data_4NXH # _entry.id 4NXH # _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 4NXH pdb_00004nxh 10.2210/pdb4nxh/pdb NDB NA2821 ? ? RCSB RCSB083778 ? ? WWPDB D_1000083778 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4NMG ;2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop ; unspecified PDB 4NLF ;2'-Trifluoromethylthiocytidine-modified E. coli 23S rRNA Sarcin Ricin Loop ; unspecified PDB 3DVZ 'Unmodified E. coli 23S rRNA Sarcin Ricin Loop' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4NXH _pdbx_database_status.recvd_initial_deposition_date 2013-12-09 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ennifar, E.' 1 'Micura, R.' 2 'Kosutic, M.' 3 # _citation.id primary _citation.title ;Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 136 _citation.page_first 6656 _citation.page_last 6663 _citation.year 2014 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 1520-5126 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24766131 _citation.pdbx_database_id_DOI 10.1021/ja5005637 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kosutic, M.' 1 ? primary 'Jud, L.' 2 ? primary 'Da Veiga, C.' 3 ? primary 'Frener, M.' 4 ? primary 'Fauster, K.' 5 ? primary 'Kreutz, C.' 6 ? primary 'Ennifar, E.' 7 ? primary 'Micura, R.' 8 ? # _cell.entry_id 4NXH _cell.length_a 29.560 _cell.length_b 29.560 _cell.length_c 76.730 _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 4NXH _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 '23S ribosomal RNA Sarcin Ricin Loop' 8830.335 1 ? ? ? ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 4 water nat water 18.015 130 ? ? ? ? # _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(6FU)CCUAGUACGAGAGGACCGGAGUG' _entity_poly.pdbx_seq_one_letter_code_can UGCXCCUAGUACGAGAGGACCGGAGUG _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 6FU 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 # _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 4NXH _struct_ref.pdbx_db_accession 4NXH _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code 'UGC(6FU)CCUAGUACGAGAGGACCGGAGUG' _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4NXH _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 4NXH _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 6FU 'RNA linking' . "2'-trifluoromethylthio-2'-deoxyuridine" ? 'C10 H14 F3 N2 O8 P S' 410.261 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 4NXH _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 35.20 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;3.2 M ammonium sulfate, 50 mM potassium MOPS, pH 7.0, 10 mM magnesium chloride, 10 mM manganese chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K ; # _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 2M' _diffrn_detector.pdbx_collection_date 2013-11-27 _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 'Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X06DA' _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X06DA _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4NXH _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F -3 _reflns.d_resolution_low 29.560 _reflns.d_resolution_high 1.158 _reflns.number_obs 22732 _reflns.number_all 22865 _reflns.percent_possible_obs 99.3 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 17.8 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 12.1 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.158 _reflns_shell.d_res_low ? _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4NXH _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 22731 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.40 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.560 _refine.ls_d_res_high 1.158 _refine.ls_percent_reflns_obs 99.41 _refine.ls_R_factor_obs 0.1170 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1154 _refine.ls_R_factor_R_free 0.1481 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.00 _refine.ls_number_reflns_R_free 1137 _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] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 0.90 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.60 _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 ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.09 _refine.pdbx_overall_phase_error 15.29 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _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_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 583 _refine_hist.pdbx_number_atoms_ligand 11 _refine_hist.number_atoms_solvent 130 _refine_hist.number_atoms_total 724 _refine_hist.d_res_high 1.158 _refine_hist.d_res_low 29.560 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.010 ? ? 718 'X-RAY DIFFRACTION' ? f_angle_d 1.740 ? ? 1122 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 12.895 ? ? 346 'X-RAY DIFFRACTION' ? f_chiral_restr 0.071 ? ? 146 'X-RAY DIFFRACTION' ? f_plane_restr 0.023 ? ? 29 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _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.redundancy_reflns_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 1.1581 1.2109 2597 0.1718 96.00 0.2227 . . 137 . . . . 'X-RAY DIFFRACTION' . 1.2109 1.2747 2713 0.1344 99.00 0.1868 . . 142 . . . . 'X-RAY DIFFRACTION' . 1.2747 1.3546 2687 0.1231 100.00 0.1734 . . 142 . . . . 'X-RAY DIFFRACTION' . 1.3546 1.4591 2708 0.1097 100.00 0.1478 . . 142 . . . . 'X-RAY DIFFRACTION' . 1.4591 1.6060 2712 0.0992 100.00 0.1297 . . 143 . . . . 'X-RAY DIFFRACTION' . 1.6060 1.8383 2727 0.0862 100.00 0.1130 . . 144 . . . . 'X-RAY DIFFRACTION' . 1.8383 2.3160 2708 0.1232 100.00 0.1554 . . 142 . . . . 'X-RAY DIFFRACTION' . 2.3160 29.5696 2742 0.1171 100.00 0.1458 . . 145 . . . . # _struct.entry_id 4NXH _struct.title ;2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4NXH _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'hairpin, structural, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # _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'" A ? ? 1_555 A 6FU 4 P A ? A C 2649 A 6FU 2650 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale2 covale both ? A C 3 "O3'" B ? ? 1_555 A 6FU 4 P B ? A C 2649 A 6FU 2650 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale3 covale one ? A 6FU 4 "O3'" ? ? ? 1_555 A C 5 P ? ? A 6FU 2650 A C 2651 1_555 ? ? ? ? ? ? ? 1.601 ? ? 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 ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A GOL 2701 ? 9 'BINDING SITE FOR RESIDUE GOL A 2701' AC2 Software A SO4 2702 ? 9 'BINDING SITE FOR RESIDUE SO4 A 2702' # 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_455 ? 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_545 ? 6 AC1 9 C A 20 ? C A 2666 . ? 1_555 ? 7 AC1 9 SO4 C . ? SO4 A 2702 . ? 1_555 ? 8 AC1 9 HOH D . ? HOH A 2836 . ? 1_555 ? 9 AC1 9 HOH D . ? HOH A 2916 . ? 1_555 ? 10 AC2 9 U A 1 ? U A 2647 . ? 1_455 ? 11 AC2 9 A A 14 ? A A 2660 . ? 1_545 ? 12 AC2 9 C A 20 ? C A 2666 . ? 1_555 ? 13 AC2 9 U A 26 ? U A 2672 . ? 4_565 ? 14 AC2 9 GOL B . ? GOL A 2701 . ? 1_555 ? 15 AC2 9 HOH D . ? HOH A 2857 . ? 1_555 ? 16 AC2 9 HOH D . ? HOH A 2868 . ? 1_455 ? 17 AC2 9 HOH D . ? HOH A 2869 . ? 1_555 ? 18 AC2 9 HOH D . ? HOH A 2877 . ? 4_565 ? # _database_PDB_matrix.entry_id 4NXH _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 4NXH _atom_sites.fract_transf_matrix[1][1] 0.033829 _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] 0.033829 _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] 0.013033 _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 F H N O P S # 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 6FU 4 2650 2650 6FU 6FU 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 2701 1 GOL GOL A . C 3 SO4 1 2702 1 SO4 SO4 A . D 4 HOH 1 2801 1 HOH HOH A . D 4 HOH 2 2802 2 HOH HOH A . D 4 HOH 3 2803 3 HOH HOH A . D 4 HOH 4 2804 4 HOH HOH A . D 4 HOH 5 2805 5 HOH HOH A . D 4 HOH 6 2806 6 HOH HOH A . D 4 HOH 7 2807 7 HOH HOH A . D 4 HOH 8 2808 8 HOH HOH A . D 4 HOH 9 2809 9 HOH HOH A . D 4 HOH 10 2810 10 HOH HOH A . D 4 HOH 11 2811 11 HOH HOH A . D 4 HOH 12 2812 12 HOH HOH A . D 4 HOH 13 2813 13 HOH HOH A . D 4 HOH 14 2814 14 HOH HOH A . D 4 HOH 15 2815 15 HOH HOH A . D 4 HOH 16 2816 16 HOH HOH A . D 4 HOH 17 2817 17 HOH HOH A . D 4 HOH 18 2818 18 HOH HOH A . D 4 HOH 19 2819 19 HOH HOH A . D 4 HOH 20 2820 20 HOH HOH A . D 4 HOH 21 2821 21 HOH HOH A . D 4 HOH 22 2822 22 HOH HOH A . D 4 HOH 23 2823 23 HOH HOH A . D 4 HOH 24 2824 24 HOH HOH A . D 4 HOH 25 2825 25 HOH HOH A . D 4 HOH 26 2826 26 HOH HOH A . D 4 HOH 27 2827 27 HOH HOH A . D 4 HOH 28 2828 28 HOH HOH A . D 4 HOH 29 2829 29 HOH HOH A . D 4 HOH 30 2830 30 HOH HOH A . D 4 HOH 31 2831 31 HOH HOH A . D 4 HOH 32 2832 32 HOH HOH A . D 4 HOH 33 2833 33 HOH HOH A . D 4 HOH 34 2834 34 HOH HOH A . D 4 HOH 35 2835 35 HOH HOH A . D 4 HOH 36 2836 36 HOH HOH A . D 4 HOH 37 2837 37 HOH HOH A . D 4 HOH 38 2838 38 HOH HOH A . D 4 HOH 39 2839 39 HOH HOH A . D 4 HOH 40 2840 40 HOH HOH A . D 4 HOH 41 2841 41 HOH HOH A . D 4 HOH 42 2842 42 HOH HOH A . D 4 HOH 43 2843 43 HOH HOH A . D 4 HOH 44 2844 44 HOH HOH A . D 4 HOH 45 2845 45 HOH HOH A . D 4 HOH 46 2846 46 HOH HOH A . D 4 HOH 47 2847 47 HOH HOH A . D 4 HOH 48 2848 48 HOH HOH A . D 4 HOH 49 2849 49 HOH HOH A . D 4 HOH 50 2850 50 HOH HOH A . D 4 HOH 51 2851 51 HOH HOH A . D 4 HOH 52 2852 52 HOH HOH A . D 4 HOH 53 2853 53 HOH HOH A . D 4 HOH 54 2854 54 HOH HOH A . D 4 HOH 55 2855 55 HOH HOH A . D 4 HOH 56 2856 56 HOH HOH A . D 4 HOH 57 2857 57 HOH HOH A . D 4 HOH 58 2858 58 HOH HOH A . D 4 HOH 59 2859 59 HOH HOH A . D 4 HOH 60 2860 60 HOH HOH A . D 4 HOH 61 2861 61 HOH HOH A . D 4 HOH 62 2862 62 HOH HOH A . D 4 HOH 63 2863 63 HOH HOH A . D 4 HOH 64 2864 64 HOH HOH A . D 4 HOH 65 2865 65 HOH HOH A . D 4 HOH 66 2866 66 HOH HOH A . D 4 HOH 67 2867 67 HOH HOH A . D 4 HOH 68 2868 68 HOH HOH A . D 4 HOH 69 2869 69 HOH HOH A . D 4 HOH 70 2870 70 HOH HOH A . D 4 HOH 71 2871 71 HOH HOH A . D 4 HOH 72 2872 72 HOH HOH A . D 4 HOH 73 2873 74 HOH HOH A . D 4 HOH 74 2874 75 HOH HOH A . D 4 HOH 75 2875 76 HOH HOH A . D 4 HOH 76 2876 77 HOH HOH A . D 4 HOH 77 2877 78 HOH HOH A . D 4 HOH 78 2878 79 HOH HOH A . D 4 HOH 79 2879 80 HOH HOH A . D 4 HOH 80 2880 81 HOH HOH A . D 4 HOH 81 2881 82 HOH HOH A . D 4 HOH 82 2882 83 HOH HOH A . D 4 HOH 83 2883 84 HOH HOH A . D 4 HOH 84 2884 85 HOH HOH A . D 4 HOH 85 2885 86 HOH HOH A . D 4 HOH 86 2886 87 HOH HOH A . D 4 HOH 87 2887 88 HOH HOH A . D 4 HOH 88 2888 89 HOH HOH A . D 4 HOH 89 2889 90 HOH HOH A . D 4 HOH 90 2890 91 HOH HOH A . D 4 HOH 91 2891 92 HOH HOH A . D 4 HOH 92 2892 93 HOH HOH A . D 4 HOH 93 2893 94 HOH HOH A . D 4 HOH 94 2894 95 HOH HOH A . D 4 HOH 95 2895 96 HOH HOH A . D 4 HOH 96 2896 97 HOH HOH A . D 4 HOH 97 2897 98 HOH HOH A . D 4 HOH 98 2898 99 HOH HOH A . D 4 HOH 99 2899 100 HOH HOH A . D 4 HOH 100 2900 101 HOH HOH A . D 4 HOH 101 2901 102 HOH HOH A . D 4 HOH 102 2902 103 HOH HOH A . D 4 HOH 103 2903 104 HOH HOH A . D 4 HOH 104 2904 105 HOH HOH A . D 4 HOH 105 2905 106 HOH HOH A . D 4 HOH 106 2906 107 HOH HOH A . D 4 HOH 107 2907 108 HOH HOH A . D 4 HOH 108 2908 109 HOH HOH A . D 4 HOH 109 2909 110 HOH HOH A . D 4 HOH 110 2910 111 HOH HOH A . D 4 HOH 111 2911 112 HOH HOH A . D 4 HOH 112 2912 113 HOH HOH A . D 4 HOH 113 2913 114 HOH HOH A . D 4 HOH 114 2914 115 HOH HOH A . D 4 HOH 115 2915 116 HOH HOH A . D 4 HOH 116 2916 117 HOH HOH A . D 4 HOH 117 2917 118 HOH HOH A . D 4 HOH 118 2918 120 HOH HOH A . D 4 HOH 119 2919 124 HOH HOH A . D 4 HOH 120 2920 125 HOH HOH A . D 4 HOH 121 2921 126 HOH HOH A . D 4 HOH 122 2922 127 HOH HOH A . D 4 HOH 123 2923 128 HOH HOH A . D 4 HOH 124 2924 129 HOH HOH A . D 4 HOH 125 2925 130 HOH HOH A . D 4 HOH 126 2926 131 HOH HOH A . D 4 HOH 127 2927 132 HOH HOH A . D 4 HOH 128 2928 133 HOH HOH A . D 4 HOH 129 2929 134 HOH HOH A . D 4 HOH 130 2930 136 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,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2014-12-10 2 'Structure model' 1 1 2022-06-15 3 'Structure model' 1 2 2023-09-20 # _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' 'Database references' 2 2 'Structure model' 'Derived calculations' 3 3 'Structure model' 'Data collection' 4 3 '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' citation 2 2 'Structure model' citation_author 3 2 'Structure model' database_2 4 2 'Structure model' struct_conn 5 2 'Structure model' struct_site 6 3 'Structure model' chem_comp_atom 7 3 'Structure model' chem_comp_bond 8 3 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.journal_volume' 7 2 'Structure model' '_citation.page_first' 8 2 'Structure model' '_citation.page_last' 9 2 'Structure model' '_citation.pdbx_database_id_DOI' 10 2 'Structure model' '_citation.pdbx_database_id_PubMed' 11 2 'Structure model' '_citation.title' 12 2 'Structure model' '_citation.year' 13 2 'Structure model' '_database_2.pdbx_DOI' 14 2 'Structure model' '_database_2.pdbx_database_accession' 15 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 16 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 17 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 18 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOLREP phasing . ? 1 PHENIX refinement '(phenix.refine: 1.8.2_1309)' ? 2 XDS 'data reduction' . ? 3 XDS 'data scaling' . ? 4 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O5'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 G _pdbx_validate_rmsd_angle.auth_seq_id_1 2655 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 P _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 G _pdbx_validate_rmsd_angle.auth_seq_id_2 2655 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 OP2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 G _pdbx_validate_rmsd_angle.auth_seq_id_3 2655 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 97.77 _pdbx_validate_rmsd_angle.angle_target_value 105.70 _pdbx_validate_rmsd_angle.angle_deviation -7.93 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.90 _pdbx_validate_rmsd_angle.linker_flag N # _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 Y _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 A _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 2654 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id "O3'" _pdbx_unobs_or_zero_occ_atoms.label_alt_id A _pdbx_unobs_or_zero_occ_atoms.label_asym_id A _pdbx_unobs_or_zero_occ_atoms.label_comp_id A _pdbx_unobs_or_zero_occ_atoms.label_seq_id 8 _pdbx_unobs_or_zero_occ_atoms.label_atom_id "O3'" # 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 6FU P P N N 1 6FU OP1 O N N 2 6FU OP2 O N N 3 6FU "O5'" O N N 4 6FU "C5'" C N N 5 6FU "C4'" C N R 6 6FU "O4'" O N N 7 6FU "C3'" C N R 8 6FU "O3'" O N N 9 6FU "C2'" C N R 10 6FU "S2'" S N N 11 6FU "C7'" C N N 12 6FU "F1'" F N N 13 6FU "F2'" F N N 14 6FU "F3'" F N N 15 6FU "C1'" C N R 16 6FU N1 N N N 17 6FU C2 C N N 18 6FU O2 O N N 19 6FU N3 N N N 20 6FU C4 C N N 21 6FU O4 O N N 22 6FU C5 C N N 23 6FU C6 C N N 24 6FU H1 H N N 25 6FU H2 H N N 26 6FU H3 H N N 27 6FU H4 H N N 28 6FU H5 H N N 29 6FU H6 H N N 30 6FU H7 H N N 31 6FU H8 H N N 32 6FU H9 H N N 33 6FU H10 H N N 34 6FU H11 H N N 35 6FU H12 H N N 36 6FU OP3 O N N 37 6FU H13 H N N 38 6FU H14 H N N 39 A OP3 O N N 40 A P P N N 41 A OP1 O N N 42 A OP2 O N N 43 A "O5'" O N N 44 A "C5'" C N N 45 A "C4'" C N R 46 A "O4'" O N N 47 A "C3'" C N S 48 A "O3'" O N N 49 A "C2'" C N R 50 A "O2'" O N N 51 A "C1'" C N R 52 A N9 N Y N 53 A C8 C Y N 54 A N7 N Y N 55 A C5 C Y N 56 A C6 C Y N 57 A N6 N N N 58 A N1 N Y N 59 A C2 C Y N 60 A N3 N Y N 61 A C4 C Y N 62 A HOP3 H N N 63 A HOP2 H N N 64 A "H5'" H N N 65 A "H5''" H N N 66 A "H4'" H N N 67 A "H3'" H N N 68 A "HO3'" H N N 69 A "H2'" H N N 70 A "HO2'" H N N 71 A "H1'" H N N 72 A H8 H N N 73 A H61 H N N 74 A H62 H N N 75 A H2 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 GOL C1 C N N 150 GOL O1 O N N 151 GOL C2 C N N 152 GOL O2 O N N 153 GOL C3 C N N 154 GOL O3 O N N 155 GOL H11 H N N 156 GOL H12 H N N 157 GOL HO1 H N N 158 GOL H2 H N N 159 GOL HO2 H N N 160 GOL H31 H N N 161 GOL H32 H N N 162 GOL HO3 H N N 163 HOH O O N N 164 HOH H1 H N N 165 HOH H2 H N N 166 SO4 S S N N 167 SO4 O1 O N N 168 SO4 O2 O N N 169 SO4 O3 O N N 170 SO4 O4 O N N 171 U OP3 O N N 172 U P P N N 173 U OP1 O N N 174 U OP2 O N N 175 U "O5'" O N N 176 U "C5'" C N N 177 U "C4'" C N R 178 U "O4'" O N N 179 U "C3'" C N S 180 U "O3'" O N N 181 U "C2'" C N R 182 U "O2'" O N N 183 U "C1'" C N R 184 U N1 N N N 185 U C2 C N N 186 U O2 O N N 187 U N3 N N N 188 U C4 C N N 189 U O4 O N N 190 U C5 C N N 191 U C6 C N N 192 U HOP3 H N N 193 U HOP2 H N N 194 U "H5'" H N N 195 U "H5''" H N N 196 U "H4'" H N N 197 U "H3'" H N N 198 U "HO3'" H N N 199 U "H2'" H N N 200 U "HO2'" H N N 201 U "H1'" H N N 202 U H3 H N N 203 U H5 H N N 204 U H6 H N N 205 # 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 6FU OP1 P sing N N 1 6FU P OP2 sing N N 2 6FU P "O5'" sing N N 3 6FU "C5'" "O5'" sing N N 4 6FU "C5'" "C4'" sing N N 5 6FU C5 C6 doub N N 6 6FU C5 C4 sing N N 7 6FU C6 N1 sing N N 8 6FU "O4'" "C4'" sing N N 9 6FU "O4'" "C1'" sing N N 10 6FU "C4'" "C3'" sing N N 11 6FU O4 C4 doub N N 12 6FU C4 N3 sing N N 13 6FU N1 "C1'" sing N N 14 6FU N1 C2 sing N N 15 6FU "C1'" "C2'" sing N N 16 6FU "C3'" "C2'" sing N N 17 6FU "C3'" "O3'" sing N N 18 6FU N3 C2 sing N N 19 6FU C2 O2 doub N N 20 6FU "C2'" "S2'" sing N N 21 6FU "S2'" "C7'" sing N N 22 6FU "F1'" "C7'" sing N N 23 6FU "C7'" "F3'" sing N N 24 6FU "C7'" "F2'" sing N N 25 6FU OP1 H1 sing N N 26 6FU OP2 H2 sing N N 27 6FU "C5'" H3 sing N N 28 6FU "C5'" H4 sing N N 29 6FU "C4'" H5 sing N N 30 6FU "C3'" H6 sing N N 31 6FU "O3'" H7 sing N N 32 6FU "C2'" H8 sing N N 33 6FU "C1'" H9 sing N N 34 6FU N3 H10 sing N N 35 6FU C5 H11 sing N N 36 6FU C6 H12 sing N N 37 6FU P OP3 sing N N 38 6FU P H13 sing N N 39 6FU OP3 H14 sing N N 40 A OP3 P sing N N 41 A OP3 HOP3 sing N N 42 A P OP1 doub N N 43 A P OP2 sing N N 44 A P "O5'" sing N N 45 A OP2 HOP2 sing N N 46 A "O5'" "C5'" sing N N 47 A "C5'" "C4'" sing N N 48 A "C5'" "H5'" sing N N 49 A "C5'" "H5''" sing N N 50 A "C4'" "O4'" sing N N 51 A "C4'" "C3'" sing N N 52 A "C4'" "H4'" sing N N 53 A "O4'" "C1'" sing N N 54 A "C3'" "O3'" sing N N 55 A "C3'" "C2'" sing N N 56 A "C3'" "H3'" sing N N 57 A "O3'" "HO3'" sing N N 58 A "C2'" "O2'" sing N N 59 A "C2'" "C1'" sing N N 60 A "C2'" "H2'" sing N N 61 A "O2'" "HO2'" sing N N 62 A "C1'" N9 sing N N 63 A "C1'" "H1'" sing N N 64 A N9 C8 sing Y N 65 A N9 C4 sing Y N 66 A C8 N7 doub Y N 67 A C8 H8 sing N N 68 A N7 C5 sing Y N 69 A C5 C6 sing Y N 70 A C5 C4 doub Y N 71 A C6 N6 sing N N 72 A C6 N1 doub Y N 73 A N6 H61 sing N N 74 A N6 H62 sing N N 75 A N1 C2 sing Y N 76 A C2 N3 doub Y N 77 A C2 H2 sing N N 78 A N3 C4 sing Y N 79 C OP3 P sing N N 80 C OP3 HOP3 sing N N 81 C P OP1 doub N N 82 C P OP2 sing N N 83 C P "O5'" sing N N 84 C OP2 HOP2 sing N N 85 C "O5'" "C5'" sing N N 86 C "C5'" "C4'" sing N N 87 C "C5'" "H5'" sing N N 88 C "C5'" "H5''" sing N N 89 C "C4'" "O4'" sing N N 90 C "C4'" "C3'" sing N N 91 C "C4'" "H4'" sing N N 92 C "O4'" "C1'" sing N N 93 C "C3'" "O3'" sing N N 94 C "C3'" "C2'" sing N N 95 C "C3'" "H3'" sing N N 96 C "O3'" "HO3'" sing N N 97 C "C2'" "O2'" sing N N 98 C "C2'" "C1'" sing N N 99 C "C2'" "H2'" sing N N 100 C "O2'" "HO2'" sing N N 101 C "C1'" N1 sing N N 102 C "C1'" "H1'" sing N N 103 C N1 C2 sing N N 104 C N1 C6 sing N N 105 C C2 O2 doub N N 106 C C2 N3 sing N N 107 C N3 C4 doub N N 108 C C4 N4 sing N N 109 C C4 C5 sing N N 110 C N4 H41 sing N N 111 C N4 H42 sing N N 112 C C5 C6 doub N N 113 C C5 H5 sing N N 114 C C6 H6 sing N N 115 G OP3 P sing N N 116 G OP3 HOP3 sing N N 117 G P OP1 doub N N 118 G P OP2 sing N N 119 G P "O5'" sing N N 120 G OP2 HOP2 sing N N 121 G "O5'" "C5'" sing N N 122 G "C5'" "C4'" sing N N 123 G "C5'" "H5'" sing N N 124 G "C5'" "H5''" sing N N 125 G "C4'" "O4'" sing N N 126 G "C4'" "C3'" sing N N 127 G "C4'" "H4'" sing N N 128 G "O4'" "C1'" sing N N 129 G "C3'" "O3'" sing N N 130 G "C3'" "C2'" sing N N 131 G "C3'" "H3'" sing N N 132 G "O3'" "HO3'" sing N N 133 G "C2'" "O2'" sing N N 134 G "C2'" "C1'" sing N N 135 G "C2'" "H2'" sing N N 136 G "O2'" "HO2'" sing N N 137 G "C1'" N9 sing N N 138 G "C1'" "H1'" sing N N 139 G N9 C8 sing Y N 140 G N9 C4 sing Y N 141 G C8 N7 doub Y N 142 G C8 H8 sing N N 143 G N7 C5 sing Y N 144 G C5 C6 sing N N 145 G C5 C4 doub Y N 146 G C6 O6 doub N N 147 G C6 N1 sing N N 148 G N1 C2 sing N N 149 G N1 H1 sing N N 150 G C2 N2 sing N N 151 G C2 N3 doub N N 152 G N2 H21 sing N N 153 G N2 H22 sing N N 154 G N3 C4 sing N N 155 GOL C1 O1 sing N N 156 GOL C1 C2 sing N N 157 GOL C1 H11 sing N N 158 GOL C1 H12 sing N N 159 GOL O1 HO1 sing N N 160 GOL C2 O2 sing N N 161 GOL C2 C3 sing N N 162 GOL C2 H2 sing N N 163 GOL O2 HO2 sing N N 164 GOL C3 O3 sing N N 165 GOL C3 H31 sing N N 166 GOL C3 H32 sing N N 167 GOL O3 HO3 sing N N 168 HOH O H1 sing N N 169 HOH O H2 sing N N 170 SO4 S O1 doub N N 171 SO4 S O2 doub N N 172 SO4 S O3 sing N N 173 SO4 S O4 sing N N 174 U OP3 P sing N N 175 U OP3 HOP3 sing N N 176 U P OP1 doub N N 177 U P OP2 sing N N 178 U P "O5'" sing N N 179 U OP2 HOP2 sing N N 180 U "O5'" "C5'" sing N N 181 U "C5'" "C4'" sing N N 182 U "C5'" "H5'" sing N N 183 U "C5'" "H5''" sing N N 184 U "C4'" "O4'" sing N N 185 U "C4'" "C3'" sing N N 186 U "C4'" "H4'" sing N N 187 U "O4'" "C1'" sing N N 188 U "C3'" "O3'" sing N N 189 U "C3'" "C2'" sing N N 190 U "C3'" "H3'" sing N N 191 U "O3'" "HO3'" sing N N 192 U "C2'" "O2'" sing N N 193 U "C2'" "C1'" sing N N 194 U "C2'" "H2'" sing N N 195 U "O2'" "HO2'" sing N N 196 U "C1'" N1 sing N N 197 U "C1'" "H1'" sing N N 198 U N1 C2 sing N N 199 U N1 C6 sing N N 200 U C2 O2 doub N N 201 U C2 N3 sing N N 202 U N3 C4 sing N N 203 U N3 H3 sing N N 204 U C4 O4 doub N N 205 U C4 C5 sing N N 206 U C5 C6 doub N N 207 U C5 H5 sing N N 208 U C6 H6 sing N N 209 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4NXH 'double helix' 4NXH 'a-form double helix' 4NXH 'mismatched base pair' 4NXH '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 -2.773 -0.939 0.257 1.855 -15.688 0.384 1 A_G2648:U2672_A A 2648 ? A 2672 ? 28 1 1 A C 3 1_555 A G 25 1_555 -0.591 0.180 0.406 -1.982 -14.715 -0.194 2 A_C2649:G2671_A A 2649 ? A 2671 ? 19 1 1 A C 5 1_555 A G 23 1_555 0.246 -0.139 -0.027 7.480 -17.574 1.408 3 A_C2651:G2669_A A 2651 ? A 2669 ? 19 1 1 A C 6 1_555 A G 22 1_555 0.333 -0.158 -0.012 -0.491 -13.249 -1.880 4 A_C2652:G2668_A A 2652 ? A 2668 ? 19 1 1 A U 7 1_555 A C 21 1_555 5.760 -2.160 -0.273 -2.637 -14.569 -13.156 5 A_U2653:C2667_A A 2653 ? A 2667 ? ? ? 1 A U 10 1_555 A A 19 1_555 4.097 -1.891 -0.656 8.957 -18.274 -101.856 6 A_U2656:A2665_A A 2656 ? A 2665 ? 24 4 1 A A 11 1_555 A G 18 1_555 -6.811 -4.319 -0.057 -1.273 2.511 -2.955 7 A_A2657:G2664_A A 2657 ? A 2664 ? 11 9 1 A C 12 1_555 A G 17 1_555 0.154 -0.111 -0.098 6.656 -3.363 0.674 8 A_C2658:G2663_A A 2658 ? A 2663 ? 19 1 1 A G 13 1_555 A A 16 1_555 7.235 -5.282 0.718 18.481 -7.482 -19.820 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 -0.412 -1.166 3.319 -3.286 4.028 44.183 -1.913 0.240 3.227 5.333 4.351 44.472 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 0.409 -3.357 5.976 4.969 11.945 61.655 -4.155 -0.003 5.326 11.519 -4.792 62.867 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 -0.665 -1.928 3.355 -1.193 9.086 33.100 -4.627 0.948 2.766 15.580 2.046 34.311 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 -0.599 -0.969 3.529 6.634 9.361 53.746 -1.637 1.065 3.242 10.224 -7.245 54.868 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 0.731 -0.793 6.192 5.387 -4.937 32.121 0.226 0.484 6.278 -8.781 -9.582 32.920 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 5.250 -1.219 3.540 -1.297 -1.949 -12.660 7.932 21.754 3.825 8.743 -5.817 -12.874 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 -0.112 -1.147 3.178 -3.614 4.621 61.443 -1.325 -0.052 3.094 4.511 3.529 61.695 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 -2.813 -1.317 2.918 -7.707 5.504 50.026 -1.893 2.772 3.139 6.442 9.020 50.858 8 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 'SULFATE ION' SO4 4 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 3DVZ _pdbx_initial_refinement_model.details 'PDB ENTRY 3DVZ' #