data_1ID9 # _entry.id 1ID9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1ID9 pdb_00001id9 10.2210/pdb1id9/pdb NDB AH0016 ? ? RCSB RCSB013179 ? ? WWPDB D_1000013179 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1ICG _pdbx_database_related.details ;Rhodium hexammine replaced by iridium hexammine ; _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1ID9 _pdbx_database_status.recvd_initial_deposition_date 2001-04-04 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cruse, W.' 1 'Saludjian, P.' 2 'Neuman, A.' 3 'Prange, T.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues.' 'Acta Crystallogr.,Sect.D' 57 1609 1613 2001 ABCRE6 DK 0907-4449 0766 ? 11679725 10.1107/S0907444901012318 1 'Structure of a Mispaired RNA Double Helix at 1.6 A Resolution and Implications for the Prediction of RNA Secondary Structure' Proc.Natl.Acad.Sci.USA 91 4160 4164 1994 PNASA6 US 0027-8424 0040 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cruse, W.' 1 ? primary 'Saludjian, P.' 2 ? primary 'Neuman, A.' 3 ? primary 'Prange, T.' 4 ? 1 'Cruse, W.' 5 ? 1 'Saludjian, P.' 6 ? 1 'Biala, E.' 7 ? 1 'Strazewski, P.' 8 ? 1 'Prange, T.' 9 ? 1 'Kennard, O.' 10 ? # _cell.entry_id 1ID9 _cell.length_a 53.730 _cell.length_b 19.390 _cell.length_c 45.830 _cell.angle_alpha 90.00 _cell.angle_beta 105.70 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ID9 _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # 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 "5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UFP))-3'" 2826.694 2 ? ? ? ? 2 non-polymer syn 'RHODIUM HEXAMINE ION' 205.089 2 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 2 ? ? ? ? 4 water nat water 18.015 50 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GCUUCGGC(UFP)' _entity_poly.pdbx_seq_one_letter_code_can GCUUCGGCN _entity_poly.pdbx_strand_id A,B _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 G n 1 2 C n 1 3 U n 1 4 U n 1 5 C n 1 6 G n 1 7 G n 1 8 C n 1 9 UFP 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 ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'phosphoramidite method' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1ID9 _struct_ref.pdbx_db_accession 1ID9 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1ID9 A 1 ? 9 ? 1ID9 1 ? 9 ? 1 9 2 1 1ID9 B 1 ? 9 ? 1ID9 1 ? 9 ? 1 9 # 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 RHD non-polymer . 'RHODIUM HEXAMINE ION' ? 'H18 N6 Rh 3' 205.089 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 UFP 'DNA linking' . "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 F N2 O8 P' 326.172 # _exptl.entry_id 1ID9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.03 _exptl_crystal.density_percent_sol 39.53 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.8 _exptl_crystal_grow.pdbx_details 'Cacodylate, MPD, rhodium(iii) hexammine, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 Cacodylate ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'rhodium(iii) hexammine' ? ? ? 1 4 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 277 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1998-10-08 _diffrn_detector.details 'Si(111)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'curvated Si(111) mirror' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.967 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'LURE BEAMLINE DW32' _diffrn_source.pdbx_synchrotron_site LURE _diffrn_source.pdbx_synchrotron_beamline DW32 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.967 # _reflns.entry_id 1ID9 _reflns.observed_criterion_sigma_I 4 _reflns.observed_criterion_sigma_F 2 _reflns.d_resolution_low 11 _reflns.d_resolution_high 1.6 _reflns.number_obs 4339 _reflns.number_all 4425 _reflns.percent_possible_obs 98 _reflns.pdbx_Rmerge_I_obs 0.041 _reflns.pdbx_Rsym_value 0.045 _reflns.pdbx_netI_over_sigmaI 21 _reflns.B_iso_Wilson_estimate 18 _reflns.pdbx_redundancy 9 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.6 _reflns_shell.d_res_low 1.7 _reflns_shell.percent_possible_all 76 _reflns_shell.Rmerge_I_obs 0.141 _reflns_shell.pdbx_Rsym_value 0.16 _reflns_shell.meanI_over_sigI_obs 4.1 _reflns_shell.pdbx_redundancy 5 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 786 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1ID9 _refine.ls_number_reflns_obs 4339 _refine.ls_number_reflns_all 4425 _refine.pdbx_ls_sigma_I 4 _refine.pdbx_ls_sigma_F 2 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_d_res_low 11 _refine.ls_d_res_high 1.6 _refine.ls_percent_reflns_obs 98 _refine.ls_R_factor_obs 0.153 _refine.ls_R_factor_all 0.155 _refine.ls_R_factor_R_work 0.156 _refine.ls_R_factor_R_free 0.195 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 410 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _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 ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;Last fluoro-uracil (chain B) refined as a two-position disorder ; _refine.pdbx_starting_model 'pdb entry 165D' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model 'Isotropic, the rhodium atoms were anisotropically refined' _refine.pdbx_stereochemistry_target_values 'personal dictionary from small molecules' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 385 _refine_hist.pdbx_number_atoms_ligand 19 _refine_hist.number_atoms_solvent 50 _refine_hist.number_atoms_total 454 _refine_hist.d_res_high 1.6 _refine_hist.d_res_low 11 # 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 s_bond_d 0.013 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.027 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.074 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.02 ? ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all . 1.6 1.7 . 0.181 76.9 0.2 0.02 . 64 . 'X-RAY DIFFRACTION' . . . 1.7 1.8 . 0.166 74.8 0.198 0.02 . 65 . 'X-RAY DIFFRACTION' . . . 1.8 2 . 0.165 77.6 0.195 0.02 . 95 . 'X-RAY DIFFRACTION' . . . 2 3 . 0.156 69.1 0.19 0.02 . 135 . 'X-RAY DIFFRACTION' . . . 3 5 . 0.117 54.4 0.2 0.02 . 42 . 'X-RAY DIFFRACTION' . . . 5 11 . 0.13 42.2 0.22 0.02 . 9 . 'X-RAY DIFFRACTION' . . # _struct.entry_id 1ID9 _struct.title 'STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF RH(NH3)6+++' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1ID9 _struct_keywords.pdbx_keywords DNA/RNA _struct_keywords.text 'RNA/DNA HYBRID, FLUORO URACIL, RHODIUM(III) HEXAMMINE, C-U MISMATCH, G-U mismatch, DNA-RNA COMPLEX' # 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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? G N N 4 ? H N N 4 ? # 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 8 "O3'" ? ? ? 1_555 A UFP 9 P ? ? A C 8 A UFP 9 1_555 ? ? ? ? ? ? ? 1.594 ? ? covale2 covale both ? B C 8 "O3'" ? ? ? 1_555 B UFP 9 P ? ? B C 8 B UFP 9 1_555 ? ? ? ? ? ? ? 1.616 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 1 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 1 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 1 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 2 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 2 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 2 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 B G 6 O6 ? ? A U 3 B G 6 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A U 3 O2 ? ? ? 1_555 B G 6 N1 ? ? A U 3 B G 6 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog9 hydrog ? ? A U 4 O4 ? ? ? 1_555 B C 5 N4 ? ? A U 4 B C 5 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog10 hydrog ? ? A C 5 N4 ? ? ? 1_555 B U 4 O4 ? ? A C 5 B U 4 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog11 hydrog ? ? A G 6 N1 ? ? ? 1_555 B U 3 O2 ? ? A G 6 B U 3 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog12 hydrog ? ? A G 6 O6 ? ? ? 1_555 B U 3 N3 ? ? A G 6 B U 3 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog13 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 8 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 8 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 8 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # 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 RHD 11 ? 5 'BINDING SITE FOR RESIDUE RHD A 11' AC2 Software A RHD 12 ? 5 'BINDING SITE FOR RESIDUE RHD A 12' # 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 5 C A 5 ? C A 5 . ? 1_555 ? 2 AC1 5 G A 6 ? G A 6 . ? 1_555 ? 3 AC1 5 G A 7 ? G A 7 . ? 1_555 ? 4 AC1 5 HOH G . ? HOH A 117 . ? 1_555 ? 5 AC1 5 HOH G . ? HOH A 119 . ? 1_555 ? 6 AC2 5 C A 5 ? C A 5 . ? 4_545 ? 7 AC2 5 G A 7 ? G A 7 . ? 1_545 ? 8 AC2 5 C A 8 ? C A 8 . ? 1_545 ? 9 AC2 5 HOH G . ? HOH A 126 . ? 4_545 ? 10 AC2 5 C B 5 ? C B 5 . ? 4_545 ? # _database_PDB_matrix.entry_id 1ID9 _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 1ID9 _atom_sites.fract_transf_matrix[1][1] 0.018605 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005230 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.051546 _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] 0.022660 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C CL F N O P RH # 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 C 2 2 2 C C A . n A 1 3 U 3 3 3 U U 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 G 6 6 6 G G A . n A 1 7 G 7 7 7 G G A . n A 1 8 C 8 8 8 C C A . n A 1 9 UFP 9 9 9 UFP +U A . n B 1 1 G 1 1 1 G G B . n B 1 2 C 2 2 2 C C B . n B 1 3 U 3 3 3 U U B . n B 1 4 U 4 4 4 U U B . n B 1 5 C 5 5 5 C C B . n B 1 6 G 6 6 6 G G B . n B 1 7 G 7 7 7 G G B . n B 1 8 C 8 8 8 C C B . n B 1 9 UFP 9 9 9 UFP +U B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 RHD 1 11 11 RHD RHO A . D 2 RHD 1 12 12 RHD RHO A . E 3 CL 1 32 32 CL CL A . F 3 CL 1 31 31 CL CL B . G 4 HOH 1 101 101 HOH HOH A . G 4 HOH 2 102 102 HOH HOH A . G 4 HOH 3 105 105 HOH HOH A . G 4 HOH 4 107 107 HOH HOH A . G 4 HOH 5 109 109 HOH HOH A . G 4 HOH 6 111 111 HOH HOH A . G 4 HOH 7 112 112 HOH HOH A . G 4 HOH 8 113 113 HOH HOH A . G 4 HOH 9 115 115 HOH HOH A . G 4 HOH 10 116 116 HOH HOH A . G 4 HOH 11 117 117 HOH HOH A . G 4 HOH 12 118 118 HOH HOH A . G 4 HOH 13 119 119 HOH HOH A . G 4 HOH 14 121 121 HOH HOH A . G 4 HOH 15 124 124 HOH HOH A . G 4 HOH 16 125 125 HOH HOH A . G 4 HOH 17 126 126 HOH HOH A . G 4 HOH 18 127 127 HOH HOH A . G 4 HOH 19 128 128 HOH HOH A . G 4 HOH 20 129 129 HOH HOH A . G 4 HOH 21 130 130 HOH HOH A . G 4 HOH 22 131 131 HOH HOH A . G 4 HOH 23 134 134 HOH HOH A . G 4 HOH 24 136 136 HOH HOH A . G 4 HOH 25 137 137 HOH HOH A . G 4 HOH 26 138 138 HOH HOH A . G 4 HOH 27 139 139 HOH HOH A . G 4 HOH 28 141 141 HOH HOH A . G 4 HOH 29 143 143 HOH HOH A . G 4 HOH 30 145 145 HOH HOH A . G 4 HOH 31 147 147 HOH HOH A . G 4 HOH 32 149 149 HOH HOH A . H 4 HOH 1 103 103 HOH HOH B . H 4 HOH 2 104 104 HOH HOH B . H 4 HOH 3 106 106 HOH HOH B . H 4 HOH 4 108 108 HOH HOH B . H 4 HOH 5 110 110 HOH HOH B . H 4 HOH 6 114 114 HOH HOH B . H 4 HOH 7 120 120 HOH HOH B . H 4 HOH 8 122 122 HOH HOH B . H 4 HOH 9 123 123 HOH HOH B . H 4 HOH 10 132 132 HOH HOH B . H 4 HOH 11 133 133 HOH HOH B . H 4 HOH 12 135 135 HOH HOH B . H 4 HOH 13 140 140 HOH HOH B . H 4 HOH 14 142 142 HOH HOH B . H 4 HOH 15 144 144 HOH HOH B . H 4 HOH 16 146 146 HOH HOH B . H 4 HOH 17 148 148 HOH HOH B . H 4 HOH 18 150 150 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _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 2001-04-12 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-09 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOSFLM 'data reduction' . ? 1 SCALA 'data scaling' . ? 2 AMoRE phasing . ? 3 SHELXL-97 refinement . ? 4 CCP4 'data scaling' '(SCALA)' ? 5 # 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 C2 A C 2 ? ? N3 A C 2 ? ? C4 A C 2 ? ? 124.07 119.90 4.17 0.50 N 2 1 N3 A C 2 ? ? C4 A C 2 ? ? C5 A C 2 ? ? 118.56 121.90 -3.34 0.40 N 3 1 C5 A C 2 ? ? C6 A C 2 ? ? N1 A C 2 ? ? 124.55 121.00 3.55 0.50 N 4 1 C2 A U 3 ? ? N3 A U 3 ? ? C4 A U 3 ? ? 121.74 127.00 -5.26 0.60 N 5 1 N3 A U 3 ? ? C4 A U 3 ? ? C5 A U 3 ? ? 118.79 114.60 4.19 0.60 N 6 1 C5 A U 3 ? ? C4 A U 3 ? ? O4 A U 3 ? ? 120.26 125.90 -5.64 0.60 N 7 1 "O5'" A U 4 ? ? "C5'" A U 4 ? ? "C4'" A U 4 ? ? 104.29 109.40 -5.11 0.80 N 8 1 N1 A U 4 ? ? C2 A U 4 ? ? N3 A U 4 ? ? 118.70 114.90 3.80 0.60 N 9 1 C2 A U 4 ? ? N3 A U 4 ? ? C4 A U 4 ? ? 122.90 127.00 -4.10 0.60 N 10 1 C5 A U 4 ? ? C4 A U 4 ? ? O4 A U 4 ? ? 121.05 125.90 -4.85 0.60 N 11 1 N3 A C 5 ? ? C4 A C 5 ? ? C5 A C 5 ? ? 119.46 121.90 -2.44 0.40 N 12 1 C4 A G 6 ? ? C5 A G 6 ? ? C6 A G 6 ? ? 114.67 118.80 -4.13 0.60 N 13 1 C5 A G 6 ? ? C6 A G 6 ? ? N1 A G 6 ? ? 116.11 111.50 4.61 0.50 N 14 1 C5 A G 6 ? ? C6 A G 6 ? ? O6 A G 6 ? ? 121.27 128.60 -7.33 0.60 N 15 1 C5 A G 7 ? ? C6 A G 7 ? ? N1 A G 7 ? ? 114.70 111.50 3.20 0.50 N 16 1 N3 A C 8 ? ? C4 A C 8 ? ? C5 A C 8 ? ? 119.49 121.90 -2.41 0.40 N 17 1 "C3'" A C 8 ? ? "O3'" A C 8 ? ? P A UFP 9 ? ? 129.28 119.70 9.58 1.20 Y 18 1 C6 B G 1 ? ? N1 B G 1 ? ? C2 B G 1 ? ? 121.21 125.10 -3.89 0.60 N 19 1 N3 B C 2 ? ? C4 B C 2 ? ? C5 B C 2 ? ? 118.58 121.90 -3.32 0.40 N 20 1 C5 B C 2 ? ? C6 B C 2 ? ? N1 B C 2 ? ? 124.25 121.00 3.25 0.50 N 21 1 C6 B U 3 ? ? N1 B U 3 ? ? C2 B U 3 ? ? 117.25 121.00 -3.75 0.60 N 22 1 N1 B U 3 ? ? C2 B U 3 ? ? N3 B U 3 ? ? 118.78 114.90 3.88 0.60 N 23 1 C2 B U 4 ? ? N3 B U 4 ? ? C4 B U 4 ? ? 123.10 127.00 -3.90 0.60 N 24 1 C5 B U 4 ? ? C4 B U 4 ? ? O4 B U 4 ? ? 122.14 125.90 -3.76 0.60 N 25 1 OP1 B C 5 ? ? P B C 5 ? ? OP2 B C 5 ? ? 110.48 119.60 -9.12 1.50 N 26 1 N3 B C 5 ? ? C4 B C 5 ? ? C5 B C 5 ? ? 118.66 121.90 -3.24 0.40 N 27 1 "O5'" B G 6 ? ? "C5'" B G 6 ? ? "C4'" B G 6 ? ? 103.38 109.40 -6.02 0.80 N 28 1 N3 B C 8 ? ? C4 B C 8 ? ? C5 B C 8 ? ? 119.27 121.90 -2.63 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 CL CL CL N N 36 G OP3 O N N 37 G P P N N 38 G OP1 O N N 39 G OP2 O N N 40 G "O5'" O N N 41 G "C5'" C N N 42 G "C4'" C N R 43 G "O4'" O N N 44 G "C3'" C N S 45 G "O3'" O N N 46 G "C2'" C N R 47 G "O2'" O N N 48 G "C1'" C N R 49 G N9 N Y N 50 G C8 C Y N 51 G N7 N Y N 52 G C5 C Y N 53 G C6 C N N 54 G O6 O N N 55 G N1 N N N 56 G C2 C N N 57 G N2 N N N 58 G N3 N N N 59 G C4 C Y N 60 G HOP3 H N N 61 G HOP2 H N N 62 G "H5'" H N N 63 G "H5''" H N N 64 G "H4'" H N N 65 G "H3'" H N N 66 G "HO3'" H N N 67 G "H2'" H N N 68 G "HO2'" H N N 69 G "H1'" H N N 70 G H8 H N N 71 G H1 H N N 72 G H21 H N N 73 G H22 H N N 74 HOH O O N N 75 HOH H1 H N N 76 HOH H2 H N N 77 RHD RH RH N N 78 RHD N1 N N N 79 RHD N2 N N N 80 RHD N3 N N N 81 RHD N4 N N N 82 RHD N5 N N N 83 RHD N6 N N N 84 RHD HN11 H N N 85 RHD HN12 H N N 86 RHD HN13 H N N 87 RHD HN21 H N N 88 RHD HN22 H N N 89 RHD HN23 H N N 90 RHD HN31 H N N 91 RHD HN32 H N N 92 RHD HN33 H N N 93 RHD HN41 H N N 94 RHD HN42 H N N 95 RHD HN43 H N N 96 RHD HN51 H N N 97 RHD HN52 H N N 98 RHD HN53 H N N 99 RHD HN61 H N N 100 RHD HN62 H N N 101 RHD HN63 H N N 102 U OP3 O N N 103 U P P N N 104 U OP1 O N N 105 U OP2 O N N 106 U "O5'" O N N 107 U "C5'" C N N 108 U "C4'" C N R 109 U "O4'" O N N 110 U "C3'" C N S 111 U "O3'" O N N 112 U "C2'" C N R 113 U "O2'" O N N 114 U "C1'" C N R 115 U N1 N N N 116 U C2 C N N 117 U O2 O N N 118 U N3 N N N 119 U C4 C N N 120 U O4 O N N 121 U C5 C N N 122 U C6 C N N 123 U HOP3 H N N 124 U HOP2 H N N 125 U "H5'" H N N 126 U "H5''" H N N 127 U "H4'" H N N 128 U "H3'" H N N 129 U "HO3'" H N N 130 U "H2'" H N N 131 U "HO2'" H N N 132 U "H1'" H N N 133 U H3 H N N 134 U H5 H N N 135 U H6 H N N 136 UFP N1 N N N 137 UFP C2 C N N 138 UFP N3 N N N 139 UFP C4 C N N 140 UFP C5 C N N 141 UFP C6 C N N 142 UFP O2 O N N 143 UFP O4 O N N 144 UFP F5 F N N 145 UFP "C1'" C N R 146 UFP "C2'" C N N 147 UFP "C3'" C N S 148 UFP "C4'" C N R 149 UFP "O3'" O N N 150 UFP "O4'" O N N 151 UFP "C5'" C N N 152 UFP "O5'" O N N 153 UFP P P N N 154 UFP O1P O N N 155 UFP O2P O N N 156 UFP O3P O N N 157 UFP HN3 H N N 158 UFP H6 H N N 159 UFP "H1'" H N N 160 UFP "H2'1" H N N 161 UFP "H2'2" H N N 162 UFP "H3'" H N N 163 UFP "H4'" H N N 164 UFP "HO3'" H N N 165 UFP "H5'1" H N N 166 UFP "H5'2" H N N 167 UFP HOP2 H N N 168 UFP HOP3 H N N 169 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 G OP3 P sing N N 37 G OP3 HOP3 sing N N 38 G P OP1 doub N N 39 G P OP2 sing N N 40 G P "O5'" sing N N 41 G OP2 HOP2 sing N N 42 G "O5'" "C5'" sing N N 43 G "C5'" "C4'" sing N N 44 G "C5'" "H5'" sing N N 45 G "C5'" "H5''" sing N N 46 G "C4'" "O4'" sing N N 47 G "C4'" "C3'" sing N N 48 G "C4'" "H4'" sing N N 49 G "O4'" "C1'" sing N N 50 G "C3'" "O3'" sing N N 51 G "C3'" "C2'" sing N N 52 G "C3'" "H3'" sing N N 53 G "O3'" "HO3'" sing N N 54 G "C2'" "O2'" sing N N 55 G "C2'" "C1'" sing N N 56 G "C2'" "H2'" sing N N 57 G "O2'" "HO2'" sing N N 58 G "C1'" N9 sing N N 59 G "C1'" "H1'" sing N N 60 G N9 C8 sing Y N 61 G N9 C4 sing Y N 62 G C8 N7 doub Y N 63 G C8 H8 sing N N 64 G N7 C5 sing Y N 65 G C5 C6 sing N N 66 G C5 C4 doub Y N 67 G C6 O6 doub N N 68 G C6 N1 sing N N 69 G N1 C2 sing N N 70 G N1 H1 sing N N 71 G C2 N2 sing N N 72 G C2 N3 doub N N 73 G N2 H21 sing N N 74 G N2 H22 sing N N 75 G N3 C4 sing N N 76 HOH O H1 sing N N 77 HOH O H2 sing N N 78 RHD RH N1 sing N N 79 RHD RH N2 sing N N 80 RHD RH N3 sing N N 81 RHD RH N4 sing N N 82 RHD RH N5 sing N N 83 RHD RH N6 sing N N 84 RHD N1 HN11 sing N N 85 RHD N1 HN12 sing N N 86 RHD N1 HN13 sing N N 87 RHD N2 HN21 sing N N 88 RHD N2 HN22 sing N N 89 RHD N2 HN23 sing N N 90 RHD N3 HN31 sing N N 91 RHD N3 HN32 sing N N 92 RHD N3 HN33 sing N N 93 RHD N4 HN41 sing N N 94 RHD N4 HN42 sing N N 95 RHD N4 HN43 sing N N 96 RHD N5 HN51 sing N N 97 RHD N5 HN52 sing N N 98 RHD N5 HN53 sing N N 99 RHD N6 HN61 sing N N 100 RHD N6 HN62 sing N N 101 RHD N6 HN63 sing N N 102 U OP3 P sing N N 103 U OP3 HOP3 sing N N 104 U P OP1 doub N N 105 U P OP2 sing N N 106 U P "O5'" sing N N 107 U OP2 HOP2 sing N N 108 U "O5'" "C5'" sing N N 109 U "C5'" "C4'" sing N N 110 U "C5'" "H5'" sing N N 111 U "C5'" "H5''" sing N N 112 U "C4'" "O4'" sing N N 113 U "C4'" "C3'" sing N N 114 U "C4'" "H4'" sing N N 115 U "O4'" "C1'" sing N N 116 U "C3'" "O3'" sing N N 117 U "C3'" "C2'" sing N N 118 U "C3'" "H3'" sing N N 119 U "O3'" "HO3'" sing N N 120 U "C2'" "O2'" sing N N 121 U "C2'" "C1'" sing N N 122 U "C2'" "H2'" sing N N 123 U "O2'" "HO2'" sing N N 124 U "C1'" N1 sing N N 125 U "C1'" "H1'" sing N N 126 U N1 C2 sing N N 127 U N1 C6 sing N N 128 U C2 O2 doub N N 129 U C2 N3 sing N N 130 U N3 C4 sing N N 131 U N3 H3 sing N N 132 U C4 O4 doub N N 133 U C4 C5 sing N N 134 U C5 C6 doub N N 135 U C5 H5 sing N N 136 U C6 H6 sing N N 137 UFP N1 C2 sing N N 138 UFP N1 C6 sing N N 139 UFP N1 "C1'" sing N N 140 UFP C2 N3 sing N N 141 UFP C2 O2 doub N N 142 UFP N3 C4 sing N N 143 UFP N3 HN3 sing N N 144 UFP C4 C5 sing N N 145 UFP C4 O4 doub N N 146 UFP C5 C6 doub N N 147 UFP C5 F5 sing N N 148 UFP C6 H6 sing N N 149 UFP "C1'" "C2'" sing N N 150 UFP "C1'" "O4'" sing N N 151 UFP "C1'" "H1'" sing N N 152 UFP "C2'" "C3'" sing N N 153 UFP "C2'" "H2'1" sing N N 154 UFP "C2'" "H2'2" sing N N 155 UFP "C3'" "C4'" sing N N 156 UFP "C3'" "O3'" sing N N 157 UFP "C3'" "H3'" sing N N 158 UFP "C4'" "O4'" sing N N 159 UFP "C4'" "C5'" sing N N 160 UFP "C4'" "H4'" sing N N 161 UFP "O3'" "HO3'" sing N N 162 UFP "C5'" "O5'" sing N N 163 UFP "C5'" "H5'1" sing N N 164 UFP "C5'" "H5'2" sing N N 165 UFP "O5'" P sing N N 166 UFP P O1P doub N N 167 UFP P O2P sing N N 168 UFP P O3P sing N N 169 UFP O2P HOP2 sing N N 170 UFP O3P HOP3 sing N N 171 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1ID9 'double helix' 1ID9 'a-form double helix' 1ID9 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B C 8 1_555 0.060 -0.150 -0.034 -5.384 -12.337 -0.423 1 A_G1:C8_B A 1 ? B 8 ? 19 1 1 A C 2 1_555 B G 7 1_555 0.111 -0.199 0.056 -2.206 -11.376 -1.567 2 A_C2:G7_B A 2 ? B 7 ? 19 1 1 A U 3 1_555 B G 6 1_555 2.418 -0.533 0.193 -1.211 -7.458 0.714 3 A_U3:G6_B A 3 ? B 6 ? 28 ? 1 A U 4 1_555 B C 5 1_555 -0.564 0.126 -0.132 1.891 -2.525 -41.505 4 A_U4:C5_B A 4 ? B 5 ? ? ? 1 A C 5 1_555 B U 4 1_555 0.553 0.045 -0.099 8.885 -2.911 -39.783 5 A_C5:U4_B A 5 ? B 4 ? ? ? 1 A G 6 1_555 B U 3 1_555 -2.442 -0.686 -0.083 3.444 -9.707 -4.135 6 A_G6:U3_B A 6 ? B 3 ? 28 ? 1 A G 7 1_555 B C 2 1_555 -0.185 -0.162 0.037 -4.888 -13.163 -0.400 7 A_G7:C2_B A 7 ? B 2 ? 19 1 1 A C 8 1_555 B G 1 1_555 0.162 -0.150 0.221 -5.646 -4.680 -0.728 8 A_C8:G1_B A 8 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 8 1_555 A C 2 1_555 B G 7 1_555 -0.718 -1.428 3.192 -3.074 8.317 31.631 -3.859 0.779 2.792 14.895 5.505 32.819 1 AA_G1C2:G7C8_BB A 1 ? B 8 ? A 2 ? B 7 ? 1 A C 2 1_555 B G 7 1_555 A U 3 1_555 B G 6 1_555 0.246 -1.377 3.302 0.683 5.998 40.677 -2.599 -0.278 3.081 8.571 -0.976 41.104 2 AA_C2U3:G6G7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A U 3 1_555 B G 6 1_555 A U 4 1_555 B C 5 1_555 -3.992 -1.938 3.174 -1.377 6.720 20.348 -7.696 10.210 2.664 18.361 3.762 21.462 3 AA_U3U4:C5G6_BB A 3 ? B 6 ? A 4 ? B 5 ? 1 A U 4 1_555 B C 5 1_555 A C 5 1_555 B U 4 1_555 -0.153 -1.941 3.404 -2.221 8.364 37.753 -3.937 -0.037 2.928 12.722 3.378 38.697 4 AA_U4C5:U4C5_BB A 4 ? B 5 ? A 5 ? B 4 ? 1 A C 5 1_555 B U 4 1_555 A G 6 1_555 B U 3 1_555 3.107 -1.707 3.443 -0.462 9.821 24.606 -6.194 -6.902 2.527 21.957 1.033 26.470 5 AA_C5G6:U3U4_BB A 5 ? B 4 ? A 6 ? B 3 ? 1 A G 6 1_555 B U 3 1_555 A G 7 1_555 B C 2 1_555 0.309 -1.734 3.540 -2.716 4.832 40.546 -3.036 -0.754 3.294 6.933 3.897 40.907 6 AA_G6G7:C2U3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A G 7 1_555 B C 2 1_555 A C 8 1_555 B G 1 1_555 0.084 -2.006 3.354 -0.315 0.791 33.937 -3.565 -0.195 3.307 1.354 0.540 33.947 7 AA_G7C8:G1C2_BB A 7 ? B 2 ? A 8 ? B 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'RHODIUM HEXAMINE ION' RHD 3 'CHLORIDE ION' CL 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 165D _pdbx_initial_refinement_model.details 'pdb entry 165D' #