data_1R2P # _entry.id 1R2P # _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 1R2P pdb_00001r2p 10.2210/pdb1r2p/pdb RCSB RCSB020362 ? ? WWPDB D_1000020362 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type BMRB 5962 'NMR data: chemical shifts of domain 5' unspecified PDB 1kxk 'crystal structure of a domain5 / domain 6 construct from ai5gamma' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1R2P _pdbx_database_status.recvd_initial_deposition_date 2003-09-29 _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 'Sigel, R.K.O.' 1 'Sashital, D.G.' 2 'Abramovitz, D.L.' 3 'Palmer III, A.G.' 4 'Butcher, S.E.' 5 'Pyle, A.M.' 6 # _citation.id primary _citation.title 'Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 11 _citation.page_first 187 _citation.page_last 192 _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 14745440 _citation.pdbx_database_id_DOI 10.1038/nsmb717 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sigel, R.K.' 1 ? primary 'Sashital, D.G.' 2 ? primary 'Abramovitz, D.L.' 3 ? primary 'Palmer, A.G.' 4 ? primary 'Butcher, S.E.' 5 ? primary 'Pyle, A.M.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 34-MER _entity.formula_weight 10970.567 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'DOMAIN 5 OF THE AI5(GAMMA) GROUP II INTRON' _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 GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC _entity_poly.pdbx_seq_one_letter_code_can GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC _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 A 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 C n 1 26 G n 1 27 U 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 ;SEQUENCE OCCURS NATURALLY IN Saccharomyces CEREVISIAE (Baker's yeast) AND WAS SYNTHESIZED IN VITRO USING 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 1R2P _struct_ref.pdbx_db_accession 1R2P _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 1R2P _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 1R2P _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.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 2 3 '2D NOESY' 3 2 4 '2D NOESY' 4 4 2 3D_13C-separated_NOESY 5 4 2 '2D 1H-13C HSQC' 6 2 2 '2D 1H-1H TOCSY' 7 4 2 '3D 1H-13C-1H HCCH TOCSY' 8 4 2 '3D 1H-13C-1H HCCH COSY' 9 3 2 '2D 2JHN HNN-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 ? 6.5 '100mM KCl' ? K 2 298 ? 6.5 '100mM KCl' ? K 3 308 ? 6.5 '100mM KCl' ? K 4 291 ? 6.5 '100mM KCl' ? K 5 303 ? 6.5 '100mM KCl' ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '0.5 - 0.7 mM D5 RNA; 0 - 200mM KCl, 0 - 20 mM MgCl2, 0.01 mM EDTA, 90% H2O, 10% D2O' '90% H2O/10% D2O' 2 '0.5 - 0.7 mM D5 RNA; 0 - 200mM KCl, 0 - 20 mM MgCl2, 0.01 mM EDTA, 99.999% D2O' '99.999% D2O' 3 '0.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA, 90% H2O, 10% D2O' '90% H2O/10% D2O' 4 '0.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA, 99.999% D2O' '99.999% D2O' 5 '0.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA, 17 mg/mL Pf1 FILAMENTOUS 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 AVANCE 600 2 ? Bruker DMX 500 3 ? Bruker DMX 750 # _pdbx_nmr_refine.entry_id 1R2P _pdbx_nmr_refine.method 'TORSION ANGLE MOLECULAR DYNAMICS CARTESIAN SPACE SIMULATED ANNEALING AND MOLECULAR DYNAMICS RESIDUAL DIPOLAR COUPLINGS' _pdbx_nmr_refine.details ;STRUCTURES BASED ON 678 NOE-DERIVED DISTANCE RESTRAINTS, 261 DIHEDRAL RESTRAINTS, 72 HYDROGEN BOND RESTRAINTS, AND 24 RESIDUAL DIPOLAR COUPLING RESTRAINTS ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1R2P _pdbx_nmr_details.text 'RESIDUAL DIPOLAR COUPLINGS WERE MEASURED USING 1H-13C HSQC COUPLED IN EITHER THE PROTON OR THE CARBON DIMENSION' # _pdbx_nmr_ensemble.entry_id 1R2P _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 1R2P _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 CNS 1.1 'structure solution' 'Brunger et. al.' 1 DYANA ? 'data analysis' 'Guntert, Mumenthaler, Wuthrich' 2 Sparky 3 'data analysis' 'Goddard and Kneller' 3 XwinNMR 2.6 processing Bruker 4 CNS 1.1 refinement 'Brunger et. al.' 5 # _exptl.entry_id 1R2P _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.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 1R2P _struct.title 'Solution structure of domain 5 from the ai5(gamma) group II intron' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1R2P _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA HAIRPIN, TETRALOOP, BULGE, METAL ION, MAGNESIUM, 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 N3 ? ? ? 1_555 A G 30 N1 ? ? A C 5 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 30 O6 ? ? A C 5 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 30 N2 ? ? A C 5 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 6 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 6 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 6 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 28 N1 ? ? A U 7 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 7 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 27 N3 ? ? A A 8 A U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 27 O4 ? ? A A 8 A U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 10 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 10 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 10 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 11 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 11 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 11 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 12 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 12 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 12 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 13 N1 ? ? ? 1_555 A U 20 N3 ? ? A A 13 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 13 N6 ? ? ? 1_555 A U 20 O4 ? ? A A 13 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 14 N3 ? ? ? 1_555 A G 19 O6 ? ? A U 14 A G 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog33 hydrog ? ? A U 14 O2 ? ? ? 1_555 A G 19 N1 ? ? A U 14 A G 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog34 hydrog ? ? A G 15 N2 ? ? ? 1_555 A A 18 N7 ? ? A G 15 A A 18 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog35 hydrog ? ? A G 15 N3 ? ? ? 1_555 A A 18 N6 ? ? A G 15 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 1R2P _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 1R2P _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 A 8 8 8 A A 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 C 25 25 25 C C A . n A 1 26 G 26 26 26 G G A . n A 1 27 U 27 27 27 U U 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 2004-02-03 2 'Structure model' 1 1 2008-04-29 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_nmr_spectrometer 4 4 'Structure model' pdbx_struct_assembly 5 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' 4 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 2 "HO2'" A G 26 ? ? "O5'" A U 27 ? ? 1.54 2 2 H3 A U 7 ? ? N1 A A 28 ? ? 1.57 3 3 "HO2'" A G 26 ? ? "O5'" A U 27 ? ? 1.43 4 4 "O2'" A C 25 ? ? H5 A U 27 ? ? 1.58 5 6 "HO2'" A G 26 ? ? "O5'" A U 27 ? ? 1.44 6 7 "HO2'" A G 26 ? ? "O5'" A U 27 ? ? 1.47 7 9 "HO2'" A G 26 ? ? "O5'" A U 27 ? ? 1.50 8 10 "HO2'" A G 26 ? ? "O5'" A U 27 ? ? 1.40 # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 8 _pdbx_validate_planes.auth_comp_id G _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 15 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.066 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1R2P 'double helix' 1R2P 'a-form double helix' 1R2P tetraloop 1R2P 'mismatched base pair' 1R2P '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 -0.203 -0.205 -0.148 -1.457 -1.721 -0.758 1 A_G1:C34_A A 1 ? A 34 ? 19 1 1 A A 2 1_555 A U 33 1_555 0.173 -0.385 -0.640 -5.284 17.697 -7.183 2 A_A2:U33_A A 2 ? A 33 ? 20 1 1 A G 3 1_555 A U 32 1_555 -1.501 -0.535 -0.904 -1.885 17.510 -14.404 3 A_G3:U32_A A 3 ? A 32 ? 28 ? 1 A C 4 1_555 A G 31 1_555 0.254 -0.257 -0.311 0.992 -6.585 -0.990 4 A_C4:G31_A A 4 ? A 31 ? 19 1 1 A C 5 1_555 A G 30 1_555 0.019 -0.777 -1.404 5.933 9.445 -9.628 5 A_C5:G30_A A 5 ? A 30 ? 19 1 1 A G 6 1_555 A C 29 1_555 -0.170 -0.519 -0.953 1.327 10.103 -4.248 6 A_G6:C29_A A 6 ? A 29 ? 19 1 1 A U 7 1_555 A A 28 1_555 -0.062 -0.581 -1.181 11.045 -1.528 6.721 7 A_U7:A28_A A 7 ? A 28 ? 20 1 1 A A 8 1_555 A U 27 1_555 1.182 -0.706 -1.807 -27.141 24.141 -55.066 8 A_A8:U27_A A 8 ? A 27 ? 20 1 1 A G 10 1_555 A C 23 1_555 -0.177 -0.516 -0.962 -23.089 32.036 -8.679 9 A_G10:C23_A A 10 ? A 23 ? 19 1 1 A C 11 1_555 A G 22 1_555 0.179 -0.229 -0.107 -17.492 18.399 -2.477 10 A_C11:G22_A A 11 ? A 22 ? 19 1 1 A G 12 1_555 A C 21 1_555 0.474 -0.057 0.368 7.717 -7.494 2.417 11 A_G12:C21_A A 12 ? A 21 ? 19 1 1 A A 13 1_555 A U 20 1_555 -0.677 -0.285 0.369 -1.024 -7.907 -12.455 12 A_A13:U20_A A 13 ? A 20 ? 20 1 1 A U 14 1_555 A G 19 1_555 2.643 -0.401 -0.184 13.254 3.322 -4.932 13 A_U14:G19_A A 14 ? A 19 ? 28 ? 1 A G 15 1_555 A A 18 1_555 6.213 -3.742 1.540 -6.792 -7.604 -9.088 14 A_G15:A18_A A 15 ? 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 34 1_555 A A 2 1_555 A U 33 1_555 -0.442 -1.520 3.716 -0.843 13.745 33.627 -4.472 0.586 2.904 22.617 1.387 36.262 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 -0.600 -1.159 4.332 1.113 -6.109 25.522 -0.308 1.729 4.454 -13.574 -2.473 26.254 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 0.652 -1.279 3.745 -0.936 -2.619 33.143 -1.729 -1.321 3.812 -4.581 1.638 33.256 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 -0.696 -0.672 3.931 1.733 -4.121 32.722 -0.338 1.579 3.943 -7.272 -3.058 33.018 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 0.368 -1.018 4.676 -3.801 -16.114 31.183 1.929 -1.461 4.571 -27.668 6.526 35.209 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 1.044 -1.121 3.476 1.685 -0.463 35.109 -1.782 -1.459 3.535 -0.768 -2.791 35.151 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 A 8 1_555 A U 27 1_555 -3.498 -2.305 5.619 7.268 -10.484 37.426 -1.288 6.654 5.309 -15.787 -10.945 39.467 7 AA_U7A8:U27A28_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 0.395 -1.710 3.900 -1.504 15.327 25.610 -6.688 -1.099 2.476 31.236 3.065 29.818 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 -0.124 -1.002 2.885 1.584 3.644 24.976 -3.199 0.678 2.700 8.358 -3.633 25.285 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 -0.578 -1.652 4.011 -3.295 5.835 27.124 -5.069 0.268 3.626 12.206 6.893 27.925 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 0.249 -1.447 2.872 1.325 -0.333 41.973 -1.988 -0.227 2.889 -0.464 -1.850 41.994 11 AA_A13U14:G19U20_AA A 13 ? A 20 ? A 14 ? A 19 ? 1 A U 14 1_555 A G 19 1_555 A G 15 1_555 A A 18 1_555 0.198 -0.866 3.959 12.053 32.580 54.228 -2.503 0.435 3.046 32.321 -11.957 63.682 12 AA_U14G15:A18G19_AA A 14 ? A 19 ? A 15 ? A 18 ? #