data_1LPW # _entry.id 1LPW # _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 1LPW pdb_00001lpw 10.2210/pdb1lpw/pdb RCSB RCSB016167 ? ? WWPDB D_1000016167 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1LMV _pdbx_database_related.details 'Solution structure of the unmodified U2 snRNA-intron branch site helix' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1LPW _pdbx_database_status.recvd_initial_deposition_date 2002-05-08 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _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 'Newby, M.I.' 1 'Greenbaum, N.L.' 2 # _citation.id primary _citation.title 'Sculpting of the Spliceosomal Branch Site Recognition Motif by a Conserved Pseudouridine' _citation.journal_abbrev Nat.Struct.Biol. _citation.journal_volume 12 _citation.page_first 958 _citation.page_last 965 _citation.year 2002 _citation.journal_id_ASTM NSBIEW _citation.country US _citation.journal_id_ISSN 1072-8368 _citation.journal_id_CSD 2024 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12426583 _citation.pdbx_database_id_DOI 10.1038/nsb873 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Newby, M.I.' 1 ? primary 'Greenbaum, N.L.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer nat "5'-R(*GP*GP*UP*GP*(PSU)P*AP*GP*UP*A)-3'" 2912.775 1 ? ? ? 'U2 snRNA' 2 polymer nat "5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3'" 3104.925 1 ? ? ? 'pre-mRNA conserved intron branch site sequence site' # 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 'GGUG(PSU)AGUA' GGUGUAGUA A ? 2 polyribonucleotide no no UACUAACACC UACUAACACC 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 U n 1 4 G n 1 5 PSU n 1 6 A n 1 7 G n 1 8 U n 1 9 A n 2 1 U n 2 2 A n 2 3 C n 2 4 U n 2 5 A n 2 6 A n 2 7 C n 2 8 A n 2 9 C n 2 10 C n # loop_ _entity_src_nat.entity_id _entity_src_nat.pdbx_src_id _entity_src_nat.pdbx_alt_source_flag _entity_src_nat.pdbx_beg_seq_num _entity_src_nat.pdbx_end_seq_num _entity_src_nat.common_name _entity_src_nat.pdbx_organism_scientific _entity_src_nat.pdbx_ncbi_taxonomy_id _entity_src_nat.genus _entity_src_nat.species _entity_src_nat.strain _entity_src_nat.tissue _entity_src_nat.tissue_fraction _entity_src_nat.pdbx_secretion _entity_src_nat.pdbx_fragment _entity_src_nat.pdbx_variant _entity_src_nat.pdbx_cell_line _entity_src_nat.pdbx_atcc _entity_src_nat.pdbx_cellular_location _entity_src_nat.pdbx_organ _entity_src_nat.pdbx_organelle _entity_src_nat.pdbx_cell _entity_src_nat.pdbx_plasmid_name _entity_src_nat.pdbx_plasmid_details _entity_src_nat.details 1 1 sample ? ? ;baker's yeast ; 'Saccharomyces cerevisiae' 4932 Saccharomyces ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample ? ? ;baker's yeast ; 'Saccharomyces cerevisiae' 4932 Saccharomyces ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1LPW 1LPW ? ? ? 2 2 PDB 1LPW 1LPW ? ? ? # 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 1LPW A 1 ? 9 ? 1LPW 1 ? 9 ? 1 9 2 2 1LPW B 1 ? 10 ? 1LPW 1 ? 10 ? 1 10 # 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 PSU 'RNA linking' n "PSEUDOURIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 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 2 2 DQF-COSY # 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 ambient 6.4 '50mM sodium chloride' ? K 2 293 ambient 6.4 '50mM sodium chloride' ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1mM U2 snRNA-intron duplex; 10mM sodium phosphate' '90% H2O/10% D2O' 2 '1mM U2 snRNA-intron duplex; 10mM sodium phosphate' '100% 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 ? Varian UNITYPLUS 720 2 ? Varian UNITYPLUS 720 # _pdbx_nmr_refine.entry_id 1LPW _pdbx_nmr_refine.method 'torsion angle molecular dynamics followed by conjugate gradient minimization' _pdbx_nmr_refine.details ;A total of 191 distance restraints were used, not including the 40 hydrogen bond distances imposed. Including the 133 dihedral restraints applied in structure calculations, 353 total restraints were applied. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1LPW _pdbx_nmr_details.text ;This structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times, so that the buildup of certain NOEs could be observed to resolve some spectral overlap. ; # _pdbx_nmr_ensemble.entry_id 1LPW _pdbx_nmr_ensemble.conformers_calculated_total_number 800 _pdbx_nmr_ensemble.conformers_submitted_total_number 9 _pdbx_nmr_ensemble.conformer_selection_criteria 'lowest energy structures that did not violate data from fluorescence experiments' _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 1LPW _pdbx_nmr_representative.conformer_id 2 _pdbx_nmr_representative.selection_criteria 'lowest energy structure that agreed best with experimental data' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal VNMR 5.3 collection 'Varian, Inc.' 1 Sparky 3.69 'data analysis' 'T.D. Goddard and D.G. Kneller' 2 VNMR 3.851 'structure solution' 'Axel Brunger' 3 X-PLOR 3.851 refinement Brunger 4 # _exptl.entry_id 1LPW _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.crystal_id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_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 ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1LPW _struct.title 'Solution structure of the yeast spliceosomal U2 snRNA-intron branch site helix featuring a conserved pseudouridine' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1LPW _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'U2 snRNA, branch site, pseudouridine, RNA' # 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 ? # _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 covale1 covale both ? A G 4 "O3'" ? ? ? 1_555 A PSU 5 P ? ? A G 4 A PSU 5 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale2 covale both ? A PSU 5 "O3'" ? ? ? 1_555 A A 6 P ? ? A PSU 5 A A 6 1_555 ? ? ? ? ? ? ? 1.610 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 1 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 1 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 1 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 2 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 2 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 2 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 B A 8 N1 ? ? A U 3 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 B A 8 N6 ? ? A U 3 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 4 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 4 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 4 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A PSU 5 N3 ? ? ? 1_555 B A 5 N1 ? ? A PSU 5 B A 5 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog13 hydrog ? ? A PSU 5 O2 ? ? ? 1_555 B A 5 N6 ? ? A PSU 5 B A 5 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog14 hydrog ? ? A A 6 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 6 B U 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 6 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 6 B U 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 6 N3 ? ? ? 1_555 B A 6 N6 ? ? A A 6 B A 6 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog17 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 7 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 7 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 7 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 2 N1 ? ? A U 8 B A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 8 O4 ? ? ? 1_555 B A 2 N6 ? ? A U 8 B A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 1 N3 ? ? A A 9 B U 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 1 O4 ? ? A A 9 B U 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1LPW _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 1LPW _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 G 2 2 2 G G A . n A 1 3 U 3 3 3 U U A . n A 1 4 G 4 4 4 G G A . n A 1 5 PSU 5 5 5 PSU PSU A . n A 1 6 A 6 6 6 A A A . n A 1 7 G 7 7 7 G G A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n B 2 1 U 1 1 1 U U B . n B 2 2 A 2 2 2 A A B . n B 2 3 C 3 3 3 C C B . n B 2 4 U 4 4 4 U U B . n B 2 5 A 5 5 5 A A B . n B 2 6 A 6 6 6 A A B . n B 2 7 C 7 7 7 C C B . n B 2 8 A 8 8 8 A A B . n B 2 9 C 9 9 9 C C B . n B 2 10 C 10 10 10 C C B . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id PSU _pdbx_struct_mod_residue.label_seq_id 5 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id PSU _pdbx_struct_mod_residue.auth_seq_id 5 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id U _pdbx_struct_mod_residue.details "PSEUDOURIDINE-5'-MONOPHOSPHATE" # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 2002-11-27 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _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 5 4 '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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_remark.id 999 _pdbx_database_remark.text ;SEQUENCE Position 35 in U2 snRNA sequences from S. cerevisiae is a pseudouridine. This corresponds to position 5 on strand A, which is a uridine in 1LMV, and a pseudouridine in 1LPW. ; # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 3 "HO2'" A A 6 ? ? H61 B A 6 ? ? 1.28 2 4 "HO2'" A A 6 ? ? H61 B A 6 ? ? 1.33 3 5 "HO2'" A A 6 ? ? H61 B A 6 ? ? 1.31 4 7 "HO2'" A A 6 ? ? H61 B A 6 ? ? 1.28 5 8 "HO2'" A A 6 ? ? H61 B A 6 ? ? 1.29 6 9 "HO2'" A A 6 ? ? H61 B A 6 ? ? 1.30 # 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 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 113.31 108.50 4.81 0.70 N 2 1 "O4'" A U 3 ? ? "C1'" A U 3 ? ? N1 A U 3 ? ? 113.48 108.50 4.98 0.70 N 3 1 "O4'" A U 8 ? ? "C1'" A U 8 ? ? N1 A U 8 ? ? 112.73 108.50 4.23 0.70 N 4 1 "O4'" A A 9 ? ? "C1'" A A 9 ? ? N9 A A 9 ? ? 113.70 108.50 5.20 0.70 N 5 1 "O4'" B U 1 ? ? "C1'" B U 1 ? ? N1 B U 1 ? ? 114.13 108.50 5.63 0.70 N 6 1 "O4'" B C 3 ? ? "C1'" B C 3 ? ? N1 B C 3 ? ? 112.82 108.50 4.32 0.70 N 7 1 "O4'" B A 8 ? ? "C1'" B A 8 ? ? N9 B A 8 ? ? 114.34 108.50 5.84 0.70 N 8 2 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 113.43 108.50 4.93 0.70 N 9 2 "O4'" A U 3 ? ? "C1'" A U 3 ? ? N1 A U 3 ? ? 113.13 108.50 4.63 0.70 N 10 2 "O4'" A A 9 ? ? "C1'" A A 9 ? ? N9 A A 9 ? ? 113.59 108.50 5.09 0.70 N 11 2 "O4'" B U 1 ? ? "C1'" B U 1 ? ? N1 B U 1 ? ? 113.48 108.50 4.98 0.70 N 12 2 "O4'" B A 2 ? ? "C1'" B A 2 ? ? N9 B A 2 ? ? 112.91 108.50 4.41 0.70 N 13 2 "O4'" B C 3 ? ? "C1'" B C 3 ? ? N1 B C 3 ? ? 113.81 108.50 5.31 0.70 N 14 2 "O4'" B A 8 ? ? "C1'" B A 8 ? ? N9 B A 8 ? ? 115.00 108.50 6.50 0.70 N 15 3 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 113.70 108.50 5.20 0.70 N 16 3 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 114.03 108.50 5.53 0.70 N 17 3 "O4'" A U 8 ? ? "C1'" A U 8 ? ? N1 A U 8 ? ? 112.77 108.50 4.27 0.70 N 18 3 "O4'" B U 1 ? ? "C1'" B U 1 ? ? N1 B U 1 ? ? 114.35 108.50 5.85 0.70 N 19 3 "O4'" B A 2 ? ? "C1'" B A 2 ? ? N9 B A 2 ? ? 113.73 108.50 5.23 0.70 N 20 3 "O4'" B C 3 ? ? "C1'" B C 3 ? ? N1 B C 3 ? ? 113.85 108.50 5.35 0.70 N 21 3 "C4'" B A 6 ? ? "C3'" B A 6 ? ? "C2'" B A 6 ? ? 96.19 102.60 -6.41 1.00 N 22 3 "O4'" B A 8 ? ? "C1'" B A 8 ? ? N9 B A 8 ? ? 115.36 108.50 6.86 0.70 N 23 3 "O4'" B C 9 ? ? "C1'" B C 9 ? ? N1 B C 9 ? ? 112.87 108.50 4.37 0.70 N 24 4 "O4'" B U 1 ? ? "C1'" B U 1 ? ? N1 B U 1 ? ? 113.28 108.50 4.78 0.70 N 25 4 "O4'" B A 2 ? ? "C1'" B A 2 ? ? N9 B A 2 ? ? 113.48 108.50 4.98 0.70 N 26 4 "O4'" B C 3 ? ? "C1'" B C 3 ? ? N1 B C 3 ? ? 113.65 108.50 5.15 0.70 N 27 4 "O4'" B A 6 ? ? "C1'" B A 6 ? ? N9 B A 6 ? ? 113.58 108.50 5.08 0.70 N 28 4 "O4'" B A 8 ? ? "C1'" B A 8 ? ? N9 B A 8 ? ? 115.57 108.50 7.07 0.70 N 29 5 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 113.89 108.50 5.39 0.70 N 30 5 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 114.50 108.50 6.00 0.70 N 31 5 "O4'" B U 1 ? ? "C1'" B U 1 ? ? N1 B U 1 ? ? 114.46 108.50 5.96 0.70 N 32 5 "O4'" B A 2 ? ? "C1'" B A 2 ? ? N9 B A 2 ? ? 113.86 108.50 5.36 0.70 N 33 5 "O4'" B C 3 ? ? "C1'" B C 3 ? ? N1 B C 3 ? ? 113.39 108.50 4.89 0.70 N 34 5 "C3'" B A 5 ? ? "C2'" B A 5 ? ? "C1'" B A 5 ? ? 96.42 101.30 -4.88 0.70 N 35 5 "O4'" B A 5 ? ? "C1'" B A 5 ? ? N9 B A 5 ? ? 113.53 108.50 5.03 0.70 N 36 5 "O4'" B A 8 ? ? "C1'" B A 8 ? ? N9 B A 8 ? ? 114.34 108.50 5.84 0.70 N 37 6 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 113.75 108.50 5.25 0.70 N 38 6 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 114.20 108.50 5.70 0.70 N 39 6 "O4'" A U 8 ? ? "C1'" A U 8 ? ? N1 A U 8 ? ? 112.79 108.50 4.29 0.70 N 40 6 "O4'" B U 1 ? ? "C1'" B U 1 ? ? N1 B U 1 ? ? 113.33 108.50 4.83 0.70 N 41 6 "O4'" B A 2 ? ? "C1'" B A 2 ? ? N9 B A 2 ? ? 113.04 108.50 4.54 0.70 N 42 6 "O4'" B C 3 ? ? "C1'" B C 3 ? ? N1 B C 3 ? ? 114.00 108.50 5.50 0.70 N 43 6 "O4'" B A 8 ? ? "C1'" B A 8 ? ? N9 B A 8 ? ? 114.63 108.50 6.13 0.70 N 44 6 "O4'" B C 9 ? ? "C1'" B C 9 ? ? N1 B C 9 ? ? 112.98 108.50 4.48 0.70 N 45 7 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 113.57 108.50 5.07 0.70 N 46 7 "O4'" B U 1 ? ? "C1'" B U 1 ? ? N1 B U 1 ? ? 114.22 108.50 5.72 0.70 N 47 7 "O4'" B A 2 ? ? "C1'" B A 2 ? ? N9 B A 2 ? ? 113.40 108.50 4.90 0.70 N 48 7 "O4'" B C 3 ? ? "C1'" B C 3 ? ? N1 B C 3 ? ? 113.77 108.50 5.27 0.70 N 49 7 "C3'" B A 5 ? ? "O3'" B A 5 ? ? P B A 6 ? ? 128.40 119.70 8.70 1.20 Y 50 7 "C4'" B A 6 ? ? "C3'" B A 6 ? ? "C2'" B A 6 ? ? 96.48 102.60 -6.12 1.00 N 51 7 "O4'" B A 8 ? ? "C1'" B A 8 ? ? N9 B A 8 ? ? 115.33 108.50 6.83 0.70 N 52 8 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 113.67 108.50 5.17 0.70 N 53 8 "O4'" A U 8 ? ? "C1'" A U 8 ? ? N1 A U 8 ? ? 112.92 108.50 4.42 0.70 N 54 8 "O4'" B U 1 ? ? "C1'" B U 1 ? ? N1 B U 1 ? ? 114.58 108.50 6.08 0.70 N 55 8 "O4'" B A 2 ? ? "C1'" B A 2 ? ? N9 B A 2 ? ? 114.16 108.50 5.66 0.70 N 56 8 "O4'" B C 3 ? ? "C1'" B C 3 ? ? N1 B C 3 ? ? 113.47 108.50 4.97 0.70 N 57 8 "C3'" B A 5 ? ? "C2'" B A 5 ? ? "C1'" B A 5 ? ? 95.68 101.30 -5.62 0.70 N 58 8 "O4'" B A 5 ? ? "C1'" B A 5 ? ? N9 B A 5 ? ? 113.18 108.50 4.68 0.70 N 59 8 "O4'" B A 8 ? ? "C1'" B A 8 ? ? N9 B A 8 ? ? 115.91 108.50 7.41 0.70 N 60 9 "O4'" A A 9 ? ? "C1'" A A 9 ? ? N9 A A 9 ? ? 113.85 108.50 5.35 0.70 N 61 9 "O4'" B U 1 ? ? "C1'" B U 1 ? ? N1 B U 1 ? ? 114.90 108.50 6.40 0.70 N 62 9 "O4'" B A 2 ? ? "C1'" B A 2 ? ? N9 B A 2 ? ? 114.44 108.50 5.94 0.70 N 63 9 "O4'" B C 3 ? ? "C1'" B C 3 ? ? N1 B C 3 ? ? 113.50 108.50 5.00 0.70 N 64 9 "C3'" B A 6 ? ? "O3'" B A 6 ? ? P B C 7 ? ? 128.18 119.70 8.48 1.20 Y 65 9 "O4'" B A 8 ? ? "C1'" B A 8 ? ? N9 B A 8 ? ? 115.18 108.50 6.68 0.70 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1LPW 'double helix' 1LPW 'a-form double helix' 1LPW 'bulge loop' 1LPW '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 B C 10 1_555 -0.746 -0.181 -0.237 -9.429 -8.344 0.105 1 A_G1:C10_B A 1 ? B 10 ? 19 1 1 A G 2 1_555 B C 9 1_555 -0.599 -0.175 -0.562 -20.026 -22.640 2.525 2 A_G2:C9_B A 2 ? B 9 ? 19 1 1 A U 3 1_555 B A 8 1_555 -0.696 0.084 -0.026 -11.755 -19.784 -5.916 3 A_U3:A8_B A 3 ? B 8 ? 20 1 1 A G 4 1_555 B C 7 1_555 -0.371 -0.066 -0.052 -22.107 -37.185 -1.670 4 A_G4:C7_B A 4 ? B 7 ? 19 1 1 A PSU 5 1_555 B A 5 1_555 -0.445 -0.033 0.017 18.676 -5.693 -6.232 5 A_PSU5:A5_B A 5 ? B 5 ? 21 1 1 A A 6 1_555 B U 4 1_555 0.136 0.042 -0.410 -5.893 2.782 -9.052 6 A_A6:U4_B A 6 ? B 4 ? 20 1 1 A G 7 1_555 B C 3 1_555 -0.599 -0.227 -0.210 -0.401 -9.229 -3.096 7 A_G7:C3_B A 7 ? B 3 ? 19 1 1 A U 8 1_555 B A 2 1_555 -0.354 0.013 -0.177 -0.627 -13.874 2.030 8 A_U8:A2_B A 8 ? B 2 ? 20 1 1 A A 9 1_555 B U 1 1_555 0.251 -0.023 0.290 5.537 2.219 3.608 9 A_A9:U1_B A 9 ? B 1 ? 20 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 B C 10 1_555 A G 2 1_555 B C 9 1_555 0.427 -1.563 3.393 4.209 12.757 32.150 -4.485 -0.098 2.636 21.881 -7.219 34.775 1 AA_G1G2:C9C10_BB A 1 ? B 10 ? A 2 ? B 9 ? 1 A G 2 1_555 B C 9 1_555 A U 3 1_555 B A 8 1_555 -0.439 -1.123 2.857 -2.924 -0.961 35.984 -1.692 0.344 2.911 -1.553 4.722 36.111 2 AA_G2U3:A8C9_BB A 2 ? B 9 ? A 3 ? B 8 ? 1 A U 3 1_555 B A 8 1_555 A G 4 1_555 B C 7 1_555 -0.538 -0.089 3.762 0.295 6.939 33.691 -1.395 0.962 3.667 11.817 -0.502 34.379 3 AA_U3G4:C7A8_BB A 3 ? B 8 ? A 4 ? B 7 ? 1 A G 4 1_555 B C 7 1_555 A PSU 5 1_555 B A 5 1_555 1.987 0.316 3.330 -23.246 -0.981 47.236 0.415 -3.623 2.187 -1.147 27.174 52.360 4 AA_G4PSU5:A5C7_BB A 4 ? B 7 ? A 5 ? B 5 ? 1 A PSU 5 1_555 B A 5 1_555 A A 6 1_555 B U 4 1_555 0.441 -1.356 5.031 6.198 -35.596 38.351 2.608 0.221 4.694 -44.137 -7.685 52.219 5 AA_PSU5A6:U4A5_BB A 5 ? B 5 ? A 6 ? B 4 ? 1 A A 6 1_555 B U 4 1_555 A G 7 1_555 B C 3 1_555 0.513 -1.658 2.970 -2.271 7.788 30.794 -4.223 -1.285 2.445 14.356 4.185 31.819 6 AA_A6G7:C3U4_BB A 6 ? B 4 ? A 7 ? B 3 ? 1 A G 7 1_555 B C 3 1_555 A U 8 1_555 B A 2 1_555 0.218 -1.898 2.999 -0.339 5.678 32.643 -4.161 -0.433 2.639 10.007 0.598 33.122 7 AA_G7U8:A2C3_BB A 7 ? B 3 ? A 8 ? B 2 ? 1 A U 8 1_555 B A 2 1_555 A A 9 1_555 B U 1 1_555 -0.006 -1.192 2.854 -6.179 10.335 32.837 -3.271 -0.758 2.347 17.562 10.501 34.918 8 AA_U8A9:U1A2_BB A 8 ? B 2 ? A 9 ? B 1 ? #