data_1NTB # _entry.id 1NTB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1NTB pdb_00001ntb 10.2210/pdb1ntb/pdb NDB DR0010 ? ? RCSB RCSB018183 ? ? WWPDB D_1000018183 ? ? # 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 2003-05-13 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 5 'Structure model' 1 4 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' 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_site 7 5 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 19 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 20 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 21 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 22 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 23 4 'Structure model' '_pdbx_struct_conn_angle.value' 24 4 'Structure model' '_struct_conn.pdbx_dist_value' 25 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 26 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 32 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 33 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 34 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 35 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 36 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 37 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 38 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 39 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 40 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 41 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NTB _pdbx_database_status.recvd_initial_deposition_date 2003-01-29 _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1NTA _pdbx_database_related.details '2.9 A crystal structure of Streptomycin RNA-aptamer (Barium form)' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Tereshko, V.' 1 'Skripkin, E.' 2 'Patel, D.J.' 3 # _citation.id primary _citation.title 'Encapsulating Streptomycin within a small 40-mer RNA' _citation.journal_abbrev CHEM.BIOL. _citation.journal_volume 10 _citation.page_first 175 _citation.page_last 187 _citation.year 2003 _citation.journal_id_ASTM CBOLE2 _citation.country UK _citation.journal_id_ISSN 1074-5521 _citation.journal_id_CSD 2050 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12618190 _citation.pdbx_database_id_DOI '10.1016/S1074-5521(03)00024-3' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Tereshko, V.' 1 ? primary 'Skripkin, E.' 2 ? primary 'Patel, D.J.' 3 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP*UP*GP*CP*C)-3'" 6988.146 1 ? ? ? ? 2 polymer syn "5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C)-3'" 5762.499 1 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 2 ? ? ? ? 4 non-polymer syn STREPTOMYCIN 581.574 1 ? ? ? ? 5 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 6 water nat water 18.015 6 ? ? ? ? # 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 GGAUCGCAUUUGGACUUCUGCC GGAUCGCAUUUGGACUUCUGCC A ? 2 polyribonucleotide no no CGGCACCACGGUCGGAUC CGGCACCACGGUCGGAUC B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'SODIUM ION' NA 4 STREPTOMYCIN SRY 5 'MAGNESIUM ION' MG 6 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 U n 1 5 C n 1 6 G n 1 7 C n 1 8 A n 1 9 U n 1 10 U n 1 11 U n 1 12 G n 1 13 G n 1 14 A n 1 15 C n 1 16 U n 1 17 U n 1 18 C n 1 19 U n 1 20 G n 1 21 C n 1 22 C n 2 1 C n 2 2 G n 2 3 G n 2 4 C n 2 5 A n 2 6 C n 2 7 C n 2 8 A n 2 9 C n 2 10 G n 2 11 G n 2 12 U n 2 13 C n 2 14 G n 2 15 G n 2 16 A n 2 17 U n 2 18 C n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 SRY non-polymer . STREPTOMYCIN 'STREPTOMYCIN A' 'C21 H39 N7 O12' 581.574 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 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 U 4 4 4 U U A . n A 1 5 C 5 5 5 C C A . n A 1 6 G 6 6 6 G G A . n A 1 7 C 7 7 7 C C A . n A 1 8 A 8 8 8 A A A . n A 1 9 U 9 9 9 U U A . n A 1 10 U 10 10 10 U U A . n A 1 11 U 11 11 11 U 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 A 14 14 14 A A A . n A 1 15 C 15 15 15 C C A . n A 1 16 U 16 16 16 U U A . n A 1 17 U 17 17 17 U U A . n A 1 18 C 18 18 18 C C A . n A 1 19 U 19 19 19 U U A . n A 1 20 G 20 20 20 G G A . n A 1 21 C 21 21 21 C C A . n A 1 22 C 22 22 22 C C A . n B 2 1 C 1 101 101 C C B . n B 2 2 G 2 102 102 G G B . n B 2 3 G 3 103 103 G G B . n B 2 4 C 4 104 104 C C B . n B 2 5 A 5 105 105 A A B . n B 2 6 C 6 106 106 C C B . n B 2 7 C 7 107 107 C C B . n B 2 8 A 8 108 108 A A B . n B 2 9 C 9 109 109 C C B . n B 2 10 G 10 110 110 G G B . n B 2 11 G 11 111 111 G G B . n B 2 12 U 12 112 112 U U B . n B 2 13 C 13 113 113 C C B . n B 2 14 G 14 114 114 G G B . n B 2 15 G 15 115 115 G G B . n B 2 16 A 16 116 116 A A B . n B 2 17 U 17 117 117 U U B . n B 2 18 C 18 118 118 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 NA 1 23 4 NA NA A . D 3 NA 1 24 5 NA NA A . E 4 SRY 1 25 6 SRY SRY A . F 5 MG 1 1 1 MG MG B . G 6 HOH 1 26 8 HOH HOH A . G 6 HOH 2 27 10 HOH HOH A . H 6 HOH 1 7 7 HOH HOH B . H 6 HOH 2 9 9 HOH HOH B . H 6 HOH 3 11 11 HOH HOH B . H 6 HOH 4 12 12 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.13 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CNS phasing . ? 4 # _cell.entry_id 1NTB _cell.length_a 82.634 _cell.length_b 82.634 _cell.length_c 49.153 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NTB _symmetry.space_group_name_H-M 'I 4' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 # _exptl.entry_id 1NTB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.29 _exptl_crystal.density_percent_sol 62.62 _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 5.6 _exptl_crystal_grow.pdbx_details 'MES buffer, Magnesium cloride, sodium cloride, MPD, pH 5.6, 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 'MES buffer' ? ? ? 1 2 1 MgCl2 ? ? ? 1 3 1 NaCl ? ? ? 1 4 1 MPD ? ? ? 1 5 2 MgCl2 ? ? ? 1 6 2 NaCl ? ? ? 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 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV++' _diffrn_detector.pdbx_collection_date 2002-05-24 _diffrn_detector.details mirrors # _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RUH3R' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 1NTB _reflns.number_all ? _reflns.number_obs 3942 _reflns.percent_possible_obs 99.8 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 2.85 _reflns.d_resolution_low 25.0 _reflns.pdbx_Rmerge_I_obs 0.045 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 9.3 _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 2.95 _reflns_shell.percent_possible_all 99.8 _reflns_shell.Rmerge_I_obs 0.45 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1NTB _refine.ls_number_reflns_obs 3394 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.00 _refine.ls_d_res_high 2.90 _refine.ls_percent_reflns_obs 99.84 _refine.ls_R_factor_obs 0.20847 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20373 _refine.ls_R_factor_R_free 0.25507 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.3 _refine.ls_number_reflns_R_free 349 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.946 _refine.correlation_coeff_Fo_to_Fc_free 0.923 _refine.B_iso_mean 45.528 _refine.aniso_B[1][1] 0.51 _refine.aniso_B[2][2] 0.51 _refine.aniso_B[3][3] -1.02 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'Barium form of streptomycin RNA-aptamer' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _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 RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 0.396 _refine.overall_SU_ML 0.299 _refine.overall_SU_B 16.131 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 842 _refine_hist.pdbx_number_atoms_ligand 43 _refine_hist.number_atoms_solvent 6 _refine_hist.number_atoms_total 891 _refine_hist.d_res_high 2.90 _refine_hist.d_res_low 20.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.010 0.021 ? 988 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 327 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.746 2.121 ? 1525 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.710 2.049 ? 854 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.412 0.200 ? 175 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 418 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.003 0.020 ? 4 'X-RAY DIFFRACTION' ? r_nbd_refined 0.179 0.200 ? 177 'X-RAY DIFFRACTION' ? r_nbd_other 0.227 0.200 ? 407 'X-RAY DIFFRACTION' ? r_nbtor_other 0.110 0.200 ? 198 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.178 0.200 ? 30 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.123 0.200 ? 18 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.225 0.200 ? 10 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.149 0.200 ? 1 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 0.853 3.000 ? 988 'X-RAY DIFFRACTION' ? r_scangle_it 1.372 4.500 ? 1525 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.900 _refine_ls_shell.d_res_low 2.974 _refine_ls_shell.number_reflns_R_work 234 _refine_ls_shell.R_factor_R_work 0.3 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.359 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 22 _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 1NTB _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 1NTB _struct.title '2.9 A crystal structure of Streptomycin RNA-aptamer complex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1NTB _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Streptomycin RNA-Aptamer, Magnesium form, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 4 ? F N N 5 ? G N N 6 ? H N N 6 ? # 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 1NTB 1NTB ? ? ? 2 2 PDB 1NTB 1NTB ? ? ? # 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 1NTB A 1 ? 22 ? 1NTB 1 ? 22 ? 1 22 2 2 1NTB B 1 ? 18 ? 1NTB 101 ? 118 ? 101 118 # _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,H # _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 metalc1 metalc ? ? A C 7 OP2 ? ? ? 1_555 C NA . NA ? ? A C 7 A NA 23 1_555 ? ? ? ? ? ? ? 2.483 ? ? metalc2 metalc ? ? A A 8 "O2'" ? ? ? 1_555 C NA . NA ? ? A A 8 A NA 23 1_555 ? ? ? ? ? ? ? 2.497 ? ? metalc3 metalc ? ? A U 10 OP2 ? ? ? 1_555 C NA . NA ? ? A U 10 A NA 23 1_555 ? ? ? ? ? ? ? 2.480 ? ? metalc4 metalc ? ? A U 10 O2 ? ? ? 1_555 F MG . MG ? ? A U 10 B MG 1 1_555 ? ? ? ? ? ? ? 2.201 ? ? metalc5 metalc ? ? A U 11 O4 ? ? ? 1_555 F MG . MG ? ? A U 11 B MG 1 1_555 ? ? ? ? ? ? ? 2.245 ? ? metalc6 metalc ? ? A C 15 OP2 ? ? ? 1_555 D NA . NA ? ? A C 15 A NA 24 1_555 ? ? ? ? ? ? ? 2.248 ? ? metalc7 metalc ? ? A U 16 O4 ? ? ? 1_555 D NA . NA ? ? A U 16 A NA 24 1_555 ? ? ? ? ? ? ? 2.200 ? ? metalc8 metalc ? ? G HOH . O ? ? ? 1_555 F MG . MG ? ? A HOH 26 B MG 1 1_555 ? ? ? ? ? ? ? 2.090 ? ? metalc9 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 1 B HOH 7 1_555 ? ? ? ? ? ? ? 2.504 ? ? metalc10 metalc ? ? F MG . MG ? ? ? 1_555 B C 9 "O5'" ? ? B MG 1 B C 109 1_555 ? ? ? ? ? ? ? 2.200 ? ? metalc11 metalc ? ? F MG . MG ? ? ? 1_555 B C 9 "O4'" ? ? B MG 1 B C 109 1_555 ? ? ? ? ? ? ? 2.191 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 18 N3 ? ? A G 2 B C 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 18 O2 ? ? A G 2 B C 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 18 N4 ? ? A G 2 B C 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 17 N3 ? ? A A 3 B U 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 17 O4 ? ? A A 3 B U 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 4 N3 ? ? ? 1_555 B A 16 N1 ? ? A U 4 B A 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 4 O4 ? ? ? 1_555 B A 16 N6 ? ? A U 4 B A 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 15 N1 ? ? A C 5 B G 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 15 O6 ? ? A C 5 B G 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 15 N2 ? ? A C 5 B G 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 6 N1 ? ? ? 1_555 A G 13 O6 ? ? A G 6 A G 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A G 6 N2 ? ? ? 1_555 A G 13 N7 ? ? A G 6 A G 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 6 B C 113 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog14 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 7 B G 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 7 B G 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 7 B G 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 9 O2 ? ? A G 12 B C 109 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog18 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 13 N3 ? ? A G 13 B C 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 13 O2 ? ? A G 13 B C 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 13 B C 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 14 N1 ? ? ? 1_555 B U 12 N3 ? ? A A 14 B U 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 14 N6 ? ? ? 1_555 B U 12 O4 ? ? A A 14 B U 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 15 B G 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 15 B G 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 15 B G 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 16 O2 ? ? ? 1_555 A C 18 N4 ? ? A U 16 A C 18 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog27 hydrog ? ? A U 17 O2 ? ? ? 1_555 B A 8 N6 ? ? A U 17 B A 108 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog28 hydrog ? ? A C 18 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 18 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 18 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 18 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 18 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 18 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 19 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 19 B A 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 19 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 19 B A 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 20 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 20 B C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 20 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 20 B C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 20 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 20 B C 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 21 B G 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 21 B G 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 21 B G 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 22 O2 ? ? ? 1_555 B G 2 N1 ? ? A C 22 B G 102 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference 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 OP2 ? A C 7 ? A C 7 ? 1_555 NA ? C NA . ? A NA 23 ? 1_555 "O2'" ? A A 8 ? A A 8 ? 1_555 113.1 ? 2 OP2 ? A C 7 ? A C 7 ? 1_555 NA ? C NA . ? A NA 23 ? 1_555 OP2 ? A U 10 ? A U 10 ? 1_555 125.8 ? 3 "O2'" ? A A 8 ? A A 8 ? 1_555 NA ? C NA . ? A NA 23 ? 1_555 OP2 ? A U 10 ? A U 10 ? 1_555 98.8 ? 4 O2 ? A U 10 ? A U 10 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 O4 ? A U 11 ? A U 11 ? 1_555 97.6 ? 5 O2 ? A U 10 ? A U 10 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 O ? G HOH . ? A HOH 26 ? 1_555 85.6 ? 6 O4 ? A U 11 ? A U 11 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 O ? G HOH . ? A HOH 26 ? 1_555 164.3 ? 7 O2 ? A U 10 ? A U 10 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 O ? H HOH . ? B HOH 7 ? 1_555 99.4 ? 8 O4 ? A U 11 ? A U 11 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 O ? H HOH . ? B HOH 7 ? 1_555 100.3 ? 9 O ? G HOH . ? A HOH 26 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 O ? H HOH . ? B HOH 7 ? 1_555 64.0 ? 10 O2 ? A U 10 ? A U 10 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 "O5'" ? B C 9 ? B C 109 ? 1_555 161.3 ? 11 O4 ? A U 11 ? A U 11 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 "O5'" ? B C 9 ? B C 109 ? 1_555 92.2 ? 12 O ? G HOH . ? A HOH 26 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 "O5'" ? B C 9 ? B C 109 ? 1_555 89.3 ? 13 O ? H HOH . ? B HOH 7 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 "O5'" ? B C 9 ? B C 109 ? 1_555 94.4 ? 14 O2 ? A U 10 ? A U 10 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 "O4'" ? B C 9 ? B C 109 ? 1_555 89.4 ? 15 O4 ? A U 11 ? A U 11 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 "O4'" ? B C 9 ? B C 109 ? 1_555 76.3 ? 16 O ? G HOH . ? A HOH 26 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 "O4'" ? B C 9 ? B C 109 ? 1_555 119.2 ? 17 O ? H HOH . ? B HOH 7 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 "O4'" ? B C 9 ? B C 109 ? 1_555 170.9 ? 18 "O5'" ? B C 9 ? B C 109 ? 1_555 MG ? F MG . ? B MG 1 ? 1_555 "O4'" ? B C 9 ? B C 109 ? 1_555 77.4 ? 19 OP2 ? A C 15 ? A C 15 ? 1_555 NA ? D NA . ? A NA 24 ? 1_555 O4 ? A U 16 ? A U 16 ? 1_555 71.6 ? # 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 MG 1 ? 5 'BINDING SITE FOR RESIDUE MG B 1' AC2 Software A NA 23 ? 3 'BINDING SITE FOR RESIDUE NA A 23' AC3 Software A NA 24 ? 2 'BINDING SITE FOR RESIDUE NA A 24' 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 5 U A 10 ? U A 10 . ? 1_555 ? 2 AC1 5 U A 11 ? U A 11 . ? 1_555 ? 3 AC1 5 HOH G . ? HOH A 26 . ? 1_555 ? 4 AC1 5 HOH H . ? HOH B 7 . ? 1_555 ? 5 AC1 5 C B 9 ? C B 109 . ? 1_555 ? 6 AC2 3 C A 7 ? C A 7 . ? 1_555 ? 7 AC2 3 A A 8 ? A A 8 . ? 1_555 ? 8 AC2 3 U A 10 ? U A 10 . ? 1_555 ? 9 AC3 2 C A 15 ? C A 15 . ? 1_555 ? 10 AC3 2 U A 16 ? U A 16 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O5'" A A 8 ? ? "C5'" A A 8 ? ? 1.350 1.420 -0.070 0.009 N 2 1 "C1'" A U 11 ? ? N1 A U 11 ? ? 1.590 1.483 0.107 0.015 N 3 1 C4 A U 11 ? ? O4 A U 11 ? ? 1.307 1.232 0.075 0.008 N 4 1 "O5'" B C 106 ? ? "C5'" B C 106 ? ? 1.625 1.440 0.185 0.016 N 5 1 P B U 112 ? ? OP2 B U 112 ? ? 1.702 1.485 0.217 0.017 N 6 1 P B U 117 ? ? OP2 B U 117 ? ? 1.700 1.485 0.215 0.017 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A G 6 ? ? "O3'" A G 6 ? ? P A C 7 ? ? 129.16 119.70 9.46 1.20 Y 2 1 "O4'" A A 8 ? ? "C1'" A A 8 ? ? N9 A A 8 ? ? 112.80 108.50 4.30 0.70 N 3 1 "O5'" B C 106 ? ? "C5'" B C 106 ? ? "C4'" B C 106 ? ? 89.73 109.40 -19.67 0.80 N 4 1 P B C 106 ? ? "O5'" B C 106 ? ? "C5'" B C 106 ? ? 109.98 120.90 -10.92 1.60 N 5 1 "C3'" B C 107 ? ? "O3'" B C 107 ? ? P B A 108 ? ? 127.06 119.70 7.36 1.20 Y 6 1 "C1'" B U 112 ? ? "O4'" B U 112 ? ? "C4'" B U 112 ? ? 102.05 109.70 -7.65 0.70 N 7 1 "C3'" B U 112 ? ? "C2'" B U 112 ? ? "C1'" B U 112 ? ? 96.98 101.30 -4.32 0.70 N 8 1 "O4'" B U 112 ? ? "C1'" B U 112 ? ? "C2'" B U 112 ? ? 115.76 107.60 8.16 0.90 N 9 1 N1 B U 112 ? ? "C1'" B U 112 ? ? "C2'" B U 112 ? ? 128.13 114.00 14.13 1.30 N 10 1 "O4'" B U 112 ? ? "C1'" B U 112 ? ? N1 B U 112 ? ? 114.33 108.50 5.83 0.70 N 11 1 N1 B U 112 ? ? C2 B U 112 ? ? N3 B U 112 ? ? 121.20 114.90 6.30 0.60 N 12 1 C2 B U 112 ? ? N3 B U 112 ? ? C4 B U 112 ? ? 121.21 127.00 -5.79 0.60 N 13 1 N3 B U 112 ? ? C4 B U 112 ? ? C5 B U 112 ? ? 118.22 114.60 3.62 0.60 N 14 1 C5 B U 112 ? ? C4 B U 112 ? ? O4 B U 112 ? ? 118.57 125.90 -7.33 0.60 N 15 1 C6 B U 112 ? ? N1 B U 112 ? ? "C1'" B U 112 ? ? 112.19 121.20 -9.01 1.40 N 16 1 C2 B U 112 ? ? N1 B U 112 ? ? "C1'" B U 112 ? ? 127.37 117.70 9.67 1.20 N 17 1 "C4'" B U 117 ? ? "C3'" B U 117 ? ? "C2'" B U 117 ? ? 112.81 102.60 10.21 1.00 N 18 1 "O4'" B U 117 ? ? "C1'" B U 117 ? ? "C2'" B U 117 ? ? 117.13 107.60 9.53 0.90 N 19 1 "O4'" B U 117 ? ? "C1'" B U 117 ? ? N1 B U 117 ? ? 115.60 108.50 7.10 0.70 N 20 1 N1 B U 117 ? ? C2 B U 117 ? ? N3 B U 117 ? ? 120.31 114.90 5.41 0.60 N 21 1 C2 B U 117 ? ? N3 B U 117 ? ? C4 B U 117 ? ? 122.05 127.00 -4.95 0.60 N 22 1 C5 B U 117 ? ? C4 B U 117 ? ? O4 B U 117 ? ? 121.69 125.90 -4.21 0.60 N 23 1 C6 B U 117 ? ? N1 B U 117 ? ? "C1'" B U 117 ? ? 111.27 121.20 -9.93 1.40 N 24 1 C2 B U 117 ? ? N1 B U 117 ? ? "C1'" B U 117 ? ? 127.21 117.70 9.51 1.20 N # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 "C3'" ? B U 112 ? 'WRONG HAND' . 2 1 "C1'" ? B U 112 ? PLANAR . 3 1 "C3'" ? B U 117 ? PLANAR . # _struct_site_keywords.site_id 1 _struct_site_keywords.text intercalation # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 13.0915 _pdbx_refine_tls.origin_y 30.3084 _pdbx_refine_tls.origin_z 0.7858 _pdbx_refine_tls.T[1][1] 0.2346 _pdbx_refine_tls.T[2][2] 0.2111 _pdbx_refine_tls.T[3][3] 0.3656 _pdbx_refine_tls.T[1][2] 0.2198 _pdbx_refine_tls.T[1][3] 0.0239 _pdbx_refine_tls.T[2][3] 0.0065 _pdbx_refine_tls.L[1][1] 4.4955 _pdbx_refine_tls.L[2][2] 5.6035 _pdbx_refine_tls.L[3][3] 9.3740 _pdbx_refine_tls.L[1][2] 0.2268 _pdbx_refine_tls.L[1][3] -0.5570 _pdbx_refine_tls.L[2][3] -3.8731 _pdbx_refine_tls.S[1][1] -0.4998 _pdbx_refine_tls.S[1][2] 0.3799 _pdbx_refine_tls.S[1][3] -0.2448 _pdbx_refine_tls.S[2][1] 0.1511 _pdbx_refine_tls.S[2][2] 0.5065 _pdbx_refine_tls.S[2][3] -0.3314 _pdbx_refine_tls.S[3][1] 0.0325 _pdbx_refine_tls.S[3][2] -0.0659 _pdbx_refine_tls.S[3][3] -0.0066 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 1 _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 22 _pdbx_refine_tls_group.end_auth_seq_id 22 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 N 0 A SRY 25 ? E SRY ? 2 1 N 0 B HOH 11 ? H HOH ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 MG MG MG N N 114 NA NA NA N N 115 SRY C11 C N R 116 SRY N11 N N N 117 SRY CA1 C N N 118 SRY NB1 N N N 119 SRY NC1 N N N 120 SRY C21 C N R 121 SRY O21 O N N 122 SRY C31 C N S 123 SRY N31 N N N 124 SRY CD1 C N N 125 SRY NE1 N N N 126 SRY NF1 N N N 127 SRY C41 C N R 128 SRY O41 O N N 129 SRY C51 C N R 130 SRY O51 O N N 131 SRY C61 C N S 132 SRY O61 O N N 133 SRY C12 C N R 134 SRY C22 C N S 135 SRY C32 C N S 136 SRY O32 O N N 137 SRY CG2 C N N 138 SRY OG2 O N N 139 SRY C42 C N S 140 SRY CH2 C N N 141 SRY O42 O N N 142 SRY O13 O N N 143 SRY C13 C N S 144 SRY C23 C N S 145 SRY N23 N N N 146 SRY CI3 C N N 147 SRY C33 C N S 148 SRY O33 O N N 149 SRY C43 C N R 150 SRY O43 O N N 151 SRY C53 C N S 152 SRY O53 O N N 153 SRY C63 C N N 154 SRY O63 O N N 155 SRY H11 H N N 156 SRY HN11 H N N 157 SRY HB11 H N N 158 SRY HB12 H N N 159 SRY HC11 H N N 160 SRY H21 H N N 161 SRY HO21 H N N 162 SRY H31 H N N 163 SRY HN31 H N N 164 SRY HE11 H N N 165 SRY HE12 H N N 166 SRY HF11 H N N 167 SRY H41 H N N 168 SRY H51 H N N 169 SRY HO51 H N N 170 SRY H61 H N N 171 SRY HO61 H N N 172 SRY H12 H N N 173 SRY H22 H N N 174 SRY HO32 H N N 175 SRY HG21 H N N 176 SRY H42 H N N 177 SRY HH21 H N N 178 SRY HH22 H N N 179 SRY HH23 H N N 180 SRY H13 H N N 181 SRY H23 H N N 182 SRY HN23 H N N 183 SRY HI31 H N N 184 SRY HI32 H N N 185 SRY HI33 H N N 186 SRY H33 H N N 187 SRY HO33 H N N 188 SRY H43 H N N 189 SRY HO43 H N N 190 SRY H53 H N N 191 SRY H631 H N N 192 SRY H632 H N N 193 SRY HO63 H N N 194 U OP3 O N N 195 U P P N N 196 U OP1 O N N 197 U OP2 O N N 198 U "O5'" O N N 199 U "C5'" C N N 200 U "C4'" C N R 201 U "O4'" O N N 202 U "C3'" C N S 203 U "O3'" O N N 204 U "C2'" C N R 205 U "O2'" O N N 206 U "C1'" C N R 207 U N1 N N N 208 U C2 C N N 209 U O2 O N N 210 U N3 N N N 211 U C4 C N N 212 U O4 O N N 213 U C5 C N N 214 U C6 C N N 215 U HOP3 H N N 216 U HOP2 H N N 217 U "H5'" H N N 218 U "H5''" H N N 219 U "H4'" H N N 220 U "H3'" H N N 221 U "HO3'" H N N 222 U "H2'" H N N 223 U "HO2'" H N N 224 U "H1'" H N N 225 U H3 H N N 226 U H5 H N N 227 U H6 H N N 228 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 SRY C11 N11 sing N N 118 SRY C11 C21 sing N N 119 SRY C11 C61 sing N N 120 SRY C11 H11 sing N N 121 SRY N11 CA1 sing N N 122 SRY N11 HN11 sing N N 123 SRY CA1 NB1 sing N N 124 SRY CA1 NC1 doub N N 125 SRY NB1 HB11 sing N N 126 SRY NB1 HB12 sing N N 127 SRY NC1 HC11 sing N N 128 SRY C21 O21 sing N N 129 SRY C21 C31 sing N N 130 SRY C21 H21 sing N N 131 SRY O21 HO21 sing N N 132 SRY C31 N31 sing N N 133 SRY C31 C41 sing N N 134 SRY C31 H31 sing N N 135 SRY N31 CD1 sing N N 136 SRY N31 HN31 sing N N 137 SRY CD1 NE1 sing N N 138 SRY CD1 NF1 doub N N 139 SRY NE1 HE11 sing N N 140 SRY NE1 HE12 sing N N 141 SRY NF1 HF11 sing N N 142 SRY C41 O41 sing N N 143 SRY C41 C51 sing N N 144 SRY C41 H41 sing N N 145 SRY O41 C12 sing N N 146 SRY C51 O51 sing N N 147 SRY C51 C61 sing N N 148 SRY C51 H51 sing N N 149 SRY O51 HO51 sing N N 150 SRY C61 O61 sing N N 151 SRY C61 H61 sing N N 152 SRY O61 HO61 sing N N 153 SRY C12 C22 sing N N 154 SRY C12 O42 sing N N 155 SRY C12 H12 sing N N 156 SRY C22 C32 sing N N 157 SRY C22 O13 sing N N 158 SRY C22 H22 sing N N 159 SRY C32 O32 sing N N 160 SRY C32 CG2 sing N N 161 SRY C32 C42 sing N N 162 SRY O32 HO32 sing N N 163 SRY CG2 OG2 doub N N 164 SRY CG2 HG21 sing N N 165 SRY C42 CH2 sing N N 166 SRY C42 O42 sing N N 167 SRY C42 H42 sing N N 168 SRY CH2 HH21 sing N N 169 SRY CH2 HH22 sing N N 170 SRY CH2 HH23 sing N N 171 SRY O13 C13 sing N N 172 SRY C13 C23 sing N N 173 SRY C13 O53 sing N N 174 SRY C13 H13 sing N N 175 SRY C23 N23 sing N N 176 SRY C23 C33 sing N N 177 SRY C23 H23 sing N N 178 SRY N23 CI3 sing N N 179 SRY N23 HN23 sing N N 180 SRY CI3 HI31 sing N N 181 SRY CI3 HI32 sing N N 182 SRY CI3 HI33 sing N N 183 SRY C33 O33 sing N N 184 SRY C33 C43 sing N N 185 SRY C33 H33 sing N N 186 SRY O33 HO33 sing N N 187 SRY C43 O43 sing N N 188 SRY C43 C53 sing N N 189 SRY C43 H43 sing N N 190 SRY O43 HO43 sing N N 191 SRY C53 O53 sing N N 192 SRY C53 C63 sing N N 193 SRY C53 H53 sing N N 194 SRY C63 O63 sing N N 195 SRY C63 H631 sing N N 196 SRY C63 H632 sing N N 197 SRY O63 HO63 sing N N 198 U OP3 P sing N N 199 U OP3 HOP3 sing N N 200 U P OP1 doub N N 201 U P OP2 sing N N 202 U P "O5'" sing N N 203 U OP2 HOP2 sing N N 204 U "O5'" "C5'" sing N N 205 U "C5'" "C4'" sing N N 206 U "C5'" "H5'" sing N N 207 U "C5'" "H5''" sing N N 208 U "C4'" "O4'" sing N N 209 U "C4'" "C3'" sing N N 210 U "C4'" "H4'" sing N N 211 U "O4'" "C1'" sing N N 212 U "C3'" "O3'" sing N N 213 U "C3'" "C2'" sing N N 214 U "C3'" "H3'" sing N N 215 U "O3'" "HO3'" sing N N 216 U "C2'" "O2'" sing N N 217 U "C2'" "C1'" sing N N 218 U "C2'" "H2'" sing N N 219 U "O2'" "HO2'" sing N N 220 U "C1'" N1 sing N N 221 U "C1'" "H1'" sing N N 222 U N1 C2 sing N N 223 U N1 C6 sing N N 224 U C2 O2 doub N N 225 U C2 N3 sing N N 226 U N3 C4 sing N N 227 U N3 H3 sing N N 228 U C4 O4 doub N N 229 U C4 C5 sing N N 230 U C5 C6 doub N N 231 U C5 H5 sing N N 232 U C6 H6 sing N N 233 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1NTB 'double helix' 1NTB 'a-form double helix' 1NTB 'internal loop' 1NTB 'triple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 2 1_555 B C 18 1_555 -0.134 -0.201 0.338 0.538 -6.520 -5.197 1 A_G2:C118_B A 2 ? B 118 ? 19 1 1 A A 3 1_555 B U 17 1_555 0.210 -0.266 -0.207 2.388 -16.245 1.092 2 A_A3:U117_B A 3 ? B 117 ? 20 1 1 A U 4 1_555 B A 16 1_555 0.276 -0.301 0.183 0.734 -16.940 3.482 3 A_U4:A116_B A 4 ? B 116 ? 20 1 1 A C 5 1_555 B G 15 1_555 -0.081 -0.283 0.149 -1.348 -7.133 -1.025 4 A_C5:G115_B A 5 ? B 115 ? 19 1 1 A C 7 1_555 B G 14 1_555 -0.275 -0.272 -0.084 -6.786 1.864 -3.722 5 A_C7:G114_B A 7 ? B 114 ? 19 1 1 A G 13 1_555 B C 13 1_555 -0.575 -0.345 -0.440 -7.623 -1.632 0.877 6 A_G13:C113_B A 13 ? B 113 ? 19 1 1 A A 14 1_555 B U 12 1_555 0.124 -0.218 -0.819 -18.198 -1.466 5.150 7 A_A14:U112_B A 14 ? B 112 ? 20 1 1 A C 15 1_555 B G 11 1_555 0.144 -0.203 -0.062 -9.190 8.462 -2.001 8 A_C15:G111_B A 15 ? B 111 ? 19 1 1 A C 18 1_555 B G 10 1_555 0.004 -0.244 0.560 -28.253 1.855 -4.275 9 A_C18:G110_B A 18 ? B 110 ? 19 1 1 B A 8 1_555 A U 17 1_555 -4.226 -1.625 -0.563 -2.804 -0.370 -62.150 10 B_A108:U17_A B 108 ? A 17 ? ? ? 1 A G 12 1_555 B C 9 1_555 0.201 5.874 -0.118 -26.126 20.254 -106.673 11 A_G12:C109_B A 12 ? B 109 ? ? 2 1 A U 19 1_555 B A 5 1_555 0.118 0.103 0.153 -4.060 -3.727 8.188 12 A_U19:A105_B A 19 ? B 105 ? 20 1 1 A G 20 1_555 B C 4 1_555 -0.937 -0.233 0.181 7.333 -16.209 4.914 13 A_G20:C104_B A 20 ? B 104 ? 19 1 1 A C 21 1_555 B G 3 1_555 -0.225 -0.089 0.290 11.775 -18.246 3.761 14 A_C21:G103_B A 21 ? B 103 ? 19 1 1 A C 22 1_555 B G 2 1_555 0.690 -0.134 0.956 -1.126 -19.455 6.976 15 A_C22:G102_B A 22 ? B 102 ? ? 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 2 1_555 B C 18 1_555 A A 3 1_555 B U 17 1_555 -0.122 -1.405 3.195 1.879 4.075 33.050 -3.092 0.509 2.994 7.122 -3.284 33.345 1 AA_G2A3:U117C118_BB A 2 ? B 118 ? A 3 ? B 117 ? 1 A A 3 1_555 B U 17 1_555 A U 4 1_555 B A 16 1_555 0.288 -1.324 3.323 -3.021 9.276 31.697 -3.817 -0.992 2.797 16.500 5.374 33.127 2 AA_A3U4:A116U117_BB A 3 ? B 117 ? A 4 ? B 116 ? 1 A U 4 1_555 B A 16 1_555 A C 5 1_555 B G 15 1_555 -0.313 -1.799 3.180 0.369 10.458 29.755 -5.033 0.638 2.420 19.617 -0.691 31.502 3 AA_U4C5:G115A116_BB A 4 ? B 116 ? A 5 ? B 115 ? 1 A C 5 1_555 B G 15 1_555 A C 7 1_555 B G 14 1_555 -0.845 -2.642 3.211 1.702 11.662 36.759 -5.242 1.461 2.260 17.935 -2.618 38.540 4 AA_C5C7:G114G115_BB A 5 ? B 115 ? A 7 ? B 114 ? 1 A C 7 1_555 B G 14 1_555 A G 13 1_555 B C 13 1_555 -2.436 -1.959 3.345 8.158 6.664 51.834 -2.605 3.231 2.707 7.535 -9.224 52.821 5 AA_C7G13:C113G114_BB A 7 ? B 114 ? A 13 ? B 113 ? 1 A G 13 1_555 B C 13 1_555 A A 14 1_555 B U 12 1_555 -0.222 -1.964 3.710 5.382 1.939 37.325 -3.315 1.118 3.542 3.009 -8.349 37.746 6 AA_G13A14:U112C113_BB A 13 ? B 113 ? A 14 ? B 112 ? 1 A A 14 1_555 B U 12 1_555 A C 15 1_555 B G 11 1_555 -0.046 -1.986 3.170 -1.507 3.572 31.661 -4.223 -0.173 2.933 6.516 2.750 31.891 7 AA_A14C15:G111U112_BB A 14 ? B 112 ? A 15 ? B 111 ? 1 A C 15 1_555 B G 11 1_555 A C 18 1_555 B G 10 1_555 -0.962 -2.926 3.745 4.862 -0.566 45.888 -3.679 1.700 3.664 -0.723 -6.215 46.134 8 AA_C15C18:G110G111_BB A 15 ? B 111 ? A 18 ? B 110 ? 1 A C 18 1_555 B G 10 1_555 B A 8 1_555 A U 17 1_555 0.126 -2.530 -2.725 -161.745 -45.168 -39.999 0.876 1.479 -1.462 23.650 -84.690 -168.664 9 AB_C18A108:U17G110_AB A 18 ? B 110 ? B 108 ? A 17 ? 1 A U 19 1_555 B A 5 1_555 A G 20 1_555 B C 4 1_555 -0.704 -1.690 2.926 -0.611 1.478 26.155 -4.081 1.408 2.844 3.263 1.348 26.203 10 AA_U19G20:C104A105_BB A 19 ? B 105 ? A 20 ? B 104 ? 1 A G 20 1_555 B C 4 1_555 A C 21 1_555 B G 3 1_555 0.073 -1.257 2.950 -2.414 5.172 37.604 -2.506 -0.381 2.749 7.967 3.719 38.019 11 AA_G20C21:G103C104_BB A 20 ? B 104 ? A 21 ? B 103 ? 1 A C 21 1_555 B G 3 1_555 A C 22 1_555 B G 2 1_555 0.479 -1.190 3.381 -1.771 7.765 38.281 -2.711 -0.929 3.066 11.687 2.666 39.070 12 AA_C21C22:G102G103_BB A 21 ? B 103 ? A 22 ? B 102 ? # _pdbx_initial_refinement_model.accession_code 1NTA _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details 'Barium form of streptomycin RNA-aptamer' # _atom_sites.entry_id 1NTB _atom_sites.fract_transf_matrix[1][1] 0.012102 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.012102 _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] 0.020345 _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 MG N NA O P # loop_