data_2F88 # _entry.id 2F88 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2F88 pdb_00002f88 10.2210/pdb2f88/pdb RCSB RCSB035573 ? ? WWPDB D_1000035573 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2F88 _pdbx_database_status.recvd_initial_deposition_date 2005-12-02 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _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 ? # _audit_author.name 'Dayie, K.T.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA' _citation.journal_abbrev Rna _citation.journal_volume 12 _citation.page_first 235 _citation.page_last 247 _citation.year 2006 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16428604 _citation.pdbx_database_id_DOI 10.1261/rna.2237806 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Seetharaman, M.' 1 ? primary 'Eldho, N.V.' 2 ? primary 'Padgett, R.A.' 3 ? primary 'Dayie, K.T.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'D5-PL RNA RIBOZYME DOMAIN' _entity.formula_weight 11009.607 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details 'Domain 5 of PL Group II intron' # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUC _entity_poly.pdbx_seq_one_letter_code_can GAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 A n 1 3 G n 1 4 C n 1 5 C n 1 6 G n 1 7 U n 1 8 G n 1 9 U n 1 10 G n 1 11 C n 1 12 G n 1 13 A n 1 14 U n 1 15 G n 1 16 A n 1 17 A n 1 18 A n 1 19 G n 1 20 U n 1 21 C n 1 22 G n 1 23 C n 1 24 A n 1 25 A n 1 26 G n 1 27 C n 1 28 A n 1 29 C n 1 30 G n 1 31 G n 1 32 U n 1 33 U n 1 34 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details ;RNA was synthesized by in vitro transcription with T7 RNA polymerase' ; # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2F88 _struct_ref.pdbx_db_accession 2F88 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2F88 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 34 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2F88 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 34 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 34 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 3 2 2 '2D TOCSY' 3 3 2 3D_13C-separated_NOESY 1 4 1 3D_15N-separated_NOESY 1 5 3 '3D 1H-13C-1H HCCH TOCSY' 1 6 3 '3D 1H-13C-1H HCCH COSY' 1 7 3 '3D 1H-13C-1H HCCH COSY TROSY' 1 8 3 '3D HCCNH' 1 9 2 3D_13C-separated_ROESY 2 10 4 '13C/15N HSQC' 1 11 4 '13C/15N TROSY' 1 # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 278 ? 6.5 '100 mM KCl' . K 2 298 ? 6.5 '100 mM KCl' . K 3 308 ? 6.5 '100 mM KCl' . K 4 318 ? 6.5 '100 mM KCl' . K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 ;1 mM fully 13C/15N A,C,G,U labeled D5-PL, 100 mM KCl, 10 mM phosphate, 0-10 mM MgCl2, 92% H2O and 8% D2O or 99.999% D2O ; '92% H2O and 8% D2O or 99.999% D2O' 2 ;1 mM A-13C/15N Uracil labeled D5-PL, 100 mM KCl, 10 mM phosphate buffer, 0-10 mM MgCl2, 92% H2O and 8% D2O or 99.999% D2O ; '92% H2O and 8% D2O or 99.999% D2O' 3 ;1 mM unlabeled D5-PL, 100 mM KCl, 10 mM phosphate buffer, 0-10 mM MgCl2, 92% H2O and 8% D2O or 99.999% D2O ; '92% H2O and 8% D2O or 99.999% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 INOVA Varian 500 ? 2 INOVA Varian 600 ? 3 AVANCE Bruker 600 ? 4 AVANCE Bruker 800 ? # _pdbx_nmr_refine.entry_id 2F88 _pdbx_nmr_refine.method ;TORSION ANGLE MOLECULAR DYNAMICS CARTESIAN SPACE SIMULATED ANNEALING RESIDUAL DIPOLAR COUPLINGS REFINEMENT ; _pdbx_nmr_refine.details ;STRUCTURES BASED ON 549 NOE-DERIVED DISTANCE RESTRAINTS, 304 DIHEDRAL RESTRAINTS, 60 HYDROGEN BOND RESTRAINTS, AND 37 RESIDUAL DIPOLAR COUPLING RESTRAINTS ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2F88 _pdbx_nmr_details.text 'The structure was determined using a battery of standard homonuclear and recently optimized triple-resonance NMR experiments' # _pdbx_nmr_ensemble.entry_id 2F88 _pdbx_nmr_ensemble.conformers_calculated_total_number 30 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations,structures with the lowest energy' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 2F88 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal processing NMRPipe 2.1 'Delaglio, Bax' 1 'data analysis' Sparky 3 'Goddard & Kneller' 2 'structure solution' CNS 1.1 Brunger 3 refinement CNS 1.1 Brunger 4 # _exptl.entry_id 2F88 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 2F88 _struct.title 'Solution NMR structure of domain 5 from the Pyaiella littoralis (PL) group II intron' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2F88 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA hairpin, GNRA Tetraloop, Internal bulge, Mg Metal binding site, RNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 # 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 hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 34 N3 ? ? A G 1 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 34 O2 ? ? A G 1 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 34 N4 ? ? A G 1 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N1 ? ? ? 1_555 A U 33 N3 ? ? A A 2 A U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 2 N6 ? ? ? 1_555 A U 33 O4 ? ? A A 2 A U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 A U 32 O2 ? ? A G 3 A U 32 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog7 hydrog ? ? A G 3 O6 ? ? ? 1_555 A U 32 N3 ? ? A G 3 A U 32 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 31 N1 ? ? A C 4 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 31 O6 ? ? A C 4 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 31 N2 ? ? A C 4 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 26 O6 ? ? A C 5 A G 26 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog12 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 30 N1 ? ? A C 5 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 30 O6 ? ? A C 5 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 30 N2 ? ? A C 5 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 6 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 6 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 6 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 28 N1 ? ? A U 7 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 7 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 27 N3 ? ? A G 8 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 27 O2 ? ? A G 8 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 27 N4 ? ? A G 8 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 10 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 10 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 10 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 11 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 11 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 11 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 12 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 12 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 12 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A A 13 N1 ? ? ? 1_555 A U 20 N3 ? ? A A 13 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A A 13 N6 ? ? ? 1_555 A U 20 O4 ? ? A A 13 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 14 N3 ? ? ? 1_555 A G 19 O6 ? ? A U 14 A G 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog35 hydrog ? ? A U 14 O2 ? ? ? 1_555 A G 19 N1 ? ? A U 14 A G 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 2F88 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2F88 _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # 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 A 2 2 2 A A A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 C 5 5 5 C C 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 G 8 8 8 G G A . n A 1 9 U 9 9 9 U U A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C 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 U 14 14 14 U U 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 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 U 20 20 20 U U A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n A 1 24 A 24 24 24 A A A . n A 1 25 A 25 25 25 A A A . n A 1 26 G 26 26 26 G G A . n A 1 27 C 27 27 27 C C A . n A 1 28 A 28 28 28 A A A . n A 1 29 C 29 29 29 C C A . n A 1 30 G 30 30 30 G G A . n A 1 31 G 31 31 31 G G A . n A 1 32 U 32 32 32 U U A . n A 1 33 U 33 33 33 U U A . n A 1 34 C 34 34 34 C C A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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_ _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 2006-02-28 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_spectrometer 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_spectrometer.model' # 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 "H2'" A C 4 ? ? "O4'" A C 5 ? ? 1.59 2 2 "H2'" A C 4 ? ? "O4'" A C 5 ? ? 1.55 3 2 "HO2'" A A 16 ? ? "O5'" A A 17 ? ? 1.58 4 3 "H2'" A C 4 ? ? "O4'" A C 5 ? ? 1.58 5 3 "HO2'" A A 16 ? ? "O5'" A A 17 ? ? 1.59 6 4 "H2'" A C 4 ? ? "O4'" A C 5 ? ? 1.56 7 4 "HO2'" A A 16 ? ? "O5'" A A 17 ? ? 1.56 8 5 "HO2'" A A 16 ? ? "O5'" A A 17 ? ? 1.56 9 5 "H2'" A C 4 ? ? "O4'" A C 5 ? ? 1.56 10 5 "O2'" A A 25 ? ? H8 A G 26 ? ? 1.58 11 6 "HO2'" A A 24 ? ? "O5'" A A 25 ? ? 1.52 12 6 "H2'" A C 4 ? ? "O4'" A C 5 ? ? 1.59 13 7 "H2'" A C 4 ? ? "O4'" A C 5 ? ? 1.55 14 7 "HO2'" A A 16 ? ? "O5'" A A 17 ? ? 1.56 15 8 "HO2'" A A 24 ? ? "O5'" A A 25 ? ? 1.54 16 8 "H2'" A C 4 ? ? "O4'" A C 5 ? ? 1.59 17 9 "H2'" A C 4 ? ? "O4'" A C 5 ? ? 1.58 18 10 "HO2'" A A 16 ? ? "O5'" A A 17 ? ? 1.59 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2F88 'a-form double helix' 2F88 'hairpin loop' 2F88 'mismatched base pair' 2F88 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 34 1_555 0.147 -0.187 -0.381 -5.907 5.756 -1.989 1 A_G1:C34_A A 1 ? A 34 ? 19 1 1 A A 2 1_555 A U 33 1_555 -0.402 -0.286 -0.307 -5.638 -0.958 3.332 2 A_A2:U33_A A 2 ? A 33 ? 20 1 1 A G 3 1_555 A U 32 1_555 -3.276 -0.669 0.043 -6.480 -3.785 7.740 3 A_G3:U32_A A 3 ? A 32 ? 28 ? 1 A C 4 1_555 A G 31 1_555 -0.140 -0.164 -0.040 9.825 -9.842 -1.582 4 A_C4:G31_A A 4 ? A 31 ? 19 1 1 A C 5 1_555 A G 30 1_555 0.861 -0.264 -0.126 1.801 -13.894 5.579 5 A_C5:G30_A A 5 ? A 30 ? 19 1 1 A G 6 1_555 A C 29 1_555 -0.803 -0.398 -0.095 -7.728 -13.617 0.830 6 A_G6:C29_A A 6 ? A 29 ? 19 1 1 A U 7 1_555 A A 28 1_555 0.501 -0.300 0.043 7.497 -12.107 2.123 7 A_U7:A28_A A 7 ? A 28 ? 20 1 1 A G 8 1_555 A C 27 1_555 -0.741 -0.299 0.000 -4.733 -4.046 0.201 8 A_G8:C27_A A 8 ? A 27 ? 19 1 1 A G 10 1_555 A C 23 1_555 -0.470 -0.238 -0.130 -0.701 -1.096 -0.895 9 A_G10:C23_A A 10 ? A 23 ? 19 1 1 A C 11 1_555 A G 22 1_555 0.285 -0.209 -0.111 6.908 0.840 -0.893 10 A_C11:G22_A A 11 ? A 22 ? 19 1 1 A G 12 1_555 A C 21 1_555 -0.675 -0.369 -0.132 -1.682 -2.574 -1.123 11 A_G12:C21_A A 12 ? A 21 ? 19 1 1 A A 13 1_555 A U 20 1_555 -0.212 -0.188 -0.278 -1.084 -0.541 -3.814 12 A_A13:U20_A A 13 ? A 20 ? 20 1 1 A U 14 1_555 A G 19 1_555 2.439 -0.312 -0.182 2.054 -1.273 -4.023 13 A_U14:G19_A A 14 ? A 19 ? 28 ? # 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 34 1_555 A A 2 1_555 A U 33 1_555 0.424 -1.817 3.789 -2.450 -7.760 27.590 -1.518 -1.530 4.085 -15.840 5.000 28.743 1 AA_G1A2:U33C34_AA A 1 ? A 34 ? A 2 ? A 33 ? 1 A A 2 1_555 A U 33 1_555 A G 3 1_555 A U 32 1_555 -0.262 -2.049 4.094 -0.196 -5.695 20.154 -2.396 0.608 4.497 -15.869 0.547 20.936 2 AA_A2G3:U32U33_AA A 2 ? A 33 ? A 3 ? A 32 ? 1 A G 3 1_555 A U 32 1_555 A C 4 1_555 A G 31 1_555 -0.943 0.043 2.882 -0.035 10.809 39.111 -1.006 1.358 2.798 15.783 0.051 40.521 3 AA_G3C4:G31U32_AA A 3 ? A 32 ? A 4 ? A 31 ? 1 A C 4 1_555 A G 31 1_555 A C 5 1_555 A G 30 1_555 1.945 -0.970 3.653 0.366 4.625 36.218 -2.253 -3.049 3.525 7.402 -0.587 36.504 4 AA_C4C5:G30G31_AA A 4 ? A 31 ? A 5 ? A 30 ? 1 A C 5 1_555 A G 30 1_555 A G 6 1_555 A C 29 1_555 -1.119 -1.581 3.173 -0.143 14.390 28.979 -5.048 1.990 2.171 26.772 0.266 32.287 5 AA_C5G6:C29G30_AA A 5 ? A 30 ? A 6 ? A 29 ? 1 A G 6 1_555 A C 29 1_555 A U 7 1_555 A A 28 1_555 0.506 -0.719 2.801 -1.264 0.491 34.735 -1.267 -1.011 2.771 0.822 2.116 34.760 6 AA_G6U7:A28C29_AA A 6 ? A 29 ? A 7 ? A 28 ? 1 A U 7 1_555 A A 28 1_555 A G 8 1_555 A C 27 1_555 0.715 -1.866 3.201 -2.165 8.362 29.544 -4.985 -1.728 2.533 15.973 4.135 30.754 7 AA_U7G8:C27A28_AA A 7 ? A 28 ? A 8 ? A 27 ? 1 A G 10 1_555 A C 23 1_555 A C 11 1_555 A G 22 1_555 -0.710 -0.475 3.268 0.280 20.954 34.833 -2.961 1.057 2.584 31.708 -0.424 40.482 8 AA_G10C11:G22C23_AA A 10 ? A 23 ? A 11 ? A 22 ? 1 A C 11 1_555 A G 22 1_555 A G 12 1_555 A C 21 1_555 0.066 -0.551 4.253 -2.268 18.797 30.189 -4.376 -0.527 3.342 32.397 3.908 35.517 9 AA_C11G12:C21G22_AA A 11 ? A 22 ? A 12 ? A 21 ? 1 A G 12 1_555 A C 21 1_555 A A 13 1_555 A U 20 1_555 0.676 -1.545 3.230 -0.090 1.155 36.938 -2.590 -1.078 3.180 1.823 0.142 36.955 10 AA_G12A13:U20C21_AA A 12 ? A 21 ? A 13 ? A 20 ? 1 A A 13 1_555 A U 20 1_555 A U 14 1_555 A G 19 1_555 -1.275 -1.100 3.328 2.567 0.734 41.581 -1.625 2.065 3.228 1.033 -3.611 41.663 11 AA_A13U14:G19U20_AA A 13 ? A 20 ? A 14 ? A 19 ? #