data_3S8U # _entry.id 3S8U # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 3S8U pdb_00003s8u 10.2210/pdb3s8u/pdb NDB NA1159 ? ? RCSB RCSB065906 ? ? WWPDB D_1000065906 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3DVZ 'Unmodified SRL RNA' unspecified PDB 3S7C ;2'-azido-uridine SRL RNA ; unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3S8U _pdbx_database_status.recvd_initial_deposition_date 2011-05-31 _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.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ennifar, E.' 1 'Micura, R.' 2 # _citation.id primary _citation.title ;2'-Azido RNA, a Versatile Tool for Chemical Biology: Synthesis, X-ray Structure, siRNA Applications, Click Labeling. ; _citation.journal_abbrev 'Acs Chem.Biol.' _citation.journal_volume 7 _citation.page_first 581 _citation.page_last 589 _citation.year 2012 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1554-8929 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22273279 _citation.pdbx_database_id_DOI 10.1021/cb200510k # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Fauster, K.' 1 ? primary 'Hartl, M.' 2 ? primary 'Santner, T.' 3 ? primary 'Aigner, M.' 4 ? primary 'Kreutz, C.' 5 ? primary 'Bister, K.' 6 ? primary 'Ennifar, E.' 7 ? primary 'Micura, R.' 8 ? # _cell.entry_id 3S8U _cell.length_a 29.570 _cell.length_b 29.570 _cell.length_c 76.340 _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 3S8U _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _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 'Ecoli 23 S rRNA Sarcin Ricin loop' 8770.275 1 ? ? ? ? 2 water nat water 18.015 162 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'UGCUCCUAGUACGAGAGGACCGG(AT7)GUG' _entity_poly.pdbx_seq_one_letter_code_can UGCUCCUAGUACGAGAGGACCGGXGUG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 G n 1 3 C n 1 4 U n 1 5 C n 1 6 C n 1 7 U n 1 8 A n 1 9 G n 1 10 U n 1 11 A n 1 12 C n 1 13 G n 1 14 A n 1 15 G n 1 16 A n 1 17 G n 1 18 G n 1 19 A n 1 20 C n 1 21 C n 1 22 G n 1 23 G n 1 24 AT7 n 1 25 G n 1 26 U n 1 27 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'Escherichia coli' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 562 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3S8U _struct_ref.pdbx_db_accession 3S8U _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code UGCUCCUAGUACGAGAGGACCGGATGUG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3S8U _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 27 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3S8U _struct_ref_seq.db_align_beg 2647 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 2673 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2647 _struct_ref_seq.pdbx_auth_seq_align_end 2673 # 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 AT7 non-polymer . "2'-deoxy-2'-triaza-1,2-dien-2-ium-1-yl-adenine-5'-monophosphate" ? 'C10 H14 N8 O6 P 1' 373.242 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 3S8U _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.90 _exptl_crystal.density_percent_sol 35.36 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;1 volume of [3.1M (NH4)2SO4, 50mM MOPS pH7.0, 10mM MgCl2, 10mM MnCl2] + 2 volumes of [RNA in 1mM EDTA, 10mM Tris pH8.0], VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2011-05-09 _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 crystal _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.92 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X06SA' _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X06SA _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.92 # _reflns.entry_id 3S8U _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 30 _reflns.d_resolution_high 1.2 _reflns.number_obs 19989 _reflns.number_all 20495 _reflns.percent_possible_obs 97.5 _reflns.pdbx_Rmerge_I_obs 0.114 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.20 _reflns_shell.d_res_low 1.23 _reflns_shell.percent_possible_all 91.1 _reflns_shell.Rmerge_I_obs 0.545 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.67 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1549 _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 3S8U _refine.ls_number_reflns_obs 19980 _refine.ls_number_reflns_all 20495 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.01 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 27.574 _refine.ls_d_res_high 1.200 _refine.ls_percent_reflns_obs 97.67 _refine.ls_R_factor_obs 0.1445 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1428 _refine.ls_R_factor_R_free 0.1785 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.01 _refine.ls_number_reflns_R_free 1000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 1.6349 _refine.aniso_B[2][2] 1.6349 _refine.aniso_B[3][3] 0.4249 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.456 _refine.solvent_model_param_bsol 59.085 _refine.pdbx_solvent_vdw_probe_radii 0.60 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.41 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 3DVZ' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.13 _refine.pdbx_overall_phase_error 15.68 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _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 0 _refine_hist.pdbx_number_atoms_nucleic_acid 581 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 162 _refine_hist.number_atoms_total 743 _refine_hist.d_res_high 1.200 _refine_hist.d_res_low 27.574 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.019 ? ? 707 ? 'X-RAY DIFFRACTION' f_angle_d 1.784 ? ? 1106 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 16.888 ? ? 348 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.100 ? ? 148 ? 'X-RAY DIFFRACTION' f_plane_restr 0.033 ? ? 29 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _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 . 1.2001 1.2634 2593 0.1908 94.00 0.2171 . . 137 . . . . 'X-RAY DIFFRACTION' . 1.2634 1.3425 2752 0.1556 99.00 0.2097 . . 145 . . . . 'X-RAY DIFFRACTION' . 1.3425 1.4462 2723 0.1429 99.00 0.1861 . . 143 . . . . 'X-RAY DIFFRACTION' . 1.4462 1.5917 2722 0.1250 99.00 0.1998 . . 143 . . . . 'X-RAY DIFFRACTION' . 1.5917 1.8220 2751 0.1145 99.00 0.1638 . . 145 . . . . 'X-RAY DIFFRACTION' . 1.8220 2.2954 2722 0.1340 98.00 0.1695 . . 144 . . . . 'X-RAY DIFFRACTION' . 2.2954 27.5810 2717 0.1530 97.00 0.1725 . . 143 . . . . 'X-RAY DIFFRACTION' # _struct.entry_id 3S8U _struct.title 'Crystal structure of a 2-azido-adenine-modified RNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3S8U _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;hairpin RNA, RNA labelling, 2'-azido-adenine, 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 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A G 23 "O3'" ? ? ? 1_555 A AT7 24 P ? ? A G 2669 A AT7 2670 1_555 ? ? ? ? ? ? ? 1.587 ? ? hydrog1 hydrog ? ? A G 2 N1 A ? ? 1_555 A U 26 O2 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A G 2 O6 A ? ? 1_555 A U 26 N3 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A C 3 N3 A ? ? 1_555 A G 25 N1 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N4 A ? ? 1_555 A G 25 O6 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 O2 A ? ? 1_555 A G 25 N2 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 7 O2 ? ? ? 1_555 A C 21 N4 ? ? A U 2653 A C 2667 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog13 hydrog ? ? A G 9 N2 ? ? ? 1_555 A U 10 O4 ? ? A G 2655 A U 2656 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog14 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 19 N7 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog15 hydrog ? ? A U 10 O2 ? ? ? 1_555 A A 19 N6 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog16 hydrog ? ? A A 11 N6 ? ? ? 1_555 A G 18 N3 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A A 11 N7 ? ? ? 1_555 A G 18 N2 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog18 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 13 N2 ? ? ? 1_555 A A 16 N7 ? ? A G 2659 A A 2662 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 3S8U _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 3S8U _atom_sites.fract_transf_matrix[1][1] 0.033818 _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] 0.033818 _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] 0.013099 _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 H 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 U 1 2647 2647 U URI A . n A 1 2 G 2 2648 2648 G GUA A . n A 1 3 C 3 2649 2649 C CYT A . n A 1 4 U 4 2650 2650 U URI A . n A 1 5 C 5 2651 2651 C CYT A . n A 1 6 C 6 2652 2652 C CYT A . n A 1 7 U 7 2653 2653 U URI A . n A 1 8 A 8 2654 2654 A ADE A . n A 1 9 G 9 2655 2655 G GUA A . n A 1 10 U 10 2656 2656 U URI A . n A 1 11 A 11 2657 2657 A ADE A . n A 1 12 C 12 2658 2658 C CYT A . n A 1 13 G 13 2659 2659 G GUA A . n A 1 14 A 14 2660 2660 A ADE A . n A 1 15 G 15 2661 2661 G GUA A . n A 1 16 A 16 2662 2662 A ADE A . n A 1 17 G 17 2663 2663 G GUA A . n A 1 18 G 18 2664 2664 G GUA A . n A 1 19 A 19 2665 2665 A ADE A . n A 1 20 C 20 2666 2666 C CYT A . n A 1 21 C 21 2667 2667 C CYT A . n A 1 22 G 22 2668 2668 G GUA A . n A 1 23 G 23 2669 2669 G GUA A . n A 1 24 AT7 24 2670 2670 AT7 AT7 A . n A 1 25 G 25 2671 2671 G GUA A . n A 1 26 U 26 2672 2672 U URI A . n A 1 27 G 27 2673 2673 G GUA A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 1 1 HOH HOH A . B 2 HOH 2 2 2 HOH HOH A . B 2 HOH 3 3 3 HOH HOH A . B 2 HOH 4 4 4 HOH HOH A . B 2 HOH 5 5 5 HOH HOH A . B 2 HOH 6 6 6 HOH HOH A . B 2 HOH 7 7 7 HOH HOH A . B 2 HOH 8 8 8 HOH HOH A . B 2 HOH 9 9 9 HOH HOH A . B 2 HOH 10 10 10 HOH HOH A . B 2 HOH 11 11 11 HOH HOH A . B 2 HOH 12 12 12 HOH HOH A . B 2 HOH 13 13 13 HOH HOH A . B 2 HOH 14 14 14 HOH HOH A . B 2 HOH 15 15 15 HOH HOH A . B 2 HOH 16 16 16 HOH HOH A . B 2 HOH 17 17 17 HOH HOH A . B 2 HOH 18 18 18 HOH HOH A . B 2 HOH 19 19 19 HOH HOH A . B 2 HOH 20 20 20 HOH HOH A . B 2 HOH 21 21 21 HOH HOH A . B 2 HOH 22 22 22 HOH HOH A . B 2 HOH 23 23 23 HOH HOH A . B 2 HOH 24 24 24 HOH HOH A . B 2 HOH 25 25 25 HOH HOH A . B 2 HOH 26 26 26 HOH HOH A . B 2 HOH 27 27 27 HOH HOH A . B 2 HOH 28 28 28 HOH HOH A . B 2 HOH 29 29 29 HOH HOH A . B 2 HOH 30 30 30 HOH HOH A . B 2 HOH 31 31 31 HOH HOH A . B 2 HOH 32 32 32 HOH HOH A . B 2 HOH 33 33 33 HOH HOH A . B 2 HOH 34 34 34 HOH HOH A . B 2 HOH 35 35 35 HOH HOH A . B 2 HOH 36 36 36 HOH HOH A . B 2 HOH 37 37 37 HOH HOH A . B 2 HOH 38 38 38 HOH HOH A . B 2 HOH 39 39 39 HOH HOH A . B 2 HOH 40 40 40 HOH HOH A . B 2 HOH 41 41 41 HOH HOH A . B 2 HOH 42 42 42 HOH HOH A . B 2 HOH 43 43 43 HOH HOH A . B 2 HOH 44 44 44 HOH HOH A . B 2 HOH 45 45 45 HOH HOH A . B 2 HOH 46 46 46 HOH HOH A . B 2 HOH 47 47 47 HOH HOH A . B 2 HOH 48 48 48 HOH HOH A . B 2 HOH 49 49 49 HOH HOH A . B 2 HOH 50 50 50 HOH HOH A . B 2 HOH 51 51 51 HOH HOH A . B 2 HOH 52 52 52 HOH HOH A . B 2 HOH 53 53 53 HOH HOH A . B 2 HOH 54 54 54 HOH HOH A . B 2 HOH 55 55 55 HOH HOH A . B 2 HOH 56 56 56 HOH HOH A . B 2 HOH 57 57 57 HOH HOH A . B 2 HOH 58 58 58 HOH HOH A . B 2 HOH 59 59 59 HOH HOH A . B 2 HOH 60 60 60 HOH HOH A . B 2 HOH 61 61 61 HOH HOH A . B 2 HOH 62 62 62 HOH HOH A . B 2 HOH 63 63 63 HOH HOH A . B 2 HOH 64 64 64 HOH HOH A . B 2 HOH 65 65 65 HOH HOH A . B 2 HOH 66 66 66 HOH HOH A . B 2 HOH 67 67 67 HOH HOH A . B 2 HOH 68 68 68 HOH HOH A . B 2 HOH 69 69 69 HOH HOH A . B 2 HOH 70 70 70 HOH HOH A . B 2 HOH 71 71 71 HOH HOH A . B 2 HOH 72 72 72 HOH HOH A . B 2 HOH 73 73 73 HOH HOH A . B 2 HOH 74 74 74 HOH HOH A . B 2 HOH 75 75 75 HOH HOH A . B 2 HOH 76 76 76 HOH HOH A . B 2 HOH 77 77 77 HOH HOH A . B 2 HOH 78 78 78 HOH HOH A . B 2 HOH 79 79 79 HOH HOH A . B 2 HOH 80 80 80 HOH HOH A . B 2 HOH 81 81 81 HOH HOH A . B 2 HOH 82 82 82 HOH HOH A . B 2 HOH 83 83 83 HOH HOH A . B 2 HOH 84 84 84 HOH HOH A . B 2 HOH 85 85 85 HOH HOH A . B 2 HOH 86 86 86 HOH HOH A . B 2 HOH 87 87 87 HOH HOH A . B 2 HOH 88 88 88 HOH HOH A . B 2 HOH 89 89 89 HOH HOH A . B 2 HOH 90 90 90 HOH HOH A . B 2 HOH 91 91 91 HOH HOH A . B 2 HOH 92 92 92 HOH HOH A . B 2 HOH 93 93 93 HOH HOH A . B 2 HOH 94 94 94 HOH HOH A . B 2 HOH 95 95 95 HOH HOH A . B 2 HOH 96 96 96 HOH HOH A . B 2 HOH 97 97 97 HOH HOH A . B 2 HOH 98 98 98 HOH HOH A . B 2 HOH 99 99 99 HOH HOH A . B 2 HOH 100 100 100 HOH HOH A . B 2 HOH 101 101 101 HOH HOH A . B 2 HOH 102 102 102 HOH HOH A . B 2 HOH 103 103 103 HOH HOH A . B 2 HOH 104 104 104 HOH HOH A . B 2 HOH 105 105 105 HOH HOH A . B 2 HOH 106 106 106 HOH HOH A . B 2 HOH 107 107 107 HOH HOH A . B 2 HOH 108 108 108 HOH HOH A . B 2 HOH 109 109 109 HOH HOH A . B 2 HOH 110 110 110 HOH HOH A . B 2 HOH 111 111 111 HOH HOH A . B 2 HOH 112 112 112 HOH HOH A . B 2 HOH 113 113 113 HOH HOH A . B 2 HOH 114 114 114 HOH HOH A . B 2 HOH 115 115 115 HOH HOH A . B 2 HOH 116 116 116 HOH HOH A . B 2 HOH 117 117 117 HOH HOH A . B 2 HOH 118 118 118 HOH HOH A . B 2 HOH 119 119 119 HOH HOH A . B 2 HOH 120 120 120 HOH HOH A . B 2 HOH 121 121 121 HOH HOH A . B 2 HOH 122 122 122 HOH HOH A . B 2 HOH 123 123 123 HOH HOH A . B 2 HOH 124 124 124 HOH HOH A . B 2 HOH 125 125 125 HOH HOH A . B 2 HOH 126 126 126 HOH HOH A . B 2 HOH 127 127 127 HOH HOH A . B 2 HOH 128 128 128 HOH HOH A . B 2 HOH 129 129 129 HOH HOH A . B 2 HOH 130 131 131 HOH HOH A . B 2 HOH 131 132 132 HOH HOH A . B 2 HOH 132 134 134 HOH HOH A . B 2 HOH 133 136 136 HOH HOH A . B 2 HOH 134 137 137 HOH HOH A . B 2 HOH 135 138 138 HOH HOH A . B 2 HOH 136 140 140 HOH HOH A . B 2 HOH 137 141 141 HOH HOH A . B 2 HOH 138 142 142 HOH HOH A . B 2 HOH 139 143 143 HOH HOH A . B 2 HOH 140 144 144 HOH HOH A . B 2 HOH 141 145 145 HOH HOH A . B 2 HOH 142 146 146 HOH HOH A . B 2 HOH 143 148 148 HOH HOH A . B 2 HOH 144 149 149 HOH HOH A . B 2 HOH 145 150 150 HOH HOH A . B 2 HOH 146 151 151 HOH HOH A . B 2 HOH 147 152 152 HOH HOH A . B 2 HOH 148 153 153 HOH HOH A . B 2 HOH 149 154 154 HOH HOH A . B 2 HOH 150 155 155 HOH HOH A . B 2 HOH 151 156 156 HOH HOH A . B 2 HOH 152 157 157 HOH HOH A . B 2 HOH 153 158 158 HOH HOH A . B 2 HOH 154 159 159 HOH HOH A . B 2 HOH 155 160 160 HOH HOH A . B 2 HOH 156 161 161 HOH HOH A . B 2 HOH 157 162 162 HOH HOH A . B 2 HOH 158 163 163 HOH HOH A . B 2 HOH 159 164 164 HOH HOH A . B 2 HOH 160 165 165 HOH HOH A . B 2 HOH 161 166 166 HOH HOH A . B 2 HOH 162 167 167 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 2012-04-11 2 'Structure model' 1 1 2023-09-13 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' pdbx_initial_refinement_model 5 2 'Structure model' struct_conn # 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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOLREP phasing . ? 1 PHENIX refinement '(phenix.refine: 1.7_650)' ? 2 XDS 'data reduction' . ? 3 XDS 'data scaling' . ? 4 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 H1 A G 2648 ? A O2 A U 2672 ? ? 1.59 2 1 O A HOH 109 ? ? O A HOH 152 ? ? 1.97 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C5'" A U 2650 ? B "C4'" A U 2650 ? ? 1.447 1.508 -0.061 0.007 N 2 1 N1 A G 2659 ? ? C2 A G 2659 ? ? 1.323 1.373 -0.050 0.008 N 3 1 "O5'" A G 2671 ? ? "C5'" A G 2671 ? ? 1.363 1.420 -0.057 0.009 N 4 1 C5 A G 2671 ? ? N7 A G 2671 ? ? 1.339 1.388 -0.049 0.006 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 C5 A G 2648 ? B N7 A G 2648 ? B C8 A G 2648 ? B 100.76 104.30 -3.54 0.50 N 2 1 N3 A C 2649 ? B C4 A C 2649 ? B N4 A C 2649 ? B 122.48 118.00 4.48 0.70 N 3 1 C5 A C 2649 ? B C4 A C 2649 ? B N4 A C 2649 ? B 115.96 120.20 -4.24 0.70 N 4 1 C2 A C 2651 ? ? N3 A C 2651 ? ? C4 A C 2651 ? ? 123.54 119.90 3.64 0.50 N 5 1 C4 A G 2655 ? ? C5 A G 2655 ? ? N7 A G 2655 ? ? 104.59 110.80 -6.21 0.40 N 6 1 C5 A G 2655 ? ? N7 A G 2655 ? ? C8 A G 2655 ? ? 109.71 104.30 5.41 0.50 N 7 1 C8 A G 2655 ? ? N9 A G 2655 ? ? C4 A G 2655 ? ? 103.62 106.40 -2.78 0.40 N 8 1 N9 A G 2655 ? ? C4 A G 2655 ? ? C5 A G 2655 ? ? 111.26 105.40 5.86 0.40 N 9 1 C6 A G 2655 ? ? C5 A G 2655 ? ? N7 A G 2655 ? ? 134.73 130.40 4.33 0.60 N 10 1 N7 A G 2661 ? ? C8 A G 2661 ? ? N9 A G 2661 ? ? 108.86 113.10 -4.24 0.50 N 11 1 N1 A G 2664 ? ? C2 A G 2664 ? ? N3 A G 2664 ? ? 119.93 123.90 -3.97 0.60 N 12 1 C2 A G 2664 ? ? N3 A G 2664 ? ? C4 A G 2664 ? ? 115.03 111.90 3.13 0.50 N 13 1 C4 A G 2664 ? ? C5 A G 2664 ? ? N7 A G 2664 ? ? 107.67 110.80 -3.13 0.40 N 14 1 N3 A G 2664 ? ? C2 A G 2664 ? ? N2 A G 2664 ? ? 124.88 119.90 4.98 0.70 N 15 1 C4 A A 2665 ? ? C5 A A 2665 ? ? C6 A A 2665 ? ? 121.39 117.00 4.39 0.50 N 16 1 N9 A A 2665 ? ? C4 A A 2665 ? ? C5 A A 2665 ? ? 108.63 105.80 2.83 0.40 N 17 1 N1 A C 2667 ? ? C2 A C 2667 ? ? O2 A C 2667 ? ? 115.12 118.90 -3.78 0.60 N 18 1 C2 A G 2669 ? ? N3 A G 2669 ? ? C4 A G 2669 ? ? 115.10 111.90 3.20 0.50 N 19 1 C8 A G 2669 ? ? N9 A G 2669 ? ? C4 A G 2669 ? ? 103.44 106.40 -2.96 0.40 N 20 1 N9 A G 2669 ? ? C4 A G 2669 ? ? C5 A G 2669 ? ? 108.52 105.40 3.12 0.40 N 21 1 C2 A G 2671 ? ? N3 A G 2671 ? ? C4 A G 2671 ? ? 107.10 111.90 -4.80 0.50 N 22 1 N3 A G 2671 ? ? C4 A G 2671 ? ? C5 A G 2671 ? ? 132.28 128.60 3.68 0.50 N 23 1 C5 A G 2671 ? ? C6 A G 2671 ? ? N1 A G 2671 ? ? 107.41 111.50 -4.09 0.50 N 24 1 N3 A G 2671 ? ? C4 A G 2671 ? ? N9 A G 2671 ? ? 121.28 126.00 -4.72 0.60 N 25 1 C5 A U 2672 ? ? C6 A U 2672 ? ? N1 A U 2672 ? ? 119.50 122.70 -3.20 0.50 N 26 1 C8 A G 2673 ? ? N9 A G 2673 ? ? C4 A G 2673 ? ? 109.36 106.40 2.96 0.40 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id G _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 2659 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.069 _pdbx_validate_planes.type 'SIDE CHAIN' # 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 AT7 P P N N 38 AT7 N1 N Y N 39 AT7 C2 C Y N 40 AT7 N3 N Y N 41 AT7 C4 C Y N 42 AT7 C5 C Y N 43 AT7 C6 C Y N 44 AT7 N6 N N N 45 AT7 N7 N Y N 46 AT7 C8 C Y N 47 AT7 N9 N Y N 48 AT7 "C1'" C N R 49 AT7 "C2'" C N R 50 AT7 "C3'" C N S 51 AT7 "N3'" N N N 52 AT7 "O3'" O N N 53 AT7 "C4'" C N R 54 AT7 "N4'" N N N 55 AT7 "O4'" O N N 56 AT7 "C5'" C N N 57 AT7 "N5'" N N N 58 AT7 "O5'" O N N 59 AT7 H2 H N N 60 AT7 H61 H N N 61 AT7 H62 H N N 62 AT7 H8 H N N 63 AT7 "H1'" H N N 64 AT7 "H2'" H N N 65 AT7 "H3'" H N N 66 AT7 "HO3'" H N N 67 AT7 "H4'" H N N 68 AT7 "H5'" H N N 69 AT7 "H5''" H N N 70 AT7 "HN5'" H N N 71 AT7 OP1 O N N 72 AT7 OP2 O N N 73 AT7 OP3 O N N 74 AT7 HOP2 H N N 75 AT7 HOP3 H N N 76 C OP3 O N N 77 C P P N N 78 C OP1 O N N 79 C OP2 O N N 80 C "O5'" O N N 81 C "C5'" C N N 82 C "C4'" C N R 83 C "O4'" O N N 84 C "C3'" C N S 85 C "O3'" O N N 86 C "C2'" C N R 87 C "O2'" O N N 88 C "C1'" C N R 89 C N1 N N N 90 C C2 C N N 91 C O2 O N N 92 C N3 N N N 93 C C4 C N N 94 C N4 N N N 95 C C5 C N N 96 C C6 C N N 97 C HOP3 H N N 98 C HOP2 H N N 99 C "H5'" H N N 100 C "H5''" H N N 101 C "H4'" H N N 102 C "H3'" H N N 103 C "HO3'" H N N 104 C "H2'" H N N 105 C "HO2'" H N N 106 C "H1'" H N N 107 C H41 H N N 108 C H42 H N N 109 C H5 H N N 110 C H6 H N N 111 G OP3 O N N 112 G P P N N 113 G OP1 O N N 114 G OP2 O N N 115 G "O5'" O N N 116 G "C5'" C N N 117 G "C4'" C N R 118 G "O4'" O N N 119 G "C3'" C N S 120 G "O3'" O N N 121 G "C2'" C N R 122 G "O2'" O N N 123 G "C1'" C N R 124 G N9 N Y N 125 G C8 C Y N 126 G N7 N Y N 127 G C5 C Y N 128 G C6 C N N 129 G O6 O N N 130 G N1 N N N 131 G C2 C N N 132 G N2 N N N 133 G N3 N N N 134 G C4 C Y N 135 G HOP3 H N N 136 G HOP2 H N N 137 G "H5'" H N N 138 G "H5''" H N N 139 G "H4'" H N N 140 G "H3'" H N N 141 G "HO3'" H N N 142 G "H2'" H N N 143 G "HO2'" H N N 144 G "H1'" H N N 145 G H8 H N N 146 G H1 H N N 147 G H21 H N N 148 G H22 H N N 149 HOH O O N N 150 HOH H1 H N N 151 HOH H2 H N N 152 U OP3 O N N 153 U P P N N 154 U OP1 O N N 155 U OP2 O N N 156 U "O5'" O N N 157 U "C5'" C N N 158 U "C4'" C N R 159 U "O4'" O N N 160 U "C3'" C N S 161 U "O3'" O N N 162 U "C2'" C N R 163 U "O2'" O N N 164 U "C1'" C N R 165 U N1 N N N 166 U C2 C N N 167 U O2 O N N 168 U N3 N N N 169 U C4 C N N 170 U O4 O N N 171 U C5 C N N 172 U C6 C N N 173 U HOP3 H N N 174 U HOP2 H N N 175 U "H5'" H N N 176 U "H5''" H N N 177 U "H4'" H N N 178 U "H3'" H N N 179 U "HO3'" H N N 180 U "H2'" H N N 181 U "HO2'" H N N 182 U "H1'" H N N 183 U H3 H N N 184 U H5 H N N 185 U H6 H N N 186 # 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 AT7 P "O5'" sing N N 40 AT7 N1 C2 doub Y N 41 AT7 N1 C6 sing Y N 42 AT7 C2 N3 sing Y N 43 AT7 C2 H2 sing N N 44 AT7 N3 C4 doub Y N 45 AT7 C4 C5 sing Y N 46 AT7 C4 N9 sing Y N 47 AT7 C5 C6 doub Y N 48 AT7 C5 N7 sing Y N 49 AT7 C6 N6 sing N N 50 AT7 N6 H61 sing N N 51 AT7 N6 H62 sing N N 52 AT7 N7 C8 doub Y N 53 AT7 C8 N9 sing Y N 54 AT7 C8 H8 sing N N 55 AT7 N9 "C1'" sing N N 56 AT7 "C1'" "C2'" sing N N 57 AT7 "C1'" "O4'" sing N N 58 AT7 "C1'" "H1'" sing N N 59 AT7 "C2'" "C3'" sing N N 60 AT7 "C2'" "N3'" sing N N 61 AT7 "C2'" "H2'" sing N N 62 AT7 "C3'" "O3'" sing N N 63 AT7 "C3'" "C4'" sing N N 64 AT7 "C3'" "H3'" sing N N 65 AT7 "N3'" "N4'" doub N N 66 AT7 "O3'" "HO3'" sing N N 67 AT7 "C4'" "O4'" sing N N 68 AT7 "C4'" "C5'" sing N N 69 AT7 "C4'" "H4'" sing N N 70 AT7 "N4'" "N5'" doub N N 71 AT7 "C5'" "O5'" sing N N 72 AT7 "C5'" "H5'" sing N N 73 AT7 "C5'" "H5''" sing N N 74 AT7 "N5'" "HN5'" sing N N 75 AT7 P OP1 doub N N 76 AT7 P OP2 sing N N 77 AT7 P OP3 sing N N 78 AT7 OP2 HOP2 sing N N 79 AT7 OP3 HOP3 sing N N 80 C OP3 P sing N N 81 C OP3 HOP3 sing N N 82 C P OP1 doub N N 83 C P OP2 sing N N 84 C P "O5'" sing N N 85 C OP2 HOP2 sing N N 86 C "O5'" "C5'" sing N N 87 C "C5'" "C4'" sing N N 88 C "C5'" "H5'" sing N N 89 C "C5'" "H5''" sing N N 90 C "C4'" "O4'" sing N N 91 C "C4'" "C3'" sing N N 92 C "C4'" "H4'" sing N N 93 C "O4'" "C1'" sing N N 94 C "C3'" "O3'" sing N N 95 C "C3'" "C2'" sing N N 96 C "C3'" "H3'" sing N N 97 C "O3'" "HO3'" sing N N 98 C "C2'" "O2'" sing N N 99 C "C2'" "C1'" sing N N 100 C "C2'" "H2'" sing N N 101 C "O2'" "HO2'" sing N N 102 C "C1'" N1 sing N N 103 C "C1'" "H1'" sing N N 104 C N1 C2 sing N N 105 C N1 C6 sing N N 106 C C2 O2 doub N N 107 C C2 N3 sing N N 108 C N3 C4 doub N N 109 C C4 N4 sing N N 110 C C4 C5 sing N N 111 C N4 H41 sing N N 112 C N4 H42 sing N N 113 C C5 C6 doub N N 114 C C5 H5 sing N N 115 C C6 H6 sing N N 116 G OP3 P sing N N 117 G OP3 HOP3 sing N N 118 G P OP1 doub N N 119 G P OP2 sing N N 120 G P "O5'" sing N N 121 G OP2 HOP2 sing N N 122 G "O5'" "C5'" sing N N 123 G "C5'" "C4'" sing N N 124 G "C5'" "H5'" sing N N 125 G "C5'" "H5''" sing N N 126 G "C4'" "O4'" sing N N 127 G "C4'" "C3'" sing N N 128 G "C4'" "H4'" sing N N 129 G "O4'" "C1'" sing N N 130 G "C3'" "O3'" sing N N 131 G "C3'" "C2'" sing N N 132 G "C3'" "H3'" sing N N 133 G "O3'" "HO3'" sing N N 134 G "C2'" "O2'" sing N N 135 G "C2'" "C1'" sing N N 136 G "C2'" "H2'" sing N N 137 G "O2'" "HO2'" sing N N 138 G "C1'" N9 sing N N 139 G "C1'" "H1'" sing N N 140 G N9 C8 sing Y N 141 G N9 C4 sing Y N 142 G C8 N7 doub Y N 143 G C8 H8 sing N N 144 G N7 C5 sing Y N 145 G C5 C6 sing N N 146 G C5 C4 doub Y N 147 G C6 O6 doub N N 148 G C6 N1 sing N N 149 G N1 C2 sing N N 150 G N1 H1 sing N N 151 G C2 N2 sing N N 152 G C2 N3 doub N N 153 G N2 H21 sing N N 154 G N2 H22 sing N N 155 G N3 C4 sing N N 156 HOH O H1 sing N N 157 HOH O H2 sing N N 158 U OP3 P sing N N 159 U OP3 HOP3 sing N N 160 U P OP1 doub N N 161 U P OP2 sing N N 162 U P "O5'" sing N N 163 U OP2 HOP2 sing N N 164 U "O5'" "C5'" sing N N 165 U "C5'" "C4'" sing N N 166 U "C5'" "H5'" sing N N 167 U "C5'" "H5''" sing N N 168 U "C4'" "O4'" sing N N 169 U "C4'" "C3'" sing N N 170 U "C4'" "H4'" sing N N 171 U "O4'" "C1'" sing N N 172 U "C3'" "O3'" sing N N 173 U "C3'" "C2'" sing N N 174 U "C3'" "H3'" sing N N 175 U "O3'" "HO3'" sing N N 176 U "C2'" "O2'" sing N N 177 U "C2'" "C1'" sing N N 178 U "C2'" "H2'" sing N N 179 U "O2'" "HO2'" sing N N 180 U "C1'" N1 sing N N 181 U "C1'" "H1'" sing N N 182 U N1 C2 sing N N 183 U N1 C6 sing N N 184 U C2 O2 doub N N 185 U C2 N3 sing N N 186 U N3 C4 sing N N 187 U N3 H3 sing N N 188 U C4 O4 doub N N 189 U C4 C5 sing N N 190 U C5 C6 doub N N 191 U C5 H5 sing N N 192 U C6 H6 sing N N 193 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3S8U 'double helix' 3S8U 'a-form double helix' 3S8U 'mismatched base pair' 3S8U 'triple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 2 1_555 A U 26 1_555 -2.743 -0.970 0.220 0.115 -15.347 -0.613 1 A_G2648:U2672_A A 2648 ? A 2672 ? 28 1 1 A C 3 1_555 A G 25 1_555 -0.787 0.139 0.423 -0.093 -13.891 1.391 2 A_C2649:G2671_A A 2649 ? A 2671 ? 19 1 1 A C 5 1_555 A G 23 1_555 0.277 -0.144 -0.006 7.050 -18.095 1.528 3 A_C2651:G2669_A A 2651 ? A 2669 ? 19 1 1 A C 6 1_555 A G 22 1_555 0.302 -0.162 0.040 -0.857 -13.591 -2.135 4 A_C2652:G2668_A A 2652 ? A 2668 ? 19 1 1 A U 7 1_555 A C 21 1_555 5.838 -2.235 -0.169 -4.389 -13.307 -13.469 5 A_U2653:C2667_A A 2653 ? A 2667 ? ? ? 1 A U 10 1_555 A A 19 1_555 4.105 -1.836 -0.796 9.392 -20.058 -102.445 6 A_U2656:A2665_A A 2656 ? A 2665 ? 24 4 1 A A 11 1_555 A G 18 1_555 -6.821 -4.328 -0.241 -0.773 6.194 -3.214 7 A_A2657:G2664_A A 2657 ? A 2664 ? 11 10 1 A C 12 1_555 A G 17 1_555 0.174 -0.118 -0.240 9.720 -5.589 0.161 8 A_C2658:G2663_A A 2658 ? A 2663 ? 19 1 1 A G 13 1_555 A A 16 1_555 7.249 -5.335 0.705 17.314 -5.891 -20.219 9 A_G2659:A2662_A A 2659 ? A 2662 ? ? ? # 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 A U 26 1_555 A C 3 1_555 A G 25 1_555 -0.151 -1.067 3.164 -3.051 5.358 45.391 -1.815 -0.057 3.029 6.906 3.932 45.786 1 AA_G2648C2649:G2671U2672_AA A 2648 ? A 2672 ? A 2649 ? A 2671 ? 1 A C 3 1_555 A G 25 1_555 A C 5 1_555 A G 23 1_555 0.009 -3.317 6.034 1.568 8.972 62.306 -3.894 0.116 5.557 8.622 -1.507 62.902 2 AA_C2649C2651:G2669G2671_AA A 2649 ? A 2671 ? A 2651 ? A 2669 ? 1 A C 5 1_555 A G 23 1_555 A C 6 1_555 A G 22 1_555 -0.686 -1.895 3.343 -0.607 9.536 31.995 -4.795 1.101 2.694 16.837 1.073 33.356 3 AA_C2651C2652:G2668G2669_AA A 2651 ? A 2669 ? A 2652 ? A 2668 ? 1 A C 6 1_555 A G 22 1_555 A U 7 1_555 A C 21 1_555 -0.672 -1.062 3.554 5.542 9.171 54.760 -1.695 1.057 3.275 9.865 -5.961 55.719 4 AA_C2652U2653:C2667G2668_AA A 2652 ? A 2668 ? A 2653 ? A 2667 ? 1 A U 7 1_555 A C 21 1_555 A U 10 1_555 A A 19 1_555 0.468 -0.876 6.178 5.476 -5.183 31.877 0.165 0.987 6.231 -9.275 -9.799 32.734 5 AA_U2653U2656:A2665C2667_AA A 2653 ? A 2667 ? A 2656 ? A 2665 ? 1 A U 10 1_555 A A 19 1_555 A A 11 1_555 A G 18 1_555 5.059 -1.310 3.652 -2.236 -1.129 -11.238 8.521 21.280 4.417 5.671 -11.238 -11.513 6 AA_U2656A2657:G2664A2665_AA A 2656 ? A 2665 ? A 2657 ? A 2664 ? 1 A A 11 1_555 A G 18 1_555 A C 12 1_555 A G 17 1_555 0.068 -1.180 3.110 -2.892 3.360 60.003 -1.333 -0.202 3.041 3.355 2.887 60.151 7 AA_A2657C2658:G2663G2664_AA A 2657 ? A 2664 ? A 2658 ? A 2663 ? 1 A C 12 1_555 A G 17 1_555 A G 13 1_555 A A 16 1_555 -2.803 -1.405 3.025 -8.834 5.583 49.982 -2.010 2.657 3.280 6.526 10.324 50.994 8 AA_C2658G2659:A2662G2663_AA A 2658 ? A 2663 ? A 2659 ? A 2662 ? # _pdbx_entity_nonpoly.entity_id 2 _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 3DVZ _pdbx_initial_refinement_model.details 'PDB ENTRY 3DVZ' #