data_2M24 # _entry.id 2M24 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2M24 RCSB RCSB103112 BMRB 18894 WWPDB D_1000103112 # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2014-04-16 _pdbx_database_PDB_obs_spr.pdb_id 2M24 _pdbx_database_PDB_obs_spr.replace_pdb_id 2K63 _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 2K63 PDB . unspecified 2K64 PDB . unspecified 2K65 PDB . unspecified 2K66 PDB . unspecified 2M1V PDB . unspecified 2M23 PDB . unspecified 18894 BMRB . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2M24 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-12-12 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kruschel, D.' 1 'Skilandat, M.' 2 'Sigel, R.K.O.' 3 # _citation.id primary _citation.title ;NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition. ; _citation.journal_abbrev Rna _citation.journal_volume 20 _citation.page_first 295 _citation.page_last 307 _citation.year 2014 _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 24448450 _citation.pdbx_database_id_DOI 10.1261/rna.041137.113 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Kruschel, D.' 1 primary 'Skilandat, M.' 2 primary 'Sigel, R.K.' 3 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'RNA (29-MER)' _entity.formula_weight 9301.547 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation 'A15C, A17C' _entity.pdbx_fragment "d3'EBS1" _entity.details 'the sequence was produced by in-vitro transcription from a synthetic dsDNA template using T7 RNA-polymerase' # _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 GGAGUAUGUAUUGGCACUGAGCAUACUCC _entity_poly.pdbx_seq_one_letter_code_can GGAGUAUGUAUUGGCACUGAGCAUACUCC _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 G n 1 3 A n 1 4 G n 1 5 U n 1 6 A n 1 7 U n 1 8 G n 1 9 U n 1 10 A n 1 11 U n 1 12 U n 1 13 G n 1 14 G n 1 15 C n 1 16 A n 1 17 C n 1 18 U n 1 19 G n 1 20 A n 1 21 G n 1 22 C n 1 23 A n 1 24 U n 1 25 A n 1 26 C n 1 27 U n 1 28 C n 1 29 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 'Saccharomyces cerevisiae' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 4932 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2M24 _struct_ref.pdbx_db_accession 2M24 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GGAGUAUGUAUUGGCACUGAGCAUACUCC _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2M24 _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 29 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2M24 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 29 _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 29 # 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.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H NOESY' 1 2 1 '2D 1H-1H TOCSY' 1 3 1 '2D 1H-1H NOESY' 2 4 2 '2D 1H-1H NOESY' 2 5 2 '2D 1H-1H NOESY' 3 6 3 '2D 1H-13C HSQC aliphatic' 3 7 3 '2D 1H-13C HSQC aromatic' 2 8 3 '2D 1H-15N HSQC' 3 9 4 '2D 1H-13C HSQC aliphatic' 3 10 4 '2D 1H-13C HSQC aromatic' 2 11 3 '2D JNN HNN COSY' 4 12 1 '2D 1H-1H NOESY' 3 13 1 '2D 1H-1H NOESY' 1 14 1 '1D 31P' 1 15 6 '2D 1H-1H NOESY' 1 16 5 '2D 1H-13C HSQC' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 10 6.8 ambient ? 293 K 2 10 6.8 ambient ? 278 K 3 10 6.8 ambient ? 298 K 4 10 6.8 ambient ? 283 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O' 1 '100% D2O' '0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O' 2 '90% H2O/10% D2O' '0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O' 3 '90% H2O/10% D2O' '0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O' 4 '90% H2O/10% D2O' '0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O' 5 '100% D2O' ;0.6 mM [3',4',5',5'',5, 100% 2H] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O ; 6 '100% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 700 Bruker Avance 1 'Bruker Avance' 600 Bruker Avance 2 'Bruker Avance' 500 Bruker Avance 3 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2M24 _pdbx_nmr_refine.method 'molecular dynamics, torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2M24 _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation 0.2 _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation 5 _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation 0.2 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2M24 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Bruker Biospin' collection TOPSPIN '1.3, 2.0, 2.1' 1 'Bruker Biospin' processing TOPSPIN '1.3, 2.0, 2.1' 2 Goddard 'chemical shift assignment' SPARKY 3.1 3 Goddard 'data analysis' SPARKY 3.1 4 Goddard 'peak picking' SPARKY 3.1 5 'Guntert, Braun and Wuthrich' 'data analysis' DYANA 1.5 6 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNSSOLVE 1.2 7 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNSSOLVE 1.2 8 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' X-PLOR_NIH 2.24 9 'Schwieters, Kuszewski, Tjandra and Clore' refinement X-PLOR_NIH 2.24 10 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2M24 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2M24 _struct.title ;NMR solution structure of the d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma ; _struct.pdbx_descriptor 29-MER _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2M24 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'group II intron, ribozyme, splicing, EBS1, hairpin, 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.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 hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 1 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 1 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 1 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 28 N3 ? ? A G 2 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 28 O2 ? ? A G 2 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 28 N4 ? ? A G 2 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 27 N3 ? ? A A 3 A U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 27 O4 ? ? A A 3 A U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 4 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 4 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 4 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A G 4 N2 ? ? ? 1_555 A U 27 O2 ? ? A G 4 A U 27 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? hydrog13 hydrog ? ? A U 5 N3 ? ? ? 1_555 A A 25 N1 ? ? A U 5 A A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A U 5 O4 ? ? ? 1_555 A A 25 N6 ? ? A U 5 A A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 24 N3 ? ? A A 6 A U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 24 O4 ? ? A A 6 A U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 23 N1 ? ? A U 7 A A 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 23 N6 ? ? A U 7 A A 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 8 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 8 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 8 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A U 9 N3 ? ? ? 1_555 A G 21 O6 ? ? A U 9 A G 21 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? hydrog23 hydrog ? ? A U 9 O2 ? ? ? 1_555 A G 21 N1 ? ? A U 9 A G 21 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? hydrog24 hydrog ? ? A A 10 N1 ? ? ? 1_555 A A 20 N6 ? ? A A 10 A A 20 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2M24 _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 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 U 5 5 5 U U A . n A 1 6 A 6 6 6 A A 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 A 10 10 10 A A A . n A 1 11 U 11 11 11 U U A . n A 1 12 U 12 12 12 U U A . n A 1 13 G 13 13 13 G G A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 A 16 16 16 A A A . n A 1 17 C 17 17 17 C C A . n A 1 18 U 18 18 18 U U A . n A 1 19 G 19 19 19 G G A . n A 1 20 A 20 20 20 A A A . n A 1 21 G 21 21 21 G G A . n A 1 22 C 22 22 22 C C A . n A 1 23 A 23 23 23 A A A . n A 1 24 U 24 24 24 U U A . n A 1 25 A 25 25 25 A A A . n A 1 26 C 26 26 26 C C A . n A 1 27 U 27 27 27 U U A . n A 1 28 C 28 28 28 C C A . n A 1 29 C 29 29 29 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 2013-12-18 2 'Structure model' 1 1 2014-02-26 3 'Structure model' 1 2 2014-03-12 # _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 ? # 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' 'Database references' 2 3 'Structure model' 'Database references' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id 'RNA (29-MER)-1' ? 0.4-1.2 mM ? 1 'potassium chloride-2' 10 ? mM ? 1 EDTA-3 10 ? uM ? 1 'RNA (29-MER)-4' ? 0.4-1.2 mM ? 2 'potassium chloride-5' 10 ? mM ? 2 EDTA-6 10 ? uM ? 2 'RNA (29-MER)-7' 0.7 ? mM '[U-100% 13C; U-100% 15N]' 3 'potassium chloride-8' 10 ? mM ? 3 EDTA-9 10 ? uM ? 3 'RNA (29-MER)-10' 0.7 ? mM '[U-100% 13C; U-100% 15N]' 4 'potassium chloride-11' 10 ? mM ? 4 EDTA-12 10 ? uM ? 4 'Pf1 phage-13' 25.6 ? mg/mL ? 4 'RNA (29-MER)-14' 0.7 ? mM '[U-100% 13C; U-100% 15N]' 5 'potassium chloride-15' 10 ? mM ? 5 EDTA-16 10 ? uM ? 5 'RNA (29-MER)-17' 0.6 ? mM ;[3',4',5',5'',5, 100% 2H] ; 6 'potassium chloride-18' 10 ? mM ? 6 EDTA-19 10 ? uM ? 6 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2M24 _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count 45 _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count 28 _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count 29 _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_other-angle_constraints_total_count 27 _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count 48 _pdbx_nmr_constraints.NOE_constraints_total 511 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 176 _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count 250 _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # 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 H3 A U 7 ? ? N1 A A 23 ? ? 1.56 2 2 "O2'" A A 10 ? ? H6 A U 11 ? ? 1.45 3 2 "O2'" A U 11 ? ? H6 A U 12 ? ? 1.51 4 4 "O2'" A A 10 ? ? H6 A U 11 ? ? 1.45 5 5 "H4'" A U 18 ? ? "O4'" A G 19 ? ? 1.51 6 5 H3 A U 7 ? ? N1 A A 23 ? ? 1.58 7 6 "O2'" A U 11 ? ? H6 A U 12 ? ? 1.44 8 6 "HO2'" A U 11 ? ? "O5'" A U 12 ? ? 1.51 9 7 "O2'" A U 11 ? ? H6 A U 12 ? ? 1.51 10 8 H3 A U 7 ? ? N1 A A 23 ? ? 1.57 11 8 "O2'" A A 10 ? ? H6 A U 11 ? ? 1.59 12 9 O4 A U 11 ? ? H61 A A 20 ? ? 1.35 13 9 H3 A U 7 ? ? N1 A A 23 ? ? 1.57 14 10 H1 A G 13 ? ? "O2'" A G 19 ? ? 1.41 15 10 "O2'" A A 10 ? ? H6 A U 11 ? ? 1.45 16 10 H3 A U 11 ? ? N1 A A 20 ? ? 1.59 17 11 "O2'" A U 11 ? ? H6 A U 12 ? ? 1.47 18 11 "O2'" A G 19 ? ? "H5'" A A 20 ? ? 1.49 19 12 "HO2'" A C 15 ? ? "O5'" A A 16 ? ? 1.39 20 12 "O2'" A U 11 ? ? H6 A U 12 ? ? 1.54 21 12 H3 A U 7 ? ? N1 A A 23 ? ? 1.56 22 12 "HO2'" A U 11 ? ? "O5'" A U 12 ? ? 1.59 23 13 "O2'" A A 10 ? ? H6 A U 11 ? ? 1.45 24 13 "O2'" A U 11 ? ? H6 A U 12 ? ? 1.50 25 13 H3 A U 7 ? ? N1 A A 23 ? ? 1.56 26 14 "HO2'" A A 10 ? ? "O5'" A U 11 ? ? 1.56 27 14 "O3'" A U 18 ? ? H8 A G 19 ? ? 1.57 28 15 "O2'" A A 10 ? ? H6 A U 11 ? ? 1.44 29 15 "O2'" A U 11 ? ? H6 A U 12 ? ? 1.54 30 16 O4 A U 11 ? ? H61 A A 20 ? ? 1.46 31 16 H3 A U 11 ? ? N1 A A 20 ? ? 1.50 32 16 "O2'" A A 10 ? ? H6 A U 11 ? ? 1.59 33 17 "O3'" A U 18 ? ? H8 A G 19 ? ? 1.52 34 18 "O2'" A A 10 ? ? H6 A U 11 ? ? 1.45 35 19 "HO2'" A A 10 ? ? "O5'" A U 11 ? ? 1.40 36 19 "O2'" A A 10 ? ? H6 A U 11 ? ? 1.49 37 19 H3 A U 7 ? ? N1 A A 23 ? ? 1.56 38 19 "H4'" A C 15 ? ? "O4'" A A 16 ? ? 1.57 39 20 "HO2'" A A 10 ? ? "O5'" A U 11 ? ? 1.41 40 20 "O2'" A U 11 ? ? H6 A U 12 ? ? 1.50 41 20 H3 A U 7 ? ? N1 A A 23 ? ? 1.55 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2M24 'double helix' 2M24 'a-form double helix' 2M24 'hairpin loop' 2M24 '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 29 1_555 -0.746 -0.380 0.131 -4.707 -3.708 -2.165 1 A_G1:C29_A A 1 ? A 29 ? 19 1 1 A G 2 1_555 A C 28 1_555 -0.773 -0.328 0.108 1.735 -3.898 0.549 2 A_G2:C28_A A 2 ? A 28 ? 19 1 1 A A 3 1_555 A U 27 1_555 -0.834 -0.122 -0.218 -7.020 1.023 -4.030 3 A_A3:U27_A A 3 ? A 27 ? 20 1 1 A G 4 1_555 A C 26 1_555 0.530 -0.213 -0.288 -5.668 -10.373 0.185 4 A_G4:C26_A A 4 ? A 26 ? 19 1 1 A U 5 1_555 A A 25 1_555 0.519 -0.320 -0.217 0.345 -5.698 12.374 5 A_U5:A25_A A 5 ? A 25 ? 20 1 1 A A 6 1_555 A U 24 1_555 -0.544 -0.315 -0.298 -0.636 -14.543 15.510 6 A_A6:U24_A A 6 ? A 24 ? 20 1 1 A U 7 1_555 A A 23 1_555 0.116 -0.402 -0.483 1.034 -9.337 10.706 7 A_U7:A23_A A 7 ? A 23 ? 20 1 1 A G 8 1_555 A C 22 1_555 0.780 -0.189 -0.427 0.601 -1.392 -6.640 8 A_G8:C22_A A 8 ? A 22 ? 19 1 1 A U 9 1_555 A G 21 1_555 1.646 -0.160 -0.292 3.928 3.395 -8.674 9 A_U9:G21_A A 9 ? A 21 ? 28 1 1 A A 10 1_555 A A 20 1_555 1.841 -0.398 -2.450 7.845 -3.090 -52.005 10 A_A10:A20_A A 10 ? A 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 A C 29 1_555 A G 2 1_555 A C 28 1_555 -0.931 -0.709 3.363 -1.031 1.004 32.501 -1.446 1.477 3.368 1.792 1.842 32.532 1 AA_G1G2:C28C29_AA A 1 ? A 29 ? A 2 ? A 28 ? 1 A G 2 1_555 A C 28 1_555 A A 3 1_555 A U 27 1_555 -0.162 -0.934 4.595 2.058 -11.576 36.100 0.712 0.632 4.651 -18.098 -3.217 37.906 2 AA_G2A3:U27C28_AA A 2 ? A 28 ? A 3 ? A 27 ? 1 A A 3 1_555 A U 27 1_555 A G 4 1_555 A C 26 1_555 0.070 -1.675 2.751 0.063 11.296 30.026 -4.567 -0.117 2.006 20.895 -0.117 32.035 3 AA_A3G4:C26U27_AA A 3 ? A 27 ? A 4 ? A 26 ? 1 A G 4 1_555 A C 26 1_555 A U 5 1_555 A A 25 1_555 -0.167 -1.158 2.868 -1.258 13.370 32.584 -3.538 0.124 2.240 22.667 2.132 35.173 4 AA_G4U5:A25C26_AA A 4 ? A 26 ? A 5 ? A 25 ? 1 A U 5 1_555 A A 25 1_555 A A 6 1_555 A U 24 1_555 -0.143 -0.852 2.986 1.763 21.627 30.393 -3.754 0.421 1.964 36.053 -2.939 37.195 5 AA_U5A6:U24A25_AA A 5 ? A 25 ? A 6 ? A 24 ? 1 A A 6 1_555 A U 24 1_555 A U 7 1_555 A A 23 1_555 -0.120 -0.977 3.516 -0.644 1.925 39.765 -1.672 0.097 3.468 2.828 0.946 39.814 6 AA_A6U7:A23U24_AA A 6 ? A 24 ? A 7 ? A 23 ? 1 A U 7 1_555 A A 23 1_555 A G 8 1_555 A C 22 1_555 -1.008 -1.688 2.992 2.686 11.742 33.627 -4.153 1.966 2.213 19.534 -4.469 35.661 7 AA_U7G8:C22A23_AA A 7 ? A 23 ? A 8 ? A 22 ? 1 A G 8 1_555 A C 22 1_555 A U 9 1_555 A G 21 1_555 -0.525 -1.488 3.287 3.175 14.908 31.633 -4.498 1.303 2.313 25.574 -5.446 35.029 8 AA_G8U9:G21C22_AA A 8 ? A 22 ? A 9 ? A 21 ? 1 A U 9 1_555 A G 21 1_555 A A 10 1_555 A A 20 1_555 -2.570 -0.640 3.929 10.475 -9.959 29.673 0.752 6.513 2.940 -18.153 -19.092 32.935 9 AA_U9A10:A20G21_AA A 9 ? A 21 ? A 10 ? A 20 ? #