data_2KEZ # _entry.id 2KEZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2KEZ pdb_00002kez 10.2210/pdb2kez/pdb RCSB RCSB101038 ? ? WWPDB D_1000101038 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 1SY4 PDB 'U6 ISL structure at pH 7.0' unspecified 1SYZ PDB 'U6 ISL structure at pH 5.7' unspecified 2KF0 PDB . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KEZ _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-02-08 _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.pdb_format_compatible Y _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 'Venditti, V.' 1 'Butcher, S.E.' 2 # loop_ _citation.id _citation.title _citation.journal_abbrev _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 _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping.' J.Mol.Biol. 391 894 905 2009 JMOBAK UK 0022-2836 0070 ? 19591840 10.1016/j.jmb.2009.07.003 1 'Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.' Rna 9 533 542 2003 RNARFU UK 1355-8382 2122 ? 12702812 ? 2 'Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change.' Biochemistry 43 13739 13747 2004 BICHAW US 0006-2960 0033 ? 15504036 10.1021/bi048815y # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Venditti, V.' 1 ? primary 'Clos, L.' 2 ? primary 'Niccolai, N.' 3 ? primary 'Butcher, S.E.' 4 ? 1 'Reiter, N.J.' 5 ? 1 'Nikstad, L.J.' 6 ? 1 'Allmann, A.M.' 7 ? 1 'Johnson, R.J.' 8 ? 1 'Butcher, S.E.' 9 ? 2 'Reiter, N.J.' 10 ? 2 'Blad, H.' 11 ? 2 'Abildgaard, F.' 12 ? 2 'Butcher, S.E.' 13 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3') ; _entity.formula_weight 7668.615 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation A62G _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 GGUUCCCCUGCAUAAGGAUGAACC _entity_poly.pdbx_seq_one_letter_code_can GGUUCCCCUGCAUAAGGAUGAACC _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 U n 1 5 C n 1 6 C n 1 7 C n 1 8 C n 1 9 U n 1 10 G n 1 11 C n 1 12 A n 1 13 U n 1 14 A n 1 15 A n 1 16 G n 1 17 G n 1 18 A n 1 19 U n 1 20 G n 1 21 A n 1 22 A n 1 23 C n 1 24 C n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2KEZ _struct_ref.pdbx_db_accession 2KEZ _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 2KEZ _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 24 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2KEZ _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 24 _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 24 # 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' 2 2 2 '2D 1H-1H NOESY' 1 3 1 '2D 1H-1H TOCSY' 1 4 3 'J-modulated (13C 1H) CT-HSQC' 1 5 3 'J-modulated (13C 1H) CT-HSQC' 1 6 3 '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 50 8.0 ambient ? 303 K 2 50 8.0 ambient ? 283 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '2 mM RNA, 100% D2O' 1 '100% D2O' '2 mM RNA, 90% H2O/10% D2O' 2 '90% H2O/10% D2O' '0.5 mM [U-100% 13C] RNA, 100% D2O' 3 '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 750 Bruker DMX 1 'Bruker DMX' 600 Bruker DMX 2 'Bruker DMX' # _pdbx_nmr_refine.entry_id 2KEZ _pdbx_nmr_refine.method 'molecular 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 12 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KEZ _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 2KEZ _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Case, D. et al.' refinement Amber 9.0 1 'Delaglio, F. et al.' processing NMRPipe ? 2 'Goddard, T. et al.' 'chemical shift assignment' Sparky ? 3 'Bruker Biospin' processing XwinNMR ? 4 # _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 2KEZ _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KEZ _struct.title 'NMR structure of U6 ISL at pH 8.0' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KEZ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'U6 RNA, stem loop, bulge, internal loop, 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 _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 24 N3 ? ? A G 1 A C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 24 O2 ? ? A G 1 A C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 24 N4 ? ? A G 1 A C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 2 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 2 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 2 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 22 N1 ? ? A U 3 A A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 22 N6 ? ? A U 3 A A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 21 N1 ? ? A U 4 A A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 21 N6 ? ? A U 4 A A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 5 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 5 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 5 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N3 ? ? ? 1_555 A U 19 N3 ? ? A C 6 A U 19 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog15 hydrog ? ? A C 6 N4 ? ? ? 1_555 A U 19 O4 ? ? A C 6 A U 19 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog16 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 7 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 7 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 7 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 8 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 8 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 8 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 9 N3 ? ? ? 1_555 A A 15 N1 ? ? A U 9 A A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 9 O4 ? ? ? 1_555 A A 15 N6 ? ? A U 9 A A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 10 N2 ? ? ? 1_555 A A 14 N7 ? ? A G 10 A A 14 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog25 hydrog ? ? A G 10 N3 ? ? ? 1_555 A A 14 N6 ? ? A G 10 A A 14 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2KEZ _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 U 3 3 3 U U A . n A 1 4 U 4 4 4 U U 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 C 7 7 7 C C A . n A 1 8 C 8 8 8 C C 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 A 12 12 12 A A A . n A 1 13 U 13 13 13 U U A . n A 1 14 A 14 14 14 A A A . n A 1 15 A 15 15 15 A A A . n A 1 16 G 16 16 16 G G A . n A 1 17 G 17 17 17 G G A . n A 1 18 A 18 18 18 A A A . n A 1 19 U 19 19 19 U U A . n A 1 20 G 20 20 20 G G A . n A 1 21 A 21 21 21 A A A . n A 1 22 A 22 22 22 A A A . n A 1 23 C 23 23 23 C C A . n A 1 24 C 24 24 24 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 2009-07-21 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 '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 3 'Structure model' database_2 2 3 'Structure model' pdbx_nmr_software 3 3 'Structure model' pdbx_struct_assembly 4 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_nmr_software.name' # 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 (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3')-1 ; 2 ? mM ? 1 ;RNA (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3')-2 ; 2 ? mM ? 2 ;RNA (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3')-3 ; 0.5 ? mM '[U-100% 13C]' 3 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C5'" A U 13 ? ? "C4'" A U 13 ? ? "C3'" A U 13 ? ? 106.40 115.20 -8.80 1.40 N 2 1 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 105.00 112.00 -7.00 1.10 N 3 2 "C5'" A G 1 ? ? "C4'" A G 1 ? ? "C3'" A G 1 ? ? 106.44 115.20 -8.76 1.40 N 4 2 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 105.20 112.00 -6.80 1.10 N 5 3 "C5'" A G 1 ? ? "C4'" A G 1 ? ? "C3'" A G 1 ? ? 106.50 115.20 -8.70 1.40 N 6 3 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 112.92 108.50 4.42 0.70 N 7 3 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 104.73 112.00 -7.27 1.10 N 8 4 "C5'" A G 1 ? ? "C4'" A G 1 ? ? "C3'" A G 1 ? ? 106.24 115.20 -8.96 1.40 N 9 4 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 112.72 108.50 4.22 0.70 N 10 4 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 104.91 112.00 -7.09 1.10 N 11 5 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 105.35 112.00 -6.65 1.10 N 12 6 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 104.73 112.00 -7.27 1.10 N 13 7 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 104.91 112.00 -7.09 1.10 N 14 8 "C5'" A G 1 ? ? "C4'" A G 1 ? ? "C3'" A G 1 ? ? 106.75 115.20 -8.45 1.40 N 15 8 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 112.94 108.50 4.44 0.70 N 16 8 "C1'" A C 11 ? ? "O4'" A C 11 ? ? "C4'" A C 11 ? ? 105.34 109.70 -4.36 0.70 N 17 8 "O4'" A A 14 ? ? "C1'" A A 14 ? ? N9 A A 14 ? ? 113.04 108.50 4.54 0.70 N 18 8 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 105.19 112.00 -6.81 1.10 N 19 9 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 105.17 112.00 -6.83 1.10 N 20 10 N9 A G 16 ? ? "C1'" A G 16 ? ? "C2'" A G 16 ? ? 104.97 112.00 -7.03 1.10 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 2 _pdbx_validate_planes.auth_comp_id U _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 13 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.065 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2KEZ 'double helix' 2KEZ 'a-form double helix' 2KEZ 'hairpin loop' 2KEZ 'bulge loop' 2KEZ '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 24 1_555 -0.195 -0.205 -0.567 -6.421 16.577 -5.647 1 A_G1:C24_A A 1 ? A 24 ? 19 1 1 A G 2 1_555 A C 23 1_555 -0.440 -0.162 -0.294 -8.007 -22.301 2.645 2 A_G2:C23_A A 2 ? A 23 ? 19 1 1 A U 3 1_555 A A 22 1_555 0.134 -0.056 -0.347 -10.508 -21.984 4.709 3 A_U3:A22_A A 3 ? A 22 ? 20 1 1 A U 4 1_555 A A 21 1_555 0.030 -0.087 -0.516 -2.197 -18.096 -0.823 4 A_U4:A21_A A 4 ? A 21 ? 20 1 1 A C 5 1_555 A G 20 1_555 0.424 -0.161 -0.318 4.214 -15.271 1.086 5 A_C5:G20_A A 5 ? A 20 ? 19 1 1 A C 6 1_555 A U 19 1_555 0.473 -1.513 -0.180 7.304 -14.931 6.994 6 A_C6:U19_A A 6 ? A 19 ? 18 1 1 A C 7 1_555 A G 17 1_555 -0.112 -0.047 -0.272 15.466 -19.473 0.220 7 A_C7:G17_A A 7 ? A 17 ? 19 1 1 A C 8 1_555 A G 16 1_555 -0.045 -0.129 -0.461 4.206 -23.563 4.208 8 A_C8:G16_A A 8 ? A 16 ? 19 1 1 A U 9 1_555 A A 15 1_555 -0.324 -0.160 -0.735 -1.838 -8.161 11.915 9 A_U9:A15_A A 9 ? A 15 ? 20 1 1 A G 10 1_555 A A 14 1_555 5.829 -4.029 -2.124 2.886 14.913 7.014 10 A_G10:A14_A A 10 ? A 14 ? 11 5 # 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 24 1_555 A G 2 1_555 A C 23 1_555 0.550 -2.059 3.611 0.590 8.863 30.614 -5.401 -0.892 2.925 16.358 -1.090 31.846 1 AA_G1G2:C23C24_AA A 1 ? A 24 ? A 2 ? A 23 ? 1 A G 2 1_555 A C 23 1_555 A U 3 1_555 A A 22 1_555 -0.204 -1.540 3.582 1.225 4.779 33.969 -3.407 0.549 3.332 8.126 -2.083 34.315 2 AA_G2U3:A22C23_AA A 2 ? A 23 ? A 3 ? A 22 ? 1 A U 3 1_555 A A 22 1_555 A U 4 1_555 A A 21 1_555 -0.229 -1.226 3.409 3.720 11.613 27.271 -4.719 1.194 2.627 23.214 -7.436 29.826 3 AA_U3U4:A21A22_AA A 3 ? A 22 ? A 4 ? A 21 ? 1 A U 4 1_555 A A 21 1_555 A C 5 1_555 A G 20 1_555 0.436 -0.643 3.447 0.854 13.168 26.555 -4.086 -0.670 2.830 26.675 -1.730 29.600 4 AA_U4C5:G20A21_AA A 4 ? A 21 ? A 5 ? A 20 ? 1 A C 5 1_555 A G 20 1_555 A C 6 1_555 A U 19 1_555 0.750 -0.621 3.898 1.413 14.641 25.509 -4.851 -1.129 3.124 30.171 -2.912 29.385 5 AA_C5C6:U19G20_AA A 5 ? A 20 ? A 6 ? A 19 ? 1 A C 6 1_555 A U 19 1_555 A C 7 1_555 A G 17 1_555 1.202 -1.983 6.035 -23.019 13.828 39.151 -4.386 -4.678 3.931 18.266 30.405 47.175 6 AA_C6C7:G17U19_AA A 6 ? A 19 ? A 7 ? A 17 ? 1 A C 7 1_555 A G 17 1_555 A C 8 1_555 A G 16 1_555 -0.594 -1.644 3.628 2.086 25.020 24.081 -6.246 1.288 1.337 46.706 -3.893 34.654 7 AA_C7C8:G16G17_AA A 7 ? A 17 ? A 8 ? A 16 ? 1 A C 8 1_555 A G 16 1_555 A U 9 1_555 A A 15 1_555 0.432 -1.308 3.994 -5.659 14.650 22.284 -6.809 -2.474 2.497 33.130 12.796 27.205 8 AA_C8U9:A15G16_AA A 8 ? A 16 ? A 9 ? A 15 ? 1 A U 9 1_555 A A 15 1_555 A G 10 1_555 A A 14 1_555 -0.169 0.766 4.335 4.888 10.403 59.902 0.085 0.482 4.377 10.315 -4.847 60.894 9 AA_U9G10:A14A15_AA A 9 ? A 15 ? A 10 ? A 14 ? #