data_1F1T # _entry.id 1F1T # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _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 1F1T pdb_00001f1t 10.2210/pdb1f1t/pdb NDB UR0011 ? ? RCSB RCSB011139 ? ? WWPDB D_1000011139 ? ? # 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 2000-09-04 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_conn_type 7 4 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 18 4 'Structure model' '_pdbx_struct_conn_angle.value' 19 4 'Structure model' '_struct_conn.conn_type_id' 20 4 'Structure model' '_struct_conn.id' 21 4 'Structure model' '_struct_conn.pdbx_dist_value' 22 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 23 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 24 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 26 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 27 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 28 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 29 4 'Structure model' '_struct_conn.ptnr1_symmetry' 30 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 31 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 32 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 33 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 34 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 35 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 36 4 'Structure model' '_struct_conn.ptnr2_symmetry' 37 4 'Structure model' '_struct_conn_type.id' 38 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 39 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 40 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1F1T _pdbx_database_status.recvd_initial_deposition_date 2000-05-19 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Baugh, C.' 1 'Grate, D.' 2 'Wilson, C.' 3 # _citation.id primary _citation.title '2.8 A crystal structure of the malachite green aptamer.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 301 _citation.page_first 117 _citation.page_last 128 _citation.year 2000 _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 10926496 _citation.pdbx_database_id_DOI 10.1006/jmbi.2000.3951 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Baugh, C.' 1 ? primary 'Grate, D.' 2 ? primary 'Wilson, C.' 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 'MALACHITE GREEN APTAMER RNA' 12711.902 1 ? ? ? 'ALL URIDINES ARE 5-BROMO-URIDINE' 2 non-polymer syn 'STRONTIUM ION' 87.620 8 ? ? ? ? 3 non-polymer syn "N,N'-TETRAMETHYL-ROSAMINE" 343.442 1 ? ? ? ? 4 water nat water 18.015 5 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GGA(5BU)CCCGAC(5BU)GGCGAGAGCCAGG(5BU)AACGAA(5BU)GGA(5BU)CC' _entity_poly.pdbx_seq_one_letter_code_can GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'STRONTIUM ION' SR 3 "N,N'-TETRAMETHYL-ROSAMINE" ROS 4 water HOH # 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 A n 1 4 5BU n 1 5 C n 1 6 C n 1 7 C n 1 8 G n 1 9 A n 1 10 C n 1 11 5BU n 1 12 G n 1 13 G n 1 14 C n 1 15 G n 1 16 A n 1 17 G n 1 18 A n 1 19 G n 1 20 C n 1 21 C n 1 22 A n 1 23 G n 1 24 G n 1 25 5BU n 1 26 A n 1 27 A n 1 28 C n 1 29 G n 1 30 A n 1 31 A n 1 32 5BU n 1 33 G n 1 34 G n 1 35 A n 1 36 5BU n 1 37 C n 1 38 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'IN VITRO T7 TRANSCRIPTION OF A LINEARIZED PLASMID TEMPLATE' # 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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 ROS non-polymer . "N,N'-TETRAMETHYL-ROSAMINE" '(6-DIMETHYLAMINO-9-PHENYL-XANTHEN-3-YLIDENE)-DIMETHYL-AMMONIUM' 'C23 H23 N2 O 1' 343.442 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 # 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 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 5BU 4 4 4 5BU +U A . n A 1 5 C 5 5 5 C C A . n A 1 6 C 6 6 6 C C A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G A . n A 1 9 A 9 9 9 A A A . n A 1 10 C 10 10 10 C C A . n A 1 11 5BU 11 11 11 5BU +U A . n A 1 12 G 12 12 12 G G A . n A 1 13 G 13 13 13 G G A . n A 1 14 C 14 14 14 C C A . n A 1 15 G 15 15 15 G G A . n A 1 16 A 16 16 16 A A A . n A 1 17 G 17 17 17 G G A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 C 20 20 20 C C A . n A 1 21 C 21 21 21 C C A . n A 1 22 A 22 22 22 A A A . n A 1 23 G 23 23 23 G G A . n A 1 24 G 24 24 24 G G A . n A 1 25 5BU 25 25 25 5BU +U A . n A 1 26 A 26 26 26 A A A . n A 1 27 A 27 27 27 A A A . n A 1 28 C 28 28 28 C C A . n A 1 29 G 29 29 29 G G A . n A 1 30 A 30 30 30 A A A . n A 1 31 A 31 31 31 A A A . n A 1 32 5BU 32 32 32 5BU +U A . n A 1 33 G 33 33 33 G G A . n A 1 34 G 34 34 34 G G A . n A 1 35 A 35 35 35 A A A . n A 1 36 5BU 36 36 36 5BU +U A . n A 1 37 C 37 37 37 C C A . n A 1 38 C 38 38 38 C C A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SR 1 201 201 SR SR A . C 2 SR 1 202 202 SR SR A . D 2 SR 1 203 203 SR SR A . E 2 SR 1 204 204 SR SR A . F 2 SR 1 205 205 SR SR A . G 2 SR 1 206 206 SR SR A . H 2 SR 1 208 208 SR SR A . I 2 SR 1 209 209 SR SR A . J 3 ROS 1 101 101 ROS ROS A . K 4 HOH 1 301 301 HOH HOH A . K 4 HOH 2 302 302 HOH HOH A . K 4 HOH 3 303 303 HOH HOH A . K 4 HOH 4 304 304 HOH HOH A . K 4 HOH 5 305 305 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHARP phasing . ? 1 CNS refinement 0.9 ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _cell.entry_id 1F1T _cell.length_a 55.297 _cell.length_b 55.297 _cell.length_c 143.92 _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1F1T _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 179 # _exptl.entry_id 1F1T _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 52.30 _exptl_crystal.density_Matthews 2.58 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.5 _exptl_crystal_grow.pdbx_details 'CACODYLATE, MGCL2, SRCL2, KCL, SPERMINE, MPD, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _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 CACODYLATE ? ? ? 1 2 1 MGCL2 ? ? ? 1 3 1 SRCL2 ? ? ? 1 4 1 KCL ? ? ? 1 5 1 SPERMINE ? ? ? 1 6 1 MPD ? ? ? 1 7 2 MPD ? ? ? # _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 MARRESEARCH _diffrn_detector.pdbx_collection_date 1999-08-25 _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 MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.92070 1.0 2 0.92090 1.0 3 0.90830 1.0 4 1.0000 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 '0.92070, 0.92090, 0.90830, 1.0000' # _reflns.entry_id 1F1T _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 2.8 _reflns.number_obs 3188 _reflns.number_all 3188 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.057 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 40.59 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 40.3 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1F1T _refine.ls_number_reflns_obs 3188 _refine.ls_number_reflns_all 3188 _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 9.0 _refine.ls_d_res_high 2.8 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.2609 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2609 _refine.ls_R_factor_R_free 0.2822 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _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 ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _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_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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 816 _refine_hist.pdbx_number_atoms_ligand 39 _refine_hist.number_atoms_solvent 5 _refine_hist.number_atoms_total 860 _refine_hist.d_res_high 2.8 _refine_hist.d_res_low 9.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.013 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.96 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1F1T _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 1F1T _struct.title 'CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1F1T _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'U-TURN, BASE QUADRUPLE, BASE TRIPLE, GNRA TETRALOOP, 5-BROMO-URIDINE, 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 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 3 ? K N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1F1T _struct_ref.pdbx_db_accession 1F1T _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1F1T _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 38 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1F1T _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 38 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 38 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K # _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.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A A 3 "O3'" ? ? ? 1_555 A 5BU 4 P ? ? A A 3 A 5BU 4 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale2 covale both ? A 5BU 4 "O3'" ? ? ? 1_555 A C 5 P ? ? A 5BU 4 A C 5 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale3 covale both ? A C 10 "O3'" ? ? ? 1_555 A 5BU 11 P ? ? A C 10 A 5BU 11 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? A 5BU 11 "O3'" ? ? ? 1_555 A G 12 P ? ? A 5BU 11 A G 12 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale5 covale both ? A G 24 "O3'" ? ? ? 1_555 A 5BU 25 P ? ? A G 24 A 5BU 25 1_555 ? ? ? ? ? ? ? 1.657 ? ? covale6 covale both ? A 5BU 25 "O3'" ? ? ? 1_555 A A 26 P ? ? A 5BU 25 A A 26 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale7 covale both ? A A 31 "O3'" ? ? ? 1_555 A 5BU 32 P ? ? A A 31 A 5BU 32 1_555 ? ? ? ? ? ? ? 1.586 ? ? covale8 covale both ? A 5BU 32 "O3'" ? ? ? 1_555 A G 33 P ? ? A 5BU 32 A G 33 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale9 covale both ? A A 35 "O3'" ? ? ? 1_555 A 5BU 36 P ? ? A A 35 A 5BU 36 1_555 ? ? ? ? ? ? ? 1.592 ? ? covale10 covale both ? A 5BU 36 "O3'" ? ? ? 1_555 A C 37 P ? ? A 5BU 36 A C 37 1_555 ? ? ? ? ? ? ? 1.601 ? ? metalc1 metalc ? ? A A 16 OP1 ? ? ? 6_434 B SR . SR ? ? A A 16 A SR 201 1_555 ? ? ? ? ? ? ? 2.859 ? ? metalc2 metalc ? ? A A 31 OP2 ? ? ? 1_555 F SR . SR ? ? A A 31 A SR 205 1_555 ? ? ? ? ? ? ? 3.204 ? ? metalc3 metalc ? ? A 5BU 32 O2 ? ? ? 1_555 B SR . SR ? ? A 5BU 32 A SR 201 1_555 ? ? ? ? ? ? ? 2.774 ? ? metalc4 metalc ? ? A G 33 OP2 ? ? ? 1_555 F SR . SR ? ? A G 33 A SR 205 1_555 ? ? ? ? ? ? ? 3.152 ? ? metalc5 metalc ? ? A G 33 OP1 ? ? ? 1_555 G SR . SR ? ? A G 33 A SR 206 1_555 ? ? ? ? ? ? ? 2.617 ? ? metalc6 metalc ? ? A G 34 OP1 ? ? ? 1_555 B SR . SR ? ? A G 34 A SR 201 1_555 ? ? ? ? ? ? ? 2.635 ? ? metalc7 metalc ? ? G SR . SR ? ? ? 1_555 K HOH . O ? ? A SR 206 A HOH 304 1_555 ? ? ? ? ? ? ? 2.722 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 1 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 1 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 1 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 37 N3 ? ? A G 2 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 37 O2 ? ? A G 2 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 37 N4 ? ? A G 2 A C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A 5BU 36 N3 ? ? A A 3 A 5BU 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A 5BU 36 O4 ? ? A A 3 A 5BU 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A 5BU 4 N3 ? ? ? 1_555 A A 35 N1 ? ? A 5BU 4 A A 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 5BU 4 O4 ? ? ? 1_555 A A 35 N6 ? ? A 5BU 4 A A 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 34 N1 ? ? A C 5 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 34 O6 ? ? A C 5 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 34 N2 ? ? A C 5 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 6 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 6 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 6 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 29 N1 ? ? A C 7 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 29 O6 ? ? A C 7 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 29 N2 ? ? A C 7 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 28 N3 ? ? A G 8 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 28 O2 ? ? A G 8 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 28 N4 ? ? A G 8 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 10 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 10 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 10 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A 5BU 11 N3 ? ? ? 1_555 A A 22 N1 ? ? A 5BU 11 A A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A 5BU 11 O4 ? ? ? 1_555 A A 22 N6 ? ? A 5BU 11 A A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A 5BU 11 O2 ? ? ? 1_555 A A 26 N6 ? ? A 5BU 11 A A 26 1_555 ? ? ? ? ? ? '5BU-A PAIR' ? ? ? hydrog29 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 12 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 12 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 12 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 13 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 20 O2 ? ? A G 13 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 20 N4 ? ? A G 13 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 14 N3 ? ? ? 1_555 A G 19 N1 ? ? A C 14 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 14 N4 ? ? ? 1_555 A G 19 O6 ? ? A C 14 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 19 N2 ? ? A C 14 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 15 N2 ? ? ? 1_555 A A 18 N7 ? ? A G 15 A A 18 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog39 hydrog ? ? A G 23 N2 ? ? ? 1_555 A A 27 N1 ? ? A G 23 A A 27 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog40 hydrog ? ? A G 23 N3 ? ? ? 1_555 A A 27 N6 ? ? A G 23 A A 27 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog41 hydrog ? ? A G 24 N1 ? ? ? 1_555 A G 29 N7 ? ? A G 24 A G 29 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog42 hydrog ? ? A G 24 N2 ? ? ? 1_555 A G 29 O6 ? ? A G 24 A G 29 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog43 hydrog ? ? A G 29 N2 ? ? ? 1_555 A A 31 N1 ? ? A G 29 A A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog44 hydrog ? ? A G 29 N3 ? ? ? 1_555 A A 31 N6 ? ? A G 29 A A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP1 ? A A 16 ? A A 16 ? 6_434 SR ? B SR . ? A SR 201 ? 1_555 O2 ? A 5BU 32 ? A 5BU 32 ? 1_555 74.9 ? 2 OP1 ? A A 16 ? A A 16 ? 6_434 SR ? B SR . ? A SR 201 ? 1_555 OP1 ? A G 34 ? A G 34 ? 1_555 88.6 ? 3 O2 ? A 5BU 32 ? A 5BU 32 ? 1_555 SR ? B SR . ? A SR 201 ? 1_555 OP1 ? A G 34 ? A G 34 ? 1_555 80.4 ? 4 OP2 ? A A 31 ? A A 31 ? 1_555 SR ? F SR . ? A SR 205 ? 1_555 OP2 ? A G 33 ? A G 33 ? 1_555 93.5 ? 5 OP1 ? A G 33 ? A G 33 ? 1_555 SR ? G SR . ? A SR 206 ? 1_555 O ? K HOH . ? A HOH 304 ? 1_555 59.7 ? # 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 SR 201 ? 3 'BINDING SITE FOR RESIDUE SR A 201' AC2 Software A SR 205 ? 2 'BINDING SITE FOR RESIDUE SR A 205' AC3 Software A SR 206 ? 2 'BINDING SITE FOR RESIDUE SR A 206' AC4 Software A ROS 101 ? 6 'BINDING SITE FOR RESIDUE ROS A 101' 1 ? ? ? ? ? ? ? # 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 3 A A 16 ? A A 16 . ? 6_434 ? 2 AC1 3 5BU A 32 ? 5BU A 32 . ? 1_555 ? 3 AC1 3 G A 34 ? G A 34 . ? 1_555 ? 4 AC2 2 A A 31 ? A A 31 . ? 1_555 ? 5 AC2 2 G A 33 ? G A 33 . ? 1_555 ? 6 AC3 2 G A 33 ? G A 33 . ? 1_555 ? 7 AC3 2 HOH K . ? HOH A 304 . ? 1_555 ? 8 AC4 6 C A 7 ? C A 7 . ? 1_555 ? 9 AC4 6 G A 8 ? G A 8 . ? 1_555 ? 10 AC4 6 G A 24 ? G A 24 . ? 1_555 ? 11 AC4 6 C A 28 ? C A 28 . ? 1_555 ? 12 AC4 6 G A 29 ? G A 29 . ? 1_555 ? 13 AC4 6 A A 30 ? A A 30 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OP2 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 5BU _pdbx_validate_close_contact.auth_seq_id_1 4 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 305 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.94 # 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 "O3'" A C 6 ? ? P A C 7 ? ? OP2 A C 7 ? ? 117.38 110.50 6.88 1.10 Y 2 1 N9 A G 8 ? ? "C1'" A G 8 ? ? "C2'" A G 8 ? ? 123.88 114.00 9.88 1.30 N 3 1 N9 A G 15 ? ? "C1'" A G 15 ? ? "C2'" A G 15 ? ? 104.31 112.00 -7.69 1.10 N 4 1 N9 A G 24 ? ? "C1'" A G 24 ? ? "C2'" A G 24 ? ? 122.34 114.00 8.34 1.30 N 5 1 N9 A G 29 ? ? "C1'" A G 29 ? ? "C2'" A G 29 ? ? 124.62 114.00 10.62 1.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 G A 23 ? ? 0.052 'SIDE CHAIN' 2 1 G A 24 ? ? 0.063 'SIDE CHAIN' # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 5BU 4 A 5BU 4 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 2 A 5BU 11 A 5BU 11 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 3 A 5BU 25 A 5BU 25 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 4 A 5BU 32 A 5BU 32 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 5 A 5BU 36 A 5BU 36 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" # _struct_site_keywords.site_id 1 _struct_site_keywords.text INTERCALATION # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 ROS C1 C Y N 148 ROS C2 C Y N 149 ROS C3 C Y N 150 ROS O2 O Y N 151 ROS C4 C Y N 152 ROS C5 C Y N 153 ROS C6 C Y N 154 ROS C7 C Y N 155 ROS C8 C Y N 156 ROS C9 C Y N 157 ROS C10 C Y N 158 ROS C11 C Y N 159 ROS C12 C Y N 160 ROS C13 C Y N 161 ROS C14 C Y N 162 ROS C15 C Y N 163 ROS C16 C Y N 164 ROS C17 C Y N 165 ROS C18 C Y N 166 ROS C19 C Y N 167 ROS N1 N N N 168 ROS C20 C N N 169 ROS C21 C N N 170 ROS N2 N N N 171 ROS C22 C N N 172 ROS C23 C N N 173 ROS H2 H N N 174 ROS H5 H N N 175 ROS H7 H N N 176 ROS H8 H N N 177 ROS H12 H N N 178 ROS H13 H N N 179 ROS H15 H N N 180 ROS H16 H N N 181 ROS H17 H N N 182 ROS H18 H N N 183 ROS H19 H N N 184 ROS H201 H N N 185 ROS H202 H N N 186 ROS H203 H N N 187 ROS H211 H N N 188 ROS H212 H N N 189 ROS H213 H N N 190 ROS H221 H N N 191 ROS H222 H N N 192 ROS H223 H N N 193 ROS H231 H N N 194 ROS H232 H N N 195 ROS H233 H N N 196 SR SR SR N N 197 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 ROS C1 C2 sing Y N 153 ROS C1 C13 sing Y N 154 ROS C1 N1 doub N N 155 ROS C2 C3 doub Y N 156 ROS C2 H2 sing N N 157 ROS C3 O2 sing Y N 158 ROS C3 C11 sing Y N 159 ROS O2 C4 sing Y N 160 ROS C4 C5 sing Y N 161 ROS C4 C9 doub Y N 162 ROS C5 C6 doub Y N 163 ROS C5 H5 sing N N 164 ROS C6 C7 sing Y N 165 ROS C6 N2 sing N N 166 ROS C7 C8 doub Y N 167 ROS C7 H7 sing N N 168 ROS C8 C9 sing Y N 169 ROS C8 H8 sing N N 170 ROS C9 C10 sing Y N 171 ROS C10 C11 doub Y N 172 ROS C10 C14 sing Y N 173 ROS C11 C12 sing Y N 174 ROS C12 C13 doub Y N 175 ROS C12 H12 sing N N 176 ROS C13 H13 sing N N 177 ROS C14 C15 doub Y N 178 ROS C14 C19 sing Y N 179 ROS C15 C16 sing Y N 180 ROS C15 H15 sing N N 181 ROS C16 C17 doub Y N 182 ROS C16 H16 sing N N 183 ROS C17 C18 sing Y N 184 ROS C17 H17 sing N N 185 ROS C18 C19 doub Y N 186 ROS C18 H18 sing N N 187 ROS C19 H19 sing N N 188 ROS N1 C20 sing N N 189 ROS N1 C21 sing N N 190 ROS C20 H201 sing N N 191 ROS C20 H202 sing N N 192 ROS C20 H203 sing N N 193 ROS C21 H211 sing N N 194 ROS C21 H212 sing N N 195 ROS C21 H213 sing N N 196 ROS N2 C22 sing N N 197 ROS N2 C23 sing N N 198 ROS C22 H221 sing N N 199 ROS C22 H222 sing N N 200 ROS C22 H223 sing N N 201 ROS C23 H231 sing N N 202 ROS C23 H232 sing N N 203 ROS C23 H233 sing N N 204 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1F1T 'double helix' 1F1T 'a-form double helix' 1F1T tetraloop 1F1T 'bulge loop' 1F1T 'mismatched base pair' 1F1T 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 38 1_555 -0.785 -0.534 0.159 -4.834 -1.906 -6.072 1 A_G1:C38_A A 1 ? A 38 ? 19 1 1 A G 2 1_555 A C 37 1_555 -0.659 -0.859 -0.304 -1.413 -19.985 3.072 2 A_G2:C37_A A 2 ? A 37 ? 19 1 1 A A 3 1_555 A 5BU 36 1_555 0.099 -0.263 0.277 7.079 -9.795 1.960 3 A_A3:5BU36_A A 3 ? A 36 ? 20 1 1 A 5BU 4 1_555 A A 35 1_555 -0.544 -0.386 -0.276 11.008 -2.274 -3.505 4 A_5BU4:A35_A A 4 ? A 35 ? 20 1 1 A C 5 1_555 A G 34 1_555 -0.262 -0.205 -0.396 12.129 -12.501 3.853 5 A_C5:G34_A A 5 ? A 34 ? 19 1 1 A C 6 1_555 A G 33 1_555 0.277 -0.017 0.048 -0.391 -8.314 3.199 6 A_C6:G33_A A 6 ? A 33 ? 19 1 1 A C 7 1_555 A G 29 1_555 0.691 0.011 0.351 2.167 -3.222 0.367 7 A_C7:G29_A A 7 ? A 29 ? 19 1 1 A G 8 1_555 A C 28 1_555 -1.097 -0.267 0.101 -2.733 2.302 -0.458 8 A_G8:C28_A A 8 ? A 28 ? 19 1 1 A C 10 1_555 A G 23 1_555 0.016 -0.317 -0.135 -4.922 1.609 -4.179 9 A_C10:G23_A A 10 ? A 23 ? 19 1 1 A 5BU 11 1_555 A A 22 1_555 0.392 -0.630 -0.096 4.327 -3.682 0.483 10 A_5BU11:A22_A A 11 ? A 22 ? 20 1 1 A G 12 1_555 A C 21 1_555 -0.015 -0.369 -0.175 2.704 -13.856 4.466 11 A_G12:C21_A A 12 ? A 21 ? 19 1 1 A G 13 1_555 A C 20 1_555 -0.182 -0.238 -0.048 1.130 -11.956 10.074 12 A_G13:C20_A A 13 ? A 20 ? 19 1 1 A C 14 1_555 A G 19 1_555 0.477 0.007 -0.248 -2.205 -0.923 -0.746 13 A_C14:G19_A A 14 ? A 19 ? 19 1 1 A G 15 1_555 A A 18 1_555 7.439 -5.000 -0.028 9.026 5.568 -24.202 14 A_G15:A18_A A 15 ? A 18 ? ? ? # 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 38 1_555 A G 2 1_555 A C 37 1_555 -0.136 -0.891 3.232 5.028 -4.007 30.090 -0.892 1.244 3.256 -7.609 -9.549 30.754 1 AA_G1G2:C37C38_AA A 1 ? A 38 ? A 2 ? A 37 ? 1 A G 2 1_555 A C 37 1_555 A A 3 1_555 A 5BU 36 1_555 0.640 -1.544 2.963 -3.744 6.957 29.989 -4.019 -1.806 2.455 13.159 7.082 30.990 2 AA_G2A3:5BU36C37_AA A 2 ? A 37 ? A 3 ? A 36 ? 1 A A 3 1_555 A 5BU 36 1_555 A 5BU 4 1_555 A A 35 1_555 0.210 -1.772 3.269 4.815 2.052 32.222 -3.506 0.452 3.151 3.667 -8.605 32.633 3 AA_A35BU4:A355BU36_AA A 3 ? A 36 ? A 4 ? A 35 ? 1 A 5BU 4 1_555 A A 35 1_555 A C 5 1_555 A G 34 1_555 -0.040 -2.501 3.331 -0.826 7.910 24.161 -7.732 -0.122 2.403 18.274 1.907 25.417 4 AA_5BU4C5:G34A35_AA A 4 ? A 35 ? A 5 ? A 34 ? 1 A C 5 1_555 A G 34 1_555 A C 6 1_555 A G 33 1_555 0.349 -2.126 3.585 -2.456 10.826 37.864 -4.444 -0.811 2.866 16.261 3.689 39.400 5 AA_C5C6:G33G34_AA A 5 ? A 34 ? A 6 ? A 33 ? 1 A C 6 1_555 A G 33 1_555 A C 7 1_555 A G 29 1_555 2.310 -1.226 3.000 -1.657 5.130 52.579 -1.673 -2.692 2.808 5.774 1.865 52.835 6 AA_C6C7:G29G33_AA A 6 ? A 33 ? A 7 ? A 29 ? 1 A C 7 1_555 A G 29 1_555 A G 8 1_555 A C 28 1_555 0.837 -2.197 7.008 1.248 12.221 4.086 -32.747 -1.364 0.224 71.299 -7.281 12.944 7 AA_C7G8:C28G29_AA A 7 ? A 29 ? A 8 ? A 28 ? 1 A G 8 1_555 A C 28 1_555 A C 10 1_555 A G 23 1_555 1.513 1.565 3.319 2.810 1.619 90.910 1.065 -1.005 3.376 1.135 -1.971 90.956 8 AA_G8C10:G23C28_AA A 8 ? A 28 ? A 10 ? A 23 ? 1 A C 10 1_555 A G 23 1_555 A 5BU 11 1_555 A A 22 1_555 -0.516 -1.588 3.089 -3.100 1.197 34.417 -2.846 0.418 3.067 2.017 5.223 34.573 9 AA_C105BU11:A22G23_AA A 10 ? A 23 ? A 11 ? A 22 ? 1 A 5BU 11 1_555 A A 22 1_555 A G 12 1_555 A C 21 1_555 -0.185 -1.652 3.259 1.885 9.014 29.000 -4.816 0.702 2.622 17.453 -3.649 30.397 10 AA_5BU11G12:C21A22_AA A 11 ? A 22 ? A 12 ? A 21 ? 1 A G 12 1_555 A C 21 1_555 A G 13 1_555 A C 20 1_555 0.665 -1.660 3.186 1.042 9.528 28.678 -4.925 -1.087 2.538 18.592 -2.033 30.206 11 AA_G12G13:C20C21_AA A 12 ? A 21 ? A 13 ? A 20 ? 1 A G 13 1_555 A C 20 1_555 A C 14 1_555 A G 19 1_555 0.368 -1.797 3.366 3.353 5.522 36.650 -3.548 -0.132 3.092 8.698 -5.282 37.196 12 AA_G13C14:G19C20_AA A 13 ? A 20 ? A 14 ? A 19 ? 1 A C 14 1_555 A G 19 1_555 A G 15 1_555 A A 18 1_555 -1.286 -2.130 2.959 1.581 5.913 49.635 -2.891 1.621 2.666 7.013 -1.875 49.988 13 AA_C14G15:A18G19_AA A 14 ? A 19 ? A 15 ? A 18 ? # _atom_sites.entry_id 1F1T _atom_sites.fract_transf_matrix[1][1] 0.018084 _atom_sites.fract_transf_matrix[1][2] 0.010441 _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] 0.020882 _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] 0.006948 _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 BR C N O P SR # loop_