data_4PQV # _entry.id 4PQV # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 4PQV pdb_00004pqv 10.2210/pdb4pqv/pdb NDB NA2945 ? ? RCSB RCSB085109 ? ? WWPDB D_1000085109 ? ? # 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 2014-04-30 2 'Structure model' 1 1 2017-11-22 3 'Structure model' 1 2 2024-02-28 # _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' 'Refinement description' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' software 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_struct_conn_angle 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_ref_seq_dif 8 3 '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 2 'Structure model' '_software.name' 2 3 'Structure model' '_database_2.pdbx_DOI' 3 3 'Structure model' '_database_2.pdbx_database_accession' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 15 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 16 3 'Structure model' '_pdbx_struct_conn_angle.value' 17 3 'Structure model' '_struct_conn.pdbx_dist_value' 18 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 19 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 20 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 21 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 22 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 23 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 24 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 25 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 26 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 27 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 28 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 29 3 'Structure model' '_struct_ref_seq_dif.details' 30 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 31 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 32 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4PQV _pdbx_database_status.recvd_initial_deposition_date 2014-03-04 _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 'Chapman, E.G.' 1 'Costantino, D.A.' 2 'Rabe, J.L.' 3 'Moon, S.L.' 4 'Wilusz, J.' 5 'Nix, J.C.' 6 'Kieft, J.S.' 7 # _citation.id primary _citation.title 'The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production.' _citation.journal_abbrev Science _citation.journal_volume 344 _citation.page_first 307 _citation.page_last 310 _citation.year 2014 _citation.journal_id_ASTM SCIEAS _citation.country US _citation.journal_id_ISSN 0036-8075 _citation.journal_id_CSD 0038 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24744377 _citation.pdbx_database_id_DOI 10.1126/science.1250897 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chapman, E.G.' 1 ? primary 'Costantino, D.A.' 2 ? primary 'Rabe, J.L.' 3 ? primary 'Moon, S.L.' 4 ? primary 'Wilusz, J.' 5 ? primary 'Nix, J.C.' 6 ? primary 'Kieft, J.S.' 7 ? # 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 'XRN1-resistant flaviviral RNA' 22095.186 1 ? 'U2G, G-U pair insertion' ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 9 ? ? ? ? 3 water nat water 18.015 7 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGGUCAGAUCGGCGAAAGUCGCCACUUCGCCGAGGAGUGCAAUCUGUGAGGCCCCAGGAGGACUGGGU _entity_poly.pdbx_seq_one_letter_code_can GGGUCAGAUCGGCGAAAGUCGCCACUUCGCCGAGGAGUGCAAUCUGUGAGGCCCCAGGAGGACUGGGU _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 G n 1 4 U n 1 5 C n 1 6 A n 1 7 G n 1 8 A n 1 9 U n 1 10 C n 1 11 G n 1 12 G n 1 13 C n 1 14 G n 1 15 A n 1 16 A n 1 17 A n 1 18 G n 1 19 U n 1 20 C n 1 21 G n 1 22 C n 1 23 C n 1 24 A n 1 25 C n 1 26 U n 1 27 U n 1 28 C n 1 29 G n 1 30 C n 1 31 C n 1 32 G n 1 33 A n 1 34 G n 1 35 G n 1 36 A n 1 37 G n 1 38 U n 1 39 G n 1 40 C n 1 41 A n 1 42 A n 1 43 U n 1 44 C n 1 45 U n 1 46 G n 1 47 U n 1 48 G n 1 49 A n 1 50 G n 1 51 G n 1 52 C n 1 53 C n 1 54 C n 1 55 C n 1 56 A n 1 57 G n 1 58 G n 1 59 A n 1 60 G n 1 61 G n 1 62 A n 1 63 C n 1 64 U n 1 65 G n 1 66 G n 1 67 G n 1 68 U 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 'Murray Valley encephalitis virus' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 11079 _pdbx_entity_src_syn.details 'RNA was prepared by in vitro transcription with T7 polymerase' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 G 3 3 3 G G A . n A 1 4 U 4 4 4 U U A . n A 1 5 C 5 5 5 C C A . n A 1 6 A 6 6 6 A A A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 U 9 9 9 U U A . n A 1 10 C 10 10 10 C C A . n A 1 11 G 11 11 11 G G A . n A 1 12 G 12 12 12 G G A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n A 1 15 A 15 15 15 A A A . n A 1 16 A 16 16 16 A A A . n A 1 17 A 17 17 17 A A A . n A 1 18 G 18 18 18 G G A . n A 1 19 U 19 19 19 U U A . n A 1 20 C 20 20 20 C C A . n A 1 21 G 21 21 21 G G A . n A 1 22 C 22 22 22 C C A . n A 1 23 C 23 23 23 C C A . n A 1 24 A 24 24 24 A A A . n A 1 25 C 25 25 25 C C A . n A 1 26 U 26 26 26 U U A . n A 1 27 U 27 27 27 U U A . n A 1 28 C 28 28 28 C C A . n A 1 29 G 29 29 29 G G A . n A 1 30 C 30 30 30 C C A . n A 1 31 C 31 31 31 C C A . n A 1 32 G 32 32 32 G G A . n A 1 33 A 33 33 33 A A A . n A 1 34 G 34 34 34 G G A . n A 1 35 G 35 35 35 G G A . n A 1 36 A 36 36 36 A A A . n A 1 37 G 37 37 37 G G A . n A 1 38 U 38 38 38 U U A . n A 1 39 G 39 39 39 G G A . n A 1 40 C 40 40 40 C C A . n A 1 41 A 41 41 41 A A A . n A 1 42 A 42 42 42 A A A . n A 1 43 U 43 43 43 U U A . n A 1 44 C 44 44 44 C C A . n A 1 45 U 45 45 45 U U A . n A 1 46 G 46 46 46 G G A . n A 1 47 U 47 47 47 U U A . n A 1 48 G 48 48 48 G G A . n A 1 49 A 49 49 49 A A A . n A 1 50 G 50 50 50 G G A . n A 1 51 G 51 51 51 G G A . n A 1 52 C 52 52 52 C C A . n A 1 53 C 53 53 53 C C A . n A 1 54 C 54 54 54 C C A . n A 1 55 C 55 55 55 C C A . n A 1 56 A 56 56 56 A A A . n A 1 57 G 57 57 57 G G A . n A 1 58 G 58 58 58 G G A . n A 1 59 A 59 59 59 A A A . n A 1 60 G 60 60 60 G G A . n A 1 61 G 61 61 61 G G A . n A 1 62 A 62 62 62 A A A . n A 1 63 C 63 63 63 C C A . n A 1 64 U 64 64 64 U U A . n A 1 65 G 65 65 65 G G A . n A 1 66 G 66 66 66 G G A . n A 1 67 G 67 67 67 G G A . n A 1 68 U 68 68 68 U U 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 MG 1 101 1 MG MG A . C 2 MG 1 102 1 MG MG A . D 2 MG 1 103 1 MG MG A . E 2 MG 1 104 1 MG MG A . F 2 MG 1 105 1 MG MG A . G 2 MG 1 106 1 MG MG A . H 2 MG 1 107 1 MG MG A . I 2 MG 1 108 1 MG MG A . J 2 MG 1 109 1 MG MG A . K 3 HOH 1 201 1 HOH HOH A . K 3 HOH 2 202 2 HOH HOH A . K 3 HOH 3 203 3 HOH HOH A . K 3 HOH 4 204 4 HOH HOH A . K 3 HOH 5 205 5 HOH HOH A . K 3 HOH 6 206 6 HOH HOH A . K 3 HOH 7 207 13 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal Blu-Ice 'data collection' Ice ? 1 PHENIX 'model building' . ? 2 PHENIX refinement '(phenix.refine: 1.8.4_1496)' ? 3 d*TREK 'data reduction' . ? 4 d*TREK 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 4PQV _cell.length_a 76.698 _cell.length_b 76.698 _cell.length_c 76.448 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 4PQV _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4PQV _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.94 _exptl_crystal.density_percent_sol 58.13 _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 7.5 _exptl_crystal_grow.pdbx_details ;drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at 13000 x g) + 2 uL 10% MPD, 40 mM sodium cacodylate, pH 6.0, 12 mM spermine, 80 mM sodium chloride, 20 mM magnesium chloride (Nucleic Acid Mini-Screen kit, Hampton Research), well: 20-35% MPD, crystals appeared within 2-3 days and grew to full size over 1-2 weeks. To obtain derivatized crystals for phasing, 5 uL 4 mM iridium (III) hexammine in RNase-free water was added directly to crystallization drops and well solutions <35% MPD were replaced with 35% MPD. Wells were then re-sealed and allowed to re-equilibrate for at least 2 days, VAPOR DIFFUSION, SITTING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CMOS _diffrn_detector.type TAURUS-1 _diffrn_detector.pdbx_collection_date 2013-09-27 _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 'Rosenbaum-Rock sagitally focused 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 1.0972 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 4.2.2' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 4.2.2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0972 # _reflns.entry_id 4PQV _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.14 _reflns.d_resolution_high 2.45 _reflns.number_obs 9499 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.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 2.45 _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 ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4PQV _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 8418 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.39 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 50.140 _refine.ls_d_res_high 2.463 _refine.ls_percent_reflns_obs 85.47 _refine.ls_R_factor_obs 0.2357 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2303 _refine.ls_R_factor_R_free 0.2835 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.91 _refine.ls_number_reflns_R_free 824 _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 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.35 _refine.pdbx_overall_phase_error 38.25 _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 1466 _refine_hist.pdbx_number_atoms_ligand 9 _refine_hist.number_atoms_solvent 7 _refine_hist.number_atoms_total 1482 _refine_hist.d_res_high 2.463 _refine_hist.d_res_low 50.140 # 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 0.006 ? ? 1641 'X-RAY DIFFRACTION' ? f_angle_d 1.247 ? ? 2560 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 14.545 ? ? 813 'X-RAY DIFFRACTION' ? f_chiral_restr 0.050 ? ? 340 'X-RAY DIFFRACTION' ? f_plane_restr 0.007 ? ? 68 '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' . 2.463 2.5422 180 0.4780 13.00 0.6652 . . 24 . . . . 'X-RAY DIFFRACTION' . 2.5422 2.6331 611 0.4380 40.00 0.4572 . . 63 . . . . 'X-RAY DIFFRACTION' . 2.6331 2.7385 1344 0.3632 91.00 0.3844 . . 142 . . . . 'X-RAY DIFFRACTION' . 2.7385 2.8631 1450 0.3357 100.00 0.3826 . . 165 . . . . 'X-RAY DIFFRACTION' . 2.8631 3.0141 1495 0.3115 100.00 0.3750 . . 165 . . . . 'X-RAY DIFFRACTION' . 3.0141 3.2029 1478 0.2623 100.00 0.2777 . . 166 . . . . 'X-RAY DIFFRACTION' . 3.2029 3.4501 1483 0.2303 100.00 0.2881 . . 166 . . . . 'X-RAY DIFFRACTION' . 3.4501 3.7972 1507 0.2166 100.00 0.2516 . . 159 . . . . 'X-RAY DIFFRACTION' . 3.7972 4.3464 1481 0.2010 100.00 0.2710 . . 164 . . . . 'X-RAY DIFFRACTION' . 4.3464 5.4749 1510 0.2051 100.00 0.2577 . . 165 . . . . 'X-RAY DIFFRACTION' . 5.4749 50.1505 1477 0.2051 99.00 0.2714 . . 163 . . . . # _database_PDB_matrix.entry_id 4PQV _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 # _struct.entry_id 4PQV _struct.title ;Crystal structure of an Xrn1-resistant RNA from the 3' untranslated region of a flavivirus (Murray Valley Encephalitis virus) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4PQV _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;flavivirus, 3' untranslated region, sfRNA, pseudoknot, Type C RNA three-way junction, Xrn1 resistant RNA, xrRNA), resists degradation, exonuclease Xrn1, small flaviviral RNA, 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 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 3 ? # _struct_ref.id 1 _struct_ref.db_name GB _struct_ref.db_code KC852196.1 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GUGUCAGAUCGCGAAAGCGCCACUUCGCCGAGGAGUGCAAUCUGUGAGGCCCCAGGAGGACUGGGU _struct_ref.pdbx_align_begin 10594 _struct_ref.pdbx_db_accession KC852196.1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4PQV _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 68 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession KC852196.1 _struct_ref_seq.db_align_beg 10594 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10659 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 68 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4PQV G A 2 ? GB KC852196.1 U 10595 'engineered mutation' 2 1 1 4PQV G A 11 ? GB KC852196.1 ? ? insertion 11 2 1 4PQV U A 19 ? GB KC852196.1 ? ? insertion 19 3 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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,E,F,G,H,I,J,K # _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 # _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 metalc1 metalc ? ? A C 5 OP2 ? ? ? 1_555 C MG . MG ? ? A C 5 A MG 102 1_555 ? ? ? ? ? ? ? 2.215 ? ? metalc2 metalc ? ? A G 11 O6 ? ? ? 1_555 H MG . MG ? ? A G 11 A MG 107 1_555 ? ? ? ? ? ? ? 2.988 ? ? metalc3 metalc ? ? A A 16 OP1 ? ? ? 1_555 E MG . MG ? ? A A 16 A MG 104 1_555 ? ? ? ? ? ? ? 2.997 ? ? metalc4 metalc ? ? A C 23 OP2 ? ? ? 1_555 C MG . MG ? ? A C 23 A MG 102 1_555 ? ? ? ? ? ? ? 1.776 ? ? metalc5 metalc ? ? A G 67 O6 ? ? ? 1_555 J MG . MG ? ? A G 67 A MG 109 1_555 ? ? ? ? ? ? ? 2.233 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 102 A HOH 201 1_555 ? ? ? ? ? ? ? 1.999 ? ? metalc7 metalc ? ? C MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 102 A HOH 202 1_555 ? ? ? ? ? ? ? 2.088 ? ? metalc8 metalc ? ? C MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 102 A HOH 203 1_555 ? ? ? ? ? ? ? 2.182 ? ? metalc9 metalc ? ? C MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 102 A HOH 207 1_555 ? ? ? ? ? ? ? 2.225 ? ? metalc10 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 104 A HOH 204 1_555 ? ? ? ? ? ? ? 2.249 ? ? metalc11 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 104 A HOH 205 1_555 ? ? ? ? ? ? ? 2.354 ? ? metalc12 metalc ? ? E MG . MG ? ? ? 1_555 K HOH . O ? ? A MG 104 A HOH 206 1_555 ? ? ? ? ? ? ? 2.769 ? ? hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 40 N3 ? ? A G 3 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 40 O2 ? ? A G 3 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 40 N4 ? ? A G 3 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 24 N7 ? ? A U 4 A A 24 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog5 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 24 N6 ? ? A U 4 A A 24 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog6 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 46 N1 ? ? A C 5 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 46 O6 ? ? A C 5 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 46 N2 ? ? A C 5 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 45 N3 ? ? A A 6 A U 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 45 O4 ? ? A A 6 A U 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 44 N3 ? ? A G 7 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 44 O2 ? ? A G 7 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 44 N4 ? ? A G 7 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 43 N3 ? ? A A 8 A U 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 43 O4 ? ? A A 8 A U 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 9 N3 ? ? ? 1_555 A A 42 N1 ? ? A U 9 A A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 9 O4 ? ? ? 1_555 A A 42 N6 ? ? A U 9 A A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 10 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 10 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 10 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog22 hydrog ? ? A G 12 N1 ? ? ? 1_555 A U 19 O2 ? ? A G 12 A U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A G 12 O6 ? ? ? 1_555 A U 19 N3 ? ? A G 12 A U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog24 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 18 N1 ? ? A C 13 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 18 O6 ? ? A C 13 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 18 N2 ? ? A C 13 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 14 N2 ? ? ? 1_555 A A 17 N7 ? ? A G 14 A A 17 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog28 hydrog ? ? A C 23 N3 ? ? ? 1_555 A G 39 N1 ? ? A C 23 A G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 23 N4 ? ? ? 1_555 A G 39 O6 ? ? A C 23 A G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 23 O2 ? ? ? 1_555 A G 39 N2 ? ? A C 23 A G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 37 N1 ? ? A C 25 A G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 37 O6 ? ? A C 25 A G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 37 N2 ? ? A C 25 A G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 26 N3 ? ? ? 1_555 A A 36 N1 ? ? A U 26 A A 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A U 26 O4 ? ? ? 1_555 A A 36 N6 ? ? A U 26 A A 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A U 27 N3 ? ? ? 1_555 A G 35 O6 ? ? A U 27 A G 35 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog37 hydrog ? ? A U 27 O2 ? ? ? 1_555 A G 35 N1 ? ? A U 27 A G 35 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog38 hydrog ? ? A C 28 N3 ? ? ? 1_555 A G 34 N1 ? ? A C 28 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 28 N4 ? ? ? 1_555 A G 34 O6 ? ? A C 28 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 28 O2 ? ? ? 1_555 A G 34 N2 ? ? A C 28 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A U 47 N3 ? ? ? 1_555 A A 49 N7 ? ? A U 47 A A 49 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog42 hydrog ? ? A U 47 O4 ? ? ? 1_555 A A 49 N6 ? ? A U 47 A A 49 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog43 hydrog ? ? A C 53 N3 ? ? ? 1_555 A G 67 N1 ? ? A C 53 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 53 N4 ? ? ? 1_555 A G 67 O6 ? ? A C 53 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 53 O2 ? ? ? 1_555 A G 67 N2 ? ? A C 53 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 54 N3 ? ? ? 1_555 A G 66 N1 ? ? A C 54 A G 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 54 N4 ? ? ? 1_555 A G 66 O6 ? ? A C 54 A G 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 54 O2 ? ? ? 1_555 A G 66 N2 ? ? A C 54 A G 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 55 N3 ? ? ? 1_555 A G 65 N1 ? ? A C 55 A G 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 55 N4 ? ? ? 1_555 A G 65 O6 ? ? A C 55 A G 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 55 O2 ? ? ? 1_555 A G 65 N2 ? ? A C 55 A G 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A A 56 N1 ? ? ? 1_555 A U 64 N3 ? ? A A 56 A U 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A A 56 N6 ? ? ? 1_555 A U 64 O4 ? ? A A 56 A U 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A G 57 N1 ? ? ? 1_555 A C 63 N3 ? ? A G 57 A C 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A G 57 N2 ? ? ? 1_555 A C 63 O2 ? ? A G 57 A C 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A G 57 O6 ? ? ? 1_555 A C 63 N4 ? ? A G 57 A C 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A G 58 N2 ? ? ? 1_555 A A 62 N7 ? ? A G 58 A A 62 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog58 hydrog ? ? A G 58 N3 ? ? ? 1_555 A A 62 N6 ? ? A G 58 A A 62 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog59 hydrog ? ? A G 66 N2 ? ? ? 1_555 A U 68 O4 ? ? A G 66 A U 68 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP2 ? A C 5 ? A C 5 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 OP2 ? A C 23 ? A C 23 ? 1_555 92.8 ? 2 OP2 ? A C 5 ? A C 5 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 201 ? 1_555 87.8 ? 3 OP2 ? A C 23 ? A C 23 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 201 ? 1_555 135.0 ? 4 OP2 ? A C 5 ? A C 5 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 202 ? 1_555 154.9 ? 5 OP2 ? A C 23 ? A C 23 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 202 ? 1_555 90.0 ? 6 O ? K HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 202 ? 1_555 107.5 ? 7 OP2 ? A C 5 ? A C 5 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 203 ? 1_555 78.5 ? 8 OP2 ? A C 23 ? A C 23 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 203 ? 1_555 155.7 ? 9 O ? K HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 203 ? 1_555 67.9 ? 10 O ? K HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 203 ? 1_555 88.8 ? 11 OP2 ? A C 5 ? A C 5 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 207 ? 1_555 64.1 ? 12 OP2 ? A C 23 ? A C 23 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 207 ? 1_555 92.8 ? 13 O ? K HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 207 ? 1_555 126.8 ? 14 O ? K HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 207 ? 1_555 90.9 ? 15 O ? K HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? K HOH . ? A HOH 207 ? 1_555 63.0 ? 16 OP1 ? A A 16 ? A A 16 ? 1_555 MG ? E MG . ? A MG 104 ? 1_555 O ? K HOH . ? A HOH 204 ? 1_555 165.5 ? 17 OP1 ? A A 16 ? A A 16 ? 1_555 MG ? E MG . ? A MG 104 ? 1_555 O ? K HOH . ? A HOH 205 ? 1_555 117.5 ? 18 O ? K HOH . ? A HOH 204 ? 1_555 MG ? E MG . ? A MG 104 ? 1_555 O ? K HOH . ? A HOH 205 ? 1_555 75.7 ? 19 OP1 ? A A 16 ? A A 16 ? 1_555 MG ? E MG . ? A MG 104 ? 1_555 O ? K HOH . ? A HOH 206 ? 1_555 142.4 ? 20 O ? K HOH . ? A HOH 204 ? 1_555 MG ? E MG . ? A MG 104 ? 1_555 O ? K HOH . ? A HOH 206 ? 1_555 50.6 ? 21 O ? K HOH . ? A HOH 205 ? 1_555 MG ? E MG . ? A MG 104 ? 1_555 O ? K HOH . ? A HOH 206 ? 1_555 48.7 ? # 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 MG 102 ? 6 'BINDING SITE FOR RESIDUE MG A 102' AC2 Software A MG 103 ? 1 'BINDING SITE FOR RESIDUE MG A 103' AC3 Software A MG 104 ? 6 'BINDING SITE FOR RESIDUE MG A 104' AC4 Software A MG 105 ? 1 'BINDING SITE FOR RESIDUE MG A 105' AC5 Software A MG 107 ? 1 'BINDING SITE FOR RESIDUE MG A 107' AC6 Software A MG 108 ? 1 'BINDING SITE FOR RESIDUE MG A 108' AC7 Software A MG 109 ? 2 'BINDING SITE FOR RESIDUE MG A 109' # 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 6 C A 5 ? C A 5 . ? 1_555 ? 2 AC1 6 C A 23 ? C A 23 . ? 1_555 ? 3 AC1 6 HOH K . ? HOH A 201 . ? 1_555 ? 4 AC1 6 HOH K . ? HOH A 202 . ? 1_555 ? 5 AC1 6 HOH K . ? HOH A 203 . ? 1_555 ? 6 AC1 6 HOH K . ? HOH A 207 . ? 1_555 ? 7 AC2 1 G A 51 ? G A 51 . ? 1_555 ? 8 AC3 6 G A 14 ? G A 14 . ? 1_555 ? 9 AC3 6 A A 16 ? A A 16 . ? 1_555 ? 10 AC3 6 G A 58 ? G A 58 . ? 5_565 ? 11 AC3 6 HOH K . ? HOH A 204 . ? 1_555 ? 12 AC3 6 HOH K . ? HOH A 205 . ? 1_555 ? 13 AC3 6 HOH K . ? HOH A 206 . ? 1_555 ? 14 AC4 1 G A 58 ? G A 58 . ? 1_555 ? 15 AC5 1 G A 11 ? G A 11 . ? 1_555 ? 16 AC6 1 A A 59 ? A A 59 . ? 5_565 ? 17 AC7 2 G A 66 ? G A 66 . ? 1_555 ? 18 AC7 2 G A 67 ? G A 67 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 205 ? ? O A HOH 206 ? ? 2.14 2 1 O A HOH 204 ? ? O A HOH 206 ? ? 2.19 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A G 21 ? ? "C1'" A G 21 ? ? N9 A G 21 ? ? 112.80 108.50 4.30 0.70 N 2 1 C6 A C 31 ? ? N1 A C 31 ? ? C2 A C 31 ? ? 117.83 120.30 -2.47 0.40 N 3 1 N1 A G 32 ? ? C2 A G 32 ? ? N3 A G 32 ? ? 128.51 123.90 4.61 0.60 N 4 1 C2 A G 32 ? ? N3 A G 32 ? ? C4 A G 32 ? ? 107.80 111.90 -4.10 0.50 N 5 1 C6 A G 32 ? ? C5 A G 32 ? ? N7 A G 32 ? ? 126.28 130.40 -4.12 0.60 N 6 1 N1 A G 32 ? ? C2 A G 32 ? ? N2 A G 32 ? ? 108.18 116.20 -8.02 0.90 N 7 1 C5 A G 48 ? ? N7 A G 48 ? ? C8 A G 48 ? ? 100.68 104.30 -3.62 0.50 N 8 1 N7 A G 48 ? ? C8 A G 48 ? ? N9 A G 48 ? ? 117.33 113.10 4.23 0.50 N 9 1 C8 A G 48 ? ? N9 A G 48 ? ? C4 A G 48 ? ? 101.92 106.40 -4.48 0.40 N 10 1 N9 A G 48 ? ? C4 A G 48 ? ? C5 A G 48 ? ? 107.96 105.40 2.56 0.40 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 MG MG MG N N 114 U OP3 O N N 115 U P P N N 116 U OP1 O N N 117 U OP2 O N N 118 U "O5'" O N N 119 U "C5'" C N N 120 U "C4'" C N R 121 U "O4'" O N N 122 U "C3'" C N S 123 U "O3'" O N N 124 U "C2'" C N R 125 U "O2'" O N N 126 U "C1'" C N R 127 U N1 N N N 128 U C2 C N N 129 U O2 O N N 130 U N3 N N N 131 U C4 C N N 132 U O4 O N N 133 U C5 C N N 134 U C6 C N N 135 U HOP3 H N N 136 U HOP2 H N N 137 U "H5'" H N N 138 U "H5''" H N N 139 U "H4'" H N N 140 U "H3'" H N N 141 U "HO3'" H N N 142 U "H2'" H N N 143 U "HO2'" H N N 144 U "H1'" H N N 145 U H3 H N N 146 U H5 H N N 147 U H6 H N N 148 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4PQV 'double helix' 4PQV 'a-form double helix' 4PQV 'hairpin loop' 4PQV tetraloop 4PQV 'bulge loop' 4PQV 'mismatched base pair' 4PQV 'three-way junction' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 3 1_555 A C 40 1_555 -0.404 -0.309 0.496 15.721 -1.973 2.174 1 A_G3:C40_A A 3 ? A 40 ? 19 1 1 A C 23 1_555 A G 39 1_555 0.307 -0.616 0.526 -4.693 -8.478 -1.097 2 A_C23:G39_A A 23 ? A 39 ? 19 1 1 A A 24 1_555 A U 4 1_555 0.267 -3.294 -0.608 8.694 -1.868 60.777 3 A_A24:U4_A A 24 ? A 4 ? 23 3 1 A C 25 1_555 A G 37 1_555 0.208 -0.204 0.276 2.914 -16.239 -3.839 4 A_C25:G37_A A 25 ? A 37 ? 19 1 1 A U 26 1_555 A A 36 1_555 -0.179 -0.231 -0.554 8.783 -24.847 -0.638 5 A_U26:A36_A A 26 ? A 36 ? 20 1 1 A U 27 1_555 A G 35 1_555 2.230 -0.808 0.216 0.491 -20.504 3.529 6 A_U27:G35_A A 27 ? A 35 ? 28 1 1 A C 28 1_555 A G 34 1_555 0.102 -0.441 0.226 0.107 -12.334 -0.550 7 A_C28:G34_A A 28 ? A 34 ? 19 1 1 A A 17 1_555 A G 14 1_555 -8.168 -4.882 1.091 -8.147 -18.741 -56.245 8 A_A17:G14_A A 17 ? A 14 ? ? ? 1 A G 18 1_555 A C 13 1_555 -0.219 -0.205 -0.302 -3.679 -7.974 -0.026 9 A_G18:C13_A A 18 ? A 13 ? 19 1 1 A U 19 1_555 A G 12 1_555 2.285 -0.026 -0.046 4.781 -8.794 3.725 10 A_U19:G12_A A 19 ? A 12 ? 28 1 1 A C 20 1_555 A G 11 1_555 0.182 0.480 0.356 -1.720 -16.407 6.798 11 A_C20:G11_A A 20 ? A 11 ? ? 1 1 A G 21 1_555 A C 10 1_555 -0.246 0.119 0.175 29.904 9.931 -9.534 12 A_G21:C10_A A 21 ? A 10 ? 19 1 1 A A 42 1_555 A U 9 1_555 0.661 -0.245 0.659 28.332 -10.192 -1.771 13 A_A42:U9_A A 42 ? A 9 ? 20 1 1 A U 43 1_555 A A 8 1_555 0.212 0.133 -0.415 8.403 -29.590 -0.035 14 A_U43:A8_A A 43 ? A 8 ? 20 1 1 A C 44 1_555 A G 7 1_555 -0.294 0.049 1.121 -8.770 -10.454 1.866 15 A_C44:G7_A A 44 ? A 7 ? 19 1 1 A U 45 1_555 A A 6 1_555 -0.474 0.154 0.427 -5.782 -21.182 4.130 16 A_U45:A6_A A 45 ? A 6 ? 20 1 1 A G 46 1_555 A C 5 1_555 0.193 -0.587 -0.159 -2.109 -12.006 -7.901 17 A_G46:C5_A A 46 ? A 5 ? 19 1 1 A U 47 1_555 A A 49 1_555 -0.226 3.047 0.319 -2.989 -9.508 -65.595 18 A_U47:A49_A A 47 ? A 49 ? 23 3 1 A C 53 1_555 A G 67 1_555 -0.319 -0.471 -0.297 5.263 -9.144 -3.873 19 A_C53:G67_A A 53 ? A 67 ? 19 1 1 A C 54 1_555 A G 66 1_555 -0.081 -0.284 -0.456 7.914 -15.760 -3.593 20 A_C54:G66_A A 54 ? A 66 ? 19 1 1 A C 55 1_555 A G 65 1_555 0.257 -0.064 0.071 -4.887 0.118 -1.246 21 A_C55:G65_A A 55 ? A 65 ? 19 1 1 A A 56 1_555 A U 64 1_555 0.038 -0.161 0.312 0.851 -6.059 3.083 22 A_A56:U64_A A 56 ? A 64 ? 20 1 1 A G 57 1_555 A C 63 1_555 -0.348 -0.317 0.029 -9.863 -10.603 2.864 23 A_G57:C63_A A 57 ? A 63 ? 19 1 1 A G 58 1_555 A A 62 1_555 6.396 -4.419 0.169 2.834 4.968 -5.020 24 A_G58:A62_A A 58 ? A 62 ? 11 10 # 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 3 1_555 A C 40 1_555 A C 23 1_555 A G 39 1_555 -1.984 -0.858 3.599 -5.183 6.712 53.950 -1.388 1.816 3.638 7.347 5.674 54.562 1 AA_G3C23:G39C40_AA A 3 ? A 40 ? A 23 ? A 39 ? 1 A C 23 1_555 A G 39 1_555 A A 24 1_555 A U 4 1_555 0.352 0.024 3.485 1.691 1.610 -4.152 -14.166 18.822 2.905 -20.246 21.268 -4.763 2 AA_C23A24:U4G39_AA A 23 ? A 39 ? A 24 ? A 4 ? 1 A A 24 1_555 A U 4 1_555 A C 25 1_555 A G 37 1_555 -0.547 -3.728 2.827 -3.777 10.277 56.483 -4.312 0.410 2.204 10.748 3.949 57.449 3 AA_A24C25:G37U4_AA A 24 ? A 4 ? A 25 ? A 37 ? 1 A C 25 1_555 A G 37 1_555 A U 26 1_555 A A 36 1_555 -0.840 -1.800 3.039 3.192 10.596 28.890 -5.069 2.087 2.157 20.322 -6.122 30.894 4 AA_C25U26:A36G37_AA A 25 ? A 37 ? A 26 ? A 36 ? 1 A U 26 1_555 A A 36 1_555 A U 27 1_555 A G 35 1_555 0.058 -0.639 3.562 -3.255 11.129 42.720 -1.961 -0.402 3.291 14.950 4.373 44.195 5 AA_U26U27:G35A36_AA A 26 ? A 36 ? A 27 ? A 35 ? 1 A U 27 1_555 A G 35 1_555 A C 28 1_555 A G 34 1_555 0.340 -1.503 3.227 5.263 0.425 30.842 -2.868 0.358 3.219 0.792 -9.806 31.280 6 AA_U27C28:G34G35_AA A 27 ? A 35 ? A 28 ? A 34 ? 1 A A 17 1_555 A G 14 1_555 A G 18 1_555 A C 13 1_555 4.583 -2.086 3.504 1.998 18.751 54.680 -3.180 -4.648 2.860 19.767 -2.106 57.603 7 AA_A17G18:C13G14_AA A 17 ? A 14 ? A 18 ? A 13 ? 1 A G 18 1_555 A C 13 1_555 A U 19 1_555 A G 12 1_555 0.488 -1.545 3.116 -1.566 4.396 41.907 -2.568 -0.828 2.927 6.124 2.181 42.154 8 AA_G18U19:G12C13_AA A 18 ? A 13 ? A 19 ? A 12 ? 1 A U 19 1_555 A G 12 1_555 A C 20 1_555 A G 11 1_555 -0.793 -2.086 3.258 0.500 8.554 22.438 -7.446 2.050 2.299 21.025 -1.229 23.999 9 AA_U19C20:G11G12_AA A 19 ? A 12 ? A 20 ? A 11 ? 1 A C 20 1_555 A G 11 1_555 A G 21 1_555 A C 10 1_555 -1.416 -1.539 2.424 -2.038 14.129 14.925 -7.908 3.434 0.850 43.504 6.275 20.625 10 AA_C20G21:C10G11_AA A 20 ? A 11 ? A 21 ? A 10 ? 1 A G 21 1_555 A C 10 1_555 A A 42 1_555 A U 9 1_555 -1.472 0.083 3.196 -9.257 4.171 51.802 -0.182 1.046 3.391 4.722 10.481 52.720 11 AA_G21A42:U9C10_AA A 21 ? A 10 ? A 42 ? A 9 ? 1 A A 42 1_555 A U 9 1_555 A U 43 1_555 A A 8 1_555 0.122 -0.740 3.709 5.080 5.925 27.304 -3.031 1.056 3.442 12.238 -10.493 28.377 12 AA_A42U43:A8U9_AA A 42 ? A 9 ? A 43 ? A 8 ? 1 A U 43 1_555 A A 8 1_555 A C 44 1_555 A G 7 1_555 0.145 -2.468 3.512 -13.747 8.219 29.511 -5.602 -2.456 2.454 14.839 24.819 33.492 13 AA_U43C44:G7A8_AA A 43 ? A 8 ? A 44 ? A 7 ? 1 A C 44 1_555 A G 7 1_555 A U 45 1_555 A A 6 1_555 -0.111 -1.345 3.003 4.968 5.556 30.318 -3.431 1.038 2.669 10.426 -9.322 31.200 14 AA_C44U45:A6G7_AA A 44 ? A 7 ? A 45 ? A 6 ? 1 A U 45 1_555 A A 6 1_555 A G 46 1_555 A C 5 1_555 -0.517 -1.242 3.270 0.872 9.559 33.603 -3.443 0.986 2.809 16.130 -1.471 34.909 15 AA_U45G46:C5A6_AA A 45 ? A 6 ? A 46 ? A 5 ? 1 A G 46 1_555 A C 5 1_555 A U 47 1_555 A A 49 1_555 -0.555 -4.407 3.034 -1.239 5.364 49.233 -5.603 0.583 2.583 6.415 1.482 49.521 16 AA_G46U47:A49C5_AA A 46 ? A 5 ? A 47 ? A 49 ? 1 A C 53 1_555 A G 67 1_555 A C 54 1_555 A G 66 1_555 0.427 -1.490 3.360 0.601 11.899 34.085 -4.022 -0.609 2.713 19.573 -0.989 36.049 17 AA_C53C54:G66G67_AA A 53 ? A 67 ? A 54 ? A 66 ? 1 A C 54 1_555 A G 66 1_555 A C 55 1_555 A G 65 1_555 -0.689 -2.062 3.667 -5.490 8.635 26.873 -6.190 0.095 2.956 17.782 11.306 28.721 18 AA_C54C55:G65G66_AA A 54 ? A 66 ? A 55 ? A 65 ? 1 A C 55 1_555 A G 65 1_555 A A 56 1_555 A U 64 1_555 0.750 -1.791 3.045 0.463 7.443 30.784 -4.479 -1.300 2.563 13.769 -0.857 31.653 19 AA_C55A56:U64G65_AA A 55 ? A 65 ? A 56 ? A 64 ? 1 A A 56 1_555 A U 64 1_555 A G 57 1_555 A C 63 1_555 0.316 -1.751 3.641 3.677 5.488 30.365 -4.401 0.166 3.296 10.324 -6.917 31.059 20 AA_A56G57:C63U64_AA A 56 ? A 64 ? A 57 ? A 63 ? 1 A G 57 1_555 A C 63 1_555 A G 58 1_555 A A 62 1_555 -0.649 -0.597 3.057 -1.372 4.508 63.917 -0.743 0.557 3.025 4.252 1.294 64.072 21 AA_G57G58:A62C63_AA A 57 ? A 63 ? A 58 ? A 62 ? # _atom_sites.entry_id 4PQV _atom_sites.fract_transf_matrix[1][1] 0.013038 _atom_sites.fract_transf_matrix[1][2] 0.007528 _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] 0.015055 _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] 0.013081 _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 MG N O P # loop_