data_1XHP # _entry.id 1XHP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1XHP pdb_00001xhp 10.2210/pdb1xhp/pdb RCSB RCSB030374 ? ? WWPDB D_1000030374 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1SY4 'Solution Structure of the Shortened U6 ISL' unspecified PDB 1R2P 'Solution Structure Of Domain 5 From The Ai5(gamma) Group II Intron' unspecified PDB 1KXK 'Crystal Structure Of A RNA Molecule Containing Domain 5 and 6 Of The Yeast Ai5G Group II Self-Splicing Intron' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1XHP _pdbx_database_status.recvd_initial_deposition_date 2004-09-20 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sashital, D.G.' 1 'Cornilescu, G.' 2 'Butcher, S.E.' 3 # _citation.id primary _citation.title 'U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 11 _citation.page_first 1237 _citation.page_last 1242 _citation.year 2004 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9993 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15543154 _citation.pdbx_database_id_DOI 10.1038/nsmb863 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sashital, D.G.' 1 ? primary 'Cornilescu, G.' 2 ? primary 'McManus, C.J.' 3 ? primary 'Brow, D.A.' 4 ? primary 'Butcher, S.E.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'U6 snRNA' _entity.formula_weight 10240.134 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 GAGCAGUUCCCCUGCAUAAGGAUGAACCGUUC _entity_poly.pdbx_seq_one_letter_code_can GAGCAGUUCCCCUGCAUAAGGAUGAACCGUUC _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 A n 1 6 G n 1 7 U n 1 8 U n 1 9 C n 1 10 C n 1 11 C n 1 12 C n 1 13 U n 1 14 G n 1 15 C n 1 16 A n 1 17 U n 1 18 A n 1 19 A n 1 20 G n 1 21 G n 1 22 A n 1 23 U n 1 24 G n 1 25 A n 1 26 A n 1 27 C n 1 28 C n 1 29 G n 1 30 U n 1 31 U n 1 32 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 'In vitro transcription of U6 nucleotides 59-88 using purified T7 RNA polymerase and synthetic DNA oligonucleotides.' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1XHP _struct_ref.pdbx_db_accession 1XHP _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 1XHP _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 32 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1XHP _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 32 _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 32 # 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.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 2 2 '2D NOESY' 3 2 2 '2D TOCSY' 4 4 2 3D_13C-separated_NOESY 5 4 2 '3D [1H-13C-1H] HCCH-TOCSY' 6 4 4 '3D [1H-13C-1H] HCCH -COSY' 7 3 3 '2D [15N-1H] HNN-COSY' 8 5 2 'J-modulated [13C-1H] CT-HSQC' # 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 1 283 ? 6.9 ? ? K 2 303 ? 7.5 ? ? K 3 298 ? 6.9 ? ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1mM extended U6 ISL RNA; 90% H2O; 10% D2O' '90% H2O/10% D2O' 2 '1mM extended U6 ISL RNA; 99.99% D2O' '99.99% D2O' 3 '1mM 13C,15N labeled extended U6 ISL RNA; 90% H2O; 10% D2O' '90% H2O/10% D2O' 4 '1mM 13C,15N labeled extended U6 ISL RNA; 99.99% D2O' '99.99% D2O' 5 '1mM 13C,15N labeled extended U6 ISL RNA; 17 mg/ml pf1 bacteriophage; 90% H2O; 10% D2O' '90% H2O/10% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Bruker DMX 600 2 ? Bruker DMX 750 3 ? Varian INOVA 600 4 ? Varian INOVA 800 # _pdbx_nmr_refine.entry_id 1XHP _pdbx_nmr_refine.method 'simulated annealing, torsion angle dynamics, molecular dynamics, residual dipolar couplings, conformational database potentials' _pdbx_nmr_refine.details '435 NOE distance constraints, 244 dihedral angle restraints, 66 hydrogen bond restraints, 77 residual dipolar couplings' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1XHP _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria '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 1XHP _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal XwinNMR 3.5 processing Bruker 1 VNMR 1.1 processing Varian 2 NMRPipe 97.027.12.56 processing Bax 3 Sparky 3.105 'data analysis' 'Goddard and Kneller' 4 CNS 1.1 'structure solution' Brunger 5 XPLOR-NIH 2.9.7 'structure solution' 'Clore, Kuszewski, Schwieters, Tjandra' 6 XPLOR-NIH 2.9.7 refinement ? 7 # _exptl.entry_id 1XHP _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 ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _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.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _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 1XHP _struct.title 'Solution Structure of the Extended U6 ISL as Observed in the U2/U6 complex from Saccharomyces cerevisiae' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1XHP _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'U6 RNA, RNA stem-loop, penta-loop, internal bulge, 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 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 32 N3 ? ? A G 1 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 32 O2 ? ? A G 1 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 32 N4 ? ? A G 1 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N1 ? ? ? 1_555 A U 31 N3 ? ? A A 2 A U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 2 N6 ? ? ? 1_555 A U 31 O4 ? ? A A 2 A U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 A U 30 O2 ? ? A G 3 A U 30 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog7 hydrog ? ? A G 3 O6 ? ? ? 1_555 A U 30 N3 ? ? A G 3 A U 30 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 29 N1 ? ? A C 4 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 29 O6 ? ? A C 4 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 29 N2 ? ? A C 4 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N6 ? ? ? 1_555 A C 28 N3 ? ? A A 5 A C 28 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog12 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 27 N3 ? ? A G 6 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 27 O2 ? ? A G 6 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 27 N4 ? ? A G 6 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 26 N1 ? ? A U 7 A A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 26 N6 ? ? A U 7 A A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 25 N1 ? ? A U 8 A A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 25 N6 ? ? A U 8 A A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 24 N1 ? ? A C 9 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 24 O6 ? ? A C 9 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 24 N2 ? ? A C 9 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 A A 22 N6 ? ? A C 10 A A 22 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog23 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 11 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 11 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 11 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 12 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 12 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 12 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 13 N3 ? ? ? 1_555 A A 19 N1 ? ? A U 13 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 13 O4 ? ? ? 1_555 A A 19 N6 ? ? A U 13 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 N2 ? ? ? 1_555 A A 18 N7 ? ? A G 14 A A 18 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog32 hydrog ? ? A G 14 N3 ? ? ? 1_555 A A 18 N6 ? ? A G 14 A A 18 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1XHP _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 1XHP _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 GUA A . n A 1 2 A 2 2 2 A ADE A . n A 1 3 G 3 3 3 G GUA A . n A 1 4 C 4 4 4 C CYT A . n A 1 5 A 5 5 5 A ADE A . n A 1 6 G 6 6 6 G GUA A . n A 1 7 U 7 7 7 U URI A . n A 1 8 U 8 8 8 U URI A . n A 1 9 C 9 9 9 C CYT A . n A 1 10 C 10 10 10 C CYT A . n A 1 11 C 11 11 11 C CYT A . n A 1 12 C 12 12 12 C CYT A . n A 1 13 U 13 13 13 U URI A . n A 1 14 G 14 14 14 G GUA A . n A 1 15 C 15 15 15 C CYT A . n A 1 16 A 16 16 16 A ADE A . n A 1 17 U 17 17 17 U URI A . n A 1 18 A 18 18 18 A ADE A . n A 1 19 A 19 19 19 A ADE A . n A 1 20 G 20 20 20 G GUA A . n A 1 21 G 21 21 21 G GUA A . n A 1 22 A 22 22 22 A ADE A . n A 1 23 U 23 23 23 U URI A . n A 1 24 G 24 24 24 G GUA A . n A 1 25 A 25 25 25 A ADE A . n A 1 26 A 26 26 26 A ADE A . n A 1 27 C 27 27 27 C CYT A . n A 1 28 C 28 28 28 C CYT A . n A 1 29 G 29 29 29 G GUA A . n A 1 30 U 30 30 30 U URI A . n A 1 31 U 31 31 31 U URI A . n A 1 32 C 32 32 32 C CYT 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 2004-11-23 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _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_software 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_software.name' # 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 H61 A A 5 ? ? H41 A C 28 ? ? 1.27 2 2 H61 A A 5 ? ? H41 A C 28 ? ? 1.28 3 3 H61 A A 5 ? ? H41 A C 28 ? ? 1.27 4 4 H61 A A 5 ? ? H41 A C 28 ? ? 1.28 5 4 "O2'" A C 15 ? ? H8 A A 16 ? ? 1.44 6 4 "O2'" A A 16 ? ? H6 A U 17 ? ? 1.55 7 5 H61 A A 5 ? ? H41 A C 28 ? ? 1.28 8 6 H61 A A 5 ? ? H41 A C 28 ? ? 1.27 9 7 H61 A A 5 ? ? H41 A C 28 ? ? 1.27 10 7 "O2'" A C 15 ? ? H8 A A 16 ? ? 1.42 11 7 "O2'" A A 16 ? ? H6 A U 17 ? ? 1.53 12 8 H61 A A 5 ? ? H41 A C 28 ? ? 1.28 13 8 "O2'" A A 16 ? ? H6 A U 17 ? ? 1.45 14 8 "O2'" A C 15 ? ? H8 A A 16 ? ? 1.46 15 9 H61 A A 5 ? ? H41 A C 28 ? ? 1.28 16 9 "O2'" A C 15 ? ? H8 A A 16 ? ? 1.48 17 9 "HO2'" A A 2 ? ? "O4'" A G 3 ? ? 1.60 18 10 H61 A A 5 ? ? H41 A C 28 ? ? 1.28 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C1'" A A 2 ? ? "O4'" A A 2 ? ? "C4'" A A 2 ? ? 105.39 109.70 -4.31 0.70 N 2 2 "C1'" A A 2 ? ? "O4'" A A 2 ? ? "C4'" A A 2 ? ? 105.06 109.70 -4.64 0.70 N 3 3 "C3'" A A 16 ? ? "O3'" A A 16 ? ? P A U 17 ? ? 128.17 119.70 8.47 1.20 Y 4 4 "C1'" A A 2 ? ? "O4'" A A 2 ? ? "C4'" A A 2 ? ? 105.22 109.70 -4.48 0.70 N 5 5 "C1'" A A 2 ? ? "O4'" A A 2 ? ? "C4'" A A 2 ? ? 105.47 109.70 -4.23 0.70 N 6 5 "C1'" A A 5 ? ? "O4'" A A 5 ? ? "C4'" A A 5 ? ? 105.44 109.70 -4.26 0.70 N 7 6 "C1'" A A 2 ? ? "O4'" A A 2 ? ? "C4'" A A 2 ? ? 105.19 109.70 -4.51 0.70 N 8 7 "C1'" A A 2 ? ? "O4'" A A 2 ? ? "C4'" A A 2 ? ? 105.32 109.70 -4.38 0.70 N 9 8 "C1'" A A 2 ? ? "O4'" A A 2 ? ? "C4'" A A 2 ? ? 105.30 109.70 -4.40 0.70 N 10 9 "C1'" A U 17 ? ? "O4'" A U 17 ? ? "C4'" A U 17 ? ? 101.57 109.70 -8.13 0.70 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1XHP 'a-form double helix' 1XHP 'hairpin loop' 1XHP 'bulge loop' 1XHP '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 32 1_555 -0.086 -0.069 0.249 2.685 -0.014 -2.128 1 A_G1:C32_A A 1 ? A 32 ? 19 1 1 A A 2 1_555 A U 31 1_555 -0.223 -0.087 0.017 13.164 -5.824 0.381 2 A_A2:U31_A A 2 ? A 31 ? 20 1 1 A G 3 1_555 A U 30 1_555 -1.886 -0.396 0.329 -2.395 -16.678 -3.006 3 A_G3:U30_A A 3 ? A 30 ? 28 1 1 A C 4 1_555 A G 29 1_555 0.453 -0.156 -0.105 0.343 -1.485 -2.144 4 A_C4:G29_A A 4 ? A 29 ? 19 1 1 A A 5 1_555 A C 28 1_555 -1.124 -0.450 -0.339 -2.583 0.929 -5.240 5 A_A5:C28_A A 5 ? A 28 ? ? ? 1 A G 6 1_555 A C 27 1_555 -0.386 -0.201 0.233 -1.351 -16.554 -3.341 6 A_G6:C27_A A 6 ? A 27 ? 19 1 1 A U 7 1_555 A A 26 1_555 0.072 -0.093 -0.170 -3.322 -9.601 1.471 7 A_U7:A26_A A 7 ? A 26 ? 20 1 1 A U 8 1_555 A A 25 1_555 0.084 -0.041 0.072 -0.533 -15.889 -3.796 8 A_U8:A25_A A 8 ? A 25 ? 20 1 1 A C 9 1_555 A G 24 1_555 1.027 -0.498 0.302 0.365 -8.119 -3.239 9 A_C9:G24_A A 9 ? A 24 ? 19 1 1 A C 10 1_555 A A 22 1_555 1.429 -0.312 -0.224 0.801 -2.976 -9.068 10 A_C10:A22_A A 10 ? A 22 ? ? ? 1 A C 11 1_555 A G 21 1_555 0.340 -0.119 -0.230 1.992 0.034 -2.199 11 A_C11:G21_A A 11 ? A 21 ? 19 1 1 A C 12 1_555 A G 20 1_555 0.117 -0.073 -0.210 2.338 -4.431 -1.738 12 A_C12:G20_A A 12 ? A 20 ? 19 1 1 A U 13 1_555 A A 19 1_555 0.673 -0.208 -0.214 1.334 -4.812 -2.032 13 A_U13:A19_A A 13 ? A 19 ? 20 1 1 A G 14 1_555 A A 18 1_555 6.681 -3.721 -0.020 -0.821 1.664 2.584 14 A_G14:A18_A A 14 ? A 18 ? 11 9 # 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 32 1_555 A A 2 1_555 A U 31 1_555 0.242 -1.544 3.134 2.814 10.615 24.749 -5.644 0.104 2.301 23.352 -6.192 27.041 1 AA_G1A2:U31C32_AA A 1 ? A 32 ? A 2 ? A 31 ? 1 A A 2 1_555 A U 31 1_555 A G 3 1_555 A U 30 1_555 -0.161 -1.679 3.567 -6.856 7.441 25.860 -5.349 -1.366 2.927 15.874 14.627 27.738 2 AA_A2G3:U30U31_AA A 2 ? A 31 ? A 3 ? A 30 ? 1 A G 3 1_555 A U 30 1_555 A C 4 1_555 A G 29 1_555 -0.271 -1.282 3.381 0.884 1.204 37.424 -2.159 0.541 3.332 1.876 -1.377 37.453 3 AA_G3C4:G29U30_AA A 3 ? A 30 ? A 4 ? A 29 ? 1 A C 4 1_555 A G 29 1_555 A A 5 1_555 A C 28 1_555 -0.221 -1.835 3.595 1.739 13.457 20.345 -8.261 1.030 1.986 33.683 -4.354 24.415 4 AA_C4A5:C28G29_AA A 4 ? A 29 ? A 5 ? A 28 ? 1 A A 5 1_555 A C 28 1_555 A G 6 1_555 A C 27 1_555 0.494 -1.425 3.213 -4.592 8.999 30.699 -4.020 -1.632 2.604 16.448 8.393 32.281 5 AA_A5G6:C27C28_AA A 5 ? A 28 ? A 6 ? A 27 ? 1 A G 6 1_555 A C 27 1_555 A U 7 1_555 A A 26 1_555 0.165 -1.083 3.696 2.267 -8.804 36.231 -0.329 0.094 3.848 -13.890 -3.577 37.317 6 AA_G6U7:A26C27_AA A 6 ? A 27 ? A 7 ? A 26 ? 1 A U 7 1_555 A A 26 1_555 A U 8 1_555 A A 25 1_555 -0.091 -1.700 2.859 0.433 12.927 30.342 -4.704 0.217 1.988 23.407 -0.785 32.924 7 AA_U7U8:A25A26_AA A 7 ? A 26 ? A 8 ? A 25 ? 1 A U 8 1_555 A A 25 1_555 A C 9 1_555 A G 24 1_555 -0.116 -1.549 3.405 0.690 -0.986 30.313 -2.752 0.366 3.449 -1.884 -1.319 30.337 8 AA_U8C9:G24A25_AA A 8 ? A 25 ? A 9 ? A 24 ? 1 A C 9 1_555 A G 24 1_555 A C 10 1_555 A A 22 1_555 2.575 -1.418 4.237 -2.314 1.338 52.677 -1.707 -3.090 4.094 1.506 2.606 52.740 9 AA_C9C10:A22G24_AA A 9 ? A 24 ? A 10 ? A 22 ? 1 A C 10 1_555 A A 22 1_555 A C 11 1_555 A G 21 1_555 0.281 -1.855 3.285 3.335 7.609 23.994 -6.257 0.252 2.598 17.639 -7.731 25.372 10 AA_C10C11:G21A22_AA A 10 ? A 22 ? A 11 ? A 21 ? 1 A C 11 1_555 A G 21 1_555 A C 12 1_555 A G 20 1_555 0.025 -1.788 3.284 2.940 9.317 26.319 -5.699 0.582 2.505 19.622 -6.193 28.044 11 AA_C11C12:G20G21_AA A 11 ? A 21 ? A 12 ? A 20 ? 1 A C 12 1_555 A G 20 1_555 A U 13 1_555 A A 19 1_555 0.199 -1.758 3.532 0.473 3.730 26.717 -4.762 -0.301 3.264 8.022 -1.017 26.976 12 AA_C12U13:A19G20_AA A 12 ? A 20 ? A 13 ? A 19 ? 1 A U 13 1_555 A A 19 1_555 A G 14 1_555 A A 18 1_555 0.324 -0.328 3.730 1.636 6.988 56.651 -0.780 -0.237 3.676 7.331 -1.716 57.066 13 AA_U13G14:A18A19_AA A 13 ? A 19 ? A 14 ? A 18 ? #