data_3LOA # _entry.id 3LOA # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3LOA pdb_00003loa 10.2210/pdb3loa/pdb NDB NA0454 ? ? RCSB RCSB057524 ? ? WWPDB D_1000057524 ? ? # 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 2010-08-04 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2019-07-17 4 'Structure model' 1 3 2024-02-21 # _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' 'Data collection' 3 3 'Structure model' 'Derived calculations' 4 3 'Structure model' 'Refinement description' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 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 3 'Structure model' software 2 3 'Structure model' struct_conn 3 4 'Structure model' chem_comp_atom 4 4 'Structure model' chem_comp_bond 5 4 'Structure model' database_2 6 4 'Structure model' struct_conn 7 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 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 3 'Structure model' '_software.version' 4 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_database_2.pdbx_DOI' 6 4 'Structure model' '_database_2.pdbx_database_accession' 7 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 19 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 20 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 21 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3LOA _pdbx_database_status.recvd_initial_deposition_date 2010-02-03 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Dibrov, S.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'A model for the study of ligand binding to the ribosomal RNA helix h44.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 38 _citation.page_first 4458 _citation.page_last 4465 _citation.year 2010 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20215440 _citation.pdbx_database_id_DOI 10.1093/nar/gkq159 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dibrov, S.M.' 1 ? primary 'Parsons, J.' 2 ? primary 'Hermann, T.' 3 ? # 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*CP*GP*CP*GP*CP*CP*CP*GP*(5BU)P*CP*AP*CP*AP*CP*CP*AP*CP*CP*CP*G)-3'" 6675.907 1 ? ? ? '16S rRNA helix 44' 2 polymer syn "5'-R(*GP*GP*GP*(5BU)P*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*UP*AP*AP*CP*GP*CP*GP*GP*C)-3'" 7593.416 1 ? ? ? '16S rRNA helix 44' 3 non-polymer syn 'MAGNESIUM ION' 24.305 3 ? ? ? ? 4 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 5 water nat water 18.015 29 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes 'CCGCGCCCG(5BU)CACACCACCCG' CCGCGCCCGUCACACCACCCG A ? 2 polyribonucleotide no yes 'GGG(5BU)GGUGAAGUCGUAACGCGGC' GGGUGGUGAAGUCGUAACGCGGC B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'MAGNESIUM ION' MG 4 'SULFATE ION' SO4 5 water HOH # 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 C n 1 3 G n 1 4 C n 1 5 G n 1 6 C n 1 7 C n 1 8 C n 1 9 G n 1 10 5BU n 1 11 C n 1 12 A n 1 13 C n 1 14 A n 1 15 C n 1 16 C n 1 17 A n 1 18 C n 1 19 C n 1 20 C n 1 21 G n 2 1 G n 2 2 G n 2 3 G n 2 4 5BU n 2 5 G n 2 6 G n 2 7 U n 2 8 G n 2 9 A n 2 10 A n 2 11 G n 2 12 U n 2 13 C n 2 14 G n 2 15 U n 2 16 A n 2 17 A n 2 18 C n 2 19 G n 2 20 C n 2 21 G n 2 22 G n 2 23 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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 C 1 1397 1397 C C A . n A 1 2 C 2 1398 1398 C C A . n A 1 3 G 3 1399 1399 G G A . n A 1 4 C 4 1400 1400 C C A . n A 1 5 G 5 1401 1401 G G A . n A 1 6 C 6 1402 1402 C C A . n A 1 7 C 7 1403 1403 C C A . n A 1 8 C 8 1404 1404 C C A . n A 1 9 G 9 1405 1405 G G A . n A 1 10 5BU 10 1406 1406 5BU 5BU A . n A 1 11 C 11 1407 1407 C C A . n A 1 12 A 12 1408 1408 A A A . n A 1 13 C 13 1409 1409 C C A . n A 1 14 A 14 1410 1410 A A A . n A 1 15 C 15 1411 1411 C C A . n A 1 16 C 16 1412 1412 C C A . n A 1 17 A 17 1413 1413 A A A . n A 1 18 C 18 1414 1414 C C A . n A 1 19 C 19 1415 1415 C C A . n A 1 20 C 20 1416 1416 C C A . n A 1 21 G 21 1417 1417 G G A . n B 2 1 G 1 1484 1484 G G B . n B 2 2 G 2 1485 1485 G G B . n B 2 3 G 3 1486 1486 G G B . n B 2 4 5BU 4 1487 1487 5BU 5BU B . n B 2 5 G 5 1488 1488 G G B . n B 2 6 G 6 1489 1489 G G B . n B 2 7 U 7 1490 1490 U U B . n B 2 8 G 8 1491 1491 G G B . n B 2 9 A 9 1492 1492 A A B . n B 2 10 A 10 1493 1493 A A B . n B 2 11 G 11 1494 1494 G G B . n B 2 12 U 12 1495 1495 U U B . n B 2 13 C 13 1496 1496 C C B . n B 2 14 G 14 1497 1497 G G B . n B 2 15 U 15 1498 1498 U U B . n B 2 16 A 16 1499 1499 A A B . n B 2 17 A 17 1500 1500 A A B . n B 2 18 C 18 1501 1501 C C B . n B 2 19 G 19 1502 1502 G G B . n B 2 20 C 20 1503 1503 C C B . n B 2 21 G 21 1504 1504 G G B . n B 2 22 G 22 1505 1505 G G B . n B 2 23 C 23 1506 1506 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 3 MG 1 1 1 MG MG A . D 4 SO4 1 1418 1 SO4 SO4 A . E 3 MG 1 1 1 MG MG B . F 3 MG 1 1507 1 MG MG B . G 4 SO4 1 1508 1 SO4 SO4 B . H 5 HOH 1 5 5 HOH HOH A . H 5 HOH 2 8 8 HOH HOH A . H 5 HOH 3 10 10 HOH HOH A . H 5 HOH 4 12 12 HOH HOH A . H 5 HOH 5 16 16 HOH HOH A . H 5 HOH 6 17 17 HOH HOH A . H 5 HOH 7 18 18 HOH HOH A . H 5 HOH 8 22 22 HOH HOH A . H 5 HOH 9 26 26 HOH HOH A . H 5 HOH 10 29 29 HOH HOH A . I 5 HOH 1 2 2 HOH HOH B . I 5 HOH 2 3 3 HOH HOH B . I 5 HOH 3 4 4 HOH HOH B . I 5 HOH 4 6 6 HOH HOH B . I 5 HOH 5 7 7 HOH HOH B . I 5 HOH 6 9 9 HOH HOH B . I 5 HOH 7 11 11 HOH HOH B . I 5 HOH 8 13 13 HOH HOH B . I 5 HOH 9 14 14 HOH HOH B . I 5 HOH 10 15 15 HOH HOH B . I 5 HOH 11 19 19 HOH HOH B . I 5 HOH 12 20 20 HOH HOH B . I 5 HOH 13 21 21 HOH HOH B . I 5 HOH 14 23 23 HOH HOH B . I 5 HOH 15 24 24 HOH HOH B . I 5 HOH 16 25 25 HOH HOH B . I 5 HOH 17 27 27 HOH HOH B . I 5 HOH 18 28 28 HOH HOH B . I 5 HOH 19 1509 1 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PHENIX refinement '(phenix.refine)' ? 1 CNS refinement . ? 2 HKL-2000 'data collection' . ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 CNS phasing . ? 6 # _cell.entry_id 3LOA _cell.length_a 57.455 _cell.length_b 57.455 _cell.length_c 58.433 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3LOA _symmetry.space_group_name_H-M 'P 64' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3LOA _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.95 _exptl_crystal.density_percent_sol 36.96 _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 289 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details '1 mM magnesium chloride, 1.95 M ammonium sulfate, 50 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2008-03-29 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si 111' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.919411 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 17-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 17-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.919411 # _reflns.entry_id 3LOA _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 28.7 _reflns.d_resolution_high 2.3 _reflns.number_obs 4941 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 36.22 _reflns.B_iso_Wilson_estimate 61.5 _reflns.pdbx_redundancy 12.5 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.30 _reflns_shell.d_res_low 2.38 _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.31 _reflns_shell.pdbx_redundancy 12.2 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 946 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3LOA _refine.ls_number_reflns_obs 4921 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.90 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 28.728 _refine.ls_d_res_high 2.299 _refine.ls_percent_reflns_obs 99.06 _refine.ls_R_factor_obs 0.1923 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1906 _refine.ls_R_factor_R_free 0.2305 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.61 _refine.ls_number_reflns_R_free 439 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.323 _refine.solvent_model_param_bsol 44.477 _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.42 _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _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 935 _refine_hist.pdbx_number_atoms_ligand 13 _refine_hist.number_atoms_solvent 29 _refine_hist.number_atoms_total 977 _refine_hist.d_res_high 2.299 _refine_hist.d_res_low 28.728 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.007 ? ? 1051 'X-RAY DIFFRACTION' ? f_angle_d 1.437 ? ? 1636 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 17.112 ? ? 436 'X-RAY DIFFRACTION' ? f_chiral_restr 0.054 ? ? 216 'X-RAY DIFFRACTION' ? f_plane_restr 0.004 ? ? 44 '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.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id . 2.2986 2.6310 3005 0.2873 98.84 0.3141 . . 165 . . . . 'X-RAY DIFFRACTION' . 2.6310 3.3140 3040 0.2432 99.56 0.2585 . . 147 . . . . 'X-RAY DIFFRACTION' . 3.3140 28.7297 3034 0.1533 98.78 0.1963 . . 127 . . . . 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3LOA _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 3LOA _struct.title 'Crystal Structure Analysis of the RNA construct with two adjacent ligand binding sites of helix h44 in 16S ribosomal RNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3LOA _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, A-site, Hygromycin B binding site, aminoglycoside' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 3 ? F N N 3 ? G N N 4 ? H N N 5 ? I N N 5 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 3LOA 3LOA 1 ? CCGCGCCCGUCACACCACCCG ? 2 PDB 3LOA 3LOA 2 ? GGGUGGUGAAGUCGUAACGCGGC ? # 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 3LOA A 1 ? 21 ? 3LOA 1397 ? 1417 ? 1397 1417 2 2 3LOA B 1 ? 23 ? 3LOA 1484 ? 1506 ? 1484 1506 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3940 ? 1 MORE -41 ? 1 'SSA (A^2)' 7850 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A G 9 "O3'" ? ? ? 1_555 A 5BU 10 P ? ? A G 1405 A 5BU 1406 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale2 covale both ? A 5BU 10 "O3'" ? ? ? 1_555 A C 11 P ? ? A 5BU 1406 A C 1407 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale3 covale both ? B G 3 "O3'" ? ? ? 1_555 B 5BU 4 P ? ? B G 1486 B 5BU 1487 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale4 covale both ? B 5BU 4 "O3'" ? ? ? 1_555 B G 5 P ? ? B 5BU 1487 B G 1488 1_555 ? ? ? ? ? ? ? 1.594 ? ? metalc1 metalc ? ? E MG . MG ? ? ? 1_555 B A 17 "O2'" ? ? B MG 1 B A 1500 1_555 ? ? ? ? ? ? ? 2.866 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 22 N1 ? ? A C 1397 B G 1505 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 22 O6 ? ? A C 1397 B G 1505 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 22 N2 ? ? A C 1397 B G 1505 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 21 N1 ? ? A C 1398 B G 1504 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 21 O6 ? ? A C 1398 B G 1504 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 21 N2 ? ? A C 1398 B G 1504 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 1399 B C 1503 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 1399 B C 1503 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 1399 B C 1503 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 1400 B G 1502 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 1400 B G 1502 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 1400 B G 1502 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 18 N3 ? ? A G 1401 B C 1501 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 18 O2 ? ? A G 1401 B C 1501 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 18 N4 ? ? A G 1401 B C 1501 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 N4 ? ? ? 1_555 B U 15 O2 ? ? A C 1402 B U 1498 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog17 hydrog ? ? A C 6 O2 ? ? ? 1_555 B A 17 N6 ? ? A C 1402 B A 1500 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog18 hydrog ? ? A C 7 N4 ? ? ? 1_555 B U 15 O2 ? ? A C 1403 B U 1498 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog19 hydrog ? ? A C 7 O2 ? ? ? 1_555 B A 16 N6 ? ? A C 1403 B A 1499 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog20 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 13 N3 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 13 O2 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A 5BU 10 N3 ? ? ? 1_555 B U 12 O2 ? ? A 5BU 1406 B U 1495 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog27 hydrog ? ? A 5BU 10 O4 ? ? ? 1_555 B U 12 N3 ? ? A 5BU 1406 B U 1495 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog28 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 12 N1 ? ? ? 1_555 B A 10 N6 ? ? A A 1408 B A 1493 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog32 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 1409 B G 1491 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 1409 B G 1491 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 1409 B G 1491 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A A 14 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 1410 B U 1490 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A A 14 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 1410 B U 1490 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 1411 B G 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 1411 B G 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 1411 B G 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 16 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 1412 B G 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 16 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 1412 B G 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 16 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 1412 B G 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A A 17 N1 ? ? ? 1_555 B 5BU 4 N3 ? ? A A 1413 B 5BU 1487 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A A 17 N6 ? ? ? 1_555 B 5BU 4 O4 ? ? A A 1413 B 5BU 1487 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 18 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 1414 B G 1486 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 18 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 1414 B G 1486 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 18 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 1414 B G 1486 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 19 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 1415 B G 1485 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 19 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 1415 B G 1485 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 19 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 1415 B G 1485 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 1416 B G 1484 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 1416 B G 1484 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 1416 B G 1484 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? 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 MG 1 ? 1 'BINDING SITE FOR RESIDUE MG A 1' AC2 Software A SO4 1418 ? 4 'BINDING SITE FOR RESIDUE SO4 A 1418' AC3 Software B MG 1 ? 4 'BINDING SITE FOR RESIDUE MG B 1' AC4 Software B MG 1507 ? 1 'BINDING SITE FOR RESIDUE MG B 1507' AC5 Software B SO4 1508 ? 5 'BINDING SITE FOR RESIDUE SO4 B 1508' # 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 1 C A 8 ? C A 1404 . ? 1_555 ? 2 AC2 4 HOH H . ? HOH A 16 . ? 1_655 ? 3 AC2 4 HOH H . ? HOH A 26 . ? 1_555 ? 4 AC2 4 C A 1 ? C A 1397 . ? 1_555 ? 5 AC2 4 C A 2 ? C A 1398 . ? 1_555 ? 6 AC3 4 A A 14 ? A A 1410 . ? 2_655 ? 7 AC3 4 C A 15 ? C A 1411 . ? 2_655 ? 8 AC3 4 A B 17 ? A B 1500 . ? 1_555 ? 9 AC3 4 C B 18 ? C B 1501 . ? 1_555 ? 10 AC4 1 G B 5 ? G B 1488 . ? 1_555 ? 11 AC5 5 C A 18 ? C A 1414 . ? 1_655 ? 12 AC5 5 C A 19 ? C A 1415 . ? 1_655 ? 13 AC5 5 C A 20 ? C A 1416 . ? 1_655 ? 14 AC5 5 HOH I . ? HOH B 4 . ? 1_555 ? 15 AC5 5 C B 23 ? C B 1506 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 OP2 B G 1488 ? ? O B HOH 15 ? ? 1.85 2 1 O3 B SO4 1508 ? ? O B HOH 4 ? ? 1.88 3 1 C2 B A 1493 ? ? O B HOH 21 ? ? 2.12 4 1 N1 B A 1493 ? ? O B HOH 21 ? ? 2.17 # 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 "C1'" B A 1492 ? ? "O4'" B A 1492 ? ? "C4'" B A 1492 ? ? 104.43 109.70 -5.27 0.70 N 2 1 "C3'" B A 1492 ? ? "C2'" B A 1492 ? ? "C1'" B A 1492 ? ? 96.26 101.30 -5.04 0.70 N 3 1 "O4'" B A 1492 ? ? "C1'" B A 1492 ? ? N9 B A 1492 ? ? 113.91 108.50 5.41 0.70 N 4 1 "C3'" B A 1492 ? ? "O3'" B A 1492 ? ? P B A 1493 ? ? 127.17 119.70 7.47 1.20 Y 5 1 "O4'" B A 1493 ? ? "C1'" B A 1493 ? ? N9 B A 1493 ? ? 114.08 108.50 5.58 0.70 N # 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 5BU 10 A 5BU 1406 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 2 B 5BU 4 B 5BU 1487 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 27 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id I _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 26.4843 _pdbx_refine_tls.origin_y 13.8319 _pdbx_refine_tls.origin_z 18.7602 _pdbx_refine_tls.T[1][1] 0.3681 _pdbx_refine_tls.T[2][2] 0.6772 _pdbx_refine_tls.T[3][3] 0.4733 _pdbx_refine_tls.T[1][2] -0.0502 _pdbx_refine_tls.T[1][3] -0.0213 _pdbx_refine_tls.T[2][3] 0.0676 _pdbx_refine_tls.L[1][1] 0.7434 _pdbx_refine_tls.L[2][2] -0.6248 _pdbx_refine_tls.L[3][3] 0.0082 _pdbx_refine_tls.L[1][2] -0.0392 _pdbx_refine_tls.L[1][3] 0.5575 _pdbx_refine_tls.L[2][3] 0.3597 _pdbx_refine_tls.S[1][1] -0.1369 _pdbx_refine_tls.S[1][2] -0.0583 _pdbx_refine_tls.S[1][3] 0.1621 _pdbx_refine_tls.S[2][1] 0.1125 _pdbx_refine_tls.S[2][2] 0.1127 _pdbx_refine_tls.S[2][3] -0.0008 _pdbx_refine_tls.S[3][1] 0.0497 _pdbx_refine_tls.S[3][2] -0.0962 _pdbx_refine_tls.S[3][3] 0.0019 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id ? _pdbx_refine_tls_group.beg_auth_seq_id ? _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id ? _pdbx_refine_tls_group.end_auth_seq_id ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details all # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 MG MG MG N N 148 SO4 S S N N 149 SO4 O1 O N N 150 SO4 O2 O N N 151 SO4 O3 O N N 152 SO4 O4 O N N 153 U OP3 O N N 154 U P P N N 155 U OP1 O N N 156 U OP2 O N N 157 U "O5'" O N N 158 U "C5'" C N N 159 U "C4'" C N R 160 U "O4'" O N N 161 U "C3'" C N S 162 U "O3'" O N N 163 U "C2'" C N R 164 U "O2'" O N N 165 U "C1'" C N R 166 U N1 N N N 167 U C2 C N N 168 U O2 O N N 169 U N3 N N N 170 U C4 C N N 171 U O4 O N N 172 U C5 C N N 173 U C6 C N N 174 U HOP3 H N N 175 U HOP2 H N N 176 U "H5'" H N N 177 U "H5''" H N N 178 U "H4'" H N N 179 U "H3'" H N N 180 U "HO3'" H N N 181 U "H2'" H N N 182 U "HO2'" H N N 183 U "H1'" H N N 184 U H3 H N N 185 U H5 H N N 186 U H6 H N N 187 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 SO4 S O1 doub N N 153 SO4 S O2 doub N N 154 SO4 S O3 sing N N 155 SO4 S O4 sing N N 156 U OP3 P sing N N 157 U OP3 HOP3 sing N N 158 U P OP1 doub N N 159 U P OP2 sing N N 160 U P "O5'" sing N N 161 U OP2 HOP2 sing N N 162 U "O5'" "C5'" sing N N 163 U "C5'" "C4'" sing N N 164 U "C5'" "H5'" sing N N 165 U "C5'" "H5''" sing N N 166 U "C4'" "O4'" sing N N 167 U "C4'" "C3'" sing N N 168 U "C4'" "H4'" sing N N 169 U "O4'" "C1'" sing N N 170 U "C3'" "O3'" sing N N 171 U "C3'" "C2'" sing N N 172 U "C3'" "H3'" sing N N 173 U "O3'" "HO3'" sing N N 174 U "C2'" "O2'" sing N N 175 U "C2'" "C1'" sing N N 176 U "C2'" "H2'" sing N N 177 U "O2'" "HO2'" sing N N 178 U "C1'" N1 sing N N 179 U "C1'" "H1'" sing N N 180 U N1 C2 sing N N 181 U N1 C6 sing N N 182 U C2 O2 doub N N 183 U C2 N3 sing N N 184 U N3 C4 sing N N 185 U N3 H3 sing N N 186 U C4 O4 doub N N 187 U C4 C5 sing N N 188 U C5 C6 doub N N 189 U C5 H5 sing N N 190 U C6 H6 sing N N 191 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3LOA 'double helix' 3LOA 'a-form double helix' 3LOA 'quadruple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 1 1_555 B G 22 1_555 0.132 -0.150 0.199 3.737 -13.554 1.898 1 A_C1397:G1505_B A 1397 ? B 1505 ? 19 1 1 A C 2 1_555 B G 21 1_555 0.404 -0.244 0.043 -1.979 -12.333 -0.451 2 A_C1398:G1504_B A 1398 ? B 1504 ? 19 1 1 A G 3 1_555 B C 20 1_555 -0.228 -0.259 0.345 -1.099 -11.007 -2.122 3 A_G1399:C1503_B A 1399 ? B 1503 ? 19 1 1 A C 4 1_555 B G 19 1_555 0.263 -0.092 0.295 1.343 -12.450 4.365 4 A_C1400:G1502_B A 1400 ? B 1502 ? 19 1 1 A G 5 1_555 B C 18 1_555 0.168 -0.147 0.105 -13.437 -25.159 0.916 5 A_G1401:C1501_B A 1401 ? B 1501 ? 19 1 1 A C 6 1_555 B A 17 1_555 3.435 -0.627 0.686 -24.601 -16.761 -10.569 6 A_C1402:A1500_B A 1402 ? B 1500 ? ? 1 1 A C 7 1_555 B U 15 1_555 -4.691 -1.368 0.581 -7.086 -2.825 25.844 7 A_C1403:U1498_B A 1403 ? B 1498 ? ? ? 1 A C 8 1_555 B G 14 1_555 0.155 -0.298 -0.006 3.592 -11.391 1.352 8 A_C1404:G1497_B A 1404 ? B 1497 ? 19 1 1 A G 9 1_555 B C 13 1_555 -0.184 0.013 -0.039 1.516 -7.217 11.700 9 A_G1405:C1496_B A 1405 ? B 1496 ? 19 1 1 A 5BU 10 1_555 B U 12 1_555 -1.895 -1.717 0.126 4.816 -20.856 9.237 10 A_5BU1406:U1495_B A 1406 ? B 1495 ? 16 1 1 A C 11 1_555 B G 11 1_555 0.026 -0.267 -0.034 -1.904 -11.616 0.190 11 A_C1407:G1494_B A 1407 ? B 1494 ? 19 1 1 A A 12 1_555 B A 10 1_555 2.398 1.980 -0.136 -19.766 15.927 -104.186 12 A_A1408:A1493_B A 1408 ? B 1493 ? ? ? 1 A C 13 1_555 B G 8 1_555 -0.121 -0.298 -0.196 -3.765 -7.190 1.727 13 A_C1409:G1491_B A 1409 ? B 1491 ? 19 1 1 A A 14 1_555 B U 7 1_555 0.151 -0.071 0.510 1.865 -13.879 13.482 14 A_A1410:U1490_B A 1410 ? B 1490 ? 20 1 1 A C 15 1_555 B G 6 1_555 0.018 -0.110 0.073 13.978 -18.088 -1.985 15 A_C1411:G1489_B A 1411 ? B 1489 ? 19 1 1 A C 16 1_555 B G 5 1_555 0.209 -0.316 0.151 6.315 -16.072 -0.955 16 A_C1412:G1488_B A 1412 ? B 1488 ? 19 1 1 A A 17 1_555 B 5BU 4 1_555 0.000 -0.273 0.249 5.271 -10.270 0.268 17 A_A1413:5BU1487_B A 1413 ? B 1487 ? 20 1 1 A C 18 1_555 B G 3 1_555 0.540 -0.149 0.008 15.172 -15.052 2.770 18 A_C1414:G1486_B A 1414 ? B 1486 ? 19 1 1 A C 19 1_555 B G 2 1_555 0.132 -0.163 -0.102 6.954 -12.973 0.171 19 A_C1415:G1485_B A 1415 ? B 1485 ? 19 1 1 A C 20 1_555 B G 1 1_555 0.803 -0.289 0.414 -0.492 -8.450 5.226 20 A_C1416:G1484_B A 1416 ? B 1484 ? 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 C 1 1_555 B G 22 1_555 A C 2 1_555 B G 21 1_555 -0.362 -1.746 3.228 0.548 7.229 32.434 -4.180 0.720 2.778 12.744 -0.967 33.213 1 AA_C1397C1398:G1504G1505_BB A 1397 ? B 1505 ? A 1398 ? B 1504 ? 1 A C 2 1_555 B G 21 1_555 A G 3 1_555 B C 20 1_555 0.096 -1.735 3.007 -1.829 10.501 28.525 -5.049 -0.487 2.232 20.433 3.559 30.413 2 AA_C1398G1399:C1503G1504_BB A 1398 ? B 1504 ? A 1399 ? B 1503 ? 1 A G 3 1_555 B C 20 1_555 A C 4 1_555 B G 19 1_555 0.839 -1.821 3.176 2.616 3.000 33.385 -3.617 -1.042 3.061 5.199 -4.534 33.615 3 AA_G1399C1400:G1502C1503_BB A 1399 ? B 1503 ? A 1400 ? B 1502 ? 1 A C 4 1_555 B G 19 1_555 A G 5 1_555 B C 18 1_555 -0.094 -1.848 3.292 3.459 13.887 35.196 -4.454 0.546 2.400 21.882 -5.451 37.909 4 AA_C1400G1401:C1501G1502_BB A 1400 ? B 1502 ? A 1401 ? B 1501 ? 1 A G 5 1_555 B C 18 1_555 A C 6 1_555 B A 17 1_555 -0.262 -1.338 3.673 2.140 12.751 45.751 -2.767 0.511 3.198 16.027 -2.690 47.448 5 AA_G1401C1402:A1500C1501_BB A 1401 ? B 1501 ? A 1402 ? B 1500 ? 1 A C 6 1_555 B A 17 1_555 A C 7 1_555 B U 15 1_555 5.483 0.370 3.503 -12.503 12.850 17.480 -1.521 -14.982 -0.073 33.020 32.130 24.990 6 AA_C1402C1403:U1498A1500_BB A 1402 ? B 1500 ? A 1403 ? B 1498 ? 1 A C 7 1_555 B U 15 1_555 A C 8 1_555 B G 14 1_555 0.126 -1.151 3.169 5.811 4.271 34.888 -2.474 0.598 2.994 7.031 -9.566 35.603 7 AA_C1403C1404:G1497U1498_BB A 1403 ? B 1498 ? A 1404 ? B 1497 ? 1 A C 8 1_555 B G 14 1_555 A G 9 1_555 B C 13 1_555 -0.096 -1.463 3.261 -1.285 14.158 26.009 -5.534 -0.055 2.191 28.875 2.621 29.582 8 AA_C1404G1405:C1496G1497_BB A 1404 ? B 1497 ? A 1405 ? B 1496 ? 1 A G 9 1_555 B C 13 1_555 A 5BU 10 1_555 B U 12 1_555 -0.412 -1.086 3.059 -4.518 6.908 27.053 -3.677 -0.107 2.735 14.349 9.384 28.262 9 AA_G14055BU1406:U1495C1496_BB A 1405 ? B 1496 ? A 1406 ? B 1495 ? 1 A 5BU 10 1_555 B U 12 1_555 A C 11 1_555 B G 11 1_555 -0.116 -0.871 3.448 2.019 4.094 45.340 -1.500 0.335 3.353 5.296 -2.612 45.557 10 AA_5BU1406C1407:G1494U1495_BB A 1406 ? B 1495 ? A 1407 ? B 1494 ? 1 A C 11 1_555 B G 11 1_555 A A 12 1_555 B A 10 1_555 -0.091 -2.857 3.334 15.882 6.586 86.694 -2.195 0.402 3.109 4.758 -11.473 88.050 11 AA_C1407A1408:A1493G1494_BB A 1407 ? B 1494 ? A 1408 ? B 1493 ? 1 A A 12 1_555 B A 10 1_555 A C 13 1_555 B G 8 1_555 2.569 0.336 3.402 3.593 22.493 -13.441 -6.274 6.509 1.110 -59.096 9.440 -26.402 12 AA_A1408C1409:G1491A1493_BB A 1408 ? B 1493 ? A 1409 ? B 1491 ? 1 A C 13 1_555 B G 8 1_555 A A 14 1_555 B U 7 1_555 0.621 -1.288 2.909 -4.304 15.868 30.851 -4.052 -1.552 1.936 27.514 7.463 34.864 13 AA_C1409A1410:U1490G1491_BB A 1409 ? B 1491 ? A 1410 ? B 1490 ? 1 A A 14 1_555 B U 7 1_555 A C 15 1_555 B G 6 1_555 -0.819 -1.026 2.960 1.145 6.287 29.174 -3.126 1.797 2.652 12.296 -2.239 29.851 14 AA_A1410C1411:G1489U1490_BB A 1410 ? B 1490 ? A 1411 ? B 1489 ? 1 A C 15 1_555 B G 6 1_555 A C 16 1_555 B G 5 1_555 0.578 -1.745 3.287 2.298 7.958 37.165 -3.645 -0.607 2.895 12.298 -3.551 38.045 15 AA_C1411C1412:G1488G1489_BB A 1411 ? B 1489 ? A 1412 ? B 1488 ? 1 A C 16 1_555 B G 5 1_555 A A 17 1_555 B 5BU 4 1_555 -0.514 -1.819 3.032 -1.874 14.257 26.663 -5.797 0.683 1.870 28.438 3.737 30.232 16 AA_C1412A1413:5BU1487G1488_BB A 1412 ? B 1488 ? A 1413 ? B 1487 ? 1 A A 17 1_555 B 5BU 4 1_555 A C 18 1_555 B G 3 1_555 0.503 -1.207 3.063 3.102 1.038 34.994 -2.145 -0.398 3.059 1.722 -5.144 35.142 17 AA_A1413C1414:G14865BU1487_BB A 1413 ? B 1487 ? A 1414 ? B 1486 ? 1 A C 18 1_555 B G 3 1_555 A C 19 1_555 B G 2 1_555 -0.463 -1.997 3.238 -2.611 11.521 28.852 -5.667 0.423 2.321 21.993 4.985 31.129 18 AA_C1414C1415:G1485G1486_BB A 1414 ? B 1486 ? A 1415 ? B 1485 ? 1 A C 19 1_555 B G 2 1_555 A C 20 1_555 B G 1 1_555 -0.092 -1.797 3.342 -4.171 9.576 36.397 -3.951 -0.371 2.791 14.956 6.514 37.817 19 AA_C1415C1416:G1484G1485_BB A 1415 ? B 1485 ? A 1416 ? B 1484 ? # _atom_sites.entry_id 3LOA _atom_sites.fract_transf_matrix[1][1] 0.017405 _atom_sites.fract_transf_matrix[1][2] 0.010049 _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] 0.020097 _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] 0.017114 _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 BR C MG N O P S # loop_