data_2JRQ # _entry.id 2JRQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 2JRQ pdb_00002jrq 10.2210/pdb2jrq/pdb RCSB RCSB100206 ? ? WWPDB D_1000100206 ? ? # 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 2007-07-24 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 5 'Structure model' 1 4 2023-12-20 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 'Structure model' 'Data collection' 7 5 '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 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_nmr_spectrometer 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 4 'Structure model' struct_conn 7 5 'Structure model' chem_comp_atom 8 5 'Structure model' chem_comp_bond 9 5 'Structure model' pdbx_database_status # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' 4 4 'Structure model' '_pdbx_nmr_spectrometer.model' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 5 'Structure model' '_pdbx_database_status.deposit_site' # _pdbx_database_status.deposit_site RCSB _pdbx_database_status.entry_id 2JRQ _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-06-28 _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_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.content_type 2JR4 PDB . unspecified 2JRG PDB . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Vendeix, F.A.P.' 1 'Dziergowska, A.' 2 'Gustilo, E.M.' 3 'Graham, W.D.' 4 'Sproat, B.' 5 'Malkiewicz, A.' 6 'Agris, P.F.' 7 # _citation.id primary _citation.title ;Wobble-Position Modifications Pre-structure tRNA's Anticodon for Ribosome-Mediated Codon Binding ; _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 'Vendeix, F.A.P.' 1 ? primary 'Dziergowska, A.' 2 ? primary 'Gustilo, E.M.' 3 ? primary 'Graham, W.D.' 4 ? primary 'Sproat, B.' 5 ? primary 'Malkiewicz, A.' 6 ? primary 'Agris, P.F.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-R(*CP*CP*UP*CP*CP*CP*UP*(CM0)P*AP*CP*AP*AP*GP*GP*AP*GP*G)-3'" _entity.formula_weight 5476.314 _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 yes _entity_poly.pdbx_seq_one_letter_code 'CCUCCCU(CM0)ACAAGGAGG' _entity_poly.pdbx_seq_one_letter_code_can CCUCCCUNACAAGGAGG _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 C n 1 2 C n 1 3 U n 1 4 C n 1 5 C n 1 6 C n 1 7 U n 1 8 CM0 n 1 9 A n 1 10 C n 1 11 A n 1 12 A n 1 13 G n 1 14 G n 1 15 A n 1 16 G n 1 17 G n # 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 CM0 'RNA linking' . ;5-(CARBOXYMETHOXY) URIDINE-5'-MONOPHOSPHATE ; ? 'C11 H15 N2 O12 P' 398.217 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_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 C 1 27 27 C C A . n A 1 2 C 2 28 28 C C A . n A 1 3 U 3 29 29 U U A . n A 1 4 C 4 30 30 C C A . n A 1 5 C 5 31 31 C C A . n A 1 6 C 6 32 32 C C A . n A 1 7 U 7 33 33 U U A . n A 1 8 CM0 8 34 34 CM0 CM0 A . n A 1 9 A 9 35 35 A A A . n A 1 10 C 10 36 36 C C A . n A 1 11 A 11 37 37 A A A . n A 1 12 A 12 38 38 A A A . n A 1 13 G 13 39 39 G G A . n A 1 14 G 14 40 40 G G A . n A 1 15 A 15 41 41 A A A . n A 1 16 G 16 42 42 G G A . n A 1 17 G 17 43 43 G G A . n # _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 2JRQ _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2JRQ _struct.title 'NMR solution structure of the anticodon of E. coli TRNA-VAL3 with 1 modification (cmo5U34)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 2JRQ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'E.coli, Valine, TRNA, ANTICODON STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, URIDINE 5-OXYACETIC ACID, CMO5U, 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_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2JRQ _struct_ref.pdbx_db_accession 2JRQ _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2JRQ _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 17 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2JRQ _struct_ref_seq.db_align_beg 27 _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 27 _struct_ref_seq.pdbx_auth_seq_align_end 43 # _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 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A U 7 "O3'" ? ? ? 1_555 A CM0 8 P ? ? A U 33 A CM0 34 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale2 covale one ? A CM0 8 "O3'" ? ? ? 1_555 A A 9 P ? ? A CM0 34 A A 35 1_555 ? ? ? ? ? ? ? 1.608 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 27 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 27 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 27 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 28 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 28 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 28 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 15 N1 ? ? A U 29 A A 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 15 N6 ? ? A U 29 A A 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 14 N1 ? ? A C 30 A G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 14 O6 ? ? A C 30 A G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 14 N2 ? ? A C 30 A G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 13 N1 ? ? A C 31 A G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 13 O6 ? ? A C 31 A G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 13 N2 ? ? A C 31 A G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 A A 12 N6 ? ? A C 32 A A 38 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _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 80 _pdbx_nmr_ensemble.conformers_submitted_total_number 11 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2JRQ _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation 0.1 _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation 5 _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation 0.5 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2JRQ _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '1.5-2 mM RNA 17mer, 90% H2O/10% D2O' 1 '90% H2O/10% D2O' '1.5-2 mM RNA 17mer, 100% D2O' 2 '100% D2O' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id 'RNA 17mer' 1.5 mM ? 1 'RNA 17mer' 1.5 mM ? 2 # 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 ? 6.2 ambient ? 295 K 2 ? 6.2 ambient ? 275 K # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 2 '2D 1H-1H COSY' 1 2 2 '2D DQF-COSY' 1 3 2 '2D 1H-1H TOCSY' 1 4 2 '2D 1H-13C HSQC' 1 5 2 '2D 1H-1H NOESY' 2 6 1 '2D 1H-1H NOESY' 1 7 2 '2D 1H-31P HETCOR' # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2JRQ _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count 28 _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 608 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count ? _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 ? _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 ? # _pdbx_nmr_refine.entry_id 2JRQ _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details 'anneal.inp protocol in CNS' _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Bruker Biospin' collection XwinNMR ? 1 Varian collection VNMR ? 2 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRDraw 3.0 3 Goddard 'data analysis' Sparky ? 4 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.1 5 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNS 1.1 6 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 CM0 P P N N 73 CM0 "O5'" O N N 74 CM0 O3P O N N 75 CM0 "C3'" C N S 76 CM0 N1 N N N 77 CM0 "C5'" C N N 78 CM0 O1P O N N 79 CM0 O2P O N N 80 CM0 "C4'" C N R 81 CM0 C2 C N N 82 CM0 C5 C N N 83 CM0 "O4'" O N N 84 CM0 "C2'" C N R 85 CM0 O2 O N N 86 CM0 N3 N N N 87 CM0 C4 C N N 88 CM0 O4 O N N 89 CM0 C6 C N N 90 CM0 C7 C N N 91 CM0 C8 C N N 92 CM0 O5 O N N 93 CM0 O8 O N N 94 CM0 "C1'" C N R 95 CM0 "O2'" O N N 96 CM0 O9 O N N 97 CM0 "O3'" O N N 98 CM0 H2P H N N 99 CM0 H3P H N N 100 CM0 "H5'1" H N N 101 CM0 "H5'2" H N N 102 CM0 "H4'" H N N 103 CM0 "H3'" H N N 104 CM0 "H1'" H N N 105 CM0 "H2'" H N N 106 CM0 H6 H N N 107 CM0 H3 H N N 108 CM0 H7C1 H N N 109 CM0 H7C2 H N N 110 CM0 H8 H N N 111 CM0 HA H N N 112 CM0 HB H N N 113 G OP3 O N N 114 G P P N N 115 G OP1 O N N 116 G OP2 O N N 117 G "O5'" O N N 118 G "C5'" C N N 119 G "C4'" C N R 120 G "O4'" O N N 121 G "C3'" C N S 122 G "O3'" O N N 123 G "C2'" C N R 124 G "O2'" O N N 125 G "C1'" C N R 126 G N9 N Y N 127 G C8 C Y N 128 G N7 N Y N 129 G C5 C Y N 130 G C6 C N N 131 G O6 O N N 132 G N1 N N N 133 G C2 C N N 134 G N2 N N N 135 G N3 N N N 136 G C4 C Y N 137 G HOP3 H N N 138 G HOP2 H N N 139 G "H5'" H N N 140 G "H5''" H N N 141 G "H4'" H N N 142 G "H3'" H N N 143 G "HO3'" H N N 144 G "H2'" H N N 145 G "HO2'" H N N 146 G "H1'" H N N 147 G H8 H N N 148 G H1 H N N 149 G H21 H N N 150 G H22 H N N 151 U OP3 O N N 152 U P P N N 153 U OP1 O N N 154 U OP2 O N N 155 U "O5'" O N N 156 U "C5'" C N N 157 U "C4'" C N R 158 U "O4'" O N N 159 U "C3'" C N S 160 U "O3'" O N N 161 U "C2'" C N R 162 U "O2'" O N N 163 U "C1'" C N R 164 U N1 N N N 165 U C2 C N N 166 U O2 O N N 167 U N3 N N N 168 U C4 C N N 169 U O4 O N N 170 U C5 C N N 171 U C6 C N N 172 U HOP3 H N N 173 U HOP2 H N N 174 U "H5'" H N N 175 U "H5''" H N N 176 U "H4'" H N N 177 U "H3'" H N N 178 U "HO3'" H N N 179 U "H2'" H N N 180 U "HO2'" H N N 181 U "H1'" H N N 182 U H3 H N N 183 U H5 H N N 184 U H6 H N N 185 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 CM0 P "O5'" sing N N 76 CM0 P O3P sing N N 77 CM0 "O5'" "C5'" sing N N 78 CM0 P O1P doub N N 79 CM0 P O2P sing N N 80 CM0 "C3'" "C4'" sing N N 81 CM0 "C5'" "C4'" sing N N 82 CM0 N1 C2 sing N N 83 CM0 "C4'" "O4'" sing N N 84 CM0 "C3'" "C2'" sing N N 85 CM0 C2 O2 doub N N 86 CM0 C2 N3 sing N N 87 CM0 C5 C4 sing N N 88 CM0 N3 C4 sing N N 89 CM0 C4 O4 doub N N 90 CM0 C5 C6 doub N N 91 CM0 N1 C6 sing N N 92 CM0 C7 C8 sing N N 93 CM0 C5 O5 sing N N 94 CM0 C7 O5 sing N N 95 CM0 C8 O8 sing N N 96 CM0 N1 "C1'" sing N N 97 CM0 "C2'" "C1'" sing N N 98 CM0 "O4'" "C1'" sing N N 99 CM0 "C2'" "O2'" sing N N 100 CM0 C8 O9 doub N N 101 CM0 "C3'" "O3'" sing N N 102 CM0 O2P H2P sing N N 103 CM0 O3P H3P sing N N 104 CM0 "C5'" "H5'1" sing N N 105 CM0 "C5'" "H5'2" sing N N 106 CM0 "C4'" "H4'" sing N N 107 CM0 "C3'" "H3'" sing N N 108 CM0 "C1'" "H1'" sing N N 109 CM0 "C2'" "H2'" sing N N 110 CM0 C6 H6 sing N N 111 CM0 N3 H3 sing N N 112 CM0 C7 H7C1 sing N N 113 CM0 C7 H7C2 sing N N 114 CM0 O8 H8 sing N N 115 CM0 "O2'" HA sing N N 116 CM0 "O3'" HB sing N N 117 G OP3 P sing N N 118 G OP3 HOP3 sing N N 119 G P OP1 doub N N 120 G P OP2 sing N N 121 G P "O5'" sing N N 122 G OP2 HOP2 sing N N 123 G "O5'" "C5'" sing N N 124 G "C5'" "C4'" sing N N 125 G "C5'" "H5'" sing N N 126 G "C5'" "H5''" sing N N 127 G "C4'" "O4'" sing N N 128 G "C4'" "C3'" sing N N 129 G "C4'" "H4'" sing N N 130 G "O4'" "C1'" sing N N 131 G "C3'" "O3'" sing N N 132 G "C3'" "C2'" sing N N 133 G "C3'" "H3'" sing N N 134 G "O3'" "HO3'" sing N N 135 G "C2'" "O2'" sing N N 136 G "C2'" "C1'" sing N N 137 G "C2'" "H2'" sing N N 138 G "O2'" "HO2'" sing N N 139 G "C1'" N9 sing N N 140 G "C1'" "H1'" sing N N 141 G N9 C8 sing Y N 142 G N9 C4 sing Y N 143 G C8 N7 doub Y N 144 G C8 H8 sing N N 145 G N7 C5 sing Y N 146 G C5 C6 sing N N 147 G C5 C4 doub Y N 148 G C6 O6 doub N N 149 G C6 N1 sing N N 150 G N1 C2 sing N N 151 G N1 H1 sing N N 152 G C2 N2 sing N N 153 G C2 N3 doub N N 154 G N2 H21 sing N N 155 G N2 H22 sing N N 156 G N3 C4 sing N N 157 U OP3 P sing N N 158 U OP3 HOP3 sing N N 159 U P OP1 doub N N 160 U P OP2 sing N N 161 U P "O5'" sing N N 162 U OP2 HOP2 sing N N 163 U "O5'" "C5'" sing N N 164 U "C5'" "C4'" sing N N 165 U "C5'" "H5'" sing N N 166 U "C5'" "H5''" sing N N 167 U "C4'" "O4'" sing N N 168 U "C4'" "C3'" sing N N 169 U "C4'" "H4'" sing N N 170 U "O4'" "C1'" sing N N 171 U "C3'" "O3'" sing N N 172 U "C3'" "C2'" sing N N 173 U "C3'" "H3'" sing N N 174 U "O3'" "HO3'" sing N N 175 U "C2'" "O2'" sing N N 176 U "C2'" "C1'" sing N N 177 U "C2'" "H2'" sing N N 178 U "O2'" "HO2'" sing N N 179 U "C1'" N1 sing N N 180 U "C1'" "H1'" sing N N 181 U N1 C2 sing N N 182 U N1 C6 sing N N 183 U C2 O2 doub N N 184 U C2 N3 sing N N 185 U N3 C4 sing N N 186 U N3 H3 sing N N 187 U C4 O4 doub N N 188 U C4 C5 sing N N 189 U C5 C6 doub N N 190 U C5 H5 sing N N 191 U C6 H6 sing N N 192 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2JRQ 'a-form double helix' 2JRQ 'hairpin loop' 2JRQ '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 C 1 1_555 A G 17 1_555 0.161 -0.064 -0.032 2.416 4.552 -4.716 1 A_C27:G43_A A 27 ? A 43 ? 19 1 1 A C 2 1_555 A G 16 1_555 0.137 -0.077 0.020 3.070 6.409 -5.587 2 A_C28:G42_A A 28 ? A 42 ? 19 1 1 A U 3 1_555 A A 15 1_555 -0.114 0.058 0.111 -0.729 2.521 -8.318 3 A_U29:A41_A A 29 ? A 41 ? 20 1 1 A C 4 1_555 A G 14 1_555 0.231 -0.117 0.140 -0.820 4.051 -2.921 4 A_C30:G40_A A 30 ? A 40 ? 19 1 1 A C 5 1_555 A G 13 1_555 0.028 -0.052 0.054 -0.679 3.739 -5.886 5 A_C31:G39_A A 31 ? A 39 ? 19 1 1 A C 6 1_555 A A 12 1_555 5.700 -2.051 2.206 -18.298 -2.051 0.226 6 A_C32:A38_A A 32 ? A 38 ? ? ? # 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 C 1 1_555 A G 17 1_555 A C 2 1_555 A G 16 1_555 -0.193 -1.700 3.348 -0.194 10.800 31.383 -4.690 0.307 2.635 19.265 0.347 33.145 1 AA_C27C28:G42G43_AA A 27 ? A 43 ? A 28 ? A 42 ? 1 A C 2 1_555 A G 16 1_555 A U 3 1_555 A A 15 1_555 -0.174 -1.803 3.533 -0.279 10.367 30.645 -5.066 0.264 2.792 18.946 0.509 32.312 2 AA_C28U29:A41G42_AA A 28 ? A 42 ? A 29 ? A 41 ? 1 A U 3 1_555 A A 15 1_555 A C 4 1_555 A G 14 1_555 0.283 -1.604 3.682 -0.423 -3.333 32.425 -2.191 -0.589 3.820 -5.949 0.756 32.594 3 AA_U29C30:G40A41_AA A 29 ? A 41 ? A 30 ? A 40 ? 1 A C 4 1_555 A G 14 1_555 A C 5 1_555 A G 13 1_555 -0.158 -1.696 3.317 1.649 11.114 31.905 -4.593 0.521 2.587 19.479 -2.891 33.777 4 AA_C30C31:G39G40_AA A 30 ? A 40 ? A 31 ? A 39 ? 1 A C 5 1_555 A G 13 1_555 A C 6 1_555 A A 12 1_555 0.158 -0.998 4.992 -2.308 2.189 52.741 -1.336 -0.404 4.940 2.462 2.595 52.830 5 AA_C31C32:A38G39_AA A 31 ? A 39 ? A 32 ? A 38 ? # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 500 Bruker AVANCE 1 'Bruker Avance' 600 Varian INOVA 2 'Varian INOVA' # _atom_sites.entry_id 2JRQ _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_