data_1KD3 # _entry.id 1KD3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1KD3 pdb_00001kd3 10.2210/pdb1kd3/pdb NDB AR0036 ? ? RCSB RCSB014828 ? ? WWPDB D_1000014828 ? ? # 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 2003-03-04 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _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' # 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_struct_conn_angle 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' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 21 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 26 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 28 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 32 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 33 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 34 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 35 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1KD3 _pdbx_database_status.recvd_initial_deposition_date 2001-11-12 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _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 'Kacer, V.' 1 'Scaringe, S.A.' 2 'Scarsdale, J.N.' 3 'Rife, J.P.' 4 # _citation.id primary _citation.title 'Crystal structures of r(GGUCACAGCCC)2.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 59 _citation.page_first 423 _citation.page_last 432 _citation.year 2003 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12595698 _citation.pdbx_database_id_DOI 10.1107/S0907444902021911 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kacer, V.' 1 ? primary 'Scaringe, S.A.' 2 ? primary 'Scarsdale, J.N.' 3 ? primary 'Rife, J.P.' 4 ? # 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*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'" 3481.146 2 ? ? ? ? 2 non-polymer syn 'THALLIUM (I) ION' 204.383 2 ? ? ? ? 3 water nat water 18.015 74 ? ? ? ? # _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 GGUCACAGCCC _entity_poly.pdbx_seq_one_letter_code_can GGUCACAGCCC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'THALLIUM (I) ION' TL 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 U n 1 4 C n 1 5 A n 1 6 C n 1 7 A n 1 8 G n 1 9 C n 1 10 C n 1 11 C n # 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 TL non-polymer . 'THALLIUM (I) ION' ? 'Tl 1' 204.383 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 U 3 3 3 U U A . n A 1 4 C 4 4 4 C C A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 A 7 7 7 A A A . n A 1 8 G 8 8 8 G G A . n A 1 9 C 9 9 9 C C A . n A 1 10 C 10 10 10 C C A . n A 1 11 C 11 11 11 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 G 2 2 2 G G B . n B 1 3 U 3 3 3 U U B . n B 1 4 C 4 4 4 C C B . n B 1 5 A 5 5 5 A A B . n B 1 6 C 6 6 6 C C B . n B 1 7 A 7 7 7 A A B . n B 1 8 G 8 8 8 G G B . n B 1 9 C 9 9 9 C C B . n B 1 10 C 10 10 10 C C B . n B 1 11 C 11 11 11 C C 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 TL 1 502 502 TL TL A . D 2 TL 1 501 501 TL TL B . E 3 HOH 1 18 18 HOH HOH A . E 3 HOH 2 19 19 HOH HOH A . E 3 HOH 3 23 23 HOH HOH A . E 3 HOH 4 26 26 HOH HOH A . E 3 HOH 5 31 31 HOH HOH A . E 3 HOH 6 32 32 HOH HOH A . E 3 HOH 7 36 36 HOH HOH A . E 3 HOH 8 37 37 HOH HOH A . E 3 HOH 9 41 41 HOH HOH A . E 3 HOH 10 47 47 HOH HOH A . E 3 HOH 11 48 48 HOH HOH A . E 3 HOH 12 49 49 HOH HOH A . E 3 HOH 13 56 56 HOH HOH A . E 3 HOH 14 64 64 HOH HOH A . E 3 HOH 15 66 66 HOH HOH A . E 3 HOH 16 67 67 HOH HOH A . E 3 HOH 17 69 69 HOH HOH A . E 3 HOH 18 73 73 HOH HOH A . E 3 HOH 19 78 78 HOH HOH A . E 3 HOH 20 80 80 HOH HOH A . E 3 HOH 21 82 82 HOH HOH A . E 3 HOH 22 83 83 HOH HOH A . E 3 HOH 23 85 85 HOH HOH A . E 3 HOH 24 86 86 HOH HOH A . E 3 HOH 25 115 115 HOH HOH A . E 3 HOH 26 121 121 HOH HOH A . E 3 HOH 27 131 131 HOH HOH A . E 3 HOH 28 169 169 HOH HOH A . E 3 HOH 29 173 173 HOH HOH A . E 3 HOH 30 218 218 HOH HOH A . E 3 HOH 31 310 310 HOH HOH A . E 3 HOH 32 317 317 HOH HOH A . E 3 HOH 33 318 318 HOH HOH A . E 3 HOH 34 412 412 HOH HOH A . F 3 HOH 1 14 14 HOH HOH B . F 3 HOH 2 16 16 HOH HOH B . F 3 HOH 3 17 17 HOH HOH B . F 3 HOH 4 20 20 HOH HOH B . F 3 HOH 5 22 22 HOH HOH B . F 3 HOH 6 25 25 HOH HOH B . F 3 HOH 7 30 30 HOH HOH B . F 3 HOH 8 34 34 HOH HOH B . F 3 HOH 9 35 35 HOH HOH B . F 3 HOH 10 38 38 HOH HOH B . F 3 HOH 11 39 39 HOH HOH B . F 3 HOH 12 40 40 HOH HOH B . F 3 HOH 13 42 42 HOH HOH B . F 3 HOH 14 45 45 HOH HOH B . F 3 HOH 15 55 55 HOH HOH B . F 3 HOH 16 57 57 HOH HOH B . F 3 HOH 17 58 58 HOH HOH B . F 3 HOH 18 59 59 HOH HOH B . F 3 HOH 19 60 60 HOH HOH B . F 3 HOH 20 61 61 HOH HOH B . F 3 HOH 21 68 68 HOH HOH B . F 3 HOH 22 70 70 HOH HOH B . F 3 HOH 23 72 72 HOH HOH B . F 3 HOH 24 74 74 HOH HOH B . F 3 HOH 25 77 77 HOH HOH B . F 3 HOH 26 79 79 HOH HOH B . F 3 HOH 27 87 87 HOH HOH B . F 3 HOH 28 112 112 HOH HOH B . F 3 HOH 29 124 124 HOH HOH B . F 3 HOH 30 142 142 HOH HOH B . F 3 HOH 31 157 157 HOH HOH B . F 3 HOH 32 161 161 HOH HOH B . F 3 HOH 33 172 172 HOH HOH B . F 3 HOH 34 215 215 HOH HOH B . F 3 HOH 35 311 311 HOH HOH B . F 3 HOH 36 314 314 HOH HOH B . F 3 HOH 37 315 315 HOH HOH B . F 3 HOH 38 316 316 HOH HOH B . F 3 HOH 39 319 319 HOH HOH B . F 3 HOH 40 411 411 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 CNS refinement . ? 3 CNS phasing . ? 4 # _cell.entry_id 1KD3 _cell.length_a 44.232 _cell.length_b 44.232 _cell.length_c 49.870 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KD3 _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting tetragonal _symmetry.Int_Tables_number 78 # _exptl.entry_id 1KD3 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 61.9 _exptl_crystal.density_Matthews 3.25 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.4 _exptl_crystal_grow.pdbx_details '50 mM tris HCl (pH 6.4), 1.4 M (NH4)2SO4, 20 mM MgCl2, 18 mM spermine, neomycin B, pH 6.4, VAPOR DIFFUSION, HANGING DROP at 293K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 'tris HCl' ? ? ? 1 2 1 '(NH4)2SO4' ? ? ? 1 3 1 MgCl2 ? ? ? 1 4 1 spermine ? ? ? 1 5 1 'neomycin B' ? ? ? 1 6 2 'tris HCl' ? ? ? 1 7 2 '(NH4)2SO4' ? ? ? 1 8 2 MgCl2 ? ? ? 1 9 2 spermine ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 98 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date 2000-05-31 _diffrn_detector.details 'Osmic confocal optics' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Osmic confocal optics' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 1KD3 _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 99 _reflns.d_resolution_high 1.80 _reflns.number_obs 9145 _reflns.number_all 9161 _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs 0.102 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 28.7 _reflns.B_iso_Wilson_estimate 30.2 _reflns.pdbx_redundancy 9.9 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.80 _reflns_shell.d_res_low 1.83 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.51 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.7 _reflns_shell.pdbx_redundancy 9.3 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 447 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1KD3 _refine.ls_number_reflns_obs 8800 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF 1381692.88 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.ls_d_res_low 21.72 _refine.ls_d_res_high 1.80 _refine.ls_percent_reflns_obs 97.9 _refine.ls_R_factor_obs 0.215 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.215 _refine.ls_R_factor_R_free 0.241 _refine.ls_R_factor_R_free_error 0.008 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.4 _refine.ls_number_reflns_R_free 911 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 24.8 _refine.aniso_B[1][1] 0.88 _refine.aniso_B[2][2] 0.88 _refine.aniso_B[3][3] -1.76 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.573747 _refine.solvent_model_param_bsol 74.6805 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'metal free r(GGUCACAGCCC)2' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _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.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.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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_analyze.entry_id 1KD3 _refine_analyze.Luzzati_coordinate_error_obs 0.22 _refine_analyze.Luzzati_sigma_a_obs 0.17 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.27 _refine_analyze.Luzzati_sigma_a_free 0.22 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 460 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 74 _refine_hist.number_atoms_total 536 _refine_hist.d_res_high 1.80 _refine_hist.d_res_low 21.72 # 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 c_bond_d 0.004 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.8 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 11.1 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.18 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.80 _refine_ls_shell.d_res_low 1.91 _refine_ls_shell.number_reflns_R_work 1288 _refine_ls_shell.R_factor_R_work 0.266 _refine_ls_shell.percent_reflns_obs 96.0 _refine_ls_shell.R_factor_R_free 0.3 _refine_ls_shell.R_factor_R_free_error 0.026 _refine_ls_shell.percent_reflns_R_free 9.6 _refine_ls_shell.number_reflns_R_free 136 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 DNA-RNA_REP.PARAM DNA-RNA.TOP 'X-RAY DIFFRACTION' 2 WATER_REP.PARAM WATER.TOP 'X-RAY DIFFRACTION' 3 ION.PARAM ION.TOP 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1KD3 _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 1KD3 _struct.title 'The Crystal Structure of r(GGUCACAGCCC)2, Thallium form' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1KD3 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA duplex, metal binding, 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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1KD3 _struct_ref.pdbx_db_accession 1KD3 _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 1KD3 A 1 ? 11 ? 1KD3 1 ? 11 ? 1 11 2 1 1KD3 B 1 ? 11 ? 1KD3 1 ? 11 ? 1 11 # _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 # _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.pdbx_parent_biol_id ? _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 4 O2 ? ? ? 1_555 C TL . TL ? ? A C 4 A TL 502 1_555 ? ? ? ? ? ? ? 2.558 ? ? metalc2 metalc ? ? A C 4 N3 ? ? ? 1_555 C TL . TL ? ? A C 4 A TL 502 1_555 ? ? ? ? ? ? ? 3.273 ? ? metalc3 metalc ? ? A A 7 N7 ? ? ? 1_555 D TL . TL ? ? A A 7 B TL 501 1_555 ? ? ? ? ? ? ? 2.972 ? ? metalc4 metalc ? ? A G 8 O6 ? ? ? 1_555 D TL . TL ? ? A G 8 B TL 501 1_555 ? ? ? ? ? ? ? 3.215 ? ? metalc5 metalc ? ? E HOH . O ? ? ? 1_555 D TL . TL ? ? A HOH 19 B TL 501 1_555 ? ? ? ? ? ? ? 2.991 ? ? metalc6 metalc ? ? C TL . TL ? ? ? 1_555 B A 7 N7 ? ? A TL 502 B A 7 1_555 ? ? ? ? ? ? ? 2.929 ? ? metalc7 metalc ? ? C TL . TL ? ? ? 1_555 B G 8 O6 ? ? A TL 502 B G 8 1_555 ? ? ? ? ? ? ? 3.199 ? ? metalc8 metalc ? ? C TL . TL ? ? ? 1_555 F HOH . O ? ? A TL 502 B HOH 20 1_555 ? ? ? ? ? ? ? 3.050 ? ? metalc9 metalc ? ? B C 4 O2 ? ? ? 1_555 D TL . TL ? ? B C 4 B TL 501 1_555 ? ? ? ? ? ? ? 2.607 ? ? metalc10 metalc ? ? B C 4 N3 ? ? ? 1_555 D TL . TL ? ? B C 4 B TL 501 1_555 ? ? ? ? ? ? ? 3.261 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 1 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 1 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 1 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 2 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 2 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 2 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 B G 8 O6 ? ? A U 3 B G 8 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A U 3 O2 ? ? ? 1_555 B G 8 N1 ? ? A U 3 B G 8 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B A 7 N6 ? ? A C 4 B A 7 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog10 hydrog ? ? A A 5 N6 ? ? ? 1_555 B C 6 N3 ? ? A A 5 B C 6 1_555 ? ? ? ? ? ? TYPE_25_PAIR ? ? ? hydrog11 hydrog ? ? A A 5 N7 ? ? ? 1_555 B C 6 N4 ? ? A A 5 B C 6 1_555 ? ? ? ? ? ? TYPE_25_PAIR ? ? ? hydrog12 hydrog ? ? A C 6 N3 ? ? ? 1_555 B A 5 N6 ? ? A C 6 B A 5 1_555 ? ? ? ? ? ? TYPE_25_PAIR ? ? ? hydrog13 hydrog ? ? A C 6 N4 ? ? ? 1_555 B A 5 N7 ? ? A C 6 B A 5 1_555 ? ? ? ? ? ? TYPE_25_PAIR ? ? ? hydrog14 hydrog ? ? A A 7 N6 ? ? ? 1_555 B C 4 O2 ? ? A A 7 B C 4 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog15 hydrog ? ? A G 8 N1 ? ? ? 1_555 B U 3 O2 ? ? A G 8 B U 3 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog16 hydrog ? ? A G 8 O6 ? ? ? 1_555 B U 3 N3 ? ? A G 8 B U 3 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog17 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 9 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 9 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 9 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 10 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 10 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 10 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # 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 O2 ? A C 4 ? A C 4 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 N3 ? A C 4 ? A C 4 ? 1_555 43.5 ? 2 O2 ? A C 4 ? A C 4 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 N7 ? B A 7 ? B A 7 ? 1_555 95.8 ? 3 N3 ? A C 4 ? A C 4 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 N7 ? B A 7 ? B A 7 ? 1_555 137.9 ? 4 O2 ? A C 4 ? A C 4 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 O6 ? B G 8 ? B G 8 ? 1_555 80.3 ? 5 N3 ? A C 4 ? A C 4 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 O6 ? B G 8 ? B G 8 ? 1_555 94.1 ? 6 N7 ? B A 7 ? B A 7 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 O6 ? B G 8 ? B G 8 ? 1_555 87.0 ? 7 O2 ? A C 4 ? A C 4 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 O ? F HOH . ? B HOH 20 ? 1_555 138.2 ? 8 N3 ? A C 4 ? A C 4 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 O ? F HOH . ? B HOH 20 ? 1_555 102.3 ? 9 N7 ? B A 7 ? B A 7 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 O ? F HOH . ? B HOH 20 ? 1_555 106.6 ? 10 O6 ? B G 8 ? B G 8 ? 1_555 TL ? C TL . ? A TL 502 ? 1_555 O ? F HOH . ? B HOH 20 ? 1_555 134.5 ? 11 N7 ? A A 7 ? A A 7 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 O6 ? A G 8 ? A G 8 ? 1_555 85.2 ? 12 N7 ? A A 7 ? A A 7 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 O ? E HOH . ? A HOH 19 ? 1_555 107.1 ? 13 O6 ? A G 8 ? A G 8 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 O ? E HOH . ? A HOH 19 ? 1_555 133.4 ? 14 N7 ? A A 7 ? A A 7 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 O2 ? B C 4 ? B C 4 ? 1_555 93.0 ? 15 O6 ? A G 8 ? A G 8 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 O2 ? B C 4 ? B C 4 ? 1_555 80.5 ? 16 O ? E HOH . ? A HOH 19 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 O2 ? B C 4 ? B C 4 ? 1_555 140.7 ? 17 N7 ? A A 7 ? A A 7 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 N3 ? B C 4 ? B C 4 ? 1_555 135.5 ? 18 O6 ? A G 8 ? A G 8 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 N3 ? B C 4 ? B C 4 ? 1_555 94.5 ? 19 O ? E HOH . ? A HOH 19 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 N3 ? B C 4 ? B C 4 ? 1_555 105.0 ? 20 O2 ? B C 4 ? B C 4 ? 1_555 TL ? D TL . ? B TL 501 ? 1_555 N3 ? B C 4 ? B C 4 ? 1_555 43.7 ? # 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 B TL 501 ? 5 'BINDING SITE FOR RESIDUE TL B 501' AC2 Software A TL 502 ? 5 'BINDING SITE FOR RESIDUE TL A 502' # 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 A A 7 ? A A 7 . ? 1_555 ? 2 AC1 5 G A 8 ? G A 8 . ? 1_555 ? 3 AC1 5 HOH E . ? HOH A 19 . ? 1_555 ? 4 AC1 5 U B 3 ? U B 3 . ? 1_555 ? 5 AC1 5 C B 4 ? C B 4 . ? 1_555 ? 6 AC2 5 U A 3 ? U A 3 . ? 1_555 ? 7 AC2 5 C A 4 ? C A 4 . ? 1_555 ? 8 AC2 5 A B 7 ? A B 7 . ? 1_555 ? 9 AC2 5 G B 8 ? G B 8 . ? 1_555 ? 10 AC2 5 HOH F . ? HOH B 20 . ? 1_555 ? # 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 TL TL TL 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 1KD3 'double helix' 1KD3 'a-form double helix' 1KD3 '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 10 1_555 -0.165 -0.158 -0.110 -6.598 -6.007 -0.623 1 A_G1:C10_B A 1 ? B 10 ? 19 1 1 A G 2 1_555 B C 9 1_555 -0.194 -0.154 -0.198 -14.336 -13.882 1.558 2 A_G2:C9_B A 2 ? B 9 ? 19 1 1 A U 3 1_555 B G 8 1_555 2.398 -0.711 0.160 -10.110 -3.201 -3.123 3 A_U3:G8_B A 3 ? B 8 ? 28 ? 1 A C 4 1_555 B A 7 1_555 6.857 -4.369 0.532 -8.398 6.152 -8.519 4 A_C4:A7_B A 4 ? B 7 ? ? 6 1 A A 5 1_555 B C 6 1_555 -3.126 -0.078 0.031 -1.558 -6.894 -97.071 5 A_A5:C6_B A 5 ? B 6 ? 25 4 1 A C 6 1_555 B A 5 1_555 3.008 -0.017 0.079 2.775 -7.302 -97.676 6 A_C6:A5_B A 6 ? B 5 ? 25 4 1 A A 7 1_555 B C 4 1_555 -6.847 -4.404 0.591 10.007 6.490 -8.696 7 A_A7:C4_B A 7 ? B 4 ? ? 6 1 A G 8 1_555 B U 3 1_555 -2.408 -0.690 0.106 10.663 -3.013 -3.288 8 A_G8:U3_B A 8 ? B 3 ? 28 ? 1 A C 9 1_555 B G 2 1_555 0.307 -0.144 -0.132 12.743 -13.160 1.657 9 A_C9:G2_B A 9 ? B 2 ? 19 1 1 A C 10 1_555 B G 1 1_555 0.268 -0.115 -0.051 6.729 -6.095 2.058 10 A_C10:G1_B A 10 ? 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 10 1_555 A G 2 1_555 B C 9 1_555 -0.036 -2.090 3.440 2.459 6.071 31.968 -4.769 0.488 2.992 10.881 -4.407 32.615 1 AA_G1G2:C9C10_BB A 1 ? B 10 ? A 2 ? B 9 ? 1 A G 2 1_555 B C 9 1_555 A U 3 1_555 B G 8 1_555 0.005 -1.373 3.174 -0.062 2.022 42.203 -2.103 -0.014 3.108 2.806 0.086 42.250 2 AA_G2U3:G8C9_BB A 2 ? B 9 ? A 3 ? B 8 ? 1 A U 3 1_555 B G 8 1_555 A C 4 1_555 B A 7 1_555 0.355 -1.197 3.256 6.666 5.944 58.257 -1.519 -0.023 3.151 6.066 -6.803 58.878 3 AA_U3C4:A7G8_BB A 3 ? B 8 ? A 4 ? B 7 ? 1 A C 4 1_555 B A 7 1_555 A A 5 1_555 B C 6 1_555 -5.369 -0.991 2.847 4.062 -1.631 -13.585 5.625 -17.545 4.119 6.674 16.617 -14.270 4 AA_C4A5:C6A7_BB A 4 ? B 7 ? A 5 ? B 6 ? 1 A A 5 1_555 B C 6 1_555 A C 6 1_555 B A 5 1_555 -0.039 -3.866 3.165 -0.538 -5.608 67.304 -3.261 0.014 3.440 -5.051 0.485 67.512 5 AA_A5C6:A5C6_BB A 5 ? B 6 ? A 6 ? B 5 ? 1 A C 6 1_555 B A 5 1_555 A A 7 1_555 B C 4 1_555 5.399 -1.029 2.781 -3.816 -2.792 -12.756 7.322 18.725 3.907 12.040 -16.455 -13.601 6 AA_C6A7:C4A5_BB A 6 ? B 5 ? A 7 ? B 4 ? 1 A A 7 1_555 B C 4 1_555 A G 8 1_555 B U 3 1_555 -0.352 -1.190 3.317 -6.263 6.613 58.538 -1.542 0.037 3.197 6.719 6.362 59.180 7 AA_A7G8:U3C4_BB A 7 ? B 4 ? A 8 ? B 3 ? 1 A G 8 1_555 B U 3 1_555 A C 9 1_555 B G 2 1_555 0.007 -1.373 3.233 -0.729 1.827 42.596 -2.068 -0.081 3.174 2.513 1.003 42.639 8 AA_G8C9:G2U3_BB A 8 ? B 3 ? A 9 ? B 2 ? 1 A C 9 1_555 B G 2 1_555 A C 10 1_555 B G 1 1_555 0.040 -2.074 3.383 -2.073 5.351 31.886 -4.645 -0.430 2.996 9.642 3.736 32.385 9 AA_C9C10:G1G2_BB A 9 ? B 2 ? A 10 ? B 1 ? # _atom_sites.entry_id 1KD3 _atom_sites.fract_transf_matrix[1][1] 0.022608 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022608 _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] 0.020052 _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 N O P TL # loop_