ? P A A 22 ? ? 128.48 119.70 8.78 1.20 Y 5 1 "O4'" A C 26 ? ? "C1'" A C 26 ? ? N1 A C 26 ? ? 112.76 108.50 4.26 0.70 N 6 1 "C5'" B A 106 ? ? "C4'" B A 106 ? ? "O4'" B A 106 ? ? 116.94 109.80 7.14 0.90 N 7 1 C5 B U 110 ? ? C4 B U 110 ? ? O4 B U 110 ? ? 122.05 125.90 -3.85 0.60 N 8 1 "C4'" B G 112 ? ? "C3'" B G 112 ? ? "C2'" B G 112 ? ? 95.96 102.60 -6.64 1.00 N 9 1 "C4'" B G 118 ? ? "C3'" B G 118 ? ? "C2'" B G 118 ? ? 94.89 102.60 -7.71 1.00 N 10 1 "O4'" B U 119 ? ? "C1'" B U 119 ? ? N1 B U 119 ? ? 116.33 108.50 7.83 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 5GP P P N N 1 5GP O1P O N N 2 5GP O2P O N N 3 5GP O3P O N N 4 5GP "O5'" O N N 5 5GP "C5'" C N N 6 5GP "C4'" C N R 7 5GP "O4'" O N N 8 5GP "C3'" C N S 9 5GP "O3'" O N N 10 5GP "C2'" C N R 11 5GP "O2'" O N N 12 5GP "C1'" C N R 13 5GP N9 N Y N 14 5GP C8 C Y N 15 5GP N7 N Y N 16 5GP C5 C Y N 17 5GP C6 C N N 18 5GP O6 O N N 19 5GP N1 N N N 20 5GP C2 C N N 21 5GP N2 N N N 22 5GP N3 N N N 23 5GP C4 C Y N 24 5GP HOP2 H N N 25 5GP HOP3 H N N 26 5GP "H5'1" H N N 27 5GP "H5'2" H N N 28 5GP "H4'" H N N 29 5GP "H3'" H N N 30 5GP "HO3'" H N N 31 5GP "H2'" H N N 32 5GP "HO2'" H N N 33 5GP "H1'" H N N 34 5GP H8 H N N 35 5GP HN1 H N N 36 5GP HN21 H N N 37 5GP HN22 H N N 38 A OP3 O N N 39 A P P N N 40 A OP1 O N N 41 A OP2 O N N 42 A "O5'" O N N 43 A "C5'" C N N 44 A "C4'" C N R 45 A "O4'" O N N 46 A "C3'" C N S 47 A "O3'" O N N 48 A "C2'" C N R 49 A "O2'" O N N 50 A "C1'" C N R 51 A N9 N Y N 52 A C8 C Y N 53 A N7 N Y N 54 A C5 C Y N 55 A C6 C Y N 56 A N6 N N N 57 A N1 N Y N 58 A C2 C Y N 59 A N3 N Y N 60 A C4 C Y N 61 A HOP3 H N N 62 A HOP2 H N N 63 A "H5'" H N N 64 A "H5''" H N N 65 A "H4'" H N N 66 A "H3'" H N N 67 A "HO3'" H N N 68 A "H2'" H N N 69 A "HO2'" H N N 70 A "H1'" H N N 71 A H8 H N N 72 A H61 H N N 73 A H62 H N N 74 A H2 H N N 75 C OP3 O N N 76 C P P N N 77 C OP1 O N N 78 C OP2 O N N 79 C "O5'" O N N 80 C "C5'" C N N 81 C "C4'" C N R 82 C "O4'" O N N 83 C "C3'" C N S 84 C "O3'" O N N 85 C "C2'" C N R 86 C "O2'" O N N 87 C "C1'" C N R 88 C N1 N N N 89 C C2 C N N 90 C O2 O N N 91 C N3 N N N 92 C C4 C N N 93 C N4 N N N 94 C C5 C N N 95 C C6 C N N 96 C HOP3 H N N 97 C HOP2 H N N 98 C "H5'" H N N 99 C "H5''" H N N 100 C "H4'" H N N 101 C "H3'" H N N 102 C "HO3'" H N N 103 C "H2'" H N N 104 C "HO2'" H N N 105 C "H1'" H N N 106 C H41 H N N 107 C H42 H N N 108 C H5 H N N 109 C H6 H N N 110 CO CO CO N N 111 G OP3 O N N 112 G P P N N 113 G OP1 O N N 114 G OP2 O N N 115 G "O5'" O N N 116 G "C5'" C N N 117 G "C4'" C N R 118 G "O4'" O N N 119 G "C3'" C N S 120 G "O3'" O N N 121 G "C2'" C N R 122 G "O2'" O N N 123 G "C1'" C N R 124 G N9 N Y N 125 G C8 C Y N 126 G N7 N Y N 127 G C5 C Y N 128 G C6 C N N 129 G O6 O N N 130 G N1 N N N 131 G C2 C N N 132 G N2 N N N 133 G N3 N N N 134 G C4 C Y N 135 G HOP3 H N N 136 G HOP2 H N N 137 G "H5'" H N N 138 G "H5''" H N N 139 G "H4'" H N N 140 G "H3'" H N N 141 G "HO3'" H N N 142 G "H2'" H N N 143 G "HO2'" H N N 144 G "H1'" H N N 145 G H8 H N N 146 G H1 H N N 147 G H21 H N N 148 G H22 H N N 149 U OP3 O N N 150 U P P N N 151 U OP1 O N N 152 U OP2 O N N 153 U "O5'" O N N 154 U "C5'" C N N 155 U "C4'" C N R 156 U "O4'" O N N 157 U "C3'" C N S 158 U "O3'" O N N 159 U "C2'" C N R 160 U "O2'" O N N 161 U "C1'" C N R 162 U N1 N N N 163 U C2 C N N 164 U O2 O N N 165 U N3 N N N 166 U C4 C N N 167 U O4 O N N 168 U C5 C N N 169 U C6 C N N 170 U HOP3 H N N 171 U HOP2 H N N 172 U "H5'" H N N 173 U "H5''" H N N 174 U "H4'" H N N 175 U "H3'" H N N 176 U "HO3'" H N N 177 U "H2'" H N N 178 U "HO2'" H N N 179 U "H1'" H N N 180 U H3 H N N 181 U H5 H N N 182 U H6 H N N 183 # 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 5GP P O1P doub N N 1 5GP P O2P sing N N 2 5GP P O3P sing N N 3 5GP P "O5'" sing N N 4 5GP O2P HOP2 sing N N 5 5GP O3P HOP3 sing N N 6 5GP "O5'" "C5'" sing N N 7 5GP "C5'" "C4'" sing N N 8 5GP "C5'" "H5'1" sing N N 9 5GP "C5'" "H5'2" sing N N 10 5GP "C4'" "O4'" sing N N 11 5GP "C4'" "C3'" sing N N 12 5GP "C4'" "H4'" sing N N 13 5GP "O4'" "C1'" sing N N 14 5GP "C3'" "O3'" sing N N 15 5GP "C3'" "C2'" sing N N 16 5GP "C3'" "H3'" sing N N 17 5GP "O3'" "HO3'" sing N N 18 5GP "C2'" "O2'" sing N N 19 5GP "C2'" "C1'" sing N N 20 5GP "C2'" "H2'" sing N N 21 5GP "O2'" "HO2'" sing N N 22 5GP "C1'" N9 sing N N 23 5GP "C1'" "H1'" sing N N 24 5GP N9 C8 sing Y N 25 5GP N9 C4 sing Y N 26 5GP C8 N7 doub Y N 27 5GP C8 H8 sing N N 28 5GP N7 C5 sing Y N 29 5GP C5 C6 sing N N 30 5GP C5 C4 doub Y N 31 5GP C6 O6 doub N N 32 5GP C6 N1 sing N N 33 5GP N1 C2 sing N N 34 5GP N1 HN1 sing N N 35 5GP C2 N2 sing N N 36 5GP C2 N3 doub N N 37 5GP N2 HN21 sing N N 38 5GP N2 HN22 sing N N 39 5GP N3 C4 sing N N 40 A OP3 P sing N N 41 A OP3 HOP3 sing N N 42 A P OP1 doub N N 43 A P OP2 sing N N 44 A P "O5'" sing N N 45 A OP2 HOP2 sing N N 46 A "O5'" "C5'" sing N N 47 A "C5'" "C4'" sing N N 48 A "C5'" "H5'" sing N N 49 A "C5'" "H5''" sing N N 50 A "C4'" "O4'" sing N N 51 A "C4'" "C3'" sing N N 52 A "C4'" "H4'" sing N N 53 A "O4'" "C1'" sing N N 54 A "C3'" "O3'" sing N N 55 A "C3'" "C2'" sing N N 56 A "C3'" "H3'" sing N N 57 A "O3'" "HO3'" sing N N 58 A "C2'" "O2'" sing N N 59 A "C2'" "C1'" sing N N 60 A "C2'" "H2'" sing N N 61 A "O2'" "HO2'" sing N N 62 A "C1'" N9 sing N N 63 A "C1'" "H1'" sing N N 64 A N9 C8 sing Y N 65 A N9 C4 sing Y N 66 A C8 N7 doub Y N 67 A C8 H8 sing N N 68 A N7 C5 sing Y N 69 A C5 C6 sing Y N 70 A C5 C4 doub Y N 71 A C6 N6 sing N N 72 A C6 N1 doub Y N 73 A N6 H61 sing N N 74 A N6 H62 sing N N 75 A N1 C2 sing Y N 76 A C2 N3 doub Y N 77 A C2 H2 sing N N 78 A N3 C4 sing Y N 79 C OP3 P sing N N 80 C OP3 HOP3 sing N N 81 C P OP1 doub N N 82 C P OP2 sing N N 83 C P "O5'" sing N N 84 C OP2 HOP2 sing N N 85 C "O5'" "C5'" sing N N 86 C "C5'" "C4'" sing N N 87 C "C5'" "H5'" sing N N 88 C "C5'" "H5''" sing N N 89 C "C4'" "O4'" sing N N 90 C "C4'" "C3'" sing N N 91 C "C4'" "H4'" sing N N 92 C "O4'" "C1'" sing N N 93 C "C3'" "O3'" sing N N 94 C "C3'" "C2'" sing N N 95 C "C3'" "H3'" sing N N 96 C "O3'" "HO3'" sing N N 97 C "C2'" "O2'" sing N N 98 C "C2'" "C1'" sing N N 99 C "C2'" "H2'" sing N N 100 C "O2'" "HO2'" sing N N 101 C "C1'" N1 sing N N 102 C "C1'" "H1'" sing N N 103 C N1 C2 sing N N 104 C N1 C6 sing N N 105 C C2 O2 doub N N 106 C C2 N3 sing N N 107 C N3 C4 doub N N 108 C C4 N4 sing N N 109 C C4 C5 sing N N 110 C N4 H41 sing N N 111 C N4 H42 sing N N 112 C C5 C6 doub N N 113 C C5 H5 sing N N 114 C C6 H6 sing N N 115 G OP3 P sing N N 116 G OP3 HOP3 sing N N 117 G P OP1 doub N N 118 G P OP2 sing N N 119 G P "O5'" sing N N 120 G OP2 HOP2 sing N N 121 G "O5'" "C5'" sing N N 122 G "C5'" "C4'" sing N N 123 G "C5'" "H5'" sing N N 124 G "C5'" "H5''" sing N N 125 G "C4'" "O4'" sing N N 126 G "C4'" "C3'" sing N N 127 G "C4'" "H4'" sing N N 128 G "O4'" "C1'" sing N N 129 G "C3'" "O3'" sing N N 130 G "C3'" "C2'" sing N N 131 G "C3'" "H3'" sing N N 132 G "O3'" "HO3'" sing N N 133 G "C2'" "O2'" sing N N 134 G "C2'" "C1'" sing N N 135 G "C2'" "H2'" sing N N 136 G "O2'" "HO2'" sing N N 137 G "C1'" N9 sing N N 138 G "C1'" "H1'" sing N N 139 G N9 C8 sing Y N 140 G N9 C4 sing Y N 141 G C8 N7 doub Y N 142 G C8 H8 sing N N 143 G N7 C5 sing Y N 144 G C5 C6 sing N N 145 G C5 C4 doub Y N 146 G C6 O6 doub N N 147 G C6 N1 sing N N 148 G N1 C2 sing N N 149 G N1 H1 sing N N 150 G C2 N2 sing N N 151 G C2 N3 doub N N 152 G N2 H21 sing N N 153 G N2 H22 sing N N 154 G N3 C4 sing N N 155 U OP3 P sing N N 156 U OP3 HOP3 sing N N 157 U P OP1 doub N N 158 U P OP2 sing N N 159 U P "O5'" sing N N 160 U OP2 HOP2 sing N N 161 U "O5'" "C5'" sing N N 162 U "C5'" "C4'" sing N N 163 U "C5'" "H5'" sing N N 164 U "C5'" "H5''" sing N N 165 U "C4'" "O4'" sing N N 166 U "C4'" "C3'" sing N N 167 U "C4'" "H4'" sing N N 168 U "O4'" "C1'" sing N N 169 U "C3'" "O3'" sing N N 170 U "C3'" "C2'" sing N N 171 U "C3'" "H3'" sing N N 172 U "O3'" "HO3'" sing N N 173 U "C2'" "O2'" sing N N 174 U "C2'" "C1'" sing N N 175 U "C2'" "H2'" sing N N 176 U "O2'" "HO2'" sing N N 177 U "C1'" N1 sing N N 178 U "C1'" "H1'" sing N N 179 U N1 C2 sing N N 180 U N1 C6 sing N N 181 U C2 O2 doub N N 182 U C2 N3 sing N N 183 U N3 C4 sing N N 184 U N3 H3 sing N N 185 U C4 O4 doub N N 186 U C4 C5 sing N N 187 U C5 C6 doub N N 188 U C5 H5 sing N N 189 U C6 H6 sing N N 190 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1NYI 'double helix' 1NYI 'a-form double helix' 1NYI 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B C 24 1_555 -0.535 -0.119 -0.201 -7.186 -11.917 -1.092 1 A_G11:C125_B A 11 ? B 125 ? 19 1 1 A U 2 1_555 B A 23 1_555 -0.264 -0.045 -0.144 5.077 -13.002 4.485 2 A_U12:A124_B A 12 ? B 124 ? 20 1 1 A G 3 1_555 B C 22 1_555 0.283 -0.341 -0.009 1.527 -6.468 -1.271 3 A_G13:C123_B A 13 ? B 123 ? 19 1 1 A G 4 1_555 B C 21 1_555 -0.308 -0.449 -0.062 -2.895 -12.832 -2.501 4 A_G14:C122_B A 14 ? B 122 ? 19 1 1 A U 5 1_555 B A 20 1_555 0.065 -0.365 -0.056 1.849 -16.261 6.533 5 A_U15:A121_B A 15 ? B 121 ? 20 1 1 A C 6 1_555 B C 19 1_555 2.391 -1.473 0.331 7.190 -15.247 28.395 6 A_C16:C120_B A 16 ? B 120 ? ? 1 1 B G 1 1_555 A C 15 1_555 -0.362 -0.166 0.279 4.616 -9.351 -2.906 7 B_G102:C25_A B 102 ? A 25 ? 19 1 1 B C 2 1_555 A G 14 1_555 -0.148 -0.232 0.037 2.730 -13.212 1.779 8 B_C103:G24_A B 103 ? A 24 ? 19 1 1 B C 3 1_555 A G 13 1_555 0.223 -0.386 0.090 1.396 -9.848 1.034 9 B_C104:G23_A B 104 ? A 23 ? 19 1 1 B G 4 1_555 A A 12 1_555 6.870 -4.357 -0.440 9.566 -9.381 -9.633 10 B_G105:A22_A B 105 ? A 22 ? 11 10 1 B A 5 1_555 A G 11 1_555 -6.638 -4.991 0.675 -23.201 9.098 -4.556 11 B_A106:G21_A B 106 ? A 21 ? 11 10 1 B A 6 1_555 A U 10 1_555 -6.380 -0.607 0.186 14.484 -6.125 57.292 12 B_A107:U20_A B 107 ? A 20 ? ? 5 1 B A 7 1_555 B U 18 1_555 0.847 1.385 -0.855 -11.085 -26.726 -37.778 13 B_A108:U119_B B 108 ? B 119 ? ? ? 1 B C 8 1_555 B G 17 1_555 0.366 -0.365 0.475 -0.203 -18.382 -1.536 14 B_C109:G118_B B 109 ? B 118 ? 19 1 1 B U 9 1_555 B A 16 1_555 -0.058 -0.320 0.085 5.875 -8.757 1.438 15 B_U110:A117_B B 110 ? B 117 ? 20 1 1 B C 10 1_555 B G 15 1_555 -0.423 -0.296 0.024 11.275 -1.177 -2.950 16 B_C111:G116_B B 111 ? B 116 ? 19 1 1 B G 11 1_555 B A 14 1_555 7.496 -5.650 0.344 0.327 -20.950 -43.867 17 B_G112:A115_B B 112 ? B 115 ? ? ? # 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 B C 24 1_555 A U 2 1_555 B A 23 1_555 -0.338 -1.457 2.949 -3.469 0.867 37.403 -2.364 0.117 2.934 1.349 5.394 37.568 1 AA_G11U12:A124C125_BB A 11 ? B 125 ? A 12 ? B 124 ? 1 A U 2 1_555 B A 23 1_555 A G 3 1_555 B C 22 1_555 -0.236 -1.439 3.316 -1.216 6.541 32.222 -3.630 0.214 2.981 11.631 2.163 32.884 2 AA_U12G13:C123A124_BB A 12 ? B 124 ? A 13 ? B 123 ? 1 A G 3 1_555 B C 22 1_555 A G 4 1_555 B C 21 1_555 0.621 -2.485 3.306 0.805 3.043 25.271 -6.482 -1.185 3.008 6.922 -1.831 25.463 3 AA_G13G14:C122C123_BB A 13 ? B 123 ? A 14 ? B 122 ? 1 A G 4 1_555 B C 21 1_555 A U 5 1_555 B A 20 1_555 -0.379 -2.604 3.075 -2.093 3.011 23.534 -7.196 0.304 2.747 7.326 5.092 23.814 4 AA_G14U15:A121C122_BB A 14 ? B 122 ? A 15 ? B 121 ? 1 A U 5 1_555 B A 20 1_555 A C 6 1_555 B C 19 1_555 0.959 -0.481 3.191 -2.894 5.517 42.327 -1.188 -1.593 3.039 7.591 3.982 42.763 5 AA_U15C16:C120A121_BB A 15 ? B 121 ? A 16 ? B 120 ? 1 B G 1 1_555 A C 15 1_555 B C 2 1_555 A G 14 1_555 0.052 -1.986 3.293 -0.462 -0.369 34.337 -3.305 -0.162 3.313 -0.624 0.783 34.342 6 BB_G102C103:G24C25_AA B 102 ? A 25 ? B 103 ? A 24 ? 1 B C 2 1_555 A G 14 1_555 B C 3 1_555 A G 13 1_555 -0.271 -1.850 3.287 -1.776 3.269 31.083 -4.034 0.174 3.092 6.073 3.299 31.300 7 BB_C103C104:G23G24_AA B 103 ? A 24 ? B 104 ? A 23 ? 1 B C 3 1_555 A G 13 1_555 B G 4 1_555 A A 12 1_555 -0.816 -0.697 3.353 2.168 -0.230 56.296 -0.725 0.989 3.325 -0.244 -2.297 56.334 8 BB_C104G105:A22G23_AA B 104 ? A 23 ? B 105 ? A 22 ? 1 B G 4 1_555 A A 12 1_555 B A 5 1_555 A G 11 1_555 1.092 -1.183 3.898 5.130 -0.648 -14.660 4.942 8.516 3.271 2.443 19.336 -15.540 9 BB_G105A106:G21A22_AA B 105 ? A 22 ? B 106 ? A 21 ? 1 B A 5 1_555 A G 11 1_555 B A 6 1_555 A U 10 1_555 3.280 -0.877 1.968 -20.057 15.231 33.994 -1.691 -5.187 -0.223 22.609 29.774 42.084 10 BB_A106A107:U20G21_AA B 106 ? A 21 ? B 107 ? A 20 ? 1 B A 6 1_555 A U 10 1_555 B A 7 1_555 B U 18 1_555 -2.335 -1.678 3.937 -4.844 9.215 75.881 -1.679 1.716 3.865 7.460 3.922 76.485 11 BB_A107A108:U119U20_BA B 107 ? A 20 ? B 108 ? B 119 ? 1 B A 7 1_555 B U 18 1_555 B C 8 1_555 B G 17 1_555 1.536 -1.026 2.943 -11.088 0.642 28.698 -2.039 -4.666 2.189 1.239 21.384 30.730 12 BB_A108C109:G118U119_BB B 108 ? B 119 ? 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 -0.133 -1.361 3.101 -1.892 2.271 34.398 -2.622 -0.050 3.010 3.831 3.192 34.521 13 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 -0.052 -1.792 3.153 -2.384 3.444 27.876 -4.430 -0.413 2.909 7.099 4.914 28.183 14 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 -4.089 -1.680 3.824 4.174 18.940 56.604 -2.700 4.338 2.897 19.356 -4.265 59.574 15 BB_C111G112:A115G116_BB B 111 ? B 116 ? B 112 ? B 115 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'urx 057' # _atom_sites.entry_id 1NYI _atom_sites.fract_transf_matrix[1][1] 0.015235 _atom_sites.fract_transf_matrix[1][2] 0.008796 _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] 0.017592 _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] 0.007274 _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_