data_2N6X # _entry.id 2N6X # _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_code _database_2.database_id _database_2.pdbx_database_accession _database_2.pdbx_DOI RCSB104498 RCSB ? ? 2N6X PDB pdb_00002n6x 10.2210/pdb2n6x/pdb 25785 BMRB ? ? D_1000104498 WWPDB ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 25785 BMRB unspecified . 2N6S PDB unspecified . 2N6T PDB unspecified . 2N6W PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2N6X _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2015-08-31 _pdbx_database_status.SG_entry Y _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 'Barnwal, R.' 1 'Godin, K.' 2 'Varani, G.' 3 'Seattle Structural Genomics Center for Infectious Disease (SSGCID)' 4 # _citation.id primary _citation.title 'Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 44 _citation.page_first 9426 _citation.page_last 9437 _citation.year 2016 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 27369378 _citation.pdbx_database_id_DOI 10.1093/nar/gkw584 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Barnwal, R.P.' 1 ? primary 'Loh, E.' 2 ? primary 'Godin, K.S.' 3 ? primary 'Yip, J.' 4 ? primary 'Lavender, H.' 5 ? primary 'Tang, C.M.' 6 ? primary 'Varani, G.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'RNA (43-MER)' _entity.formula_weight 13741.121 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGUGAGUACGUAGAGUAUACUUCGGUAUACUUAUAUACUUACC _entity_poly.pdbx_seq_one_letter_code_can GGUGAGUACGUAGAGUAUACUUCGGUAUACUUAUAUACUUACC _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 U n 1 4 G n 1 5 A n 1 6 G n 1 7 U n 1 8 A n 1 9 C n 1 10 G n 1 11 U n 1 12 A n 1 13 G n 1 14 A n 1 15 G n 1 16 U n 1 17 A n 1 18 U n 1 19 A n 1 20 C n 1 21 U n 1 22 U n 1 23 C n 1 24 G n 1 25 G n 1 26 U n 1 27 A n 1 28 U n 1 29 A n 1 30 C n 1 31 U n 1 32 U n 1 33 A n 1 34 U n 1 35 A n 1 36 U n 1 37 A n 1 38 C n 1 39 U n 1 40 U n 1 41 A n 1 42 C n 1 43 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 'Neisseria meningitidis' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 487 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2N6X _struct_ref.pdbx_db_accession 2N6X _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 2N6X _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 43 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2N6X _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 43 _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 43 # 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-15N HSQC' 1 2 1 '2D 1H-13C HSQC' 1 3 1 '2D 1H-1H TOCSY' 1 4 1 '2D DQF-COSY' 1 5 1 '2D 1H-1H NOESY' 1 6 1 '3D 1H-13C NOESY' 1 7 1 '3D HCCH-TOCSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH 6.0 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 280 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents ;0.4-1.1 mM CssA5 RNA (43-MER), 0.4-1.1 mM 13C/15N-uniformly labeled CssA5 RNA (43-MER), 0.4-1.1 mM 13C/15N-AU labeled CssA5 RNA (43-MER), 0.4-1.1 mM partially deuterated CssA5 RNA (43-MER), 95% H2O/5% D2O ; _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '95% H2O/5% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 800 Bruker AVANCE 1 'Bruker Avance' 600 Bruker AVANCE 2 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2N6X _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 least restraint violations' _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2N6X _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2N6X _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 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' 'X-PLOR NIH' ? 1 'Schwieters, Kuszewski, Tjandra and Clore' refinement 'X-PLOR NIH' ? 2 'Bruker Biospin' collection TopSpin ? 3 'Bruker Biospin' processing TopSpin ? 4 Goddard 'chemical shift assignment' Sparky ? 5 Goddard 'data analysis' Sparky ? 6 Goddard 'peak picking' Sparky ? 7 # _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 2N6X _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2N6X _struct.title 'NMR Assignment and structure of CssA5 (middle region) of CssA thermometer from Neisseria meningitidis' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2N6X _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;RNA regulation, pathogen, RNA thermometer, RNA, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID ; # _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 covale1 covale both ? A G 1 "O3'" ? ? ? 1_555 A G 2 P ? ? A G 1 A G 2 1_555 ? ? ? ? ? ? ? 1.615 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 42 N3 ? ? A G 2 A C 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 42 O2 ? ? A G 2 A C 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 42 N4 ? ? A G 2 A C 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 41 N1 ? ? A U 3 A A 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 41 N6 ? ? A U 3 A A 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 4 N1 ? ? ? 1_555 A U 40 O2 ? ? A G 4 A U 40 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog7 hydrog ? ? A G 4 O6 ? ? ? 1_555 A U 40 N3 ? ? A G 4 A U 40 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 39 N3 ? ? A A 5 A U 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 39 O4 ? ? A A 5 A U 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 6 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 6 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 6 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 37 N1 ? ? A U 7 A A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 37 N6 ? ? A U 7 A A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 36 N3 ? ? A A 8 A U 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 36 O4 ? ? A A 8 A U 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 12 N1 ? ? ? 1_555 A A 33 N6 ? ? A A 12 A A 33 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog18 hydrog ? ? A A 14 N1 ? ? ? 1_555 A U 31 N3 ? ? A A 14 A U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 14 N6 ? ? ? 1_555 A U 31 O4 ? ? A A 14 A U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 15 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 15 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 15 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 15 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 15 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 15 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 29 N1 ? ? A U 16 A A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 29 N6 ? ? A U 16 A A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A A 17 N1 ? ? ? 1_555 A U 28 N3 ? ? A A 17 A U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 17 N6 ? ? ? 1_555 A U 28 O4 ? ? A A 17 A U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 18 N3 ? ? ? 1_555 A A 27 N1 ? ? A U 18 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 18 O4 ? ? ? 1_555 A A 27 N6 ? ? A U 18 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 19 N1 ? ? ? 1_555 A U 26 N3 ? ? A A 19 A U 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 19 N6 ? ? ? 1_555 A U 26 O4 ? ? A A 19 A U 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 20 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 20 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 20 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 20 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 20 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 20 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 21 O2 ? ? ? 1_555 A G 24 N1 ? ? A U 21 A G 24 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog35 hydrog ? ? A U 21 N3 ? ? ? 1_555 A G 25 O6 ? ? A U 21 A G 25 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog36 hydrog ? ? A U 21 O2 ? ? ? 1_555 A G 25 N1 ? ? A U 21 A G 25 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2N6X _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 Q # 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 A 5 5 5 A A 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 C 9 9 9 C C A . n A 1 10 G 10 10 10 G G A . n A 1 11 U 11 11 11 U U A . n A 1 12 A 12 12 12 A A A . n A 1 13 G 13 13 13 G G A . n A 1 14 A 14 14 14 A A A . n A 1 15 G 15 15 15 G G A . n A 1 16 U 16 16 16 U U A . n A 1 17 A 17 17 17 A A A . n A 1 18 U 18 18 18 U U A . n A 1 19 A 19 19 19 A A A . n A 1 20 C 20 20 20 C C A . n A 1 21 U 21 21 21 U U A . n A 1 22 U 22 22 22 U U A . n A 1 23 C 23 23 23 C C A . n A 1 24 G 24 24 24 G G A . n A 1 25 G 25 25 25 G G A . n A 1 26 U 26 26 26 U U A . n A 1 27 A 27 27 27 A A A . n A 1 28 U 28 28 28 U U A . n A 1 29 A 29 29 29 A A A . n A 1 30 C 30 30 30 C C A . n A 1 31 U 31 31 31 U U A . n A 1 32 U 32 32 32 U U A . n A 1 33 A 33 33 33 A A A . n A 1 34 U 34 34 34 U U A . n A 1 35 A 35 35 35 A A A . n A 1 36 U 36 36 36 U U A . n A 1 37 A 37 37 37 A A A . n A 1 38 C 38 38 38 C C A . n A 1 39 U 39 39 39 U U A . n A 1 40 U 40 40 40 U U A . n A 1 41 A 41 41 41 A A A . n A 1 42 C 42 42 42 C C A . n A 1 43 C 43 43 43 C C A . n # _pdbx_SG_project.full_name_of_center 'Seattle Structural Genomics Center for Infectious Disease' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center SSGCID _pdbx_SG_project.project_name ? # _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 2016-08-03 2 'Structure model' 1 1 2016-11-23 3 'Structure model' 1 2 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 '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 3 'Structure model' database_2 2 3 'Structure model' pdbx_database_status 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' pdbx_nmr_spectrometer 5 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 3 'Structure model' '_pdbx_nmr_software.name' 5 3 'Structure model' '_pdbx_nmr_spectrometer.model' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # 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 'CssA5 RNA (43-MER)-1' ? 0.4-1.1 mM ? 1 'CssA5 RNA (43-MER)-2' ? 0.4-1.1 mM '13C/15N-uniformly labeled' 1 'CssA5 RNA (43-MER)-3' ? 0.4-1.1 mM '13C/15N-AU labeled' 1 'CssA5 RNA (43-MER)-4' ? 0.4-1.1 mM 'partially deuterated' 1 # 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 U 26 ? ? "O4'" A A 27 ? ? 1.49 2 2 "HO2'" A C 30 ? ? "O4'" A U 31 ? ? 1.53 3 2 "HO2'" A G 15 ? ? "O4'" A U 16 ? ? 1.56 4 2 "HO2'" A U 36 ? ? "O4'" A A 37 ? ? 1.57 5 4 "HO2'" A G 2 ? ? "O4'" A U 3 ? ? 1.59 6 6 "HO2'" A U 26 ? ? "O4'" A A 27 ? ? 1.59 7 8 "HO2'" A U 36 ? ? "O4'" A A 37 ? ? 1.45 8 8 "HO2'" A U 26 ? ? "O4'" A A 27 ? ? 1.46 9 8 "HO2'" A A 5 ? ? "O4'" A G 6 ? ? 1.51 10 9 "HO2'" A U 36 ? ? "O4'" A A 37 ? ? 1.48 11 9 "HO2'" A A 35 ? ? "O4'" A U 36 ? ? 1.55 12 10 "HO2'" A A 35 ? ? "O4'" A U 36 ? ? 1.48 13 10 "HO2'" A A 19 ? ? "O4'" A C 20 ? ? 1.52 14 10 "HO2'" A G 25 ? ? "O4'" A U 26 ? ? 1.57 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2N6X 'double helix' 2N6X 'a-form double helix' 2N6X tetraloop 2N6X 'mismatched base pair' 2N6X '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 2 1_555 A C 42 1_555 -0.584 -0.192 -0.316 -0.075 3.171 3.319 1 A_G2:C42_A A 2 ? A 42 ? 19 1 1 A U 3 1_555 A A 41 1_555 0.764 -0.213 -0.404 6.645 2.105 3.260 2 A_U3:A41_A A 3 ? A 41 ? 20 1 1 A G 4 1_555 A U 40 1_555 -2.746 -0.832 -0.306 0.439 -0.611 -2.460 3 A_G4:U40_A A 4 ? A 40 ? 28 1 1 A A 5 1_555 A U 39 1_555 -0.604 -0.352 -0.941 2.792 -6.581 -4.375 4 A_A5:U39_A A 5 ? A 39 ? 20 1 1 A G 6 1_555 A C 38 1_555 0.161 -0.162 -0.356 -4.767 -9.495 4.155 5 A_G6:C38_A A 6 ? A 38 ? 19 1 1 A U 7 1_555 A A 37 1_555 0.504 -0.274 -0.623 -0.911 -0.117 3.453 6 A_U7:A37_A A 7 ? A 37 ? 20 1 1 A A 8 1_555 A U 36 1_555 -0.075 0.018 -0.200 -5.445 -5.262 -5.862 7 A_A8:U36_A A 8 ? A 36 ? 20 1 1 A A 12 1_555 A A 33 1_555 1.662 0.869 2.316 20.970 9.001 40.951 8 A_A12:A33_A A 12 ? A 33 ? ? 1 1 A A 14 1_555 A U 31 1_555 -0.763 -0.165 -0.367 3.442 -3.044 -0.755 9 A_A14:U31_A A 14 ? A 31 ? 20 1 1 A G 15 1_555 A C 30 1_555 -0.416 -0.123 -0.244 -2.570 1.826 3.579 10 A_G15:C30_A A 15 ? A 30 ? 19 1 1 A U 16 1_555 A A 29 1_555 0.332 -0.202 -0.171 3.295 0.173 2.873 11 A_U16:A29_A A 16 ? A 29 ? 20 1 1 A A 17 1_555 A U 28 1_555 -0.718 -0.155 -0.141 -3.140 -1.456 1.458 12 A_A17:U28_A A 17 ? A 28 ? 20 1 1 A U 18 1_555 A A 27 1_555 0.735 -0.181 -0.273 5.212 1.735 2.892 13 A_U18:A27_A A 18 ? A 27 ? 20 1 1 A A 19 1_555 A U 26 1_555 -0.480 -0.179 -0.490 -3.129 1.082 -3.876 14 A_A19:U26_A A 19 ? A 26 ? 20 1 1 A C 20 1_555 A G 25 1_555 0.745 -0.257 -0.607 8.357 8.494 -2.245 15 A_C20:G25_A A 20 ? A 25 ? 19 1 1 A U 21 1_555 A G 24 1_555 0.139 -5.980 -0.403 -2.676 -9.689 -116.547 16 A_U21:G24_A A 21 ? A 24 ? ? 6 # 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 2 1_555 A C 42 1_555 A U 3 1_555 A A 41 1_555 -0.054 -0.833 4.285 0.308 -8.515 30.393 0.600 0.177 4.352 -15.854 -0.574 31.537 1 AA_G2U3:A41C42_AA A 2 ? A 42 ? A 3 ? A 41 ? 1 A U 3 1_555 A A 41 1_555 A G 4 1_555 A U 40 1_555 -0.104 -0.651 4.547 1.081 -23.286 22.822 4.915 0.468 3.670 -46.146 -2.143 32.512 2 AA_U3G4:U40A41_AA A 3 ? A 41 ? A 4 ? A 40 ? 1 A G 4 1_555 A U 40 1_555 A A 5 1_555 A U 39 1_555 0.251 -0.800 4.219 2.973 -12.127 35.577 0.865 0.128 4.265 -19.135 -4.691 37.637 3 AA_G4A5:U39U40_AA A 4 ? A 40 ? A 5 ? A 39 ? 1 A A 5 1_555 A U 39 1_555 A G 6 1_555 A C 38 1_555 0.114 -0.616 4.774 -2.176 -11.164 34.365 1.357 -0.642 4.724 -18.285 3.564 36.145 4 AA_A5G6:C38U39_AA A 5 ? A 39 ? A 6 ? A 38 ? 1 A G 6 1_555 A C 38 1_555 A U 7 1_555 A A 37 1_555 0.457 -0.886 4.161 1.221 -10.328 32.387 0.663 -0.525 4.250 -17.948 -2.123 33.973 5 AA_G6U7:A37C38_AA A 6 ? A 38 ? A 7 ? A 37 ? 1 A U 7 1_555 A A 37 1_555 A A 8 1_555 A U 36 1_555 -1.118 -0.922 4.481 -1.803 -9.877 28.182 1.143 1.633 4.596 -19.516 3.563 29.883 6 AA_U7A8:U36A37_AA A 7 ? A 37 ? A 8 ? A 36 ? 1 A A 14 1_555 A U 31 1_555 A G 15 1_555 A C 30 1_555 1.016 -0.658 4.725 0.120 -11.902 30.460 1.897 -1.776 4.653 -21.643 -0.219 32.652 7 AA_A14G15:C30U31_AA A 14 ? A 31 ? A 15 ? A 30 ? 1 A G 15 1_555 A C 30 1_555 A U 16 1_555 A A 29 1_555 -0.216 -1.127 4.350 -0.527 -13.643 29.025 1.433 0.257 4.427 -25.516 0.985 32.013 8 AA_G15U16:A29C30_AA A 15 ? A 30 ? A 16 ? A 29 ? 1 A U 16 1_555 A A 29 1_555 A A 17 1_555 A U 28 1_555 0.100 -0.657 5.022 2.615 -20.488 29.803 3.610 0.435 4.536 -35.037 -4.472 36.127 9 AA_U16A17:U28A29_AA A 16 ? A 29 ? A 17 ? A 28 ? 1 A A 17 1_555 A U 28 1_555 A U 18 1_555 A A 27 1_555 0.138 -0.717 4.285 0.007 -12.653 29.280 1.831 -0.250 4.227 -23.684 -0.012 31.842 10 AA_A17U18:A27U28_AA A 17 ? A 28 ? A 18 ? A 27 ? 1 A U 18 1_555 A A 27 1_555 A A 19 1_555 A U 26 1_555 -0.619 -0.480 5.057 -1.563 -20.896 29.461 4.014 0.642 4.457 -35.928 2.688 36.018 11 AA_U18A19:U26A27_AA A 18 ? A 27 ? A 19 ? A 26 ? 1 A A 19 1_555 A U 26 1_555 A C 20 1_555 A G 25 1_555 0.128 -1.114 4.027 -1.049 -12.628 28.820 1.032 -0.494 4.134 -23.962 1.990 31.429 12 AA_A19C20:G25U26_AA A 19 ? A 26 ? A 20 ? A 25 ? 1 A C 20 1_555 A G 25 1_555 A U 21 1_555 A G 24 1_555 -0.701 -0.438 3.501 14.973 10.448 100.957 -0.446 0.686 3.364 6.734 -9.650 102.149 13 AA_C20U21:G24G25_AA A 20 ? A 25 ? A 21 ? A 24 ? #