data_2OE6 # _entry.id 2OE6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 2OE6 pdb_00002oe6 10.2210/pdb2oe6/pdb NDB AR0072 ? ? RCSB RCSB041022 ? ? WWPDB D_1000041022 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2OE5 ;1.5 A X-ray crystal structure of Apramycin complex with RNA fragment GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC containing the human ribosomal decoding A site: RNA construct with 3'-overhang ; unspecified PDB 2OE8 ;1.8 A X-ray crystal structure of Apramycin complex with RNA fragment GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC containing the human ribosomal decoding A site: RNA construct with 5'-overhang ; unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2OE6 _pdbx_database_status.recvd_initial_deposition_date 2006-12-28 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hermann, T.' 1 'Tereshko, V.' 2 'Skripkin, E.' 3 'Patel, D.J.' 4 # _citation.id primary _citation.title 'Apramycin recognition by the human ribosomal decoding site.' _citation.journal_abbrev 'Blood Cells Mol.Dis.' _citation.journal_volume 38 _citation.page_first 193 _citation.page_last 198 _citation.year 2007 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1079-9796 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17258916 _citation.pdbx_database_id_DOI 10.1016/j.bcmd.2006.11.006 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hermann, T.' 1 ? primary 'Tereshko, V.' 2 ? primary 'Skripkin, E.' 3 ? primary 'Patel, D.J.' 4 ? # _cell.entry_id 2OE6 _cell.length_a 28.157 _cell.length_b 36.416 _cell.length_c 87.325 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 2OE6 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 syn ;RNA (5'-R(*GP*GP*GP*CP*GP*UP*CP*GP*CP*UP*AP*GP*UP*AP*CP*C)-3') ; 5129.095 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*CP*GP*GP*UP*AP*CP*UP*AP*AP*AP*AP*GP*UP*CP*GP*CP*C)-3') ; 5426.301 1 ? ? ? ? 3 water nat water 18.015 71 ? ? ? ? # 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 GGGCGUCGCUAGUACC GGGCGUCGCUAGUACC A ? 2 polyribonucleotide no no CGGUACUAAAAGUCGCC CGGUACUAAAAGUCGCC B ? # 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 U n 1 7 C n 1 8 G n 1 9 C n 1 10 U n 1 11 A n 1 12 G n 1 13 U n 1 14 A n 1 15 C n 1 16 C n 2 1 C n 2 2 G n 2 3 G n 2 4 U n 2 5 A n 2 6 C n 2 7 U n 2 8 A n 2 9 A n 2 10 A n 2 11 A n 2 12 G n 2 13 U n 2 14 C n 2 15 G n 2 16 C n 2 17 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? 'Chemically synthesized' 2 1 sample ? ? ? ? ? 'Chemically synthesized' # 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 2OE6 2OE6 ? ? ? 2 2 PDB 2OE6 2OE6 ? ? ? # 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 2OE6 A 1 ? 16 ? 2OE6 1 ? 16 ? 1 16 2 2 2OE6 B 1 ? 17 ? 2OE6 83 ? 99 ? 83 99 # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 2OE6 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.12 _exptl_crystal.density_percent_sol 42.00 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.pdbx_details '0.05M MES BUFFER, 15-20% MPD, 0.02-0.04M MAGNESIUM ACETATE, 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 MPD ? ? ? 1 3 1 'MAGNESIUM ACETATE' ? ? ? 1 4 2 MPD ? ? ? 1 5 2 'MAGNESIUM ACETATE' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2000-04-01 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X9A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X9A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0000 # _reflns.entry_id 2OE6 _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 2.4 _reflns.d_resolution_low 20 _reflns.number_all 3649 _reflns.number_obs 3649 _reflns.percent_possible_obs 95.55 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 2OE6 _refine.ls_number_reflns_obs 3468 _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 18.73 _refine.ls_d_res_high 2.40 _refine.ls_percent_reflns_obs 95.55 _refine.ls_R_factor_obs 0.21173 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20935 _refine.ls_R_factor_R_free 0.25246 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 181 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.948 _refine.correlation_coeff_Fo_to_Fc_free 0.923 _refine.B_iso_mean 25.171 _refine.aniso_B[1][1] 0.00 _refine.aniso_B[2][2] 0.01 _refine.aniso_B[3][3] -0.01 _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 ? _refine.pdbx_starting_model 2OE5 _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 0.731 _refine.pdbx_overall_ESU_R_Free 0.295 _refine.overall_SU_ML 0.197 _refine.overall_SU_B 8.865 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _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 698 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 71 _refine_hist.number_atoms_total 769 _refine_hist.d_res_high 2.40 _refine_hist.d_res_low 18.73 # 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 0.017 0.021 ? 779 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 270 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.865 3.000 ? 1211 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.039 3.000 ? 705 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.092 0.200 ? 132 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.011 0.020 ? 341 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.136 0.300 ? 116 'X-RAY DIFFRACTION' ? r_nbd_other 0.232 0.300 ? 339 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.209 0.500 ? 56 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other 0.117 0.500 ? 2 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.131 0.300 ? 9 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.202 0.300 ? 11 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.168 0.500 ? 8 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 3.754 3.000 ? 779 'X-RAY DIFFRACTION' ? r_scangle_it 4.775 4.500 ? 1211 '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 2.40 _refine_ls_shell.d_res_low 2.462 _refine_ls_shell.number_reflns_R_work 225 _refine_ls_shell.R_factor_R_work 0.418 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.545 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 9 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2OE6 _struct.title ;2.4A X-ray crystal structure of unliganded RNA fragment GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC containing the human ribosomal decoding A site: RNA construct with 5'-overhang ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2OE6 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Ribosomal decoding site, A site, Homo sapiens, RNA duplex, 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 ? # _struct_biol.id 1 # 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 hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 17 N3 ? ? A G 2 B C 99 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 17 O2 ? ? A G 2 B C 99 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 17 N4 ? ? A G 2 B C 99 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 16 N3 ? ? A G 3 B C 98 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 16 O2 ? ? A G 3 B C 98 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 16 N4 ? ? A G 3 B C 98 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 15 N1 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 15 O6 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 15 N2 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 14 N3 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 14 O2 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 14 N4 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 6 O4 ? ? ? 1_555 B U 13 N3 ? ? A U 1406 B U 1495 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog14 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 8 N2 ? ? ? 1_555 B A 11 N7 ? ? A G 1408 B A 1493 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog18 hydrog ? ? A C 9 N4 ? ? ? 1_555 B A 10 N3 ? ? A C 1409 B A 1492 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog19 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 8 N1 ? ? A U 1410 B A 1490 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 8 N6 ? ? A U 1410 B A 1490 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 11 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 1411 B U 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 11 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 1411 B U 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 1412 B C 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 1412 B C 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 1412 B C 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 13 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 1413 B A 1487 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 13 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 1413 B A 1487 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 14 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 14 B U 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 14 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 14 B U 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 15 B G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 15 B G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 15 B G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 16 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 16 B G 84 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 2OE6 _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 2OE6 _atom_sites.fract_transf_matrix[1][1] 0.035515 _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] 0.027460 _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] 0.011451 _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 N O P # 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 G 3 3 3 G G A . n A 1 4 C 4 1404 1404 C C A . n A 1 5 G 5 1405 1405 G G A . n A 1 6 U 6 1406 1406 U U A . n A 1 7 C 7 1407 1407 C C A . n A 1 8 G 8 1408 1408 G G A . n A 1 9 C 9 1409 1409 C C A . n A 1 10 U 10 1410 1410 U U A . n A 1 11 A 11 1411 1411 A A A . n A 1 12 G 12 1412 1412 G G A . n A 1 13 U 13 1413 1413 U U 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 C 16 16 16 C C A . n B 2 1 C 1 83 83 C C B . n B 2 2 G 2 84 84 G G B . n B 2 3 G 3 85 85 G G B . n B 2 4 U 4 86 86 U U B . n B 2 5 A 5 1487 1487 A A B . n B 2 6 C 6 1488 1488 C C B . n B 2 7 U 7 1489 1489 U U B . n B 2 8 A 8 1490 1490 A A B . n B 2 9 A 9 1491 1491 A A B . n B 2 10 A 10 1492 1492 A A B . n B 2 11 A 11 1493 1493 A A B . n B 2 12 G 12 1494 1494 G G B . n B 2 13 U 13 1495 1495 U U B . n B 2 14 C 14 1496 1496 C C B . n B 2 15 G 15 1497 1497 G G B . n B 2 16 C 16 98 98 C C B . n B 2 17 C 17 99 99 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 HOH 1 103 103 HOH HOH A . C 3 HOH 2 104 104 HOH HOH A . C 3 HOH 3 106 106 HOH HOH A . C 3 HOH 4 107 107 HOH HOH A . C 3 HOH 5 109 109 HOH HOH A . C 3 HOH 6 111 111 HOH HOH A . C 3 HOH 7 112 112 HOH HOH A . C 3 HOH 8 113 113 HOH HOH A . C 3 HOH 9 115 115 HOH HOH A . C 3 HOH 10 116 116 HOH HOH A . C 3 HOH 11 119 119 HOH HOH A . C 3 HOH 12 122 122 HOH HOH A . C 3 HOH 13 123 123 HOH HOH A . C 3 HOH 14 125 125 HOH HOH A . C 3 HOH 15 126 126 HOH HOH A . C 3 HOH 16 127 127 HOH HOH A . C 3 HOH 17 128 128 HOH HOH A . C 3 HOH 18 129 129 HOH HOH A . C 3 HOH 19 130 130 HOH HOH A . C 3 HOH 20 132 132 HOH HOH A . C 3 HOH 21 134 134 HOH HOH A . C 3 HOH 22 136 136 HOH HOH A . C 3 HOH 23 139 139 HOH HOH A . C 3 HOH 24 141 141 HOH HOH A . C 3 HOH 25 144 144 HOH HOH A . C 3 HOH 26 145 145 HOH HOH A . C 3 HOH 27 147 147 HOH HOH A . C 3 HOH 28 149 149 HOH HOH A . C 3 HOH 29 153 153 HOH HOH A . C 3 HOH 30 154 154 HOH HOH A . C 3 HOH 31 156 156 HOH HOH A . C 3 HOH 32 158 158 HOH HOH A . C 3 HOH 33 159 159 HOH HOH A . C 3 HOH 34 160 160 HOH HOH A . C 3 HOH 35 166 166 HOH HOH A . C 3 HOH 36 168 168 HOH HOH A . C 3 HOH 37 169 169 HOH HOH A . C 3 HOH 38 170 170 HOH HOH A . C 3 HOH 39 171 171 HOH HOH A . D 3 HOH 1 101 101 HOH HOH B . D 3 HOH 2 102 102 HOH HOH B . D 3 HOH 3 105 105 HOH HOH B . D 3 HOH 4 108 108 HOH HOH B . D 3 HOH 5 110 110 HOH HOH B . D 3 HOH 6 114 114 HOH HOH B . D 3 HOH 7 117 117 HOH HOH B . D 3 HOH 8 118 118 HOH HOH B . D 3 HOH 9 120 120 HOH HOH B . D 3 HOH 10 121 121 HOH HOH B . D 3 HOH 11 124 124 HOH HOH B . D 3 HOH 12 131 131 HOH HOH B . D 3 HOH 13 133 133 HOH HOH B . D 3 HOH 14 135 135 HOH HOH B . D 3 HOH 15 137 137 HOH HOH B . D 3 HOH 16 138 138 HOH HOH B . D 3 HOH 17 140 140 HOH HOH B . D 3 HOH 18 142 142 HOH HOH B . D 3 HOH 19 143 143 HOH HOH B . D 3 HOH 20 146 146 HOH HOH B . D 3 HOH 21 148 148 HOH HOH B . D 3 HOH 22 150 150 HOH HOH B . D 3 HOH 23 151 151 HOH HOH B . D 3 HOH 24 152 152 HOH HOH B . D 3 HOH 25 155 155 HOH HOH B . D 3 HOH 26 157 157 HOH HOH B . D 3 HOH 27 161 161 HOH HOH B . D 3 HOH 28 162 162 HOH HOH B . D 3 HOH 29 163 163 HOH HOH B . D 3 HOH 30 164 164 HOH HOH B . D 3 HOH 31 165 165 HOH HOH B . D 3 HOH 32 167 167 HOH HOH B . # _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _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 2007-02-13 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-30 # _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' Advisory 3 3 'Structure model' 'Refinement description' 4 3 'Structure model' 'Version format compliance' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 '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_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' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 18.2980 _pdbx_refine_tls.origin_y -1.5100 _pdbx_refine_tls.origin_z 43.2400 _pdbx_refine_tls.T[1][1] 0.0096 _pdbx_refine_tls.T[2][2] 0.0144 _pdbx_refine_tls.T[3][3] 0.0861 _pdbx_refine_tls.T[1][2] 0.0065 _pdbx_refine_tls.T[1][3] 0.0241 _pdbx_refine_tls.T[2][3] 0.0102 _pdbx_refine_tls.L[1][1] 0.7951 _pdbx_refine_tls.L[2][2] 0.3289 _pdbx_refine_tls.L[3][3] 2.1983 _pdbx_refine_tls.L[1][2] 0.1624 _pdbx_refine_tls.L[1][3] -0.4628 _pdbx_refine_tls.L[2][3] -0.2822 _pdbx_refine_tls.S[1][1] 0.1293 _pdbx_refine_tls.S[2][2] 0.0068 _pdbx_refine_tls.S[3][3] -0.1362 _pdbx_refine_tls.S[1][2] 0.0158 _pdbx_refine_tls.S[1][3] 0.1185 _pdbx_refine_tls.S[2][3] -0.0209 _pdbx_refine_tls.S[2][1] 0.0557 _pdbx_refine_tls.S[3][1] -0.0639 _pdbx_refine_tls.S[3][2] 0.0238 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 1 A 3 ? . . . . ? 'X-RAY DIFFRACTION' 2 1 A 1404 A 1413 ? . . . . ? 'X-RAY DIFFRACTION' 3 1 A 14 A 16 ? . . . . ? 'X-RAY DIFFRACTION' 4 1 B 83 B 86 ? . . . . ? 'X-RAY DIFFRACTION' 5 1 B 1487 B 1497 ? . . . . ? 'X-RAY DIFFRACTION' 6 1 B 98 B 99 ? . . . . ? 'X-RAY DIFFRACTION' 7 1 A 103 A 171 ? . . . . ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.0 ? 1 HKL-2000 'data collection' . ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 AMoRE phasing . ? 5 # _pdbx_database_remark.id 999 _pdbx_database_remark.text ;SEQUENCE THE RESIDUES THAT ARE NATURALLY OCCURING IN THE HUMAN RIBOSOMAL DECODING A SITE ARE NUMBERED 1404-1413 (CHAIN A) AND 1487-1497 (CHAIN B). THIS NUMBERING IS ADAPTED FROM THE BACTERIAL ESCHERICHIA COLI SEQUENCE. IN BOTH STRANDS TERMINAL RESIDUES ARE DISTINCT FROM HUMAN AND WERE INCORPORATED FOR CRYSTALLIZATION PURPOSES. THE INCORPORATED RESIDUES ARE NUMBERED 1-3, 14-16 (CHAIN A) AND 83-86,98-99 (CHAIN B). ; # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O5'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 A _pdbx_validate_rmsd_bond.auth_seq_id_1 1490 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C5'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 A _pdbx_validate_rmsd_bond.auth_seq_id_2 1490 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.363 _pdbx_validate_rmsd_bond.bond_target_value 1.420 _pdbx_validate_rmsd_bond.bond_deviation -0.057 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.009 _pdbx_validate_rmsd_bond.linker_flag 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 "O4'" A G 3 ? ? "C1'" A G 3 ? ? N9 A G 3 ? ? 113.29 108.50 4.79 0.70 N 2 1 N1 A C 16 ? ? "C1'" A C 16 ? ? "C2'" A C 16 ? ? 105.17 112.00 -6.83 1.10 N 3 1 "O4'" A C 16 ? ? "C1'" A C 16 ? ? N1 A C 16 ? ? 115.63 108.50 7.13 0.70 N 4 1 "O4'" B A 1493 ? ? "C1'" B A 1493 ? ? N9 B A 1493 ? ? 112.71 108.50 4.21 0.70 N 5 1 "C3'" B G 1494 ? ? "O3'" B G 1494 ? ? P B U 1495 ? ? 126.99 119.70 7.29 1.20 Y 6 1 "O3'" B G 1494 ? ? P B U 1495 ? ? OP2 B U 1495 ? ? 117.78 110.50 7.28 1.10 Y # 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 U OP3 O N N 114 U P P N N 115 U OP1 O N N 116 U OP2 O N N 117 U "O5'" O N N 118 U "C5'" C N N 119 U "C4'" C N R 120 U "O4'" O N N 121 U "C3'" C N S 122 U "O3'" O N N 123 U "C2'" C N R 124 U "O2'" O N N 125 U "C1'" C N R 126 U N1 N N N 127 U C2 C N N 128 U O2 O N N 129 U N3 N N N 130 U C4 C N N 131 U O4 O N N 132 U C5 C N N 133 U C6 C N N 134 U HOP3 H N N 135 U HOP2 H N N 136 U "H5'" H N N 137 U "H5''" H N N 138 U "H4'" H N N 139 U "H3'" H N N 140 U "HO3'" H N N 141 U "H2'" H N N 142 U "HO2'" H N N 143 U "H1'" H N N 144 U H3 H N N 145 U H5 H N N 146 U H6 H N N 147 # 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 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2OE6 'double helix' 2OE6 'a-form double helix' 2OE6 'bulge loop' 2OE6 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 2 1_555 B C 17 1_555 -0.556 -0.079 -0.011 -1.681 -8.583 2.032 1 A_G2:C99_B A 2 ? B 99 ? 19 1 1 A G 3 1_555 B C 16 1_555 -0.271 -0.254 0.143 1.331 -14.397 -5.968 2 A_G3:C98_B A 3 ? B 98 ? 19 1 1 A C 4 1_555 B G 15 1_555 0.344 -0.124 -0.002 1.431 -12.754 -0.350 3 A_C1404:G1497_B A 1404 ? B 1497 ? 19 1 1 A G 5 1_555 B C 14 1_555 -0.367 -0.087 -0.004 -4.514 -11.627 1.532 4 A_G1405:C1496_B A 1405 ? B 1496 ? 19 1 1 A U 6 1_555 B U 13 1_555 -2.496 -1.614 -0.001 8.641 -16.993 -2.168 5 A_U1406:U1495_B A 1406 ? B 1495 ? ? ? 1 A C 7 1_555 B G 12 1_555 0.130 -0.165 -0.175 7.325 -13.189 3.609 6 A_C1407:G1494_B A 1407 ? B 1494 ? 19 1 1 A G 8 1_555 B A 11 1_555 7.766 -5.085 -0.239 -15.247 -24.316 -50.690 7 A_G1408:A1493_B A 1408 ? B 1493 ? ? ? 1 A C 9 1_555 B A 10 1_555 -5.440 -0.763 0.399 17.519 -17.437 67.622 8 A_C1409:A1492_B A 1409 ? B 1492 ? ? 5 1 A U 10 1_555 B A 8 1_555 0.217 -0.221 -0.331 -1.501 -17.548 2.635 9 A_U1410:A1490_B A 1410 ? B 1490 ? 20 1 1 A A 11 1_555 B U 7 1_555 0.042 -0.285 0.153 -1.978 -13.200 2.346 10 A_A1411:U1489_B A 1411 ? B 1489 ? 20 1 1 A G 12 1_555 B C 6 1_555 -0.168 -0.119 -0.170 -6.817 -18.381 3.326 11 A_G1412:C1488_B A 1412 ? B 1488 ? 19 1 1 A U 13 1_555 B A 5 1_555 -0.225 -0.236 0.127 -0.967 -11.488 3.324 12 A_U1413:A1487_B A 1413 ? B 1487 ? 20 1 1 A A 14 1_555 B U 4 1_555 -0.035 -0.070 -0.316 -7.501 -16.315 4.909 13 A_A14:U86_B A 14 ? B 86 ? 20 1 1 A C 15 1_555 B G 3 1_555 0.130 -0.162 0.017 0.813 -12.593 -0.859 14 A_C15:G85_B A 15 ? B 85 ? 19 1 1 A C 16 1_555 B G 2 1_555 -0.029 0.308 0.008 4.996 -13.587 7.632 15 A_C16:G84_B A 16 ? B 84 ? ? 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 17 1_555 A G 3 1_555 B C 16 1_555 -0.230 -1.635 3.176 -4.103 3.931 33.139 -3.436 -0.238 2.974 6.829 7.128 33.609 1 AA_G2G3:C98C99_BB A 2 ? B 99 ? A 3 ? B 98 ? 1 A G 3 1_555 B C 16 1_555 A C 4 1_555 B G 15 1_555 0.237 -1.668 3.218 3.018 1.357 37.458 -2.761 0.016 3.166 2.107 -4.689 37.599 2 AA_G3C1404:G1497C98_BB A 3 ? B 98 ? A 1404 ? B 1497 ? 1 A C 4 1_555 B G 15 1_555 A G 5 1_555 B C 14 1_555 0.562 -1.577 3.262 0.687 14.592 26.386 -5.668 -0.959 2.129 29.286 -1.378 30.097 3 AA_C1404G1405:C1496G1497_BB A 1404 ? B 1497 ? A 1405 ? B 1496 ? 1 A G 5 1_555 B C 14 1_555 A U 6 1_555 B U 13 1_555 -0.136 -2.023 2.626 -3.685 6.146 23.313 -6.194 -0.518 2.031 14.768 8.856 24.375 4 AA_G1405U1406:U1495C1496_BB A 1405 ? B 1496 ? A 1406 ? B 1495 ? 1 A U 6 1_555 B U 13 1_555 A C 7 1_555 B G 12 1_555 0.196 -1.146 3.351 1.321 6.965 46.089 -2.033 -0.137 3.160 8.835 -1.676 46.601 5 AA_U1406C1407:G1494U1495_BB A 1406 ? B 1495 ? A 1407 ? B 1494 ? 1 A C 7 1_555 B G 12 1_555 A G 8 1_555 B A 11 1_555 -4.095 -1.960 4.239 -0.002 17.049 64.649 -2.618 3.728 3.681 15.659 0.002 66.623 6 AA_C1407G1408:A1493G1494_BB A 1407 ? B 1494 ? A 1408 ? B 1493 ? 1 A C 9 1_555 B A 10 1_555 A U 10 1_555 B A 8 1_555 -0.913 0.763 3.601 -0.558 8.783 77.911 0.332 0.706 3.662 6.964 0.442 78.328 7 AA_C1409U1410:A1490A1492_BB A 1409 ? B 1492 ? A 1410 ? B 1490 ? 1 A U 10 1_555 B A 8 1_555 A A 11 1_555 B U 7 1_555 0.110 -0.964 3.307 -5.496 11.545 31.539 -3.426 -1.033 2.740 20.231 9.630 33.971 8 AA_U1410A1411:U1489A1490_BB A 1410 ? B 1490 ? A 1411 ? B 1489 ? 1 A A 11 1_555 B U 7 1_555 A G 12 1_555 B C 6 1_555 -0.282 -1.170 3.305 2.253 11.822 32.465 -3.703 0.805 2.702 20.296 -3.867 34.568 9 AA_A1411G1412:C1488U1489_BB A 1411 ? B 1489 ? A 1412 ? B 1488 ? 1 A G 12 1_555 B C 6 1_555 A U 13 1_555 B A 5 1_555 0.585 -1.080 3.146 -2.145 7.807 30.149 -3.369 -1.461 2.740 14.678 4.034 31.193 10 AA_G1412U1413:A1487C1488_BB A 1412 ? B 1488 ? A 1413 ? B 1487 ? 1 A U 13 1_555 B A 5 1_555 A A 14 1_555 B U 4 1_555 0.595 -1.452 3.365 4.788 15.674 33.168 -4.310 -0.325 2.511 25.604 -7.821 36.894 11 AA_U1413A14:U86A1487_BB A 1413 ? B 1487 ? A 14 ? B 86 ? 1 A A 14 1_555 B U 4 1_555 A C 15 1_555 B G 3 1_555 -0.824 -1.408 3.049 -3.546 5.840 29.018 -3.842 0.932 2.797 11.454 6.956 29.795 12 AA_A14C15:G85U86_BB A 14 ? B 86 ? A 15 ? B 85 ? 1 A C 15 1_555 B G 3 1_555 A C 16 1_555 B G 2 1_555 0.059 -1.352 3.128 -0.195 9.027 32.070 -3.719 -0.133 2.659 15.948 0.345 33.284 13 AA_C15C16:G84G85_BB A 15 ? B 85 ? A 16 ? B 84 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _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.accession_code 2OE5 _pdbx_initial_refinement_model.details ? #