data_4RC0 # _entry.id 4RC0 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4RC0 pdb_00004rc0 10.2210/pdb4rc0/pdb NDB NA3177 ? ? RCSB RCSB087157 ? ? WWPDB D_1000087157 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4RBY . unspecified PDB 4RBZ . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4RC0 _pdbx_database_status.recvd_initial_deposition_date 2014-09-13 _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 'Pallan, P.S.' 1 'Egli, M.' 2 # _citation.id primary _citation.title 'Crystal Structure, Stability and siRNA Activity of Phosphorodithioate-Modified RNAs' _citation.journal_abbrev 'To be Published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pallan, P.S.' 1 ? primary 'Yang, X.' 2 ? primary 'Sierant, M.' 3 ? primary 'Abeydeera, N.D.' 4 ? primary 'Hassell, T.' 5 ? primary 'Martinez, C.' 6 ? primary 'Janicka, M.' 7 ? primary 'Nawrot, B.' 8 ? primary 'Egli, M.' 9 ? # _cell.entry_id 4RC0 _cell.length_a 40.914 _cell.length_b 34.836 _cell.length_c 32.274 _cell.angle_alpha 90.00 _cell.angle_beta 127.50 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4RC0 _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 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(A2M)P*(2SG)P*CP*G)-3'" 3899.534 1 ? ? ? 'Guanosine phosphorodithioate RNA' 2 water nat water 18.015 69 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'CGCGAAUU(A2M)(2SG)CG' _entity_poly.pdbx_seq_one_letter_code_can CGCGAAUUAXCG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 C n 1 4 G n 1 5 A n 1 6 A n 1 7 U n 1 8 U n 1 9 A2M n 1 10 2SG n 1 11 C n 1 12 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4RC0 _struct_ref.pdbx_db_accession 4RC0 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code 'CGCGAAUU(A2M)(2SG)CG' _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4RC0 _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 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4RC0 _struct_ref_seq.db_align_beg 101 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 112 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 101 _struct_ref_seq.pdbx_auth_seq_align_end 112 # 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 2SG 'RNA linking' n 'guanosine phosphorodithioate' ? 'C10 H16 N5 O6 P S2' 397.368 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 A2M 'RNA linking' n ;2'-O-methyladenosine 5'-(dihydrogen phosphate) ; ? 'C11 H16 N5 O7 P' 361.248 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 4RC0 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.34 _exptl_crystal.density_percent_sol 47.43 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;20 mM sodium cacodylate, 40 mM sodium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _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 CCD _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.pdbx_collection_date 2013-10-03 _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 'diamond(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97857 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 21-ID-G' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 21-ID-G _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97857 # _reflns.entry_id 4RC0 _reflns.observed_criterion_sigma_I 5 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.13 _reflns.number_obs 12968 _reflns.number_all 13579 _reflns.percent_possible_obs 95.5 _reflns.pdbx_Rmerge_I_obs 0.049 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 49.21 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.6 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.13 _reflns_shell.d_res_low 1.17 _reflns_shell.percent_possible_all 90.7 _reflns_shell.Rmerge_I_obs 0.212 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.83 _reflns_shell.pdbx_redundancy 3.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1234 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4RC0 _refine.ls_number_reflns_obs 12297 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _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 _refine.ls_d_res_high 1.13 _refine.ls_percent_reflns_obs 95.5 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.181 _refine.ls_R_factor_R_free 0.211 _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 653 _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 ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 2Q1R' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _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 ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 255 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 69 _refine_hist.number_atoms_total 324 _refine_hist.d_res_high 1.13 _refine_hist.d_res_low 50 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id s_bond_d 0.011 ? ? ? ? 'X-RAY DIFFRACTION' s_angle_d 0.035 ? ? ? ? 'X-RAY DIFFRACTION' # _pdbx_refine.entry_id 4RC0 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.R_factor_obs_no_cutoff 0.181 _pdbx_refine.free_R_factor_no_cutoff 0.211 _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? # _struct.entry_id 4RC0 _struct.title 'X-ray structure of RNA containing guanosine phosphorodithioate' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4RC0 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'phosphorodithioate RNA, guanosine phosphorodithioate, phosphorothioate, guanosine analogue, hydrophobic, backbone, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A U 8 "O3'" A ? ? 1_555 A A2M 9 P A ? A U 108 A A2M 109 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale2 covale both ? A U 8 "O3'" B ? ? 1_555 A A2M 9 P B ? A U 108 A A2M 109 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale3 covale one ? A A2M 9 "O3'" A ? ? 1_555 A 2SG 10 P ? ? A A2M 109 A 2SG 110 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale4 covale one ? A A2M 9 "O3'" B ? ? 1_555 A 2SG 10 P ? ? A A2M 109 A 2SG 110 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale5 covale both ? A 2SG 10 "O3'" ? ? ? 1_555 A C 11 P ? ? A 2SG 110 A C 111 1_555 ? ? ? ? ? ? ? 1.600 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 12 N1 ? ? A C 101 A G 112 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 12 O6 ? ? A C 101 A G 112 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 12 N2 ? ? A C 101 A G 112 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 11 N3 ? ? A G 102 A C 111 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 11 O2 ? ? A G 102 A C 111 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 11 N4 ? ? A G 102 A C 111 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 A A2M 9 N1 ? ? A G 104 A A2M 109 2_556 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog8 hydrog ? ? A G 4 O6 ? ? ? 1_555 A A2M 9 N6 ? ? A G 104 A A2M 109 2_556 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog9 hydrog ? ? A A 5 N6 A ? ? 1_555 A U 8 O4 A ? A A 105 A U 108 2_556 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog10 hydrog ? ? A U 8 O4 A ? ? 1_555 A A 5 N6 A ? A U 108 A A 105 2_556 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog11 hydrog ? ? A A2M 9 N1 ? ? ? 1_555 A G 4 N1 ? ? A A2M 109 A G 104 2_556 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog12 hydrog ? ? A A2M 9 N6 ? ? ? 1_555 A G 4 O6 ? ? A A2M 109 A G 104 2_556 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog13 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 2 N1 ? ? A C 111 A G 102 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 2 O6 ? ? A C 111 A G 102 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 2 N2 ? ? A C 111 A G 102 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 1 N3 ? ? A G 112 A C 101 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 1 O2 ? ? A G 112 A C 101 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 1 N4 ? ? A G 112 A C 101 2_556 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 4RC0 _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 4RC0 _atom_sites.fract_transf_matrix[1][1] 0.024442 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.018755 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.028706 _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] 0.039055 _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 N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 101 101 C C A . n A 1 2 G 2 102 102 G G A . n A 1 3 C 3 103 103 C C A . n A 1 4 G 4 104 104 G G A . n A 1 5 A 5 105 105 A A A . n A 1 6 A 6 106 106 A A A . n A 1 7 U 7 107 107 U U A . n A 1 8 U 8 108 108 U U A . n A 1 9 A2M 9 109 109 A2M A2M A . n A 1 10 2SG 10 110 110 2SG GUS A . n A 1 11 C 11 111 111 C C A . n A 1 12 G 12 112 112 G G A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 201 201 HOH HOH A . B 2 HOH 2 202 202 HOH HOH A . B 2 HOH 3 203 203 HOH HOH A . B 2 HOH 4 204 204 HOH HOH A . B 2 HOH 5 205 205 HOH HOH A . B 2 HOH 6 206 206 HOH HOH A . B 2 HOH 7 207 207 HOH HOH A . B 2 HOH 8 208 208 HOH HOH A . B 2 HOH 9 209 209 HOH HOH A . B 2 HOH 10 210 210 HOH HOH A . B 2 HOH 11 211 211 HOH HOH A . B 2 HOH 12 212 212 HOH HOH A . B 2 HOH 13 213 213 HOH HOH A . B 2 HOH 14 214 214 HOH HOH A . B 2 HOH 15 215 215 HOH HOH A . B 2 HOH 16 216 216 HOH HOH A . B 2 HOH 17 217 217 HOH HOH A . B 2 HOH 18 218 218 HOH HOH A . B 2 HOH 19 219 219 HOH HOH A . B 2 HOH 20 220 220 HOH HOH A . B 2 HOH 21 221 221 HOH HOH A . B 2 HOH 22 222 222 HOH HOH A . B 2 HOH 23 223 223 HOH HOH A . B 2 HOH 24 224 224 HOH HOH A . B 2 HOH 25 225 225 HOH HOH A . B 2 HOH 26 226 226 HOH HOH A . B 2 HOH 27 227 227 HOH HOH A . B 2 HOH 28 228 228 HOH HOH A . B 2 HOH 29 229 229 HOH HOH A . B 2 HOH 30 230 230 HOH HOH A . B 2 HOH 31 231 231 HOH HOH A . B 2 HOH 32 232 232 HOH HOH A . B 2 HOH 33 233 233 HOH HOH A . B 2 HOH 34 234 234 HOH HOH A . B 2 HOH 35 235 235 HOH HOH A . B 2 HOH 36 236 236 HOH HOH A . B 2 HOH 37 237 237 HOH HOH A . B 2 HOH 38 238 238 HOH HOH A . B 2 HOH 39 239 239 HOH HOH A . B 2 HOH 40 240 240 HOH HOH A . B 2 HOH 41 241 241 HOH HOH A . B 2 HOH 42 242 242 HOH HOH A . B 2 HOH 43 243 243 HOH HOH A . B 2 HOH 44 244 244 HOH HOH A . B 2 HOH 45 245 245 HOH HOH A . B 2 HOH 46 246 246 HOH HOH A . B 2 HOH 47 247 247 HOH HOH A . B 2 HOH 48 248 248 HOH HOH A . B 2 HOH 49 249 249 HOH HOH A . B 2 HOH 50 250 250 HOH HOH A . B 2 HOH 51 251 251 HOH HOH A . B 2 HOH 52 252 252 HOH HOH A . B 2 HOH 53 253 253 HOH HOH A . B 2 HOH 54 254 254 HOH HOH A . B 2 HOH 55 255 255 HOH HOH A . B 2 HOH 56 256 256 HOH HOH A . B 2 HOH 57 257 257 HOH HOH A . B 2 HOH 58 258 258 HOH HOH A . B 2 HOH 59 259 259 HOH HOH A . B 2 HOH 60 260 260 HOH HOH A . B 2 HOH 61 261 261 HOH HOH A . B 2 HOH 62 262 262 HOH HOH A . B 2 HOH 63 263 263 HOH HOH A . B 2 HOH 64 264 264 HOH HOH A . B 2 HOH 65 265 265 HOH HOH A . B 2 HOH 66 266 266 HOH HOH A . B 2 HOH 67 267 267 HOH HOH A . B 2 HOH 68 268 268 HOH HOH A . B 2 HOH 69 269 269 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A A2M 9 A A2M 109 ? A ? 2 A 2SG 10 A 2SG 110 ? G 'GUANOSINE PHOSPHORODITHIOATE' # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 -19.6471663598 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 25.6046857046 # 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 2015-09-16 2 'Structure model' 1 1 2017-07-12 3 'Structure model' 1 2 2023-09-20 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Refinement description' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' pdbx_refine 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_initial_refinement_model 6 3 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MD2 'data collection' 'diffractometer software from EMBL (with LS-CAT developed extensions)' ? 1 MOLREP phasing '(CCP4)' ? 2 SHELXL-97 refinement . ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 C6 _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 A _pdbx_validate_rmsd_bond.auth_seq_id_1 106 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 B _pdbx_validate_rmsd_bond.auth_atom_id_2 N1 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 A _pdbx_validate_rmsd_bond.auth_seq_id_2 106 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 B _pdbx_validate_rmsd_bond.bond_value 1.307 _pdbx_validate_rmsd_bond.bond_target_value 1.351 _pdbx_validate_rmsd_bond.bond_deviation -0.044 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.007 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A G 104 ? ? "C1'" A G 104 ? ? N9 A G 104 ? ? 113.21 108.50 4.71 0.70 N 2 1 C6 A A 106 ? B N1 A A 106 ? B C2 A A 106 ? B 137.16 118.60 18.56 0.60 N 3 1 N1 A A 106 ? A C2 A A 106 ? A N3 A A 106 ? A 126.02 129.30 -3.28 0.50 N 4 1 N1 A A 106 ? B C2 A A 106 ? B N3 A A 106 ? B 122.69 129.30 -6.61 0.50 N 5 1 C2 A A 106 ? B N3 A A 106 ? B C4 A A 106 ? B 101.79 110.60 -8.81 0.50 N 6 1 N3 A A 106 ? A C4 A A 106 ? A C5 A A 106 ? A 131.64 126.80 4.84 0.70 N 7 1 N3 A A 106 ? B C4 A A 106 ? B C5 A A 106 ? B 139.23 126.80 12.43 0.70 N 8 1 C4 A A 106 ? A C5 A A 106 ? A C6 A A 106 ? A 112.93 117.00 -4.07 0.50 N 9 1 C4 A A 106 ? B C5 A A 106 ? B C6 A A 106 ? B 112.67 117.00 -4.33 0.50 N 10 1 C5 A A 106 ? B C6 A A 106 ? B N1 A A 106 ? B 106.46 117.70 -11.24 0.50 N 11 1 N3 A A 106 ? B C4 A A 106 ? B N9 A A 106 ? B 116.21 127.40 -11.19 0.80 N 12 1 N1 A A 106 ? B C6 A A 106 ? B N6 A A 106 ? B 122.36 118.60 3.76 0.60 N 13 1 C5 A A 106 ? B C6 A A 106 ? B N6 A A 106 ? B 131.18 123.70 7.48 0.80 N 14 1 C4 A A 106 ? B N9 A A 106 ? B "C1'" A A 106 ? B 114.54 126.30 -11.76 1.80 N 15 1 C2 A U 107 ? B N3 A U 107 ? B C4 A U 107 ? B 133.61 127.00 6.61 0.60 N 16 1 C5 A U 107 ? B C6 A U 107 ? B N1 A U 107 ? B 125.96 122.70 3.26 0.50 N # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag Y _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id A _pdbx_unobs_or_zero_occ_atoms.auth_comp_id G _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 104 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id "C2'" _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id A _pdbx_unobs_or_zero_occ_atoms.label_comp_id G _pdbx_unobs_or_zero_occ_atoms.label_seq_id 4 _pdbx_unobs_or_zero_occ_atoms.label_atom_id "C2'" # 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 2SG P P N N 1 2SG SP1 S N N 2 2SG SP2 S N N 3 2SG "O5'" O N N 4 2SG "C5'" C N N 5 2SG "C4'" C N R 6 2SG "C3'" C N S 7 2SG "O3'" O N N 8 2SG "C2'" C N R 9 2SG "O2'" O N N 10 2SG "C1'" C N R 11 2SG "O4'" O N N 12 2SG N9 N Y N 13 2SG C4 C Y N 14 2SG C5 C Y N 15 2SG N7 N Y N 16 2SG C8 C Y N 17 2SG N3 N N N 18 2SG C2 C N N 19 2SG N2 N N N 20 2SG N1 N N N 21 2SG C6 C N N 22 2SG O6 O N N 23 2SG H1 H N N 24 2SG H2 H N N 25 2SG H3 H N N 26 2SG H4 H N N 27 2SG H5 H N N 28 2SG H6 H N N 29 2SG H7 H N N 30 2SG H8 H N N 31 2SG H9 H N N 32 2SG H10 H N N 33 2SG H11 H N N 34 2SG H13 H N N 35 2SG H14 H N N 36 2SG OP3 O N N 37 2SG H15 H N N 38 2SG H12 H N N 39 2SG H16 H N N 40 A OP3 O N N 41 A P P N N 42 A OP1 O N N 43 A OP2 O N N 44 A "O5'" O N N 45 A "C5'" C N N 46 A "C4'" C N R 47 A "O4'" O N N 48 A "C3'" C N S 49 A "O3'" O N N 50 A "C2'" C N R 51 A "O2'" O N N 52 A "C1'" C N R 53 A N9 N Y N 54 A C8 C Y N 55 A N7 N Y N 56 A C5 C Y N 57 A C6 C Y N 58 A N6 N N N 59 A N1 N Y N 60 A C2 C Y N 61 A N3 N Y N 62 A C4 C Y N 63 A HOP3 H N N 64 A HOP2 H N N 65 A "H5'" H N N 66 A "H5''" H N N 67 A "H4'" H N N 68 A "H3'" H N N 69 A "HO3'" H N N 70 A "H2'" H N N 71 A "HO2'" H N N 72 A "H1'" H N N 73 A H8 H N N 74 A H61 H N N 75 A H62 H N N 76 A H2 H N N 77 A2M P P N N 78 A2M OP1 O N N 79 A2M OP3 O N N 80 A2M "O5'" O N N 81 A2M "C5'" C N N 82 A2M "C4'" C N R 83 A2M "O4'" O N N 84 A2M "C3'" C N R 85 A2M "O3'" O N N 86 A2M "C2'" C N R 87 A2M "O2'" O N N 88 A2M "C1'" C N R 89 A2M "CM'" C N N 90 A2M N9 N Y N 91 A2M C8 C Y N 92 A2M N7 N Y N 93 A2M C5 C Y N 94 A2M C6 C Y N 95 A2M N6 N N N 96 A2M N1 N Y N 97 A2M C2 C Y N 98 A2M N3 N Y N 99 A2M C4 C Y N 100 A2M HOP3 H N N 101 A2M "H5'" H N N 102 A2M "H5''" H N N 103 A2M "H4'" H N N 104 A2M "H3'" H N N 105 A2M "HO3'" H N N 106 A2M "H2'" H N N 107 A2M "H1'" H N N 108 A2M "HM'1" H N N 109 A2M "HM'2" H N N 110 A2M "HM'3" H N N 111 A2M H8 H N N 112 A2M H61 H N N 113 A2M H62 H N N 114 A2M H2 H N N 115 A2M OP2 O N N 116 A2M HOP2 H N N 117 C OP3 O N N 118 C P P N N 119 C OP1 O N N 120 C OP2 O N N 121 C "O5'" O N N 122 C "C5'" C N N 123 C "C4'" C N R 124 C "O4'" O N N 125 C "C3'" C N S 126 C "O3'" O N N 127 C "C2'" C N R 128 C "O2'" O N N 129 C "C1'" C N R 130 C N1 N N N 131 C C2 C N N 132 C O2 O N N 133 C N3 N N N 134 C C4 C N N 135 C N4 N N N 136 C C5 C N N 137 C C6 C N N 138 C HOP3 H N N 139 C HOP2 H N N 140 C "H5'" H N N 141 C "H5''" H N N 142 C "H4'" H N N 143 C "H3'" H N N 144 C "HO3'" H N N 145 C "H2'" H N N 146 C "HO2'" H N N 147 C "H1'" H N N 148 C H41 H N N 149 C H42 H N N 150 C H5 H N N 151 C H6 H N N 152 G OP3 O N N 153 G P P N N 154 G OP1 O N N 155 G OP2 O N N 156 G "O5'" O N N 157 G "C5'" C N N 158 G "C4'" C N R 159 G "O4'" O N N 160 G "C3'" C N S 161 G "O3'" O N N 162 G "C2'" C N R 163 G "O2'" O N N 164 G "C1'" C N R 165 G N9 N Y N 166 G C8 C Y N 167 G N7 N Y N 168 G C5 C Y N 169 G C6 C N N 170 G O6 O N N 171 G N1 N N N 172 G C2 C N N 173 G N2 N N N 174 G N3 N N N 175 G C4 C Y N 176 G HOP3 H N N 177 G HOP2 H N N 178 G "H5'" H N N 179 G "H5''" H N N 180 G "H4'" H N N 181 G "H3'" H N N 182 G "HO3'" H N N 183 G "H2'" H N N 184 G "HO2'" H N N 185 G "H1'" H N N 186 G H8 H N N 187 G H1 H N N 188 G H21 H N N 189 G H22 H N N 190 HOH O O N N 191 HOH H1 H N N 192 HOH H2 H N N 193 U OP3 O N N 194 U P P N N 195 U OP1 O N N 196 U OP2 O N N 197 U "O5'" O N N 198 U "C5'" C N N 199 U "C4'" C N R 200 U "O4'" O N N 201 U "C3'" C N S 202 U "O3'" O N N 203 U "C2'" C N R 204 U "O2'" O N N 205 U "C1'" C N R 206 U N1 N N N 207 U C2 C N N 208 U O2 O N N 209 U N3 N N N 210 U C4 C N N 211 U O4 O N N 212 U C5 C N N 213 U C6 C N N 214 U HOP3 H N N 215 U HOP2 H N N 216 U "H5'" H N N 217 U "H5''" H N N 218 U "H4'" H N N 219 U "H3'" H N N 220 U "HO3'" H N N 221 U "H2'" H N N 222 U "HO2'" H N N 223 U "H1'" H N N 224 U H3 H N N 225 U H5 H N N 226 U H6 H N N 227 # 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 2SG "O3'" "C3'" sing N N 1 2SG "O2'" "C2'" sing N N 2 2SG "C2'" "C3'" sing N N 3 2SG "C2'" "C1'" sing N N 4 2SG "C3'" "C4'" sing N N 5 2SG "C4'" "C5'" sing N N 6 2SG "C4'" "O4'" sing N N 7 2SG "C5'" "O5'" sing N N 8 2SG "C1'" "O4'" sing N N 9 2SG "C1'" N9 sing N N 10 2SG N2 C2 sing N N 11 2SG N3 C2 doub N N 12 2SG N3 C4 sing N N 13 2SG "O5'" P sing N N 14 2SG N9 C4 sing Y N 15 2SG N9 C8 sing Y N 16 2SG C2 N1 sing N N 17 2SG C4 C5 doub Y N 18 2SG SP1 P sing N N 19 2SG C8 N7 doub Y N 20 2SG P SP2 sing N N 21 2SG N1 C6 sing N N 22 2SG C5 N7 sing Y N 23 2SG C5 C6 sing N N 24 2SG C6 O6 doub N N 25 2SG SP1 H1 sing N N 26 2SG SP2 H2 sing N N 27 2SG "C5'" H3 sing N N 28 2SG "C5'" H4 sing N N 29 2SG "C4'" H5 sing N N 30 2SG "C3'" H6 sing N N 31 2SG "O3'" H7 sing N N 32 2SG "C2'" H8 sing N N 33 2SG "O2'" H9 sing N N 34 2SG "C1'" H10 sing N N 35 2SG C8 H11 sing N N 36 2SG N2 H13 sing N N 37 2SG N2 H14 sing N N 38 2SG P OP3 sing N N 39 2SG P H15 sing N N 40 2SG N1 H12 sing N N 41 2SG OP3 H16 sing N N 42 A OP3 P sing N N 43 A OP3 HOP3 sing N N 44 A P OP1 doub N N 45 A P OP2 sing N N 46 A P "O5'" sing N N 47 A OP2 HOP2 sing N N 48 A "O5'" "C5'" sing N N 49 A "C5'" "C4'" sing N N 50 A "C5'" "H5'" sing N N 51 A "C5'" "H5''" sing N N 52 A "C4'" "O4'" sing N N 53 A "C4'" "C3'" sing N N 54 A "C4'" "H4'" sing N N 55 A "O4'" "C1'" sing N N 56 A "C3'" "O3'" sing N N 57 A "C3'" "C2'" sing N N 58 A "C3'" "H3'" sing N N 59 A "O3'" "HO3'" sing N N 60 A "C2'" "O2'" sing N N 61 A "C2'" "C1'" sing N N 62 A "C2'" "H2'" sing N N 63 A "O2'" "HO2'" sing N N 64 A "C1'" N9 sing N N 65 A "C1'" "H1'" sing N N 66 A N9 C8 sing Y N 67 A N9 C4 sing Y N 68 A C8 N7 doub Y N 69 A C8 H8 sing N N 70 A N7 C5 sing Y N 71 A C5 C6 sing Y N 72 A C5 C4 doub Y N 73 A C6 N6 sing N N 74 A C6 N1 doub Y N 75 A N6 H61 sing N N 76 A N6 H62 sing N N 77 A N1 C2 sing Y N 78 A C2 N3 doub Y N 79 A C2 H2 sing N N 80 A N3 C4 sing Y N 81 A2M P OP1 doub N N 82 A2M P OP3 sing N N 83 A2M P "O5'" sing N N 84 A2M OP3 HOP3 sing N N 85 A2M "O5'" "C5'" sing N N 86 A2M "C5'" "C4'" sing N N 87 A2M "C5'" "H5'" sing N N 88 A2M "C5'" "H5''" sing N N 89 A2M "C4'" "O4'" sing N N 90 A2M "C4'" "C3'" sing N N 91 A2M "C4'" "H4'" sing N N 92 A2M "O4'" "C1'" sing N N 93 A2M "C3'" "O3'" sing N N 94 A2M "C3'" "C2'" sing N N 95 A2M "C3'" "H3'" sing N N 96 A2M "O3'" "HO3'" sing N N 97 A2M "C2'" "O2'" sing N N 98 A2M "C2'" "C1'" sing N N 99 A2M "C2'" "H2'" sing N N 100 A2M "O2'" "CM'" sing N N 101 A2M "C1'" N9 sing N N 102 A2M "C1'" "H1'" sing N N 103 A2M "CM'" "HM'1" sing N N 104 A2M "CM'" "HM'2" sing N N 105 A2M "CM'" "HM'3" sing N N 106 A2M N9 C8 sing Y N 107 A2M N9 C4 sing Y N 108 A2M C8 N7 doub Y N 109 A2M C8 H8 sing N N 110 A2M N7 C5 sing Y N 111 A2M C5 C6 sing Y N 112 A2M C5 C4 doub Y N 113 A2M C6 N6 sing N N 114 A2M C6 N1 doub Y N 115 A2M N6 H61 sing N N 116 A2M N6 H62 sing N N 117 A2M N1 C2 sing Y N 118 A2M C2 N3 doub Y N 119 A2M C2 H2 sing N N 120 A2M N3 C4 sing Y N 121 A2M P OP2 sing N N 122 A2M OP2 HOP2 sing N N 123 C OP3 P sing N N 124 C OP3 HOP3 sing N N 125 C P OP1 doub N N 126 C P OP2 sing N N 127 C P "O5'" sing N N 128 C OP2 HOP2 sing N N 129 C "O5'" "C5'" sing N N 130 C "C5'" "C4'" sing N N 131 C "C5'" "H5'" sing N N 132 C "C5'" "H5''" sing N N 133 C "C4'" "O4'" sing N N 134 C "C4'" "C3'" sing N N 135 C "C4'" "H4'" sing N N 136 C "O4'" "C1'" sing N N 137 C "C3'" "O3'" sing N N 138 C "C3'" "C2'" sing N N 139 C "C3'" "H3'" sing N N 140 C "O3'" "HO3'" sing N N 141 C "C2'" "O2'" sing N N 142 C "C2'" "C1'" sing N N 143 C "C2'" "H2'" sing N N 144 C "O2'" "HO2'" sing N N 145 C "C1'" N1 sing N N 146 C "C1'" "H1'" sing N N 147 C N1 C2 sing N N 148 C N1 C6 sing N N 149 C C2 O2 doub N N 150 C C2 N3 sing N N 151 C N3 C4 doub N N 152 C C4 N4 sing N N 153 C C4 C5 sing N N 154 C N4 H41 sing N N 155 C N4 H42 sing N N 156 C C5 C6 doub N N 157 C C5 H5 sing N N 158 C C6 H6 sing N N 159 G OP3 P sing N N 160 G OP3 HOP3 sing N N 161 G P OP1 doub N N 162 G P OP2 sing N N 163 G P "O5'" sing N N 164 G OP2 HOP2 sing N N 165 G "O5'" "C5'" sing N N 166 G "C5'" "C4'" sing N N 167 G "C5'" "H5'" sing N N 168 G "C5'" "H5''" sing N N 169 G "C4'" "O4'" sing N N 170 G "C4'" "C3'" sing N N 171 G "C4'" "H4'" sing N N 172 G "O4'" "C1'" sing N N 173 G "C3'" "O3'" sing N N 174 G "C3'" "C2'" sing N N 175 G "C3'" "H3'" sing N N 176 G "O3'" "HO3'" sing N N 177 G "C2'" "O2'" sing N N 178 G "C2'" "C1'" sing N N 179 G "C2'" "H2'" sing N N 180 G "O2'" "HO2'" sing N N 181 G "C1'" N9 sing N N 182 G "C1'" "H1'" sing N N 183 G N9 C8 sing Y N 184 G N9 C4 sing Y N 185 G C8 N7 doub Y N 186 G C8 H8 sing N N 187 G N7 C5 sing Y N 188 G C5 C6 sing N N 189 G C5 C4 doub Y N 190 G C6 O6 doub N N 191 G C6 N1 sing N N 192 G N1 C2 sing N N 193 G N1 H1 sing N N 194 G C2 N2 sing N N 195 G C2 N3 doub N N 196 G N2 H21 sing N N 197 G N2 H22 sing N N 198 G N3 C4 sing N N 199 HOH O H1 sing N N 200 HOH O H2 sing N N 201 U OP3 P sing N N 202 U OP3 HOP3 sing N N 203 U P OP1 doub N N 204 U P OP2 sing N N 205 U P "O5'" sing N N 206 U OP2 HOP2 sing N N 207 U "O5'" "C5'" sing N N 208 U "C5'" "C4'" sing N N 209 U "C5'" "H5'" sing N N 210 U "C5'" "H5''" sing N N 211 U "C4'" "O4'" sing N N 212 U "C4'" "C3'" sing N N 213 U "C4'" "H4'" sing N N 214 U "O4'" "C1'" sing N N 215 U "C3'" "O3'" sing N N 216 U "C3'" "C2'" sing N N 217 U "C3'" "H3'" sing N N 218 U "O3'" "HO3'" sing N N 219 U "C2'" "O2'" sing N N 220 U "C2'" "C1'" sing N N 221 U "C2'" "H2'" sing N N 222 U "O2'" "HO2'" sing N N 223 U "C1'" N1 sing N N 224 U "C1'" "H1'" sing N N 225 U N1 C2 sing N N 226 U N1 C6 sing N N 227 U C2 O2 doub N N 228 U C2 N3 sing N N 229 U N3 C4 sing N N 230 U N3 H3 sing N N 231 U C4 O4 doub N N 232 U C4 C5 sing N N 233 U C5 C6 doub N N 234 U C5 H5 sing N N 235 U C6 H6 sing N N 236 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4RC0 'double helix' 4RC0 'mismatched base pair' 4RC0 'internal loop' # 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 C 1 1_555 A G 12 2_556 0.121 -0.115 -0.013 7.886 -14.049 -0.058 1 A_C101:G112_A A 101 ? A 112 ? 19 1 1 A G 2 1_555 A C 11 2_556 -0.263 -0.151 0.036 -4.427 -16.745 1.008 2 A_G102:C111_A A 102 ? A 111 ? 19 1 1 A G 4 1_555 A A2M 9 2_556 -0.028 1.469 -0.446 5.288 -11.702 -15.772 3 A_G104:A2M109_A A 104 ? A 109 ? 8 1 1 A A 5 1_555 A U 8 2_556 -0.670 0.332 0.313 0.622 -13.704 -8.404 4 A_A105:U108_A A 105 ? A 108 ? ? ? 1 A C 1 1_555 A G 12 1_555 0.121 -0.115 -0.013 7.886 -14.049 -0.058 5 A_C101:G112_A A 101 ? A 112 ? 19 1 1 A G 2 1_555 A C 11 1_555 -0.263 -0.151 0.036 -4.427 -16.745 1.008 6 A_G102:C111_A A 102 ? A 111 ? 19 1 1 A G 4 1_555 A A2M 9 1_555 -0.028 1.469 -0.446 5.288 -11.702 -15.772 7 A_G104:A2M109_A A 104 ? A 109 ? 8 1 1 A A 5 1_555 A U 8 1_555 -0.670 0.332 0.313 0.622 -13.704 -8.404 8 A_A105:U108_A A 105 ? A 108 ? ? ? # 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 C 1 1_555 A G 12 2_556 A G 2 1_555 A C 11 2_556 -0.370 -1.724 3.372 -3.240 12.986 31.991 -4.779 0.153 2.527 22.377 5.584 34.611 1 AA_C101G102:C111G112_AA A 101 ? A 112 ? A 102 ? A 111 ? 1 A G 2 1_555 A C 11 2_556 A G 4 1_555 A A2M 9 2_556 -1.481 -2.721 6.298 -1.198 14.848 61.385 -3.829 1.318 5.599 14.320 1.155 62.995 2 AA_G102G104:A2M109C111_AA A 102 ? A 111 ? A 104 ? A 109 ? 1 A G 4 1_555 A A2M 9 2_556 A A 5 1_555 A U 8 2_556 0.556 -1.582 3.217 -4.677 12.624 30.838 -4.563 -1.638 2.305 22.446 8.316 33.583 3 AA_G104A105:U108A2M109_AA A 104 ? A 109 ? A 105 ? A 108 ? 1 A C 1 1_555 A G 12 1_555 A G 2 1_555 A C 11 1_555 -0.370 -1.724 3.372 -3.240 12.986 31.991 -4.779 0.153 2.527 22.377 5.584 34.611 4 AA_C101G102:C111G112_AA A 101 ? A 112 ? A 102 ? A 111 ? 1 A G 2 1_555 A C 11 1_555 A G 4 1_555 A A2M 9 1_555 -1.481 -2.721 6.298 -1.198 14.848 61.385 -3.829 1.318 5.599 14.320 1.155 62.995 5 AA_G102G104:A2M109C111_AA A 102 ? A 111 ? A 104 ? A 109 ? 1 A G 4 1_555 A A2M 9 1_555 A A 5 1_555 A U 8 1_555 0.556 -1.582 3.217 -4.677 12.624 30.838 -4.563 -1.638 2.305 22.446 8.316 33.583 6 AA_G104A105:U108A2M109_AA A 104 ? A 109 ? A 105 ? A 108 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2Q1R _pdbx_initial_refinement_model.details 'PDB ENTRY 2Q1R' #