data_2JLT # _entry.id 2JLT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 2JLT pdb_00002jlt 10.2210/pdb2jlt/pdb PDBE EBI-37170 ? ? WWPDB D_1290037170 ? ? # 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 2009-08-18 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-04-19 4 'Structure model' 1 3 2017-07-12 5 'Structure model' 1 4 2024-05-08 # _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' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Data collection' 4 4 'Structure model' 'Refinement description' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' 8 5 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_database_status 6 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 4 'Structure model' '_software.name' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_pdbx_database_status.status_code_sf' 5 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2JLT _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2008-09-15 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'DiPrimo, C.' 1 ? 'Fribourg, S.' 2 ? # _citation.id primary _citation.title 'Exploring Tar-RNA Aptamer Loop-Loop Interaction by X-Ray Crystallography, Uv Spectroscopy and Surface Plasmon Resonance.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 36 _citation.page_first 7146 _citation.page_last ? _citation.year 2008 _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 18996893 _citation.pdbx_database_id_DOI 10.1093/NAR/GKN831 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lebars, I.' 1 ? primary 'Legrand, P.' 2 ? primary 'Aime, A.' 3 ? primary 'Pinaud, N.' 4 ? primary 'Fribourg, S.' 5 ? primary 'Di Primo, C.' 6 ? # 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 R06 5841.395 1 ? ? ? ? 2 polymer syn TAR 5247.030 1 ? ? ? ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 ;5'-R(*GP*GP*5BUP*CP*GP*GP*UP*CP*CP*CP*AP *GP*AP*CP*GP*AP*CP*C)-3' ; 2 ;5'-R(*GP*GP*AP*GP*CP*CP*UP*GP*GP*GP *AP*GP*CP*5BUP*CP*C)-3' ; # 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 'GG(5BU)CGGUCCCAGACGACC' GGUCGGUCCCAGACGACC A ? 2 polyribonucleotide no yes 'GGAGCCUGGGAGC(5BU)CC' GGAGCCUGGGAGCUCC B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 5BU n 1 4 C n 1 5 G n 1 6 G n 1 7 U n 1 8 C n 1 9 C n 1 10 C n 1 11 A n 1 12 G n 1 13 A n 1 14 C n 1 15 G n 1 16 A n 1 17 C n 1 18 C n 2 1 G n 2 2 G n 2 3 A n 2 4 G n 2 5 C n 2 6 C n 2 7 U n 2 8 G n 2 9 G n 2 10 G n 2 11 A n 2 12 G n 2 13 C n 2 14 5BU n 2 15 C n 2 16 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? 'ESCHERICHIA COLI' ? 562 ? 2 1 sample ? ? 'ESCHERICHIA COLI' ? 562 ? # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 5BU 3 3 3 5BU 5BU 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 U 7 7 7 U U A . n A 1 8 C 8 8 8 C C A . n A 1 9 C 9 9 9 C C A . n A 1 10 C 10 10 10 C C A . n A 1 11 A 11 11 11 A A A . n A 1 12 G 12 12 12 G G A . n A 1 13 A 13 13 13 A A A . n A 1 14 C 14 14 14 C C A . n A 1 15 G 15 15 15 G G A . n A 1 16 A 16 16 16 A A A . n A 1 17 C 17 17 17 C C A . n A 1 18 C 18 18 18 C C A . n B 2 1 G 1 1 1 G G B . n B 2 2 G 2 2 2 G G B . n B 2 3 A 3 3 3 A A B . n B 2 4 G 4 4 4 G G B . n B 2 5 C 5 5 5 C C B . n B 2 6 C 6 6 6 C C B . n B 2 7 U 7 7 7 U U B . n B 2 8 G 8 8 8 G G B . n B 2 9 G 9 9 9 G G B . n B 2 10 G 10 10 10 G G B . n B 2 11 A 11 11 11 A A B . n B 2 12 G 12 12 12 G G B . n B 2 13 C 13 13 13 C C B . n B 2 14 5BU 14 14 14 5BU 5BU B . n B 2 15 C 15 15 15 C C B . n B 2 16 C 16 16 16 C C B . n # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language REFMAC refinement 5.5.0054 ? 1 ? ? ? ? XDS 'data reduction' . ? 2 ? ? ? ? SCALA 'data scaling' . ? 3 ? ? ? ? autoSHARP phasing . ? 4 ? ? ? ? # _cell.entry_id 2JLT _cell.length_a 85.000 _cell.length_b 85.000 _cell.length_c 85.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2JLT _symmetry.space_group_name_H-M 'P 21 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 # _exptl.entry_id 2JLT _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.28 _exptl_crystal.density_percent_sol 46 _exptl_crystal.description NONE _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'NA CITRATE 100MM, MPD 35%, pH 4.6' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2007-03-03 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.91 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength 0.91 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2JLT _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.00 _reflns.d_resolution_high 2.90 _reflns.number_obs 10330 _reflns.number_all ? _reflns.percent_possible_obs 98.9 _reflns.pdbx_Rmerge_I_obs 0.08 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 18.66 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.43 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.90 _reflns_shell.d_res_low 3.07 _reflns_shell.percent_possible_all 96.6 _reflns_shell.Rmerge_I_obs 0.38 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.45 _reflns_shell.pdbx_redundancy 6.09 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2JLT _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.ls_number_reflns_obs 4510 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 60.08 _refine.ls_d_res_high 2.90 _refine.ls_percent_reflns_obs 99.6 _refine.ls_R_factor_obs 0.189 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.187 _refine.ls_R_factor_R_free 0.227 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.600 _refine.ls_number_reflns_R_free 216 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.952 _refine.correlation_coeff_Fo_to_Fc_free 0.921 _refine.B_iso_mean 26.54 _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 MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUAL ONLY' _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.370 _refine.pdbx_overall_ESU_R_Free 0.269 _refine.overall_SU_ML 0.205 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 25.930 _refine.overall_SU_R_Cruickshank_DPI ? _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 725 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 725 _refine_hist.d_res_high 2.90 _refine_hist.d_res_low 60.08 # 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 r_bond_refined_d 0.009 0.021 ? 809 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.468 3.000 ? 1260 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.048 0.200 ? 168 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.004 0.020 ? 357 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 0.751 3.000 ? 809 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 1.168 4.500 ? 1260 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.90 _refine_ls_shell.d_res_low 2.98 _refine_ls_shell.number_reflns_R_work 344 _refine_ls_shell.R_factor_R_work 0.3330 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.2940 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 6 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 2JLT _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 2JLT _struct.title 'Crystal structure of an RNA kissing complex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2JLT _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, KISSING COMPLEX' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 2JLT 1 ? ? 2JLT ? 2 PDB 2JLT 2 ? ? 2JLT ? # 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 2JLT A 1 ? 18 ? 2JLT 1 ? 18 ? 1 18 2 2 2JLT B 1 ? 16 ? 2JLT 1 ? 16 ? 1 16 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PQS _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)' 1020 ? 1 MORE 4.0 ? 1 'SSA (A^2)' 7240 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _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 2 "O3'" ? ? ? 1_555 A 5BU 3 P ? ? A G 2 A 5BU 3 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale2 covale both ? A 5BU 3 "O3'" ? ? ? 1_555 A C 4 P ? ? A 5BU 3 A C 4 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale3 covale both ? B C 13 "O3'" ? ? ? 1_555 B 5BU 14 P ? ? B C 13 B 5BU 14 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale4 covale both ? B 5BU 14 "O3'" ? ? ? 1_555 B C 15 P ? ? B 5BU 14 B C 15 1_555 ? ? ? ? ? ? ? 1.603 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 2 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 17 O2 ? ? A G 2 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 17 N4 ? ? A G 2 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A 5BU 3 N3 ? ? ? 1_555 A A 16 N1 ? ? A 5BU 3 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A 5BU 3 O4 ? ? ? 1_555 A A 16 N6 ? ? A 5BU 3 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 4 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 4 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 4 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 5 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 5 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 5 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 A A 13 N1 ? ? A G 6 A A 13 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog16 hydrog ? ? A G 6 O6 ? ? ? 1_555 A A 13 N6 ? ? A G 6 A A 13 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog17 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 11 N1 ? ? A U 7 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 11 N6 ? ? A U 7 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 9 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 9 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 9 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 10 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 10 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 10 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 11 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 11 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 11 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 11 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 12 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 12 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 12 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B G 1 N1 ? ? ? 1_555 B C 16 N3 ? ? B G 1 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B G 1 N2 ? ? ? 1_555 B C 16 O2 ? ? B G 1 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 1 O6 ? ? ? 1_555 B C 16 N4 ? ? B G 1 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B G 2 N1 ? ? ? 1_555 B C 15 N3 ? ? B G 2 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B G 2 N2 ? ? ? 1_555 B C 15 O2 ? ? B G 2 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B G 2 O6 ? ? ? 1_555 B C 15 N4 ? ? B G 2 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B A 3 N1 ? ? ? 1_555 B 5BU 14 N3 ? ? B A 3 B 5BU 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B A 3 N6 ? ? ? 1_555 B 5BU 14 O4 ? ? B A 3 B 5BU 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B G 4 N1 ? ? ? 1_555 B C 13 N3 ? ? B G 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B G 4 N2 ? ? ? 1_555 B C 13 O2 ? ? B G 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B G 4 O6 ? ? ? 1_555 B C 13 N4 ? ? B G 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B C 5 N3 ? ? ? 1_555 B G 12 N1 ? ? B C 5 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? B C 5 N4 ? ? ? 1_555 B G 12 O6 ? ? B C 5 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? B C 5 O2 ? ? ? 1_555 B G 12 N2 ? ? B C 5 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 A _pdbx_validate_rmsd_angle.auth_seq_id_1 11 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 A _pdbx_validate_rmsd_angle.auth_seq_id_2 11 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N9 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 A _pdbx_validate_rmsd_angle.auth_seq_id_3 11 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 112.98 _pdbx_validate_rmsd_angle.angle_target_value 108.50 _pdbx_validate_rmsd_angle.angle_deviation 4.48 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.70 _pdbx_validate_rmsd_angle.linker_flag 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 3 A 5BU 3 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 2 B 5BU 14 B 5BU 14 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" # _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 -1.7090 _pdbx_refine_tls.origin_y -23.8950 _pdbx_refine_tls.origin_z -24.3520 _pdbx_refine_tls.T[1][1] 0.4363 _pdbx_refine_tls.T[2][2] 0.5888 _pdbx_refine_tls.T[3][3] 0.3942 _pdbx_refine_tls.T[1][2] 0.1034 _pdbx_refine_tls.T[1][3] -0.0262 _pdbx_refine_tls.T[2][3] -0.0528 _pdbx_refine_tls.L[1][1] 2.5556 _pdbx_refine_tls.L[2][2] 5.8291 _pdbx_refine_tls.L[3][3] 0.1108 _pdbx_refine_tls.L[1][2] -2.9570 _pdbx_refine_tls.L[1][3] 0.4150 _pdbx_refine_tls.L[2][3] -0.4585 _pdbx_refine_tls.S[1][1] 0.0240 _pdbx_refine_tls.S[1][2] 0.6143 _pdbx_refine_tls.S[1][3] 0.0444 _pdbx_refine_tls.S[2][1] -0.4119 _pdbx_refine_tls.S[2][2] 0.1042 _pdbx_refine_tls.S[2][3] -0.2838 _pdbx_refine_tls.S[3][1] 0.0117 _pdbx_refine_tls.S[3][2] 0.0951 _pdbx_refine_tls.S[3][3] -0.1282 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _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 'X-RAY DIFFRACTION' 1 1 A 1 ? ? A 18 ? ? ? ? 'X-RAY DIFFRACTION' 2 1 B 1 ? ? B 16 ? ? ? ? # 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 U OP3 O N N 145 U P P N N 146 U OP1 O N N 147 U OP2 O N N 148 U "O5'" O N N 149 U "C5'" C N N 150 U "C4'" C N R 151 U "O4'" O N N 152 U "C3'" C N S 153 U "O3'" O N N 154 U "C2'" C N R 155 U "O2'" O N N 156 U "C1'" C N R 157 U N1 N N N 158 U C2 C N N 159 U O2 O N N 160 U N3 N N N 161 U C4 C N N 162 U O4 O N N 163 U C5 C N N 164 U C6 C N N 165 U HOP3 H N N 166 U HOP2 H N N 167 U "H5'" H N N 168 U "H5''" H N N 169 U "H4'" H N N 170 U "H3'" H N N 171 U "HO3'" H N N 172 U "H2'" H N N 173 U "HO2'" H N N 174 U "H1'" H N N 175 U H3 H N N 176 U H5 H N N 177 U H6 H N N 178 # 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 U OP3 P sing N N 151 U OP3 HOP3 sing N N 152 U P OP1 doub N N 153 U P OP2 sing N N 154 U P "O5'" sing N N 155 U OP2 HOP2 sing N N 156 U "O5'" "C5'" sing N N 157 U "C5'" "C4'" sing N N 158 U "C5'" "H5'" sing N N 159 U "C5'" "H5''" sing N N 160 U "C4'" "O4'" sing N N 161 U "C4'" "C3'" sing N N 162 U "C4'" "H4'" sing N N 163 U "O4'" "C1'" sing N N 164 U "C3'" "O3'" sing N N 165 U "C3'" "C2'" sing N N 166 U "C3'" "H3'" sing N N 167 U "O3'" "HO3'" sing N N 168 U "C2'" "O2'" sing N N 169 U "C2'" "C1'" sing N N 170 U "C2'" "H2'" sing N N 171 U "O2'" "HO2'" sing N N 172 U "C1'" N1 sing N N 173 U "C1'" "H1'" sing N N 174 U N1 C2 sing N N 175 U N1 C6 sing N N 176 U C2 O2 doub N N 177 U C2 N3 sing N N 178 U N3 C4 sing N N 179 U N3 H3 sing N N 180 U C4 O4 doub N N 181 U C4 C5 sing N N 182 U C5 C6 doub N N 183 U C5 H5 sing N N 184 U C6 H6 sing N N 185 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2JLT 'a-form double helix' 2JLT 'hairpin loop' 2JLT 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 18 1_555 0.409 -0.237 0.319 0.179 -1.965 -2.491 1 A_G1:C18_A A 1 ? A 18 ? 19 1 1 A G 2 1_555 A C 17 1_555 -0.736 -0.011 0.393 -4.314 -16.982 9.028 2 A_G2:C17_A A 2 ? A 17 ? 19 1 1 A 5BU 3 1_555 A A 16 1_555 -0.885 -0.230 0.142 2.926 -16.255 -1.715 3 A_5BU3:A16_A A 3 ? A 16 ? 20 1 1 A C 4 1_555 A G 15 1_555 -0.170 -0.216 0.134 -3.060 -20.049 3.515 4 A_C4:G15_A A 4 ? A 15 ? 19 1 1 A G 5 1_555 A C 14 1_555 0.000 -0.128 -0.015 -12.211 -19.590 1.615 5 A_G5:C14_A A 5 ? A 14 ? 19 1 1 A G 6 1_555 A A 13 1_555 0.291 1.538 -0.403 18.496 -11.150 -15.771 6 A_G6:A13_A A 6 ? A 13 ? 8 1 1 B C 6 1_555 A G 12 1_555 0.101 -0.140 -0.020 5.889 -13.823 -0.594 7 B_C6:G12_A B 6 ? A 12 ? 19 1 1 B U 7 1_555 A A 11 1_555 0.035 -0.152 0.485 -0.903 -7.242 2.360 8 B_U7:A11_A B 7 ? A 11 ? 20 1 1 B G 8 1_555 A C 10 1_555 -0.191 -0.049 0.006 2.058 1.426 4.589 9 B_G8:C10_A B 8 ? A 10 ? 19 1 1 B G 9 1_555 A C 9 1_555 -0.379 -0.028 -0.281 4.529 -2.509 6.897 10 B_G9:C9_A B 9 ? A 9 ? 19 1 1 B G 10 1_555 A C 8 1_555 -0.319 -0.324 -0.476 -4.657 -6.404 3.489 11 B_G10:C8_A B 10 ? A 8 ? 19 1 1 B A 11 1_555 A U 7 1_555 0.422 -0.151 -0.308 -15.442 3.507 1.653 12 B_A11:U7_A B 11 ? A 7 ? 20 1 1 B G 12 1_555 B C 5 1_555 0.073 -0.011 -0.148 -7.472 6.356 5.288 13 B_G12:C5_B B 12 ? B 5 ? 19 1 1 B C 13 1_555 B G 4 1_555 0.286 -0.068 -0.201 5.469 -4.732 4.217 14 B_C13:G4_B B 13 ? B 4 ? 19 1 1 B 5BU 14 1_555 B A 3 1_555 -0.333 -0.159 -0.230 9.813 -11.808 0.197 15 B_5BU14:A3_B B 14 ? B 3 ? 20 1 1 B C 15 1_555 B G 2 1_555 0.510 -0.152 0.282 -3.717 -9.161 7.028 16 B_C15:G2_B B 15 ? B 2 ? 19 1 1 B C 16 1_555 B G 1 1_555 -0.232 -0.176 0.188 -3.686 -4.834 3.806 17 B_C16:G1_B B 16 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 18 1_555 A G 2 1_555 A C 17 1_555 0.791 -1.948 3.405 0.571 4.179 27.886 -4.974 -1.491 3.101 8.609 -1.177 28.197 1 AA_G1G2:C17C18_AA A 1 ? A 18 ? A 2 ? A 17 ? 1 A G 2 1_555 A C 17 1_555 A 5BU 3 1_555 A A 16 1_555 -1.369 -1.587 2.989 -2.748 5.402 32.292 -3.633 2.000 2.798 9.608 4.886 32.841 2 AA_G25BU3:A16C17_AA A 2 ? A 17 ? A 3 ? A 16 ? 1 A 5BU 3 1_555 A A 16 1_555 A C 4 1_555 A G 15 1_555 1.284 -1.341 3.377 3.083 8.734 33.096 -3.640 -1.693 3.039 14.971 -5.285 34.333 3 AA_5BU3C4:G15A16_AA A 3 ? A 16 ? A 4 ? A 15 ? 1 A C 4 1_555 A G 15 1_555 A G 5 1_555 A C 14 1_555 0.149 -1.699 3.113 3.729 22.261 35.561 -4.277 0.110 1.797 32.708 -5.480 41.923 4 AA_C4G5:C14G15_AA A 4 ? A 15 ? A 5 ? A 14 ? 1 A G 5 1_555 A C 14 1_555 A G 6 1_555 A A 13 1_555 -1.494 -0.672 2.680 4.857 4.617 28.359 -2.108 3.784 2.262 9.261 -9.743 29.125 5 AA_G5G6:A13C14_AA A 5 ? A 14 ? A 6 ? A 13 ? 1 A G 6 1_555 A A 13 1_555 B C 6 1_555 A G 12 1_555 -0.213 -1.674 3.423 -5.649 1.602 40.765 -2.561 -0.333 3.357 2.285 8.059 41.168 6 AB_G6C6:G12A13_AA A 6 ? A 13 ? B 6 ? A 12 ? 1 B C 6 1_555 A G 12 1_555 B U 7 1_555 A A 11 1_555 -0.801 -2.343 3.235 -8.265 8.543 33.857 -4.956 0.192 2.700 14.139 13.680 35.825 7 BB_C6U7:A11G12_AA B 6 ? A 12 ? B 7 ? A 11 ? 1 B U 7 1_555 A A 11 1_555 B G 8 1_555 A C 10 1_555 -0.549 -1.427 2.728 1.797 18.029 32.988 -3.934 1.024 1.717 29.174 -2.908 37.514 8 BB_U7G8:C10A11_AA B 7 ? A 11 ? B 8 ? A 10 ? 1 B G 8 1_555 A C 10 1_555 B G 9 1_555 A C 9 1_555 0.264 -1.355 3.159 0.328 14.305 29.714 -4.536 -0.417 2.286 26.077 -0.598 32.910 9 BB_G8G9:C9C10_AA B 8 ? A 10 ? B 9 ? A 9 ? 1 B G 9 1_555 A C 9 1_555 B G 10 1_555 A C 8 1_555 0.262 -1.987 3.297 0.135 15.356 33.774 -4.957 -0.396 2.218 24.897 -0.219 37.008 10 BB_G9G10:C8C9_AA B 9 ? A 9 ? B 10 ? A 8 ? 1 B G 10 1_555 A C 8 1_555 B A 11 1_555 A U 7 1_555 0.441 -2.156 3.510 1.419 9.542 38.095 -4.346 -0.488 2.921 14.340 -2.132 39.254 11 BB_G10A11:U7C8_AA B 10 ? A 8 ? B 11 ? A 7 ? 1 B A 11 1_555 A U 7 1_555 B G 12 1_555 B C 5 1_555 2.432 -1.268 3.044 4.215 3.662 42.180 -2.100 -2.948 3.146 5.061 -5.827 42.531 12 BB_A11G12:C5U7_BA B 11 ? A 7 ? B 12 ? B 5 ? 1 B G 12 1_555 B C 5 1_555 B C 13 1_555 B G 4 1_555 0.183 -1.733 3.099 1.381 13.296 22.734 -6.696 -0.101 1.828 30.569 -3.175 26.328 13 BB_G12C13:G4C5_BB B 12 ? B 5 ? B 13 ? B 4 ? 1 B C 13 1_555 B G 4 1_555 B 5BU 14 1_555 B A 3 1_555 -0.838 -2.197 3.128 -3.345 9.597 28.011 -6.011 1.026 2.345 19.050 6.640 29.763 14 BB_C135BU14:A3G4_BB B 13 ? B 4 ? B 14 ? B 3 ? 1 B 5BU 14 1_555 B A 3 1_555 B C 15 1_555 B G 2 1_555 1.041 -1.822 3.573 -0.577 8.087 36.016 -4.008 -1.725 3.090 12.878 0.918 36.888 15 BB_5BU14C15:G2A3_BB B 14 ? B 3 ? B 15 ? B 2 ? 1 B C 15 1_555 B G 2 1_555 B C 16 1_555 B G 1 1_555 0.025 -2.310 3.121 2.354 6.042 26.625 -6.191 0.459 2.537 12.878 -5.017 27.389 16 BB_C15C16:G1G2_BB B 15 ? B 2 ? B 16 ? B 1 ? # _atom_sites.entry_id 2JLT _atom_sites.fract_transf_matrix[1][1] 0.011765 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.011765 _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] 0.011765 _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_