data_3DW4 # _entry.id 3DW4 # _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 3DW4 pdb_00003dw4 10.2210/pdb3dw4/pdb NDB UR0162 ? ? RCSB RCSB048562 ? ? WWPDB D_1000048562 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1q9a 'Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution' unspecified PDB 3DVZ . unspecified PDB 3DW5 . unspecified PDB 3DW6 . unspecified PDB 3DW7 . unspecified PDB 483D . unspecified # _pdbx_database_status.entry_id 3DW4 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-07-21 _pdbx_database_status.status_code REL _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Olieric, V.' 1 'Rieder, U.' 2 'Lang, K.' 3 'Serganov, A.' 4 'Schulze-Briese, C.' 5 'Micura, R.' 6 'Dumas, P.' 7 'Ennifar, E.' 8 # _citation.id primary _citation.title 'A fast selenium derivatization strategy for crystallization and phasing of RNA structures.' _citation.journal_abbrev Rna _citation.journal_volume 15 _citation.page_first 707 _citation.page_last 715 _citation.year 2009 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19228585 _citation.pdbx_database_id_DOI 10.1261/rna.1499309 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Olieric, V.' 1 ? primary 'Rieder, U.' 2 ? primary 'Lang, K.' 3 ? primary 'Serganov, A.' 4 ? primary 'Schulze-Briese, C.' 5 ? primary 'Micura, R.' 6 ? primary 'Dumas, P.' 7 ? primary 'Ennifar, E.' 8 ? # _cell.entry_id 3DW4 _cell.length_a 29.630 _cell.length_b 29.630 _cell.length_c 76.330 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DW4 _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 # 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 'Sarcin/Ricin Domain from E. Coli 23 S rRNA' 8758.282 1 ? ? ? ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 water nat water 18.015 178 ? ? ? ? # _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 'UGC(OMU)CCUAGUACGAGAGGACCGGAGUG' _entity_poly.pdbx_seq_one_letter_code_can UGCUCCUAGUACGAGAGGACCGGAGUG _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 OMU 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 A n 1 25 G n 1 26 U n 1 27 G n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3DW4 _struct_ref.pdbx_db_accession 3DW4 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 2647 _struct_ref.pdbx_seq_one_letter_code UGCUCCUAGUACGAGAGGACCGGAGUG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3DW4 _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 3DW4 _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 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HOH non-polymer . WATER ? 'H2 O' 18.015 OMU 'RNA linking' n ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; ? 'C10 H15 N2 O9 P' 338.208 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.crystals_number 1 _exptl.entry_id 3DW4 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.91 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 35.70 _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.pH 7.0 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details '3.2 M (NH4)2SO4, 50 mM K-MOPS pH 7.0, 10 mM MgCl2, 10 mM MnCl2, vapor diffusion, hanging drop, temperature 293K' _exptl_crystal_grow.temp_details ? _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.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 '(NH4)2SO4' ? ? ? 1 2 1 K-MOPS ? ? ? 1 3 1 MgCl2 ? ? ? 1 4 1 MnCl2 ? ? ? 1 5 1 H2O ? ? ? 1 6 2 '(NH4)2SO4' ? ? ? 1 7 2 K-MOPS ? ? ? 1 8 2 MgCl2 ? ? ? 1 9 2 MnCl2 ? ? ? 1 10 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 90 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'PSI PILATUS 6M' _diffrn_detector.pdbx_collection_date 2008-04-22 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.85 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X06SA' _diffrn_source.pdbx_wavelength_list 0.85 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X06SA # _reflns.entry_id 3DW4 _reflns.d_resolution_high 0.970 _reflns.number_obs 38820 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_netI_over_sigmaI 31.950 _reflns.percent_possible_obs 99.900 _reflns.B_iso_Wilson_estimate 12.748 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.number_all ? _reflns.pdbx_Rsym_value 0.036 _reflns.pdbx_redundancy 12.7 _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 0.97 _reflns_shell.d_res_low 0.98 _reflns_shell.number_measured_obs 12059 _reflns_shell.number_measured_all ? _reflns_shell.number_unique_obs 1194 _reflns_shell.Rmerge_I_obs ? _reflns_shell.meanI_over_sigI_obs 3.4 _reflns_shell.pdbx_Rsym_value 0.637 _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.percent_possible_all 98.60 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3DW4 _refine.ls_d_res_high 0.970 _refine.ls_d_res_low 27.622 _refine.pdbx_ls_sigma_F 1.99 _refine.ls_percent_reflns_obs 99.950 _refine.ls_number_reflns_obs 38820 _refine.ls_R_factor_obs 0.139 _refine.ls_R_factor_R_work 0.139 _refine.ls_R_factor_R_free 0.150 _refine.ls_percent_reflns_R_free 5.020 _refine.ls_number_reflns_R_free 1947 _refine.B_iso_mean 14.005 _refine.solvent_model_param_bsol 55.530 _refine.solvent_model_param_ksol 0.454 _refine.aniso_B[1][1] -1.345 _refine.aniso_B[2][2] -1.345 _refine.aniso_B[3][3] 2.691 _refine.aniso_B[1][2] -0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] -0.000 _refine.overall_SU_ML 0.100 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.110 _refine.pdbx_solvent_shrinkage_radii 0.900 _refine.pdbx_method_to_determine_struct ? _refine.pdbx_stereochemistry_target_values ML _refine.B_iso_max 48.11 _refine.B_iso_min 7.49 _refine.occupancy_max 1.00 _refine.occupancy_min 0.00 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model 1q9a _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_isotropic_thermal_model ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_ion_probe_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 0 _refine_hist.pdbx_number_atoms_nucleic_acid 580 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 178 _refine_hist.number_atoms_total 764 _refine_hist.d_res_high 0.970 _refine_hist.d_res_low 27.622 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 666 0.004 ? ? 'X-RAY DIFFRACTION' ? f_angle_d 1044 1.173 ? ? 'X-RAY DIFFRACTION' ? f_chiral_restr 131 0.054 ? ? 'X-RAY DIFFRACTION' ? f_plane_restr 27 0.011 ? ? 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 293 28.932 ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 0.970 0.994 14 99.000 2621 . 0.195 0.190 . 165 . 2786 . . 'X-RAY DIFFRACTION' 0.994 1.021 14 100.000 2646 . 0.172 0.211 . 143 . 2789 . . 'X-RAY DIFFRACTION' 1.021 1.051 14 100.000 2619 . 0.148 0.150 . 136 . 2755 . . 'X-RAY DIFFRACTION' 1.051 1.085 14 100.000 2619 . 0.139 0.168 . 131 . 2750 . . 'X-RAY DIFFRACTION' 1.085 1.124 14 100.000 2622 . 0.132 0.136 . 141 . 2763 . . 'X-RAY DIFFRACTION' 1.124 1.169 14 100.000 2618 . 0.124 0.153 . 131 . 2749 . . 'X-RAY DIFFRACTION' 1.169 1.222 14 100.000 2612 . 0.124 0.156 . 143 . 2755 . . 'X-RAY DIFFRACTION' 1.222 1.287 14 100.000 2683 . 0.125 0.131 . 124 . 2807 . . 'X-RAY DIFFRACTION' 1.287 1.367 14 100.000 2624 . 0.135 0.162 . 134 . 2758 . . 'X-RAY DIFFRACTION' 1.367 1.473 14 100.000 2617 . 0.139 0.163 . 156 . 2773 . . 'X-RAY DIFFRACTION' 1.473 1.621 14 100.000 2633 . 0.135 0.132 . 141 . 2774 . . 'X-RAY DIFFRACTION' 1.621 1.855 14 100.000 2637 . 0.120 0.142 . 137 . 2774 . . 'X-RAY DIFFRACTION' 1.855 2.338 14 100.000 2642 . 0.145 0.157 . 133 . 2775 . . 'X-RAY DIFFRACTION' 2.338 27.633 14 100.000 2680 . 0.143 0.143 . 132 . 2812 . . 'X-RAY DIFFRACTION' # _struct.entry_id 3DW4 _struct.title 'Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-OCH3 modified' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3DW4 _struct_keywords.text 'RNA, Sarcin Ricin Loop' _struct_keywords.pdbx_keywords 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 ? # _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 C 3 "O3'" ? ? ? 1_555 A OMU 4 P ? ? A C 2649 A OMU 2650 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale2 covale both ? A OMU 4 "O3'" ? ? ? 1_555 A C 5 P ? ? A OMU 2650 A C 2651 1_555 ? ? ? ? ? ? ? 1.601 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 26 O2 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 26 N3 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A OMU 4 N3 ? ? ? 1_555 A A 24 N1 ? ? A OMU 2650 A A 2670 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A OMU 4 O4 ? ? ? 1_555 A A 24 N6 ? ? A OMU 2650 A A 2670 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 O2 ? ? ? 1_555 A C 21 N4 ? ? A U 2653 A C 2667 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog15 hydrog ? ? A G 9 N2 ? ? ? 1_555 A U 10 O4 ? ? A G 2655 A U 2656 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog16 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 19 N7 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog17 hydrog ? ? A U 10 O2 ? ? ? 1_555 A A 19 N6 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog18 hydrog ? ? A A 11 N6 ? ? ? 1_555 A G 18 N3 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog19 hydrog ? ? A A 11 N7 ? ? ? 1_555 A G 18 N2 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog20 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 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 ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id GOL _struct_site.pdbx_auth_seq_id 1 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 9 _struct_site.details 'BINDING SITE FOR RESIDUE GOL A 1' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 U A 1 ? U A 2647 . ? 1_545 ? 2 AC1 9 U A 7 ? U A 2653 . ? 1_555 ? 3 AC1 9 A A 8 ? A A 2654 . ? 1_555 ? 4 AC1 9 U A 10 ? U A 2656 . ? 1_555 ? 5 AC1 9 A A 14 ? A A 2660 . ? 1_455 ? 6 AC1 9 C A 20 ? C A 2666 . ? 1_555 ? 7 AC1 9 HOH C . ? HOH A 2719 . ? 1_555 ? 8 AC1 9 HOH C . ? HOH A 2757 . ? 1_545 ? 9 AC1 9 HOH C . ? HOH A 2802 . ? 1_555 ? # _atom_sites.entry_id 3DW4 _atom_sites.fract_transf_matrix[1][1] 0.033750 _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] 0.033750 _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] 0.013101 _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 U A . n A 1 2 G 2 2648 2648 G G A . n A 1 3 C 3 2649 2649 C C A . n A 1 4 OMU 4 2650 2650 OMU OMU A . n A 1 5 C 5 2651 2651 C C A . n A 1 6 C 6 2652 2652 C C A . n A 1 7 U 7 2653 2653 U U A . n A 1 8 A 8 2654 2654 A A A . n A 1 9 G 9 2655 2655 G G A . n A 1 10 U 10 2656 2656 U U A . n A 1 11 A 11 2657 2657 A A A . n A 1 12 C 12 2658 2658 C C A . n A 1 13 G 13 2659 2659 G G A . n A 1 14 A 14 2660 2660 A A A . n A 1 15 G 15 2661 2661 G G A . n A 1 16 A 16 2662 2662 A A A . n A 1 17 G 17 2663 2663 G G A . n A 1 18 G 18 2664 2664 G G A . n A 1 19 A 19 2665 2665 A A A . n A 1 20 C 20 2666 2666 C C A . n A 1 21 C 21 2667 2667 C C A . n A 1 22 G 22 2668 2668 G G A . n A 1 23 G 23 2669 2669 G G A . n A 1 24 A 24 2670 2670 A A A . n A 1 25 G 25 2671 2671 G G A . n A 1 26 U 26 2672 2672 U U A . n A 1 27 G 27 2673 2673 G G 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 GOL 1 1 1 GOL GOL A . C 3 HOH 1 2674 2674 HOH HOH A . C 3 HOH 2 2675 2675 HOH HOH A . C 3 HOH 3 2676 2676 HOH HOH A . C 3 HOH 4 2677 2677 HOH HOH A . C 3 HOH 5 2678 2678 HOH HOH A . C 3 HOH 6 2679 2679 HOH HOH A . C 3 HOH 7 2680 2680 HOH HOH A . C 3 HOH 8 2681 2681 HOH HOH A . C 3 HOH 9 2682 2682 HOH HOH A . C 3 HOH 10 2683 2683 HOH HOH A . C 3 HOH 11 2684 2684 HOH HOH A . C 3 HOH 12 2685 2685 HOH HOH A . C 3 HOH 13 2686 2686 HOH HOH A . C 3 HOH 14 2687 2687 HOH HOH A . C 3 HOH 15 2688 2688 HOH HOH A . C 3 HOH 16 2689 2689 HOH HOH A . C 3 HOH 17 2690 2690 HOH HOH A . C 3 HOH 18 2691 2691 HOH HOH A . C 3 HOH 19 2692 2692 HOH HOH A . C 3 HOH 20 2693 2693 HOH HOH A . C 3 HOH 21 2694 2694 HOH HOH A . C 3 HOH 22 2695 2695 HOH HOH A . C 3 HOH 23 2696 2696 HOH HOH A . C 3 HOH 24 2697 2697 HOH HOH A . C 3 HOH 25 2698 2698 HOH HOH A . C 3 HOH 26 2699 2699 HOH HOH A . C 3 HOH 27 2700 2700 HOH HOH A . C 3 HOH 28 2701 2701 HOH HOH A . C 3 HOH 29 2702 2702 HOH HOH A . C 3 HOH 30 2703 2703 HOH HOH A . C 3 HOH 31 2704 2704 HOH HOH A . C 3 HOH 32 2705 2705 HOH HOH A . C 3 HOH 33 2706 2706 HOH HOH A . C 3 HOH 34 2707 2707 HOH HOH A . C 3 HOH 35 2708 2708 HOH HOH A . C 3 HOH 36 2709 2709 HOH HOH A . C 3 HOH 37 2710 2710 HOH HOH A . C 3 HOH 38 2711 2711 HOH HOH A . C 3 HOH 39 2712 2712 HOH HOH A . C 3 HOH 40 2713 2713 HOH HOH A . C 3 HOH 41 2714 2714 HOH HOH A . C 3 HOH 42 2715 2715 HOH HOH A . C 3 HOH 43 2716 2716 HOH HOH A . C 3 HOH 44 2717 2717 HOH HOH A . C 3 HOH 45 2718 2718 HOH HOH A . C 3 HOH 46 2719 2719 HOH HOH A . C 3 HOH 47 2720 2720 HOH HOH A . C 3 HOH 48 2721 2721 HOH HOH A . C 3 HOH 49 2722 2722 HOH HOH A . C 3 HOH 50 2723 2723 HOH HOH A . C 3 HOH 51 2724 2724 HOH HOH A . C 3 HOH 52 2725 2725 HOH HOH A . C 3 HOH 53 2726 2726 HOH HOH A . C 3 HOH 54 2727 2727 HOH HOH A . C 3 HOH 55 2728 2728 HOH HOH A . C 3 HOH 56 2729 2729 HOH HOH A . C 3 HOH 57 2730 2730 HOH HOH A . C 3 HOH 58 2731 2731 HOH HOH A . C 3 HOH 59 2732 2732 HOH HOH A . C 3 HOH 60 2733 2733 HOH HOH A . C 3 HOH 61 2734 2734 HOH HOH A . C 3 HOH 62 2735 2735 HOH HOH A . C 3 HOH 63 2736 2736 HOH HOH A . C 3 HOH 64 2737 2737 HOH HOH A . C 3 HOH 65 2738 2738 HOH HOH A . C 3 HOH 66 2739 2739 HOH HOH A . C 3 HOH 67 2740 2740 HOH HOH A . C 3 HOH 68 2741 2741 HOH HOH A . C 3 HOH 69 2742 2742 HOH HOH A . C 3 HOH 70 2743 2743 HOH HOH A . C 3 HOH 71 2744 2744 HOH HOH A . C 3 HOH 72 2745 2745 HOH HOH A . C 3 HOH 73 2746 2746 HOH HOH A . C 3 HOH 74 2747 2747 HOH HOH A . C 3 HOH 75 2748 2748 HOH HOH A . C 3 HOH 76 2749 2749 HOH HOH A . C 3 HOH 77 2750 2750 HOH HOH A . C 3 HOH 78 2751 2751 HOH HOH A . C 3 HOH 79 2752 2752 HOH HOH A . C 3 HOH 80 2753 2753 HOH HOH A . C 3 HOH 81 2754 2754 HOH HOH A . C 3 HOH 82 2755 2755 HOH HOH A . C 3 HOH 83 2756 2756 HOH HOH A . C 3 HOH 84 2757 2757 HOH HOH A . C 3 HOH 85 2758 2758 HOH HOH A . C 3 HOH 86 2759 2759 HOH HOH A . C 3 HOH 87 2760 2760 HOH HOH A . C 3 HOH 88 2761 2761 HOH HOH A . C 3 HOH 89 2762 2762 HOH HOH A . C 3 HOH 90 2763 2763 HOH HOH A . C 3 HOH 91 2764 2764 HOH HOH A . C 3 HOH 92 2765 2765 HOH HOH A . C 3 HOH 93 2766 2766 HOH HOH A . C 3 HOH 94 2767 2767 HOH HOH A . C 3 HOH 95 2768 2768 HOH HOH A . C 3 HOH 96 2769 2769 HOH HOH A . C 3 HOH 97 2770 2770 HOH HOH A . C 3 HOH 98 2771 2771 HOH HOH A . C 3 HOH 99 2772 2772 HOH HOH A . C 3 HOH 100 2773 2773 HOH HOH A . C 3 HOH 101 2774 2774 HOH HOH A . C 3 HOH 102 2775 2775 HOH HOH A . C 3 HOH 103 2776 2776 HOH HOH A . C 3 HOH 104 2777 2777 HOH HOH A . C 3 HOH 105 2778 2778 HOH HOH A . C 3 HOH 106 2779 2779 HOH HOH A . C 3 HOH 107 2780 2780 HOH HOH A . C 3 HOH 108 2781 2781 HOH HOH A . C 3 HOH 109 2782 2782 HOH HOH A . C 3 HOH 110 2783 2783 HOH HOH A . C 3 HOH 111 2784 2784 HOH HOH A . C 3 HOH 112 2785 2785 HOH HOH A . C 3 HOH 113 2786 2786 HOH HOH A . C 3 HOH 114 2787 2787 HOH HOH A . C 3 HOH 115 2788 2788 HOH HOH A . C 3 HOH 116 2789 2789 HOH HOH A . C 3 HOH 117 2790 2790 HOH HOH A . C 3 HOH 118 2791 2791 HOH HOH A . C 3 HOH 119 2792 2792 HOH HOH A . C 3 HOH 120 2793 2793 HOH HOH A . C 3 HOH 121 2794 2794 HOH HOH A . C 3 HOH 122 2795 2795 HOH HOH A . C 3 HOH 123 2796 2796 HOH HOH A . C 3 HOH 124 2797 2797 HOH HOH A . C 3 HOH 125 2798 2798 HOH HOH A . C 3 HOH 126 2799 2799 HOH HOH A . C 3 HOH 127 2800 2800 HOH HOH A . C 3 HOH 128 2801 2801 HOH HOH A . C 3 HOH 129 2802 2802 HOH HOH A . C 3 HOH 130 2803 2803 HOH HOH A . C 3 HOH 131 2804 2804 HOH HOH A . C 3 HOH 132 2805 2805 HOH HOH A . C 3 HOH 133 2806 2806 HOH HOH A . C 3 HOH 134 2807 2807 HOH HOH A . C 3 HOH 135 2808 2808 HOH HOH A . C 3 HOH 136 2809 2809 HOH HOH A . C 3 HOH 137 2810 2810 HOH HOH A . C 3 HOH 138 2811 2811 HOH HOH A . C 3 HOH 139 2812 2812 HOH HOH A . C 3 HOH 140 2813 2813 HOH HOH A . C 3 HOH 141 2814 2814 HOH HOH A . C 3 HOH 142 2815 2815 HOH HOH A . C 3 HOH 143 2816 2816 HOH HOH A . C 3 HOH 144 2817 2817 HOH HOH A . C 3 HOH 145 2818 2818 HOH HOH A . C 3 HOH 146 2819 2819 HOH HOH A . C 3 HOH 147 2820 2820 HOH HOH A . C 3 HOH 148 2821 2821 HOH HOH A . C 3 HOH 149 2822 2822 HOH HOH A . C 3 HOH 150 2823 2823 HOH HOH A . C 3 HOH 151 2824 2824 HOH HOH A . C 3 HOH 152 2825 2825 HOH HOH A . C 3 HOH 153 2826 2826 HOH HOH A . C 3 HOH 154 2827 2827 HOH HOH A . C 3 HOH 155 2828 2828 HOH HOH A . C 3 HOH 156 2829 2829 HOH HOH A . C 3 HOH 157 2830 2830 HOH HOH A . C 3 HOH 158 2831 2831 HOH HOH A . C 3 HOH 159 2832 2832 HOH HOH A . C 3 HOH 160 2833 2833 HOH HOH A . C 3 HOH 161 2834 2834 HOH HOH A . C 3 HOH 162 2835 2835 HOH HOH A . C 3 HOH 163 2836 2836 HOH HOH A . C 3 HOH 164 2837 2837 HOH HOH A . C 3 HOH 165 2838 2838 HOH HOH A . C 3 HOH 166 2839 2839 HOH HOH A . C 3 HOH 167 2840 2840 HOH HOH A . C 3 HOH 168 2841 2841 HOH HOH A . C 3 HOH 169 2842 2842 HOH HOH A . C 3 HOH 170 2843 2843 HOH HOH A . C 3 HOH 171 2844 2844 HOH HOH A . C 3 HOH 172 2845 2845 HOH HOH A . C 3 HOH 173 2846 2846 HOH HOH A . C 3 HOH 174 2847 2847 HOH HOH A . C 3 HOH 175 2848 2848 HOH HOH A . C 3 HOH 176 2849 2849 HOH HOH A . C 3 HOH 177 2850 2850 HOH HOH A . C 3 HOH 178 2851 2851 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id OMU _pdbx_struct_mod_residue.label_seq_id 4 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id OMU _pdbx_struct_mod_residue.auth_seq_id 2650 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id U _pdbx_struct_mod_residue.details ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; # _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,C # _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 2009-03-24 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 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' 'Non-polymer description' 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' Advisory 4 3 'Structure model' 'Refinement description' 5 4 'Structure model' Advisory 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Database references' 8 4 'Structure model' 'Derived calculations' 9 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 3 'Structure model' pdbx_unobs_or_zero_occ_atoms 2 3 'Structure model' software 3 4 'Structure model' chem_comp_atom 4 4 'Structure model' chem_comp_bond 5 4 'Structure model' database_2 6 4 'Structure model' pdbx_initial_refinement_model 7 4 'Structure model' pdbx_unobs_or_zero_occ_atoms 8 4 'Structure model' struct_conn 9 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 1 PHENIX . ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 RemDAq . ? ? ? ? 'data collection' ? ? ? 4 XDS . ? ? ? ? 'data reduction' ? ? ? 5 MOLREP . ? ? ? ? phasing ? ? ? 6 # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag N _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 0 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id A _pdbx_unobs_or_zero_occ_atoms.auth_comp_id HOH _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 2801 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id O _pdbx_unobs_or_zero_occ_atoms.label_alt_id A _pdbx_unobs_or_zero_occ_atoms.label_asym_id C _pdbx_unobs_or_zero_occ_atoms.label_comp_id HOH _pdbx_unobs_or_zero_occ_atoms.label_seq_id ? _pdbx_unobs_or_zero_occ_atoms.label_atom_id O # 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 GOL C1 C N N 111 GOL O1 O N N 112 GOL C2 C N N 113 GOL O2 O N N 114 GOL C3 C N N 115 GOL O3 O N N 116 GOL H11 H N N 117 GOL H12 H N N 118 GOL HO1 H N N 119 GOL H2 H N N 120 GOL HO2 H N N 121 GOL H31 H N N 122 GOL H32 H N N 123 GOL HO3 H N N 124 HOH O O N N 125 HOH H1 H N N 126 HOH H2 H N N 127 OMU N1 N N N 128 OMU C2 C N N 129 OMU N3 N N N 130 OMU C4 C N N 131 OMU C5 C N N 132 OMU C6 C N N 133 OMU O2 O N N 134 OMU O4 O N N 135 OMU "C1'" C N R 136 OMU "C2'" C N R 137 OMU "O2'" O N N 138 OMU CM2 C N N 139 OMU "C3'" C N R 140 OMU "C4'" C N R 141 OMU "O3'" O N N 142 OMU "O4'" O N N 143 OMU "C5'" C N N 144 OMU "O5'" O N N 145 OMU P P N N 146 OMU OP1 O N N 147 OMU OP2 O N N 148 OMU OP3 O N N 149 OMU HN3 H N N 150 OMU H5 H N N 151 OMU H6 H N N 152 OMU "H1'" H N N 153 OMU "H2'" H N N 154 OMU HM21 H N N 155 OMU HM22 H N N 156 OMU HM23 H N N 157 OMU "H3'" H N N 158 OMU "H4'" H N N 159 OMU "HO3'" H N N 160 OMU "H5'" H N N 161 OMU "H5''" H N N 162 OMU HOP2 H N N 163 OMU HOP3 H N N 164 U OP3 O N N 165 U P P N N 166 U OP1 O N N 167 U OP2 O N N 168 U "O5'" O N N 169 U "C5'" C N N 170 U "C4'" C N R 171 U "O4'" O N N 172 U "C3'" C N S 173 U "O3'" O N N 174 U "C2'" C N R 175 U "O2'" O N N 176 U "C1'" C N R 177 U N1 N N N 178 U C2 C N N 179 U O2 O N N 180 U N3 N N N 181 U C4 C N N 182 U O4 O N N 183 U C5 C N N 184 U C6 C N N 185 U HOP3 H N N 186 U HOP2 H N N 187 U "H5'" H N N 188 U "H5''" H N N 189 U "H4'" H N N 190 U "H3'" H N N 191 U "HO3'" H N N 192 U "H2'" H N N 193 U "HO2'" H N N 194 U "H1'" H N N 195 U H3 H N N 196 U H5 H N N 197 U H6 H N N 198 # 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 GOL C1 O1 sing N N 116 GOL C1 C2 sing N N 117 GOL C1 H11 sing N N 118 GOL C1 H12 sing N N 119 GOL O1 HO1 sing N N 120 GOL C2 O2 sing N N 121 GOL C2 C3 sing N N 122 GOL C2 H2 sing N N 123 GOL O2 HO2 sing N N 124 GOL C3 O3 sing N N 125 GOL C3 H31 sing N N 126 GOL C3 H32 sing N N 127 GOL O3 HO3 sing N N 128 HOH O H1 sing N N 129 HOH O H2 sing N N 130 OMU N1 C2 sing N N 131 OMU N1 C6 sing N N 132 OMU N1 "C1'" sing N N 133 OMU C2 N3 sing N N 134 OMU C2 O2 doub N N 135 OMU N3 C4 sing N N 136 OMU N3 HN3 sing N N 137 OMU C4 C5 sing N N 138 OMU C4 O4 doub N N 139 OMU C5 C6 doub N N 140 OMU C5 H5 sing N N 141 OMU C6 H6 sing N N 142 OMU "C1'" "C2'" sing N N 143 OMU "C1'" "O4'" sing N N 144 OMU "C1'" "H1'" sing N N 145 OMU "C2'" "O2'" sing N N 146 OMU "C2'" "C3'" sing N N 147 OMU "C2'" "H2'" sing N N 148 OMU "O2'" CM2 sing N N 149 OMU CM2 HM21 sing N N 150 OMU CM2 HM22 sing N N 151 OMU CM2 HM23 sing N N 152 OMU "C3'" "C4'" sing N N 153 OMU "C3'" "O3'" sing N N 154 OMU "C3'" "H3'" sing N N 155 OMU "C4'" "O4'" sing N N 156 OMU "C4'" "C5'" sing N N 157 OMU "C4'" "H4'" sing N N 158 OMU "O3'" "HO3'" sing N N 159 OMU "C5'" "O5'" sing N N 160 OMU "C5'" "H5'" sing N N 161 OMU "C5'" "H5''" sing N N 162 OMU "O5'" P sing N N 163 OMU P OP1 doub N N 164 OMU P OP2 sing N N 165 OMU P OP3 sing N N 166 OMU OP2 HOP2 sing N N 167 OMU OP3 HOP3 sing N N 168 U OP3 P sing N N 169 U OP3 HOP3 sing N N 170 U P OP1 doub N N 171 U P OP2 sing N N 172 U P "O5'" sing N N 173 U OP2 HOP2 sing N N 174 U "O5'" "C5'" sing N N 175 U "C5'" "C4'" sing N N 176 U "C5'" "H5'" sing N N 177 U "C5'" "H5''" sing N N 178 U "C4'" "O4'" sing N N 179 U "C4'" "C3'" sing N N 180 U "C4'" "H4'" sing N N 181 U "O4'" "C1'" sing N N 182 U "C3'" "O3'" sing N N 183 U "C3'" "C2'" sing N N 184 U "C3'" "H3'" sing N N 185 U "O3'" "HO3'" sing N N 186 U "C2'" "O2'" sing N N 187 U "C2'" "C1'" sing N N 188 U "C2'" "H2'" sing N N 189 U "O2'" "HO2'" sing N N 190 U "C1'" N1 sing N N 191 U "C1'" "H1'" sing N N 192 U N1 C2 sing N N 193 U N1 C6 sing N N 194 U C2 O2 doub N N 195 U C2 N3 sing N N 196 U N3 C4 sing N N 197 U N3 H3 sing N N 198 U C4 O4 doub N N 199 U C4 C5 sing N N 200 U C5 C6 doub N N 201 U C5 H5 sing N N 202 U C6 H6 sing N N 203 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3DW4 'double helix' 3DW4 'a-form double helix' 3DW4 'mismatched base pair' 3DW4 '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 -2.394 -0.528 0.246 5.383 -12.727 2.044 1 A_G2648:U2672_A A 2648 ? A 2672 ? 28 ? 1 A C 3 1_555 A G 25 1_555 0.263 -0.235 0.152 6.936 -20.110 -0.811 2 A_C2649:G2671_A A 2649 ? A 2671 ? 19 1 1 A OMU 4 1_555 A A 24 1_555 -0.174 -0.047 0.191 3.322 -13.788 1.207 3 A_OMU2650:A2670_A A 2650 ? A 2670 ? 20 1 1 A C 5 1_555 A G 23 1_555 0.281 -0.150 0.018 6.215 -17.306 2.044 4 A_C2651:G2669_A A 2651 ? A 2669 ? 19 1 1 A C 6 1_555 A G 22 1_555 0.298 -0.158 0.050 -2.551 -12.345 -2.249 5 A_C2652:G2668_A A 2652 ? A 2668 ? 19 1 1 A U 7 1_555 A C 21 1_555 5.708 -2.179 -0.184 -2.998 -11.763 -13.033 6 A_U2653:C2667_A A 2653 ? A 2667 ? ? ? 1 A U 10 1_555 A A 19 1_555 4.103 -1.743 -0.789 7.342 -20.945 -104.208 7 A_U2656:A2665_A A 2656 ? A 2665 ? 24 4 1 A A 11 1_555 A G 18 1_555 -6.842 -4.310 -0.069 -2.369 3.197 -3.389 8 A_A2657:G2664_A A 2657 ? A 2664 ? 11 10 1 A C 12 1_555 A G 17 1_555 0.154 -0.087 -0.222 6.926 -1.395 0.901 9 A_C2658:G2663_A A 2658 ? A 2663 ? 19 1 1 A G 13 1_555 A A 16 1_555 7.203 -5.271 0.784 18.711 -4.001 -18.999 10 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 0.006 -1.123 3.135 -0.491 3.426 44.479 -1.776 -0.051 3.044 4.517 0.647 44.607 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 OMU 4 1_555 A A 24 1_555 -0.665 -1.797 3.204 -4.338 8.893 27.909 -5.241 0.464 2.593 17.748 8.657 29.578 2 AA_C2649OMU2650:A2670G2671_AA A 2649 ? A 2671 ? A 2650 ? A 2670 ? 1 A OMU 4 1_555 A A 24 1_555 A C 5 1_555 A G 23 1_555 0.341 -1.100 3.086 0.472 4.471 35.269 -2.404 -0.495 2.933 7.343 -0.775 35.545 3 AA_OMU2650C2651:G2669A2670_AA A 2650 ? A 2670 ? 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 -0.632 -1.909 3.379 -0.268 7.727 32.173 -4.617 1.066 2.861 13.698 0.474 33.065 4 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 -0.443 -0.963 3.470 7.301 8.741 54.513 -1.557 0.913 3.214 9.427 -7.875 55.600 5 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 0.393 -0.883 6.301 4.752 -3.486 32.696 -0.407 0.864 6.351 -6.129 -8.356 33.209 6 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 5.240 -1.335 3.576 -2.146 -2.620 -11.955 9.948 21.119 4.063 12.261 -10.045 -12.424 7 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 0.208 -1.204 3.153 -1.474 4.052 59.951 -1.392 -0.277 3.068 4.050 1.473 60.091 8 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 -2.822 -1.387 2.917 -7.654 6.642 49.513 -2.065 2.804 3.095 7.836 9.029 50.475 9 AA_C2658G2659:A2662G2663_AA A 2658 ? A 2663 ? A 2659 ? A 2662 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 water 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 1Q9A _pdbx_initial_refinement_model.details ? #