data_406D # _entry.id 406D # _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 406D pdb_0000406d 10.2210/pdb406d/pdb RCSB AR0003 ? ? WWPDB D_1000179206 ? ? # 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 1999-02-05 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-11-16 5 'Structure model' 2 0 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 5 'Structure model' 'Atomic model' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 '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 5 'Structure model' atom_site 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_atom_site.occupancy' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 406D _pdbx_database_status.recvd_initial_deposition_date 1998-06-22 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Shah, S.A.' 1 'Brunger, A.T.' 2 # _citation.id primary _citation.title ;The 1.8 A crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure. ; _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 285 _citation.page_first 1577 _citation.page_last 1588 _citation.year 1999 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9917398 _citation.pdbx_database_id_DOI 10.1006/jmbi.1998.2385 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Shah, S.A.' 1 ? primary 'Brunger, A.T.' 2 ? # 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 man ;RNA (5'-R(*CP*AP*CP*CP*GP*GP*AP*UP*GP*GP*UP*(5BU)P*CP*GP*GP*UP*G)-3') ; 5554.181 2 ? ? ? ? 2 water nat water 18.015 34 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'CACCGGAUGGU(5BU)CGGUG' _entity_poly.pdbx_seq_one_letter_code_can CACCGGAUGGUUCGGUG _entity_poly.pdbx_strand_id A,E _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 A n 1 3 C n 1 4 C n 1 5 G n 1 6 G n 1 7 A n 1 8 U n 1 9 G n 1 10 G n 1 11 U n 1 12 5BU n 1 13 C n 1 14 G n 1 15 G n 1 16 U n 1 17 G 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 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 1 1 C C A . n A 1 2 A 2 2 2 A A A . n A 1 3 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 G 6 6 6 G G A . n A 1 7 A 7 7 7 A A A . n A 1 8 U 8 8 8 U U A . n A 1 9 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n A 1 11 U 11 11 11 U U A . n A 1 12 5BU 12 12 12 5BU 5BU A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n A 1 15 G 15 15 15 G G A . n A 1 16 U 16 16 16 U U A . n A 1 17 G 17 17 17 G G A . n B 1 1 C 1 18 18 C C E . n B 1 2 A 2 19 19 A A E . n B 1 3 C 3 20 20 C C E . n B 1 4 C 4 21 21 C C E . n B 1 5 G 5 22 22 G G E . n B 1 6 G 6 23 23 G G E . n B 1 7 A 7 24 24 A A E . n B 1 8 U 8 25 25 U U E . n B 1 9 G 9 26 26 G G E . n B 1 10 G 10 27 27 G G E . n B 1 11 U 11 28 28 U U E . n B 1 12 5BU 12 29 29 5BU 5BU E . n B 1 13 C 13 30 30 C C E . n B 1 14 G 14 31 31 G G E . n B 1 15 G 15 32 32 G G E . n B 1 16 U 16 33 33 U U E . n B 1 17 G 17 34 34 G G E . 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 HOH 1 18 18 HOH HOH A . C 2 HOH 2 19 19 HOH HOH A . C 2 HOH 3 20 20 HOH HOH A . C 2 HOH 4 21 21 HOH HOH A . C 2 HOH 5 22 22 HOH HOH A . C 2 HOH 6 23 23 HOH HOH A . C 2 HOH 7 24 24 HOH HOH A . C 2 HOH 8 25 25 HOH HOH A . C 2 HOH 9 26 26 HOH HOH A . C 2 HOH 10 27 27 HOH HOH A . C 2 HOH 11 28 28 HOH HOH A . C 2 HOH 12 29 29 HOH HOH A . C 2 HOH 13 30 30 HOH HOH A . C 2 HOH 14 31 31 HOH HOH A . C 2 HOH 15 32 32 HOH HOH A . C 2 HOH 16 33 33 HOH HOH A . C 2 HOH 17 34 34 HOH HOH A . C 2 HOH 18 35 35 HOH HOH A . C 2 HOH 19 36 36 HOH HOH A . D 2 HOH 1 35 35 HOH HOH E . D 2 HOH 2 36 36 HOH HOH E . D 2 HOH 3 37 37 HOH HOH E . D 2 HOH 4 38 38 HOH HOH E . D 2 HOH 5 39 39 HOH HOH E . D 2 HOH 6 40 40 HOH HOH E . D 2 HOH 7 41 41 HOH HOH E . D 2 HOH 8 42 42 HOH HOH E . D 2 HOH 9 43 43 HOH HOH E . D 2 HOH 10 44 44 HOH HOH E . D 2 HOH 11 45 45 HOH HOH E . D 2 HOH 12 46 46 HOH HOH E . D 2 HOH 13 47 47 HOH HOH E . D 2 HOH 14 48 48 HOH HOH E . D 2 HOH 15 49 49 HOH HOH E . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 0.3 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CNS phasing 0.3 ? 4 # _cell.entry_id 406D _cell.length_a 39.627 _cell.length_b 39.627 _cell.length_c 91.018 _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 406D _symmetry.space_group_name_H-M 'P 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? # _exptl.entry_id 406D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.71 _exptl_crystal.density_percent_sol 38.0000 _exptl_crystal.description ;The crystal packing of 17-bp RNA duplex is statically disordered. As a result, the asymmetric unit of the crystal contains four superimposed orientations of the duplex that are out of register, such that backbones superimpose, but base identity differs. ; _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 293.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.50 _exptl_crystal_grow.pdbx_details 'pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'PEG 300' ? ? ? 1 2 1 NACL ? ? ? 1 3 1 'SODIUM ACETATE' ? ? ? 1 4 2 'PEG 300' ? ? ? 1 5 2 NACL ? ? ? 1 6 2 'SODIUM ACETATE' ? ? ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 110.00 ? 1 2 ? ? 1 3 ? ? 1 4 ? ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 'IMAGE PLATE' MARRESEARCH 1995-11-10 ? 2 ? ? ? ? 3 ? ? ? ? 4 ? ? ? ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M ? 'SINGLE WAVELENGTH' x-ray 2 2 M ? 'SINGLE WAVELENGTH' x-ray 3 3 M ? 'SINGLE WAVELENGTH' x-ray 4 4 M ? 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 . 1.0 2 . 1.0 3 . 1.0 4 . 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'NSLS BEAMLINE X12B' NSLS X12B ? ? 2 ? ? ? ? ? ? 3 ? ? ? ? ? ? 4 ? ? ? ? ? ? # _reflns.entry_id 406D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F 0.000 _reflns.d_resolution_low 50.000 _reflns.d_resolution_high 1.800 _reflns.number_obs 8052 _reflns.number_all 8052 _reflns.percent_possible_obs 98.300 _reflns.pdbx_Rmerge_I_obs 0.084 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 19.4000 _reflns.B_iso_Wilson_estimate 9.50 _reflns.pdbx_redundancy 4.700 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1,2,3,4 _reflns.pdbx_ordinal 1 # _refine.entry_id 406D _refine.ls_number_reflns_obs 14484 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF 382611.750 _refine.pdbx_data_cutoff_low_absF 0.0000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 15.000 _refine.ls_d_res_high 1.800 _refine.ls_percent_reflns_obs 97.700 _refine.ls_R_factor_obs 0.262 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.262 _refine.ls_R_factor_R_free 0.294 _refine.ls_R_factor_R_free_error 0.008 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.500 _refine.ls_number_reflns_R_free 1524 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 12.00 _refine.aniso_B[1][1] -0.210 _refine.aniso_B[2][2] -0.210 _refine.aniso_B[3][3] 0.4300 _refine.aniso_B[1][2] -0.530 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;BULK SOLVENT MODEL USED. The structure of statically disordered 17-bp RNA duplex is represented by four models in the asymmetric unit, each model for a distinct conformation of the duplex. The sum of all models contribute to the observed diffraction data. To generate the contents of the entire asymmetric unit from the four disordered duplexes, a strict non-crystallographic hypersymmetry was applied. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model GROUP _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _refine.correlation_coeff_Fo_to_Fc ? _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.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_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_analyze.entry_id 406D _refine_analyze.Luzzati_coordinate_error_obs 0.26 _refine_analyze.Luzzati_sigma_a_obs 0.12 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.31 _refine_analyze.Luzzati_sigma_a_free 0.16 _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 726 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 34 _refine_hist.number_atoms_total 760 _refine_hist.d_res_high 1.800 _refine_hist.d_res_low 15.000 # 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 0.006 ? ? ? '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 1.00 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 10.7 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.42 ? ? ? '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_restr_ncs.dom_id 1 _refine_ls_restr_ncs.ncs_model_details CONSTR _refine_ls_restr_ncs.rms_dev_position ? _refine_ls_restr_ncs.weight_position ? _refine_ls_restr_ncs.rms_dev_B_iso ? _refine_ls_restr_ncs.weight_B_iso ? _refine_ls_restr_ncs.pdbx_type . _refine_ls_restr_ncs.pdbx_auth_asym_id . _refine_ls_restr_ncs.pdbx_ens_id 1 _refine_ls_restr_ncs.pdbx_number ? _refine_ls_restr_ncs.pdbx_rms ? _refine_ls_restr_ncs.pdbx_weight ? _refine_ls_restr_ncs.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_restr_ncs.pdbx_ordinal 1 _refine_ls_restr_ncs.pdbx_asym_id ? # _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 2079 _refine_ls_shell.R_factor_R_work 0.264 _refine_ls_shell.percent_reflns_obs 94.40 _refine_ls_shell.R_factor_R_free 0.337 _refine_ls_shell.R_factor_R_free_error 0.02 _refine_ls_shell.percent_reflns_R_free 9.80 _refine_ls_shell.number_reflns_R_free 227 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # 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.PA DNA-RNA_REP.PARAM 'X-RAY DIFFRACTION' 2 BR.PAR ? 'X-RAY DIFFRACTION' # loop_ _struct_ncs_oper.id _struct_ncs_oper.code _struct_ncs_oper.details _struct_ncs_oper.matrix[1][1] _struct_ncs_oper.matrix[1][2] _struct_ncs_oper.matrix[1][3] _struct_ncs_oper.matrix[2][1] _struct_ncs_oper.matrix[2][2] _struct_ncs_oper.matrix[2][3] _struct_ncs_oper.matrix[3][1] _struct_ncs_oper.matrix[3][2] _struct_ncs_oper.matrix[3][3] _struct_ncs_oper.vector[1] _struct_ncs_oper.vector[2] _struct_ncs_oper.vector[3] 1 given ? 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 2 given ? 1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000 0.00000 68.64000 182.03600 # _struct_ncs_dom.id 1 _struct_ncs_dom.pdbx_ens_id 1 _struct_ncs_dom.details ? # _struct_ncs_ens.id 1 _struct_ncs_ens.details ? # _database_PDB_matrix.entry_id 406D _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 406D _struct.title ;5'-R(*CP*AP*CP*CP*GP*GP*AP*UP*GP*GP*UP*(BRO) UP*CP*GP*GP*UP*G)-3' ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 406D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'DISORDERED, RNA, DOUBLE HELIX' # 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 406D _struct_ref.pdbx_db_accession 406D _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 406D A 1 ? 17 ? 406D 1 ? 17 ? 1 17 2 1 406D E 1 ? 17 ? 406D 18 ? 34 ? 18 34 # _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 # _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 U 11 "O3'" A ? ? 1_555 A 5BU 12 P A ? A U 11 A 5BU 12 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A 5BU 12 "O3'" A ? ? 1_555 A C 13 P A ? A 5BU 12 A C 13 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale3 covale both ? B U 11 "O3'" A ? ? 1_555 B 5BU 12 P A ? E U 28 E 5BU 29 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale4 covale both ? B 5BU 12 "O3'" A ? ? 1_555 B C 13 P A ? E 5BU 29 E C 30 1_555 ? ? ? ? ? ? ? 1.600 ? ? hydrog1 hydrog ? ? A C 1 N3 A ? ? 1_555 B G 17 N1 A ? A C 1 E G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 A ? ? 1_555 B G 17 O6 A ? A C 1 E G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 A ? ? 1_555 B G 17 N2 A ? A C 1 E G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N1 A ? ? 1_555 B U 16 N3 A ? A A 2 E U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 2 N6 A ? ? 1_555 B U 16 O4 A ? A A 2 E U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 N3 A ? ? 1_555 B G 15 N1 A ? A C 3 E G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N4 A ? ? 1_555 B G 15 O6 A ? A C 3 E G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 O2 A ? ? 1_555 B G 15 N2 A ? A C 3 E G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 A ? ? 1_555 B G 14 N1 A ? A C 4 E G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 A ? ? 1_555 B G 14 O6 A ? A C 4 E G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 A ? ? 1_555 B G 14 N2 A ? A C 4 E G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 A ? ? 1_555 B C 13 N3 A ? A G 5 E C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 A ? ? 1_555 B C 13 O2 A ? A G 5 E C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 A ? ? 1_555 B C 13 N4 A ? A G 5 E C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 A ? ? 1_555 B 5BU 12 O2 A ? A G 6 E 5BU 29 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog16 hydrog ? ? A G 6 O6 A ? ? 1_555 B 5BU 12 N3 A ? A G 6 E 5BU 29 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog17 hydrog ? ? A A 7 N1 A ? ? 1_555 B U 11 N3 A ? A A 7 E U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 7 N6 A ? ? 1_555 B U 11 O4 A ? A A 7 E U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 8 N3 A ? ? 1_555 B G 10 O6 A ? A U 8 E G 27 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog20 hydrog ? ? A U 8 O2 A ? ? 1_555 B G 10 N1 A ? A U 8 E G 27 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A G 9 N1 A ? ? 1_555 B G 9 N7 A ? A G 9 E G 26 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog22 hydrog ? ? A G 10 N1 A ? ? 1_555 B U 8 O2 A ? A G 10 E U 25 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A G 10 O6 A ? ? 1_555 B U 8 N3 A ? A G 10 E U 25 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog24 hydrog ? ? A U 11 N3 A ? ? 1_555 B A 7 N1 A ? A U 11 E A 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 11 O4 A ? ? 1_555 B A 7 N6 A ? A U 11 E A 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A 5BU 12 N3 A ? ? 1_555 B G 6 O6 A ? A 5BU 12 E G 23 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog27 hydrog ? ? A 5BU 12 O2 A ? ? 1_555 B G 6 N1 A ? A 5BU 12 E G 23 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog28 hydrog ? ? A C 13 N3 A ? ? 1_555 B G 5 N1 A ? A C 13 E G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 N4 A ? ? 1_555 B G 5 O6 A ? A C 13 E G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 13 O2 A ? ? 1_555 B G 5 N2 A ? A C 13 E G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 N1 A ? ? 1_555 B C 4 N3 A ? A G 14 E C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 14 N2 A ? ? 1_555 B C 4 O2 A ? A G 14 E C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 14 O6 A ? ? 1_555 B C 4 N4 A ? A G 14 E C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 15 N1 A ? ? 1_555 B C 3 N3 A ? A G 15 E C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 15 N2 A ? ? 1_555 B C 3 O2 A ? A G 15 E C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 15 O6 A ? ? 1_555 B C 3 N4 A ? A G 15 E C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A U 16 N3 A ? ? 1_555 B A 2 N1 A ? A U 16 E A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 16 O4 A ? ? 1_555 B A 2 N6 A ? A U 16 E A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 17 N1 A ? ? 1_555 B C 1 N3 A ? A G 17 E C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 17 N2 A ? ? 1_555 B C 1 O2 A ? A G 17 E C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 17 O6 A ? ? 1_555 B C 1 N4 A ? A G 17 E C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 3 O A HOH 69 ? ? O A HOH 77 ? ? 1.90 2 3 O A HOH 33 ? ? O A HOH 130 ? ? 2.03 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 32 ? ? 1_555 O A HOH 32 ? ? 2_775 1.67 2 3 O E HOH 50 ? ? 1_555 O E HOH 50 ? ? 2_765 1.21 # 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 12 A 5BU 12 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 2 B 5BU 12 E 5BU 29 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 18 ? C HOH . 2 1 A HOH 19 ? C HOH . 3 1 A HOH 30 ? C HOH . 4 1 E HOH 35 ? D HOH . 5 1 E HOH 36 ? D HOH . 6 1 E HOH 37 ? D HOH . 7 1 E HOH 38 ? D HOH . 8 1 E HOH 39 ? D HOH . 9 1 E HOH 41 ? D HOH . 10 1 E HOH 42 ? D HOH . 11 3 A HOH 22 ? C HOH . 12 3 A HOH 24 ? C HOH . 13 3 A HOH 35 ? C HOH . 14 3 A HOH 37 ? C HOH . 15 3 A HOH 54 ? C HOH . 16 3 A HOH 103 ? C HOH . 17 3 E HOH 36 ? D HOH . 18 3 E HOH 37 ? D HOH . 19 3 E HOH 38 ? D HOH . 20 3 E HOH 39 ? D HOH . 21 3 E HOH 46 ? D HOH . # _pdbx_entry_details.entry_id 406D _pdbx_entry_details.compound_details 'THE CRYSTAL IS MADE OF STATICALLY DISORDERED 17-BP RNA DUPLEX. ALL CONFIRMATIONS ARE REPRESENTED BY FOUR MODELS.' _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # 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 U OP3 O N N 148 U P P N N 149 U OP1 O N N 150 U OP2 O N N 151 U "O5'" O N N 152 U "C5'" C N N 153 U "C4'" C N R 154 U "O4'" O N N 155 U "C3'" C N S 156 U "O3'" O N N 157 U "C2'" C N R 158 U "O2'" O N N 159 U "C1'" C N R 160 U N1 N N N 161 U C2 C N N 162 U O2 O N N 163 U N3 N N N 164 U C4 C N N 165 U O4 O N N 166 U C5 C N N 167 U C6 C N N 168 U HOP3 H N N 169 U HOP2 H N N 170 U "H5'" H N N 171 U "H5''" H N N 172 U "H4'" H N N 173 U "H3'" H N N 174 U "HO3'" H N N 175 U "H2'" H N N 176 U "HO2'" H N N 177 U "H1'" H N N 178 U H3 H N N 179 U H5 H N N 180 U H6 H N N 181 # 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 U OP3 P sing N N 153 U OP3 HOP3 sing N N 154 U P OP1 doub N N 155 U P OP2 sing N N 156 U P "O5'" sing N N 157 U OP2 HOP2 sing N N 158 U "O5'" "C5'" sing N N 159 U "C5'" "C4'" sing N N 160 U "C5'" "H5'" sing N N 161 U "C5'" "H5''" sing N N 162 U "C4'" "O4'" sing N N 163 U "C4'" "C3'" sing N N 164 U "C4'" "H4'" sing N N 165 U "O4'" "C1'" sing N N 166 U "C3'" "O3'" sing N N 167 U "C3'" "C2'" sing N N 168 U "C3'" "H3'" sing N N 169 U "O3'" "HO3'" sing N N 170 U "C2'" "O2'" sing N N 171 U "C2'" "C1'" sing N N 172 U "C2'" "H2'" sing N N 173 U "O2'" "HO2'" sing N N 174 U "C1'" N1 sing N N 175 U "C1'" "H1'" sing N N 176 U N1 C2 sing N N 177 U N1 C6 sing N N 178 U C2 O2 doub N N 179 U C2 N3 sing N N 180 U N3 C4 sing N N 181 U N3 H3 sing N N 182 U C4 O4 doub N N 183 U C4 C5 sing N N 184 U C5 C6 doub N N 185 U C5 H5 sing N N 186 U C6 H6 sing N N 187 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 406D 'mismatched base pair' 406D '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 17 1_555 0.162 -0.029 -0.340 20.171 -20.900 -0.275 1 A_C1:G34_E A 1 ? E 34 ? 19 1 1 A A 2 1_555 B U 16 1_555 -0.112 -0.218 -0.302 -1.139 -17.734 6.653 2 A_A2:U33_E A 2 ? E 33 ? 20 1 1 A C 3 1_555 B G 15 1_555 0.294 -0.204 -0.881 11.422 -18.306 6.489 3 A_C3:G32_E A 3 ? E 32 ? 19 1 1 A C 4 1_555 B G 14 1_555 0.264 -0.093 -0.155 6.960 -12.845 1.020 4 A_C4:G31_E A 4 ? E 31 ? 19 1 1 A G 5 1_555 B C 13 1_555 -0.131 0.025 -0.390 -0.314 -7.832 2.530 5 A_G5:C30_E A 5 ? E 30 ? 19 1 1 A G 6 1_555 B 5BU 12 1_555 -2.108 -0.359 -0.285 -1.376 -7.130 -0.817 6 A_G6:5BU29_E A 6 ? E 29 ? 28 ? 1 A A 7 1_555 B U 11 1_555 -0.044 -0.074 -0.061 -7.139 -15.020 5.584 7 A_A7:U28_E A 7 ? E 28 ? 20 1 1 A U 8 1_555 B G 10 1_555 2.620 -0.347 -0.068 5.251 -11.784 0.515 8 A_U8:G27_E A 8 ? E 27 ? 28 ? 1 A G 9 1_555 B G 9 1_555 1.118 4.611 -0.091 -16.760 0.349 -73.796 9 A_G9:G26_E A 9 ? E 26 ? ? 3 1 A G 10 1_555 B U 8 1_555 -2.580 -0.413 0.234 -1.415 -8.112 -0.173 10 A_G10:U25_E A 10 ? E 25 ? 28 ? 1 A U 11 1_555 B A 7 1_555 -0.010 -0.161 0.061 -4.462 -10.334 7.047 11 A_U11:A24_E A 11 ? E 24 ? 20 1 1 A 5BU 12 1_555 B G 6 1_555 2.582 -0.568 -0.343 2.087 -7.684 -1.507 12 A_5BU12:G23_E A 12 ? E 23 ? 28 ? 1 A C 13 1_555 B G 5 1_555 0.210 -0.074 -0.139 1.802 -4.150 1.113 13 A_C13:G22_E A 13 ? E 22 ? 19 1 1 A G 14 1_555 B C 4 1_555 -0.208 -0.074 -0.272 -8.108 -8.194 0.253 14 A_G14:C21_E A 14 ? E 21 ? 19 1 1 A G 15 1_555 B C 3 1_555 -0.341 -0.198 -0.949 -16.475 -15.995 4.418 15 A_G15:C20_E A 15 ? E 20 ? 19 1 1 A U 16 1_555 B A 2 1_555 0.065 -0.122 -0.186 -0.193 -14.474 8.054 16 A_U16:A19_E A 16 ? E 19 ? 20 1 1 A G 17 1_555 B C 1 1_555 -0.095 -0.028 0.342 1.727 -11.316 -2.141 17 A_G17:C18_E A 17 ? E 18 ? 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 17 1_555 A A 2 1_555 B U 16 1_555 0.145 -1.771 3.486 -3.505 25.317 32.948 -4.926 -0.541 1.729 38.289 5.301 41.481 1 AA_C1A2:U33G34_EE A 1 ? E 34 ? A 2 ? E 33 ? 1 A A 2 1_555 B U 16 1_555 A C 3 1_555 B G 15 1_555 -0.436 -0.538 2.748 2.471 10.934 35.244 -2.051 0.959 2.444 17.518 -3.958 36.930 2 AA_A2C3:G32U33_EE A 2 ? E 33 ? A 3 ? E 32 ? 1 A C 3 1_555 B G 15 1_555 A C 4 1_555 B G 14 1_555 0.387 -1.872 3.600 -2.931 13.334 26.733 -6.282 -1.334 2.365 26.738 5.878 29.961 3 AA_C3C4:G31G32_EE A 3 ? E 32 ? A 4 ? E 31 ? 1 A C 4 1_555 B G 14 1_555 A G 5 1_555 B C 13 1_555 0.537 -1.763 3.604 2.940 6.037 28.083 -4.955 -0.387 3.201 12.220 -5.952 28.859 4 AA_C4G5:C30G31_EE A 4 ? E 31 ? A 5 ? E 30 ? 1 A G 5 1_555 B C 13 1_555 A G 6 1_555 B 5BU 12 1_555 -0.323 -2.233 3.095 -5.608 8.322 21.427 -7.769 -0.774 2.108 20.964 14.127 23.635 5 AA_G5G6:5BU29C30_EE A 5 ? E 30 ? A 6 ? E 29 ? 1 A G 6 1_555 B 5BU 12 1_555 A A 7 1_555 B U 11 1_555 0.060 -1.292 3.637 -2.114 6.720 37.512 -2.893 -0.379 3.356 10.338 3.252 38.144 6 AA_G6A7:U285BU29_EE A 6 ? E 29 ? A 7 ? E 28 ? 1 A A 7 1_555 B U 11 1_555 A U 8 1_555 B G 10 1_555 -0.061 -1.144 2.979 0.429 6.561 40.780 -2.247 0.127 2.770 9.342 -0.611 41.284 7 AA_A7U8:G27U28_EE A 7 ? E 28 ? A 8 ? E 27 ? 1 A U 8 1_555 B G 10 1_555 A G 9 1_555 B G 9 1_555 0.309 -4.001 3.209 9.959 6.559 61.500 -4.131 0.123 2.827 6.350 -9.642 62.534 8 AA_U8G9:G26G27_EE A 8 ? E 27 ? A 9 ? E 26 ? 1 A G 9 1_555 B G 9 1_555 A G 10 1_555 B U 8 1_555 -1.569 0.174 3.469 -9.463 4.669 -25.276 -1.496 -5.604 2.646 -10.126 -20.523 -27.357 9 AA_G9G10:U25G26_EE A 9 ? E 26 ? A 10 ? E 25 ? 1 A G 10 1_555 B U 8 1_555 A U 11 1_555 B A 7 1_555 0.208 -1.236 3.414 0.642 7.181 41.458 -2.476 -0.222 3.169 10.053 -0.899 42.053 10 AA_G10U11:A24U25_EE A 10 ? E 25 ? A 11 ? E 24 ? 1 A U 11 1_555 B A 7 1_555 A 5BU 12 1_555 B G 6 1_555 -0.170 -1.282 3.140 2.563 6.615 39.714 -2.553 0.516 2.882 9.643 -3.737 40.318 11 AA_U115BU12:G23A24_EE A 11 ? E 24 ? A 12 ? E 23 ? 1 A 5BU 12 1_555 B G 6 1_555 A C 13 1_555 B G 5 1_555 0.318 -2.434 3.203 3.659 4.354 18.333 -9.296 0.720 2.574 13.257 -11.141 19.187 12 AA_5BU12C13:G22G23_EE A 12 ? E 23 ? A 13 ? E 22 ? 1 A C 13 1_555 B G 5 1_555 A G 14 1_555 B C 4 1_555 -0.447 -1.941 3.617 -0.741 6.154 27.773 -5.425 0.733 3.134 12.622 1.520 28.443 13 AA_C13G14:C21G22_EE A 13 ? E 22 ? A 14 ? E 21 ? 1 A G 14 1_555 B C 4 1_555 A G 15 1_555 B C 3 1_555 -0.066 -1.737 3.533 2.194 17.078 27.151 -6.022 0.490 2.091 32.554 -4.182 32.064 14 AA_G14G15:C20C21_EE A 14 ? E 21 ? A 15 ? E 20 ? 1 A G 15 1_555 B C 3 1_555 A U 16 1_555 B A 2 1_555 0.593 -0.870 2.821 -4.118 5.065 33.163 -2.179 -1.575 2.573 8.769 7.128 33.782 15 AA_G15U16:A19C20_EE A 15 ? E 20 ? A 16 ? E 19 ? 1 A U 16 1_555 B A 2 1_555 A G 17 1_555 B C 1 1_555 -0.454 -1.839 3.204 -0.643 6.592 29.671 -4.727 0.748 2.750 12.674 1.237 30.385 16 AA_U16G17:C18A19_EE A 16 ? E 19 ? A 17 ? E 18 ? # _atom_sites.entry_id 406D _atom_sites.fract_transf_matrix[1][1] 0.025235 _atom_sites.fract_transf_matrix[1][2] 0.014570 _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] 0.029139 _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] 0.010987 _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 N O P # loop_