data_2M57 # _entry.id 2M57 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 2M57 pdb_00002m57 10.2210/pdb2m57/pdb RCSB RCSB103223 ? ? BMRB 19039 ? ? WWPDB D_1000103223 ? ? # _pdbx_database_related.db_id 19039 _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2M57 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-02-15 _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 _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Pechlaner, M.' 1 'Donghi, D.' 2 'Zelenay, V.' 3 'Sigel, R.K.O.' 4 # _citation.id primary _citation.title 'Acid-base equilibria near neutral pH in the catalytic triad and the bulge of domain 5 of a bacterial group II intron' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pechlaner, M.' 1 ? primary 'Donghi, D.' 2 ? primary 'Zelenay, V.' 3 ? primary 'Sigel, R.K.O.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'RNA_(35-MER)' _entity.formula_weight 11268.708 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'group II intron Domain 5 (D5)' _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 GGAGCCGUAUGCGGUAGUUCCGCACGUACGGAUCU _entity_poly.pdbx_seq_one_letter_code_can GGAGCCGUAUGCGGUAGUUCCGCACGUACGGAUCU _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 C n 1 6 C n 1 7 G n 1 8 U n 1 9 A n 1 10 U n 1 11 G n 1 12 C n 1 13 G n 1 14 G n 1 15 U n 1 16 A n 1 17 G n 1 18 U n 1 19 U n 1 20 C 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 A n 1 33 U n 1 34 C n 1 35 U 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 'Azotobacter vinelandii' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 354 _pdbx_entity_src_syn.details ;the sequence occurs naturally as part of Intron 5 from A.vinelandii and was transcribed in vitro using T7 RNA polymerase from a dsDNA template ; # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2M57 _struct_ref.pdbx_db_accession 2M57 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2M57 _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 35 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2M57 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 35 _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 35 # 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 5 '2D 1H-1H NOESY' 2 3 2 '2D 1H-1H NOESY' 1 4 1 '2D 1H-1H TOCSY' 2 5 4 '2D 1H-15N HSQC' 1 6 3 '2D 1H-13C HSQC aromatic' 1 7 3 '2D 1H-13C HSQC aliphatic' 2 8 4 '2D JNN HNN COSY' 3 9 1 '2D 1H-1H NOESY' 4 10 1 '2D 1H-1H NOESY' 5 11 2 '2D 1H-1H NOESY' 6 12 2 '2D 1H-1H NOESY' 3 13 3 '2D 1H-13C HSQC aromatic' 4 14 3 '2D 1H-13C HSQC aromatic' 4 15 3 '2D 1H-13C HSQC aliphatic' 5 16 4 '2D 1H-15N HSQC' 6 17 4 '2D 1H-15N HSQC' 5 18 4 '2D JNN HNN COSY' 6 19 4 '2D JNN HNN COSY' # 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 60 ? ambient ? 300 K 2 60 7.8 ambient ? 275 K 5 60 5.2 ambient ? 275 K 6 60 6.7 ambient ? 275 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '0.5-1 mM RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 100% D2O' 1 '100% D2O' '0.5-1 mM RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O' 2 '90% H2O/10% D2O' '0.5-1 mM [100% 13C; 100% 15N] RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 100% D2O' 3 '100% D2O' '0.5-1 mM [100% 13C; 100% 15N] RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O' 4 '90% H2O/10% D2O' ;0.5-1 mM [3',4',5',5'',5]-100% 2D RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 100% D2O ; 5 '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 2M57 _pdbx_nmr_refine.method '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 2M57 _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 ? _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 2M57 _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 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNS 1.2 1 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.2 2 'Schwieters, Kuszewski, Tjandra and Clore' refinement 'X-PLOR NIH' 2.3 3 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' 'X-PLOR NIH' 2.3 4 'Koradi, Billeter and Wuthrich' 'data analysis' MOLMOL ? 5 Goddard 'chemical shift assignment' Sparky ? 6 Goddard 'peak picking' Sparky ? 7 Goddard 'data analysis' Sparky ? 8 'Bruker Biospin' processing TopSpin 3.0.a 9 'Bruker Biospin' 'data analysis' TopSpin 3.0.a 10 Lavery 'data analysis' Curves ? 11 # _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 2M57 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2M57 _struct.title 'NMR solution structure of domain 5 from Azotobacter vinelandii Intron 5 at pH 7.8' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2M57 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, ribozyme, group II intron, hairpin' # _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 _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A U 35 O2 ? ? A G 1 A U 35 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A G 1 O6 ? ? ? 1_555 A U 35 N3 ? ? A G 1 A U 35 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 34 N3 ? ? A G 2 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 34 O2 ? ? A G 2 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 34 N4 ? ? A G 2 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 31 N1 ? ? A C 5 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 31 O6 ? ? A C 5 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 31 N2 ? ? A C 5 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 30 N1 ? ? A C 6 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 30 O6 ? ? A C 6 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 30 N2 ? ? A C 6 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 7 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 7 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 7 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 28 N1 ? ? A U 8 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 8 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 9 N6 ? ? ? 1_555 A C 25 O2 ? ? A A 9 A C 25 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog18 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 11 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 11 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 11 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 11 N3 ? ? ? 1_555 A G 26 N2 ? ? A G 11 A G 26 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog22 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 12 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 12 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 12 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 13 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 13 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 13 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 14 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 14 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 14 N2 ? ? ? 1_555 A C 20 O2 ? ? A G 14 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 O6 ? ? ? 1_555 A C 20 N4 ? ? A G 14 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2M57 _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 C 5 5 5 C C A . n A 1 6 C 6 6 6 C C 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 A 1 10 U 10 10 10 U U A . n A 1 11 G 11 11 11 G G A . n A 1 12 C 12 12 12 C C 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 U 15 15 15 U U A . n A 1 16 A 16 16 16 A A A . n A 1 17 G 17 17 17 G G A . n A 1 18 U 18 18 18 U U A . n A 1 19 U 19 19 19 U U A . n A 1 20 C 20 20 20 C C 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 A 32 32 32 A A A . n A 1 33 U 33 33 33 U U A . n A 1 34 C 34 34 34 C C A . n A 1 35 U 35 35 35 U U 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 2014-02-26 2 'Structure model' 1 1 2023-06-14 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' Other # 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 2 'Structure model' database_2 2 2 'Structure model' pdbx_database_status 3 2 'Structure model' pdbx_nmr_software 4 2 'Structure model' pdbx_nmr_spectrometer # 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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 2 'Structure model' '_pdbx_nmr_software.name' 5 2 'Structure model' '_pdbx_nmr_spectrometer.model' # 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 (35-MER)-1' ? 0.5-1 mM ? 1 'potassium chloride-2' 60 ? mM ? 1 EDTA-3 10 ? uM ? 1 'RNA (35-MER)-4' ? 0.5-1 mM ? 2 'potassium chloride-5' 60 ? mM ? 2 EDTA-6 10 ? uM ? 2 'RNA (35-MER)-7' ? 0.5-1 mM '[100% 13C; 100% 15N]' 3 'potassium chloride-8' 60 ? mM ? 3 EDTA-9 10 ? uM ? 3 'RNA (35-MER)-10' ? 0.5-1 mM '[100% 13C; 100% 15N]' 4 'potassium chloride-11' 60 ? mM ? 4 EDTA-12 10 ? uM ? 4 'RNA (35-MER)-13' ? 0.5-1 mM ;[3',4',5',5'',5]-100% 2D ; 5 'potassium chloride-14' 60 ? mM ? 5 EDTA-15 10 ? uM ? 5 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2M57 _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count 56 _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total 660 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 238 _pdbx_nmr_constraints.NOE_long_range_total_count 98 _pdbx_nmr_constraints.NOE_medium_range_total_count 14 _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count 310 _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 "HO2'" A G 4 ? ? "O5'" A C 5 ? ? 1.59 2 3 "O2'" A G 11 ? ? H21 A G 26 ? ? 1.37 3 3 "HO2'" A G 4 ? ? "O5'" A C 5 ? ? 1.57 4 4 "HO2'" A A 16 ? ? "O5'" A G 17 ? ? 1.51 5 5 H61 A A 16 ? ? O4 A U 18 ? ? 1.50 6 5 "O2'" A U 10 ? ? "H5'" A G 11 ? ? 1.60 7 6 "O2'" A G 17 ? ? "H5''" A U 18 ? ? 1.51 8 6 "O2'" A U 19 ? ? H6 A C 20 ? ? 1.55 9 7 "H2'" A U 19 ? ? "O4'" A C 20 ? ? 1.55 10 8 "O2'" A U 19 ? ? H6 A C 20 ? ? 1.52 11 8 "O2'" A G 17 ? ? "H5''" A U 18 ? ? 1.52 12 10 "O2'" A U 10 ? ? "H5'" A G 11 ? ? 1.57 13 12 "HO2'" A A 24 ? ? "O5'" A C 25 ? ? 1.37 14 14 "H2'" A U 15 ? ? "O4'" A A 16 ? ? 1.52 15 14 "H4'" A C 25 ? ? "O4'" A G 26 ? ? 1.54 16 15 H61 A A 16 ? ? O4 A U 18 ? ? 1.40 17 15 "H2'" A U 19 ? ? "O4'" A C 20 ? ? 1.51 18 16 "O2'" A U 19 ? ? H6 A C 20 ? ? 1.49 19 17 "H2'" A G 31 ? ? "O4'" A A 32 ? ? 1.57 20 18 "HO2'" A A 16 ? ? "O5'" A G 17 ? ? 1.53 21 18 "H2'" A U 19 ? ? "O4'" A C 20 ? ? 1.54 22 19 "O2'" A G 17 ? ? "H5''" A U 18 ? ? 1.52 23 19 H8 A G 17 ? ? O4 A U 19 ? ? 1.59 24 20 "H2'" A G 31 ? ? "O4'" A A 32 ? ? 1.50 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2M57 'double helix' 2M57 'a-form double helix' 2M57 'hairpin loop' 2M57 '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 U 35 1_555 -1.980 -0.281 -0.338 -1.514 1.903 7.282 1 A_G1:U35_A A 1 ? A 35 ? 28 1 1 A G 2 1_555 A C 34 1_555 -0.659 -0.039 0.007 0.702 -0.475 2.954 2 A_G2:C34_A A 2 ? A 34 ? 19 1 1 A C 5 1_555 A G 31 1_555 0.540 -0.070 -0.062 4.869 3.924 -2.511 3 A_C5:G31_A A 5 ? A 31 ? 19 1 1 A C 6 1_555 A G 30 1_555 -0.619 0.067 -0.059 -1.904 -2.116 2.928 4 A_C6:G30_A A 6 ? A 30 ? 19 1 1 A G 7 1_555 A C 29 1_555 0.516 0.060 0.019 -0.988 -1.331 0.794 5 A_G7:C29_A A 7 ? A 29 ? 19 1 1 A U 8 1_555 A A 28 1_555 -0.380 -0.060 -0.003 -0.544 0.946 -5.381 6 A_U8:A28_A A 8 ? A 28 ? 20 1 1 A A 9 1_555 A C 25 1_555 -6.035 -1.244 -1.067 -25.364 16.505 4.901 7 A_A9:C25_A A 9 ? A 25 ? ? ? 1 A G 11 1_555 A C 23 1_555 0.398 0.100 0.022 1.173 -0.291 0.105 8 A_G11:C23_A A 11 ? A 23 ? 19 1 1 A C 12 1_555 A G 22 1_555 -0.638 -0.023 -0.041 -0.612 -1.875 -3.883 9 A_C12:G22_A A 12 ? A 22 ? 19 1 1 A G 13 1_555 A C 21 1_555 0.628 -0.048 -0.049 -4.142 -1.420 -6.156 10 A_G13:C21_A A 13 ? A 21 ? 19 1 1 A G 14 1_555 A C 20 1_555 -0.588 0.029 -0.070 -1.634 3.816 2.025 11 A_G14:C20_A A 14 ? A 20 ? 19 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 U 35 1_555 A G 2 1_555 A C 34 1_555 -0.594 -0.877 4.098 -2.319 -2.536 37.030 -0.947 0.540 4.175 -3.982 3.642 37.183 1 AA_G1G2:C34U35_AA A 1 ? A 35 ? A 2 ? A 34 ? 1 A C 5 1_555 A G 31 1_555 A C 6 1_555 A G 30 1_555 0.252 -1.133 4.266 1.010 15.324 23.354 -6.775 -0.232 2.977 33.597 -2.214 27.893 2 AA_C5C6:G30G31_AA A 5 ? A 31 ? A 6 ? A 30 ? 1 A C 6 1_555 A G 30 1_555 A G 7 1_555 A C 29 1_555 0.402 -0.450 4.199 -1.984 3.363 33.637 -1.463 -1.097 4.106 5.786 3.415 33.857 3 AA_C6G7:C29G30_AA A 6 ? A 30 ? A 7 ? A 29 ? 1 A G 7 1_555 A C 29 1_555 A U 8 1_555 A A 28 1_555 -0.222 -1.595 3.752 -0.071 11.234 25.846 -6.043 0.440 2.826 23.738 0.151 28.144 4 AA_G7U8:A28C29_AA A 7 ? A 29 ? A 8 ? A 28 ? 1 A U 8 1_555 A A 28 1_555 A A 9 1_555 A C 25 1_555 4.488 1.273 3.492 29.862 -3.994 33.673 2.242 -1.584 5.438 -5.687 -42.521 44.891 5 AA_U8A9:C25A28_AA A 8 ? A 28 ? A 9 ? A 25 ? 1 A A 9 1_555 A C 25 1_555 A G 11 1_555 A C 23 1_555 1.639 -3.229 6.044 -6.247 17.666 68.556 -3.851 -1.791 5.045 15.394 5.444 70.768 6 AA_A9G11:C23C25_AA A 9 ? A 25 ? A 11 ? A 23 ? 1 A G 11 1_555 A C 23 1_555 A C 12 1_555 A G 22 1_555 -0.346 -0.737 4.348 -1.068 -2.854 31.751 -0.645 0.370 4.404 -5.202 1.946 31.894 7 AA_G11C12:G22C23_AA A 11 ? A 23 ? A 12 ? A 22 ? 1 A C 12 1_555 A G 22 1_555 A G 13 1_555 A C 21 1_555 -0.054 -1.079 3.744 -0.310 19.024 35.537 -3.895 0.041 2.833 28.769 0.469 40.164 8 AA_C12G13:C21G22_AA A 12 ? A 22 ? A 13 ? A 21 ? 1 A G 13 1_555 A C 21 1_555 A G 14 1_555 A C 20 1_555 0.744 -1.680 4.036 -0.701 -5.116 22.458 -1.894 -2.179 4.282 -12.917 1.771 23.036 9 AA_G13G14:C20C21_AA A 13 ? A 21 ? A 14 ? A 20 ? #