data_1DK1 # _entry.id 1DK1 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.351 _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 1DK1 pdb_00001dk1 10.2210/pdb1dk1/pdb NDB RR0005 ? ? RCSB RCSB010146 ? ? WWPDB D_1000010146 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DK1 _pdbx_database_status.recvd_initial_deposition_date 1999-12-06 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nikulin, A.' 1 'Serganov, A.' 2 'Ennifar, E.' 3 'Tischenko, S.' 4 'Nevskaya, N.' 5 # _citation.id primary _citation.title 'Crystal structure of the S15-rRNA complex.' _citation.journal_abbrev Nat.Struct.Biol. _citation.journal_volume 7 _citation.page_first 273 _citation.page_last 277 _citation.year 2000 _citation.journal_id_ASTM NSBIEW _citation.country US _citation.journal_id_ISSN 1072-8368 _citation.journal_id_CSD 2024 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10742169 _citation.pdbx_database_id_DOI 10.1038/74028 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nikulin, A.' 1 ? primary 'Serganov, A.' 2 ? primary 'Ennifar, E.' 3 ? primary 'Tishchenko, S.' 4 ? primary 'Nevskaya, N.' 5 ? primary 'Shepard, W.' 6 ? primary 'Portier, C.' 7 ? primary 'Garber, M.' 8 ? primary 'Ehresmann, B.' 9 ? primary 'Ehresmann, C.' 10 ? primary 'Nikonov, S.' 11 ? primary 'Dumas, P.' 12 ? # _cell.entry_id 1DK1 _cell.length_a 128.800 _cell.length_b 128.800 _cell.length_c 65.100 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 1DK1 _symmetry.space_group_name_H-M 'P 64 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? # 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 man 'RRNA FRAGMENT' 18464.963 1 ? ? ? ? 2 polymer man '30S RIBOSOMAL PROTEIN S15' 10498.702 1 ? 'ILE11MSE, ALA79MSE' 'RESIDUES 2-87' ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 9 ? ? ? ? 4 non-polymer syn 'SODIUM ION' 22.990 2 ? ? ? ? 5 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 6 water nat water 18.015 25 ? ? ? ? # 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 GGGCGGCCUUCGGGCUAGACGGUGGGAGAGGCUUCGGCUGGUCCACCCGUGACGCUC GGGCGGCCUUCGGGCUAGACGGUGGGAGAGGCUUCGGCUGGUCCACCCGUGACGCUC B ? 2 'polypeptide(L)' no yes ;PITKEEKQKV(MSE)QEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLL(MSE)(MSE)VGQRRRLLRY LQREDPERYR(MSE)LIEKLGI ; ;PITKEEKQKVMQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRML IEKLGI ; A ? # 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 G n 1 4 C n 1 5 G n 1 6 G n 1 7 C n 1 8 C n 1 9 U n 1 10 U n 1 11 C n 1 12 G n 1 13 G n 1 14 G n 1 15 C n 1 16 U n 1 17 A n 1 18 G n 1 19 A n 1 20 C n 1 21 G n 1 22 G n 1 23 U n 1 24 G n 1 25 G n 1 26 G n 1 27 A n 1 28 G n 1 29 A n 1 30 G n 1 31 G n 1 32 C n 1 33 U n 1 34 U n 1 35 C n 1 36 G n 1 37 G n 1 38 C n 1 39 U n 1 40 G n 1 41 G n 1 42 U n 1 43 C n 1 44 C n 1 45 A n 1 46 C n 1 47 C n 1 48 C n 1 49 G n 1 50 U n 1 51 G n 1 52 A n 1 53 C n 1 54 G n 1 55 C n 1 56 U n 1 57 C n 2 1 PRO n 2 2 ILE n 2 3 THR n 2 4 LYS n 2 5 GLU n 2 6 GLU n 2 7 LYS n 2 8 GLN n 2 9 LYS n 2 10 VAL n 2 11 MSE n 2 12 GLN n 2 13 GLU n 2 14 PHE n 2 15 ALA n 2 16 ARG n 2 17 PHE n 2 18 PRO n 2 19 GLY n 2 20 ASP n 2 21 THR n 2 22 GLY n 2 23 SER n 2 24 THR n 2 25 GLU n 2 26 VAL n 2 27 GLN n 2 28 VAL n 2 29 ALA n 2 30 LEU n 2 31 LEU n 2 32 THR n 2 33 LEU n 2 34 ARG n 2 35 ILE n 2 36 ASN n 2 37 ARG n 2 38 LEU n 2 39 SER n 2 40 GLU n 2 41 HIS n 2 42 LEU n 2 43 LYS n 2 44 VAL n 2 45 HIS n 2 46 LYS n 2 47 LYS n 2 48 ASP n 2 49 HIS n 2 50 HIS n 2 51 SER n 2 52 HIS n 2 53 ARG n 2 54 GLY n 2 55 LEU n 2 56 LEU n 2 57 MSE n 2 58 MSE n 2 59 VAL n 2 60 GLY n 2 61 GLN n 2 62 ARG n 2 63 ARG n 2 64 ARG n 2 65 LEU n 2 66 LEU n 2 67 ARG n 2 68 TYR n 2 69 LEU n 2 70 GLN n 2 71 ARG n 2 72 GLU n 2 73 ASP n 2 74 PRO n 2 75 GLU n 2 76 ARG n 2 77 TYR n 2 78 ARG n 2 79 MSE n 2 80 LEU n 2 81 ILE n 2 82 GLU n 2 83 LYS n 2 84 LEU n 2 85 GLY n 2 86 ILE n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample ? ? ? ? Thermus ? ? ? ? ? ? ? 'Thermus thermophilus' 274 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 Escherichia ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample ? ? ? ? Thermus ? ? ? ? ? ? ? 'Thermus thermophilus' 274 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 Escherichia ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 UNP RS15_THETH 2 P80378 ? ? ? 2 PDB 1DK1 1 1DK1 ? ? ? # 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 1DK1 A 1 ? 86 ? P80378 1 ? 86 ? 101 186 2 2 1DK1 B 1 ? 57 ? 1DK1 1 ? 57 ? 1 57 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 1DK1 MSE A 11 ? UNP P80378 ILE 11 'engineered mutation' 111 1 1 1DK1 MSE A 79 ? UNP P80378 ALA 79 'engineered mutation' 179 2 1 1DK1 MSE A 57 ? UNP P80378 MET 57 'engineered mutation' 157 3 1 1DK1 MSE A 58 ? UNP P80378 MET 58 'engineered mutation' 158 4 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 1DK1 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.69 _exptl_crystal.density_percent_sol 54.29 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 295.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.2 _exptl_crystal_grow.pdbx_details '100MM SODIUM CACODYLATE, 30 MM KCL, 1M (NH4)2SO4, 1.5 MM MGCL2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 22K' _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 'SODIUM CACODYLATE' ? ? ? 1 2 1 KCL ? ? ? 1 3 1 '(NH4)2SO4' ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 2 KCL ? ? ? 1 6 2 '(NH4)2SO4' ? ? ? 1 7 2 MGCL2 ? ? ? # _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 1999-10-18 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.94654 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE BW7A' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline BW7A _diffrn_source.pdbx_wavelength 0.94654 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1DK1 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 2.80 _reflns.number_obs 8164 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.0380000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.1 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.80 _reflns_shell.d_res_low 2.90 _reflns_shell.percent_possible_all 99.5 _reflns_shell.Rmerge_I_obs 0.2090000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 8.3 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1DK1 _refine.ls_number_reflns_obs 7679 _refine.ls_number_reflns_all 8164 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.00 _refine.ls_d_res_high 2.80 _refine.ls_percent_reflns_obs 98.1 _refine.ls_R_factor_obs 0.2130000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2130000 _refine.ls_R_factor_R_free 0.2910000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 8.3 _refine.ls_number_reflns_R_free 640 _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_overall_phase_error ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 722 _refine_hist.pdbx_number_atoms_nucleic_acid 1221 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 25 _refine_hist.number_atoms_total 1980 _refine_hist.d_res_high 2.80 _refine_hist.d_res_low 8.00 # 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 c_bond_d 0.007 ? ? ? '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 1.4 ? ? ? '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' ? # _struct.entry_id 1DK1 _struct.title 'DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DK1 _struct_keywords.pdbx_keywords RIBOSOME _struct_keywords.text 'RIBOSOME, S15, PROTEIN, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 3 ? K N N 3 ? L N N 4 ? M N N 4 ? N N N 5 ? O N N 6 ? P N N 6 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 THR B 3 ? ALA B 15 ? THR A 103 ALA A 115 1 ? 13 HELX_P HELX_P2 2 THR B 24 ? HIS B 45 ? THR A 124 HIS A 145 1 ? 22 HELX_P HELX_P3 3 HIS B 49 ? ASP B 73 ? HIS A 149 ASP A 173 1 ? 25 HELX_P HELX_P4 4 ASP B 73 ? ILE B 81 ? ASP A 173 ILE A 181 1 ? 9 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 ? B VAL 10 C ? ? ? 1_555 B MSE 11 N ? ? A VAL 110 A MSE 111 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale2 covale both ? B MSE 11 C ? ? ? 1_555 B GLN 12 N ? ? A MSE 111 A GLN 112 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale3 covale both ? B LEU 56 C ? ? ? 1_555 B MSE 57 N ? ? A LEU 156 A MSE 157 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale4 covale both ? B MSE 57 C ? ? ? 1_555 B MSE 58 N ? ? A MSE 157 A MSE 158 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale5 covale both ? B MSE 58 C ? ? ? 1_555 B VAL 59 N ? ? A MSE 158 A VAL 159 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale6 covale both ? B ARG 78 C ? ? ? 1_555 B MSE 79 N ? ? A ARG 178 A MSE 179 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale7 covale both ? B MSE 79 C ? ? ? 1_555 B LEU 80 N ? ? A MSE 179 A LEU 180 1_555 ? ? ? ? ? ? ? 1.329 ? ? metalc1 metalc ? ? A C 4 O2 ? ? ? 1_555 M NA . NA ? ? B C 4 B NA 211 1_555 ? ? ? ? ? ? ? 2.813 ? ? metalc2 metalc ? ? L NA . NA ? ? ? 1_555 O HOH . O ? ? B NA 210 B HOH 319 1_555 ? ? ? ? ? ? ? 2.700 ? ? metalc3 metalc ? ? B HIS 50 NE2 ? ? ? 1_555 N K . K ? ? A HIS 150 A K 213 1_555 ? ? ? ? ? ? ? 2.999 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 57 N3 ? ? B G 1 B C 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 57 O2 ? ? B G 1 B C 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 57 N4 ? ? B G 1 B C 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 56 O2 ? ? B G 2 B U 56 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 56 N3 ? ? B G 2 B U 56 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 55 N3 ? ? B G 3 B C 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 55 O2 ? ? B G 3 B C 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 55 N4 ? ? B G 3 B C 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 54 N1 ? ? B C 4 B G 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 54 O6 ? ? B C 4 B G 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 54 N2 ? ? B C 4 B G 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 15 N3 ? ? B G 6 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 15 O2 ? ? B G 6 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 15 N4 ? ? B G 6 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 14 N1 ? ? B C 7 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 14 O6 ? ? B C 7 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 14 N2 ? ? B C 7 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 13 N1 ? ? B C 8 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 13 O6 ? ? B C 8 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 13 N2 ? ? B C 8 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 9 O2 ? ? ? 1_555 A G 12 N1 ? ? B U 9 B G 12 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog22 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 52 N7 ? ? B U 16 B A 52 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog23 hydrog ? ? A U 16 O2 ? ? ? 1_555 A A 52 N6 ? ? B U 16 B A 52 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog24 hydrog ? ? A G 18 O6 ? ? ? 1_555 A G 51 N2 ? ? B G 18 B G 51 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog25 hydrog ? ? A G 18 N1 ? ? ? 1_555 A C 53 N3 ? ? B G 18 B C 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 18 N2 ? ? ? 1_555 A C 53 O2 ? ? B G 18 B C 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 18 O6 ? ? ? 1_555 A C 53 N4 ? ? B G 18 B C 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 19 N1 ? ? ? 1_555 A U 50 N3 ? ? B A 19 B U 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 19 N6 ? ? ? 1_555 A U 50 O4 ? ? B A 19 B U 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 20 N3 ? ? ? 1_555 A G 49 N1 ? ? B C 20 B G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 20 N4 ? ? ? 1_555 A G 49 O6 ? ? B C 20 B G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 20 O2 ? ? ? 1_555 A G 49 N2 ? ? B C 20 B G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 21 N1 ? ? ? 1_555 A C 48 N3 ? ? B G 21 B C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 21 N2 ? ? ? 1_555 A C 48 O2 ? ? B G 21 B C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 21 O6 ? ? ? 1_555 A C 48 N4 ? ? B G 21 B C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 22 N1 ? ? ? 1_555 A C 46 N3 ? ? B G 22 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 22 N2 ? ? ? 1_555 A C 46 O2 ? ? B G 22 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 22 O6 ? ? ? 1_555 A C 46 N4 ? ? B G 22 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 23 N3 ? ? ? 1_555 A A 45 N1 ? ? B U 23 B A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A U 23 O4 ? ? ? 1_555 A A 45 N6 ? ? B U 23 B A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 24 N1 ? ? ? 1_555 A C 44 N3 ? ? B G 24 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 24 N2 ? ? ? 1_555 A C 44 O2 ? ? B G 24 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 24 O6 ? ? ? 1_555 A C 44 N4 ? ? B G 24 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 25 N1 ? ? ? 1_555 A C 43 N3 ? ? B G 25 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 25 N2 ? ? ? 1_555 A C 43 O2 ? ? B G 25 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 25 O6 ? ? ? 1_555 A C 43 N4 ? ? B G 25 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 26 N1 ? ? ? 1_555 A U 42 O2 ? ? B G 26 B U 42 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog48 hydrog ? ? A G 26 O6 ? ? ? 1_555 A U 42 N3 ? ? B G 26 B U 42 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog49 hydrog ? ? A A 27 N1 A ? ? 1_555 A G 41 N1 ? ? B A 27 B G 41 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog50 hydrog ? ? A A 27 N6 A ? ? 1_555 A G 41 O6 ? ? B A 27 B G 41 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog51 hydrog ? ? A G 28 N2 A ? ? 1_555 A G 40 O6 ? ? B G 28 B G 40 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog52 hydrog ? ? A G 30 N1 ? ? ? 1_555 A U 39 O2 ? ? B G 30 B U 39 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog53 hydrog ? ? A G 30 O6 ? ? ? 1_555 A U 39 N3 ? ? B G 30 B U 39 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog54 hydrog ? ? A G 31 N1 ? ? ? 1_555 A C 38 N3 ? ? B G 31 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A G 31 N2 ? ? ? 1_555 A C 38 O2 ? ? B G 31 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A G 31 O6 ? ? ? 1_555 A C 38 N4 ? ? B G 31 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A C 32 N3 ? ? ? 1_555 A G 37 N1 ? ? B C 32 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A C 32 N4 ? ? ? 1_555 A G 37 O6 ? ? B C 32 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A C 32 O2 ? ? ? 1_555 A G 37 N2 ? ? B C 32 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A U 33 N3 ? ? ? 1_555 A G 36 O6 ? ? B U 33 B G 36 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog61 hydrog ? ? A U 33 O2 ? ? ? 1_555 A G 36 N1 ? ? B U 33 B G 36 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog62 hydrog ? ? A G 51 N3 ? ? ? 1_555 A C 53 N4 ? ? B G 51 B C 53 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # 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 201 ? 1 'BINDING SITE FOR RESIDUE MG B 201' AC2 Software B MG 202 ? 2 'BINDING SITE FOR RESIDUE MG B 202' AC3 Software B MG 205 ? 1 'BINDING SITE FOR RESIDUE MG B 205' AC4 Software B MG 208 ? 1 'BINDING SITE FOR RESIDUE MG B 208' AC5 Software B MG 209 ? 1 'BINDING SITE FOR RESIDUE MG B 209' AC6 Software B NA 210 ? 1 'BINDING SITE FOR RESIDUE NA B 210' AC7 Software B NA 211 ? 3 'BINDING SITE FOR RESIDUE NA B 211' AC8 Software A K 213 ? 1 'BINDING SITE FOR RESIDUE K A 213' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 1 G A 26 ? G B 26 . ? 1_555 ? 2 AC2 2 C A 48 ? C B 48 . ? 1_555 ? 3 AC2 2 G A 49 ? G B 49 . ? 1_555 ? 4 AC3 1 U A 39 ? U B 39 . ? 1_555 ? 5 AC4 1 U A 42 ? U B 42 . ? 1_555 ? 6 AC5 1 A A 52 ? A B 52 . ? 1_555 ? 7 AC6 1 HOH O . ? HOH B 319 . ? 1_555 ? 8 AC7 3 C A 4 ? C B 4 . ? 1_555 ? 9 AC7 3 G A 54 ? G B 54 . ? 1_555 ? 10 AC7 3 C A 55 ? C B 55 . ? 1_555 ? 11 AC8 1 HIS B 50 ? HIS A 150 . ? 1_555 ? # _database_PDB_matrix.entry_id 1DK1 _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 # _atom_sites.entry_id 1DK1 _atom_sites.fract_transf_matrix[1][1] 0.007764 _atom_sites.fract_transf_matrix[1][2] 0.004483 _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] 0.008965 _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] 0.015361 _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 K MG N NA O P SE # loop_ _database_PDB_caveat.text ;C3' of G5 has incorrect chirality ; # 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 B . n A 1 2 G 2 2 2 G G B . n A 1 3 G 3 3 3 G G B . n A 1 4 C 4 4 4 C C B . n A 1 5 G 5 5 5 G G B . n A 1 6 G 6 6 6 G G B . n A 1 7 C 7 7 7 C C B . n A 1 8 C 8 8 8 C C B . n A 1 9 U 9 9 9 U U B . n A 1 10 U 10 10 10 U U B . n A 1 11 C 11 11 11 C C B . n A 1 12 G 12 12 12 G G B . n A 1 13 G 13 13 13 G G B . n A 1 14 G 14 14 14 G G B . n A 1 15 C 15 15 15 C C B . n A 1 16 U 16 16 16 U U B . n A 1 17 A 17 17 17 A A B . n A 1 18 G 18 18 18 G G B . n A 1 19 A 19 19 19 A A B . n A 1 20 C 20 20 20 C C B . n A 1 21 G 21 21 21 G G B . n A 1 22 G 22 22 22 G G B . n A 1 23 U 23 23 23 U U B . n A 1 24 G 24 24 24 G G B . n A 1 25 G 25 25 25 G G B . n A 1 26 G 26 26 26 G G B . n A 1 27 A 27 27 27 A A B . n A 1 28 G 28 28 28 G G B . n A 1 29 A 29 29 29 A A B . n A 1 30 G 30 30 30 G G B . n A 1 31 G 31 31 31 G G B . n A 1 32 C 32 32 32 C C B . n A 1 33 U 33 33 33 U U B . n A 1 34 U 34 34 34 U U B . n A 1 35 C 35 35 35 C C B . n A 1 36 G 36 36 36 G G B . n A 1 37 G 37 37 37 G G B . n A 1 38 C 38 38 38 C C B . n A 1 39 U 39 39 39 U U B . n A 1 40 G 40 40 40 G G B . n A 1 41 G 41 41 41 G G B . n A 1 42 U 42 42 42 U U B . n A 1 43 C 43 43 43 C C B . n A 1 44 C 44 44 44 C C B . n A 1 45 A 45 45 45 A A B . n A 1 46 C 46 46 46 C C B . n A 1 47 C 47 47 47 C C B . n A 1 48 C 48 48 48 C C B . n A 1 49 G 49 49 49 G G B . n A 1 50 U 50 50 50 U U B . n A 1 51 G 51 51 51 G G B . n A 1 52 A 52 52 52 A A B . n A 1 53 C 53 53 53 C C B . n A 1 54 G 54 54 54 G G B . n A 1 55 C 55 55 55 C C B . n A 1 56 U 56 56 56 U U B . n A 1 57 C 57 57 57 C C B . n B 2 1 PRO 1 101 101 PRO PRO A . n B 2 2 ILE 2 102 102 ILE ILE A . n B 2 3 THR 3 103 103 THR THR A . n B 2 4 LYS 4 104 104 LYS LYS A . n B 2 5 GLU 5 105 105 GLU GLU A . n B 2 6 GLU 6 106 106 GLU GLU A . n B 2 7 LYS 7 107 107 LYS LYS A . n B 2 8 GLN 8 108 108 GLN GLN A . n B 2 9 LYS 9 109 109 LYS LYS A . n B 2 10 VAL 10 110 110 VAL VAL A . n B 2 11 MSE 11 111 111 MSE MSE A . n B 2 12 GLN 12 112 112 GLN GLN A . n B 2 13 GLU 13 113 113 GLU GLU A . n B 2 14 PHE 14 114 114 PHE PHE A . n B 2 15 ALA 15 115 115 ALA ALA A . n B 2 16 ARG 16 116 116 ARG ARG A . n B 2 17 PHE 17 117 117 PHE PHE A . n B 2 18 PRO 18 118 118 PRO PRO A . n B 2 19 GLY 19 119 119 GLY GLY A . n B 2 20 ASP 20 120 120 ASP ASP A . n B 2 21 THR 21 121 121 THR THR A . n B 2 22 GLY 22 122 122 GLY GLY A . n B 2 23 SER 23 123 123 SER SER A . n B 2 24 THR 24 124 124 THR THR A . n B 2 25 GLU 25 125 125 GLU GLU A . n B 2 26 VAL 26 126 126 VAL VAL A . n B 2 27 GLN 27 127 127 GLN GLN A . n B 2 28 VAL 28 128 128 VAL VAL A . n B 2 29 ALA 29 129 129 ALA ALA A . n B 2 30 LEU 30 130 130 LEU LEU A . n B 2 31 LEU 31 131 131 LEU LEU A . n B 2 32 THR 32 132 132 THR THR A . n B 2 33 LEU 33 133 133 LEU LEU A . n B 2 34 ARG 34 134 134 ARG ARG A . n B 2 35 ILE 35 135 135 ILE ILE A . n B 2 36 ASN 36 136 136 ASN ASN A . n B 2 37 ARG 37 137 137 ARG ARG A . n B 2 38 LEU 38 138 138 LEU LEU A . n B 2 39 SER 39 139 139 SER SER A . n B 2 40 GLU 40 140 140 GLU GLU A . n B 2 41 HIS 41 141 141 HIS HIS A . n B 2 42 LEU 42 142 142 LEU LEU A . n B 2 43 LYS 43 143 143 LYS LYS A . n B 2 44 VAL 44 144 144 VAL VAL A . n B 2 45 HIS 45 145 145 HIS HIS A . n B 2 46 LYS 46 146 146 LYS LYS A . n B 2 47 LYS 47 147 147 LYS LYS A . n B 2 48 ASP 48 148 148 ASP ASP A . n B 2 49 HIS 49 149 149 HIS HIS A . n B 2 50 HIS 50 150 150 HIS HIS A . n B 2 51 SER 51 151 151 SER SER A . n B 2 52 HIS 52 152 152 HIS HIS A . n B 2 53 ARG 53 153 153 ARG ARG A . n B 2 54 GLY 54 154 154 GLY GLY A . n B 2 55 LEU 55 155 155 LEU LEU A . n B 2 56 LEU 56 156 156 LEU LEU A . n B 2 57 MSE 57 157 157 MSE MSE A . n B 2 58 MSE 58 158 158 MSE MSE A . n B 2 59 VAL 59 159 159 VAL VAL A . n B 2 60 GLY 60 160 160 GLY GLY A . n B 2 61 GLN 61 161 161 GLN GLN A . n B 2 62 ARG 62 162 162 ARG ARG A . n B 2 63 ARG 63 163 163 ARG ARG A . n B 2 64 ARG 64 164 164 ARG ARG A . n B 2 65 LEU 65 165 165 LEU LEU A . n B 2 66 LEU 66 166 166 LEU LEU A . n B 2 67 ARG 67 167 167 ARG ARG A . n B 2 68 TYR 68 168 168 TYR TYR A . n B 2 69 LEU 69 169 169 LEU LEU A . n B 2 70 GLN 70 170 170 GLN GLN A . n B 2 71 ARG 71 171 171 ARG ARG A . n B 2 72 GLU 72 172 172 GLU GLU A . n B 2 73 ASP 73 173 173 ASP ASP A . n B 2 74 PRO 74 174 174 PRO PRO A . n B 2 75 GLU 75 175 175 GLU GLU A . n B 2 76 ARG 76 176 176 ARG ARG A . n B 2 77 TYR 77 177 177 TYR TYR A . n B 2 78 ARG 78 178 178 ARG ARG A . n B 2 79 MSE 79 179 179 MSE MSE A . n B 2 80 LEU 80 180 180 LEU LEU A . n B 2 81 ILE 81 181 181 ILE ILE A . n B 2 82 GLU 82 182 182 GLU GLU A . n B 2 83 LYS 83 183 183 LYS LYS A . n B 2 84 LEU 84 184 184 LEU LEU A . n B 2 85 GLY 85 185 185 GLY GLY A . n B 2 86 ILE 86 186 186 ILE ILE 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 C 3 MG 1 200 200 MG MG B . D 3 MG 1 201 201 MG MG B . E 3 MG 1 202 202 MG MG B . F 3 MG 1 203 203 MG MG B . G 3 MG 1 204 204 MG MG B . H 3 MG 1 205 205 MG MG B . I 3 MG 1 206 206 MG MG B . J 3 MG 1 208 208 MG MG B . K 3 MG 1 209 209 MG MG B . L 4 NA 1 210 210 NA NA B . M 4 NA 1 211 211 NA NA B . N 5 K 1 213 213 K K A . O 6 HOH 1 301 301 HOH WAT B . O 6 HOH 2 305 305 HOH WAT B . O 6 HOH 3 307 307 HOH WAT B . O 6 HOH 4 308 308 HOH WAT B . O 6 HOH 5 309 309 HOH WAT B . O 6 HOH 6 310 310 HOH WAT B . O 6 HOH 7 311 311 HOH WAT B . O 6 HOH 8 313 313 HOH WAT B . O 6 HOH 9 314 314 HOH WAT B . O 6 HOH 10 315 315 HOH WAT B . O 6 HOH 11 316 316 HOH WAT B . O 6 HOH 12 317 317 HOH WAT B . O 6 HOH 13 318 318 HOH WAT B . O 6 HOH 14 319 319 HOH WAT B . O 6 HOH 15 322 322 HOH WAT B . O 6 HOH 16 323 323 HOH WAT B . O 6 HOH 17 324 324 HOH WAT B . P 6 HOH 1 300 300 HOH WAT A . P 6 HOH 2 302 302 HOH WAT A . P 6 HOH 3 303 303 HOH WAT A . P 6 HOH 4 304 304 HOH WAT A . P 6 HOH 5 306 306 HOH WAT A . P 6 HOH 6 312 312 HOH WAT A . P 6 HOH 7 320 320 HOH WAT A . P 6 HOH 8 321 321 HOH WAT A . # 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 B MSE 11 A MSE 111 ? MET SELENOMETHIONINE 2 B MSE 57 A MSE 157 ? MET SELENOMETHIONINE 3 B MSE 58 A MSE 158 ? MET SELENOMETHIONINE 4 B MSE 79 A MSE 179 ? MET SELENOMETHIONINE # _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,I,J,K,L,M,N,O,P # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 301 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id O _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 2000-04-02 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-12-28 5 'Structure model' 1 4 2018-01-31 6 'Structure model' 1 5 2021-11-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' Advisory 4 5 'Structure model' 'Experimental preparation' 5 6 'Structure model' 'Data collection' 6 6 'Structure model' 'Database references' 7 6 '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 5 'Structure model' exptl_crystal_grow 2 6 'Structure model' database_2 3 6 'Structure model' diffrn_source 4 6 'Structure model' struct_conn 5 6 'Structure model' struct_ref_seq_dif 6 6 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_exptl_crystal_grow.temp' 2 6 'Structure model' '_database_2.pdbx_DOI' 3 6 'Structure model' '_database_2.pdbx_database_accession' 4 6 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 5 6 'Structure model' '_struct_conn.pdbx_dist_value' 6 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 6 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 6 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 6 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 6 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 6 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 6 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 6 'Structure model' '_struct_conn.ptnr1_label_seq_id' 14 6 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 15 6 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 16 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 6 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 6 'Structure model' '_struct_conn.ptnr2_label_atom_id' 19 6 'Structure model' '_struct_conn.ptnr2_label_comp_id' 20 6 'Structure model' '_struct_conn.ptnr2_label_seq_id' 21 6 'Structure model' '_struct_ref_seq_dif.details' 22 6 'Structure model' '_struct_site.pdbx_auth_asym_id' 23 6 'Structure model' '_struct_site.pdbx_auth_comp_id' 24 6 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHARP phasing . ? 1 CNS refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # 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 "C4'" B G 5 ? ? "C3'" B G 5 ? ? "O3'" B G 5 ? ? 125.86 113.00 12.86 2.00 N 2 1 "C2'" B G 5 ? ? "C3'" B G 5 ? ? "O3'" B G 5 ? ? 126.77 113.70 13.07 1.60 N 3 1 N1 B U 16 ? ? "C1'" B U 16 ? ? "C2'" B U 16 ? ? 122.24 114.00 8.24 1.30 N 4 1 "C2'" B A 52 ? ? "C3'" B A 52 ? ? "O3'" B A 52 ? ? 130.03 113.70 16.33 1.60 N 5 1 C A PHE 117 ? ? N A PRO 118 ? ? CA A PRO 118 ? ? 129.61 119.30 10.31 1.50 Y # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ILE A 102 ? ? 76.52 -71.77 2 1 THR A 103 ? ? 76.53 166.49 3 1 GLU A 105 ? ? -65.31 22.85 4 1 GLU A 106 ? ? -149.71 -68.68 5 1 PRO A 118 ? ? -46.34 60.19 6 1 THR A 121 ? ? -141.06 -2.05 7 1 SER A 123 ? ? -79.37 30.00 8 1 THR A 124 ? ? 75.66 -60.15 9 1 ALA A 129 ? ? -49.74 -71.55 10 1 ARG A 137 ? ? -41.89 -17.07 11 1 LEU A 142 ? ? -37.05 -32.69 12 1 HIS A 145 ? ? -119.67 77.62 13 1 HIS A 149 ? ? 60.35 -71.29 14 1 ASP A 173 ? ? -151.95 71.88 15 1 ILE A 181 ? ? -58.57 0.27 16 1 LEU A 184 ? ? -155.36 -47.77 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 U B 9 ? ? 0.066 'SIDE CHAIN' 2 1 U B 16 ? ? 0.063 'SIDE CHAIN' 3 1 G B 24 ? ? 0.050 'SIDE CHAIN' 4 1 G B 49 ? ? 0.058 'SIDE CHAIN' # 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 G 5 ? PLANAR . 2 1 "C3'" ? B A 52 ? PLANAR . # loop_ _pdbx_validate_polymer_linkage.id _pdbx_validate_polymer_linkage.PDB_model_num _pdbx_validate_polymer_linkage.auth_atom_id_1 _pdbx_validate_polymer_linkage.auth_asym_id_1 _pdbx_validate_polymer_linkage.auth_comp_id_1 _pdbx_validate_polymer_linkage.auth_seq_id_1 _pdbx_validate_polymer_linkage.PDB_ins_code_1 _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.auth_atom_id_2 _pdbx_validate_polymer_linkage.auth_asym_id_2 _pdbx_validate_polymer_linkage.auth_comp_id_2 _pdbx_validate_polymer_linkage.auth_seq_id_2 _pdbx_validate_polymer_linkage.PDB_ins_code_2 _pdbx_validate_polymer_linkage.label_alt_id_2 _pdbx_validate_polymer_linkage.dist 1 1 "O3'" B G 26 ? ? P B A 27 ? B 2.96 2 1 "O3'" B A 29 ? A P B G 30 ? ? 2.19 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1DK1 'double helix' 1DK1 'a-form double helix' 1DK1 tetraloop 1DK1 'bulge loop' 1DK1 'mismatched base pair' 1DK1 'three-way junction' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 57 1_555 0.566 -0.042 -0.442 -0.975 1.425 -6.385 1 B_G1:C57_B B 1 ? B 57 ? 19 1 1 A G 2 1_555 A U 56 1_555 -1.993 -0.800 0.261 0.767 -14.823 -1.596 2 B_G2:U56_B B 2 ? B 56 ? 28 1 1 A G 3 1_555 A C 55 1_555 -0.034 -0.229 0.152 0.212 -4.418 -4.792 3 B_G3:C55_B B 3 ? B 55 ? 19 1 1 A C 4 1_555 A G 54 1_555 -0.053 -0.171 0.296 -3.156 -1.766 -2.531 4 B_C4:G54_B B 4 ? B 54 ? 19 1 1 A G 12 1_555 A U 9 1_555 -0.743 5.265 0.527 14.490 1.865 104.125 5 B_G12:U9_B B 12 ? B 9 ? ? 2 1 A G 13 1_555 A C 8 1_555 0.311 -0.088 -0.387 -8.560 -8.083 6.423 6 B_G13:C8_B B 13 ? B 8 ? 19 1 1 A G 14 1_555 A C 7 1_555 0.227 -0.220 -0.175 -15.974 -9.248 4.132 7 B_G14:C7_B B 14 ? B 7 ? 19 1 1 A C 15 1_555 A G 6 1_555 -0.200 -0.435 0.014 -14.558 -10.926 -2.506 8 B_C15:G6_B B 15 ? B 6 ? 19 1 1 A A 52 1_555 A U 16 1_555 -4.005 -1.675 -0.077 -2.429 4.796 -105.689 9 B_A52:U16_B B 52 ? B 16 ? 24 4 1 A G 18 1_555 A C 53 1_555 0.104 -0.238 -0.182 9.562 1.001 -5.249 10 B_G18:C53_B B 18 ? B 53 ? 19 1 1 A A 19 1_555 A U 50 1_555 0.279 -0.235 0.472 7.904 -4.569 -5.655 11 B_A19:U50_B B 19 ? B 50 ? 20 1 1 A C 20 1_555 A G 49 1_555 0.454 -0.334 0.394 5.210 -1.696 0.906 12 B_C20:G49_B B 20 ? B 49 ? 19 1 1 A G 21 1_555 A C 48 1_555 -0.339 -0.169 -0.036 -0.843 -9.710 0.335 13 B_G21:C48_B B 21 ? B 48 ? 19 1 1 A G 22 1_555 A C 46 1_555 -0.871 -0.457 -0.104 -4.837 -8.920 -7.183 14 B_G22:C46_B B 22 ? B 46 ? 19 1 1 A U 23 1_555 A A 45 1_555 -0.969 -0.569 -0.006 -4.838 -7.923 1.827 15 B_U23:A45_B B 23 ? B 45 ? 20 1 1 A G 24 1_555 A C 44 1_555 -0.613 -0.602 -0.086 -1.011 -6.725 0.125 16 B_G24:C44_B B 24 ? B 44 ? 19 1 1 A G 25 1_555 A C 43 1_555 -0.721 -0.246 0.145 -1.226 -13.974 -0.288 17 B_G25:C43_B B 25 ? B 43 ? 19 1 1 A G 26 1_555 A U 42 1_555 -2.066 -0.467 0.068 -11.046 -15.307 -2.344 18 B_G26:U42_B B 26 ? B 42 ? 28 1 1 A A 27 1_555 A G 41 1_555 -0.909 1.546 -0.212 -11.675 -9.443 -19.335 19 B_A27:G41_B B 27 ? B 41 ? 8 1 1 A G 28 1_555 A G 40 1_555 5.207 1.877 0.376 -11.137 11.584 7.878 20 B_G28:G40_B B 28 ? B 40 ? ? ? 1 A G 30 1_555 A U 39 1_555 -3.244 -0.839 -0.614 -8.728 -10.348 0.469 21 B_G30:U39_B B 30 ? B 39 ? 28 ? 1 A G 31 1_555 A C 38 1_555 0.563 -0.488 -0.150 -3.766 -4.694 -6.634 22 B_G31:C38_B B 31 ? B 38 ? 19 1 1 A C 32 1_555 A G 37 1_555 0.720 -0.573 -0.194 11.626 2.030 1.491 23 B_C32:G37_B B 32 ? B 37 ? 19 1 1 A U 33 1_555 A G 36 1_555 4.502 -1.872 -1.506 15.688 -8.064 17.609 24 B_U33:G36_B B 33 ? B 36 ? 28 5 # 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 57 1_555 A G 2 1_555 A U 56 1_555 0.983 -2.000 3.308 -9.333 7.362 20.562 -6.938 -5.019 1.876 18.738 23.756 23.719 1 BB_G1G2:U56C57_BB B 1 ? B 57 ? B 2 ? B 56 ? 1 A G 2 1_555 A U 56 1_555 A G 3 1_555 A C 55 1_555 -0.421 -1.749 3.133 -2.802 5.372 41.847 -2.937 0.317 2.917 7.474 3.898 42.264 2 BB_G2G3:C55U56_BB B 2 ? B 56 ? B 3 ? B 55 ? 1 A G 3 1_555 A C 55 1_555 A C 4 1_555 A G 54 1_555 0.708 -1.769 3.294 0.394 4.151 34.386 -3.595 -1.131 3.073 6.990 -0.663 34.630 3 BB_G3C4:G54C55_BB B 3 ? B 55 ? B 4 ? B 54 ? 1 A G 12 1_555 A U 9 1_555 A G 13 1_555 A C 8 1_555 -1.982 -3.529 0.306 105.403 -124.123 61.835 -1.418 1.306 1.362 -65.223 -55.386 165.292 4 BB_G12G13:C8U9_BB B 12 ? B 9 ? B 13 ? B 8 ? 1 A G 13 1_555 A C 8 1_555 A G 14 1_555 A C 7 1_555 -0.101 -2.231 3.405 0.074 9.066 29.173 -5.934 0.205 2.610 17.474 -0.142 30.520 5 BB_G13G14:C7C8_BB B 13 ? B 8 ? B 14 ? B 7 ? 1 A G 14 1_555 A C 7 1_555 A C 15 1_555 A G 6 1_555 0.487 -2.209 3.244 3.366 0.698 28.389 -4.630 -0.229 3.224 1.416 -6.832 28.592 6 BB_G14C15:G6C7_BB B 14 ? B 7 ? B 15 ? B 6 ? 1 A C 15 1_555 A G 6 1_555 A A 52 1_555 A U 16 1_555 -0.689 -4.214 -0.889 -137.812 -104.451 25.276 -1.642 -0.273 2.824 -53.895 71.108 173.094 7 BB_C15A52:U16G6_BB B 15 ? B 6 ? B 52 ? B 16 ? 1 A A 52 1_555 A U 16 1_555 A G 18 1_555 A C 53 1_555 -1.984 -2.974 -3.017 163.716 -51.607 -86.176 1.206 -1.894 -1.335 26.200 83.116 -173.910 8 BB_A52G18:C53U16_BB B 52 ? B 16 ? B 18 ? B 53 ? 1 A G 18 1_555 A C 53 1_555 A A 19 1_555 A U 50 1_555 2.442 -1.207 2.899 4.885 4.273 56.977 -1.468 -2.306 2.992 4.463 -5.102 57.315 9 BB_G18A19:U50C53_BB B 18 ? B 53 ? B 19 ? B 50 ? 1 A A 19 1_555 A U 50 1_555 A C 20 1_555 A G 49 1_555 0.659 -1.763 3.353 -0.817 3.676 30.860 -3.988 -1.385 3.109 6.875 1.529 31.083 10 BB_A19C20:G49U50_BB B 19 ? B 50 ? B 20 ? B 49 ? 1 A C 20 1_555 A G 49 1_555 A G 21 1_555 A C 48 1_555 0.461 -2.425 3.230 2.383 3.700 28.622 -5.626 -0.424 2.927 7.430 -4.785 28.951 11 BB_C20G21:C48G49_BB B 20 ? B 49 ? B 21 ? B 48 ? 1 A G 21 1_555 A C 48 1_555 A G 22 1_555 A C 46 1_555 1.038 -1.824 3.292 1.158 11.613 46.894 -3.091 -1.184 2.814 14.334 -1.429 48.244 12 BB_G21G22:C46C48_BB B 21 ? B 48 ? B 22 ? B 46 ? 1 A G 22 1_555 A C 46 1_555 A U 23 1_555 A A 45 1_555 0.820 -1.255 3.399 -2.652 9.125 29.122 -4.134 -2.064 2.803 17.567 5.106 30.601 13 BB_G22U23:A45C46_BB B 22 ? B 46 ? B 23 ? B 45 ? 1 A U 23 1_555 A A 45 1_555 A G 24 1_555 A C 44 1_555 0.629 -1.199 3.048 0.721 7.333 32.932 -3.133 -0.979 2.738 12.738 -1.252 33.724 14 BB_U23G24:C44A45_BB B 23 ? B 45 ? B 24 ? B 44 ? 1 A G 24 1_555 A C 44 1_555 A G 25 1_555 A C 43 1_555 0.721 -2.415 3.227 1.674 6.459 28.916 -5.960 -1.086 2.673 12.722 -3.298 29.660 15 BB_G24G25:C43C44_BB B 24 ? B 44 ? B 25 ? B 43 ? 1 A G 25 1_555 A C 43 1_555 A G 26 1_555 A U 42 1_555 0.567 -2.012 3.323 1.155 9.950 28.520 -5.720 -0.873 2.515 19.453 -2.258 30.194 16 BB_G25G26:U42C43_BB B 25 ? B 43 ? B 26 ? B 42 ? 1 A G 26 1_555 A U 42 1_555 A A 27 1_555 A G 41 1_555 -1.138 -1.770 3.195 2.764 2.109 38.476 -2.923 2.044 3.012 3.192 -4.184 38.627 17 BB_G26A27:G41U42_BB B 26 ? B 42 ? B 27 ? B 41 ? 1 A A 27 1_555 A G 41 1_555 A G 28 1_555 A G 40 1_555 1.394 -1.357 3.616 -0.983 -1.759 39.880 -1.763 -2.167 3.636 -2.577 1.439 39.929 18 BB_A27G28:G40G41_BB B 27 ? B 41 ? B 28 ? B 40 ? 1 A G 28 1_555 A G 40 1_555 A G 30 1_555 A U 39 1_555 -1.282 -3.790 3.355 7.407 2.354 11.253 -17.814 11.328 1.421 10.514 -33.086 13.669 19 BB_G28G30:U39G40_BB B 28 ? B 40 ? B 30 ? B 39 ? 1 A G 30 1_555 A U 39 1_555 A G 31 1_555 A C 38 1_555 -0.848 -1.287 3.117 -5.620 2.753 40.678 -2.118 0.624 3.113 3.932 8.027 41.136 20 BB_G30G31:C38U39_BB B 30 ? B 39 ? B 31 ? B 38 ? 1 A G 31 1_555 A C 38 1_555 A C 32 1_555 A G 37 1_555 0.485 -1.452 3.000 0.878 -2.792 34.342 -2.045 -0.691 3.116 -4.717 -1.484 34.462 21 BB_G31C32:G37C38_BB B 31 ? B 38 ? B 32 ? B 37 ? 1 A C 32 1_555 A G 37 1_555 A U 33 1_555 A G 36 1_555 -0.230 -1.308 3.747 7.146 3.986 28.112 -3.550 2.176 3.374 7.994 -14.331 29.255 22 BB_C32U33:G36G37_BB B 32 ? B 37 ? B 33 ? B 36 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'MAGNESIUM ION' MG 4 'SODIUM ION' NA 5 'POTASSIUM ION' K 6 water HOH #