data_2KRV # _entry.id 2KRV # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 2KRV pdb_00002krv 10.2210/pdb2krv/pdb RCSB RCSB101496 ? ? BMRB 16650 ? 10.13018/BMR16650 WWPDB D_1000101496 ? ? # 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 2010-12-01 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 2 0 2024-05-01 # _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' 5 3 'Structure model' 'Polymer sequence' # 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' chem_comp 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' entity_poly 6 3 'Structure model' pdbx_nmr_software 7 3 'Structure model' pdbx_nmr_spectrometer 8 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' '_chem_comp.mon_nstd_flag' 2 3 'Structure model' '_database_2.pdbx_DOI' 3 3 'Structure model' '_database_2.pdbx_database_accession' 4 3 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 5 3 'Structure model' '_pdbx_nmr_software.name' 6 3 'Structure model' '_pdbx_nmr_spectrometer.model' 7 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KRV _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-12-22 _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.content_type _pdbx_database_related.details 16650 BMRB unspecified . 2KRY PDB unspecified . 2KRW PDB unspecified . 2KRZ PDB unspecified . 2KRQ PDB unspecified . 2KRP PDB unspecified . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Bilbille, Y.' 1 'Agris, P.F.' 2 # _citation.id primary _citation.title 'Solution structure of the tRNA-Arg-1 (ICG) ASL containg the 2-thiocytidine modification in position 32.' _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 'Bilbille, Y.' 1 ? primary 'Cantara, W.A.' 2 ? primary 'Kim, J.' 3 ? primary 'Agris, P.F.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*CP*UP*CP*GP*GP*(RSP)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3') ; _entity.formula_weight 5458.367 _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 'CUCGG(RSP)UICGAACCGAG' _entity_poly.pdbx_seq_one_letter_code_can CUCGGCUICGAACCGAG _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 U n 1 3 C n 1 4 G n 1 5 G n 1 6 RSP n 1 7 U n 1 8 I n 1 9 C n 1 10 G n 1 11 A n 1 12 A n 1 13 C n 1 14 C n 1 15 G n 1 16 A 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 I 'RNA linking' y 'INOSINIC ACID' ? 'C10 H13 N4 O8 P' 348.206 RSP 'RNA linking' n '4-amino-1-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidine-2(1H)-thione' ? 'C9 H14 N3 O7 P S' 339.262 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 1 1 C C A . n A 1 2 U 2 2 2 U U A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 RSP 6 6 6 RSP RSP A . n A 1 7 U 7 7 7 U U A . n A 1 8 I 8 8 8 I I 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 A 11 11 11 A A A . n A 1 12 A 12 12 12 A A A . n A 1 13 C 13 13 13 C C A . n A 1 14 C 14 14 14 C C A . n A 1 15 G 15 15 15 G G A . n A 1 16 A 16 16 16 A A A . n A 1 17 G 17 17 17 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 2KRV _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KRV _struct.title 'Solution structure of the E. coli tRNA-Arg1 (ICG) ASL containing the 2-thiocytidine modification' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KRV _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, tRNA, 2-thiocytidine, modification, ASL' # _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.db_name PDB _struct_ref.db_code 2KRV _struct_ref.pdbx_db_accession 2KRV _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code CUCGGXUICGAACCGAG _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2KRV _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 2KRV _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 17 _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 17 # _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 _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 5 "O3'" ? ? ? 1_555 A RSP 6 P ? ? A G 5 A RSP 6 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale both ? A RSP 6 "O3'" ? ? ? 1_555 A U 7 P ? ? A RSP 6 A U 7 1_555 ? ? ? ? ? ? ? 1.609 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 1 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 1 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 1 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 A A 16 N1 ? ? A U 2 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 A A 16 N6 ? ? A U 2 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 3 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 3 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 3 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 4 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 4 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 4 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 5 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 5 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 5 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 3 "H4'" A C 9 ? ? "O5'" A G 10 ? ? 1.57 2 7 "H4'" A C 9 ? ? "O5'" A G 10 ? ? 1.54 3 9 "H4'" A C 9 ? ? "O5'" A G 10 ? ? 1.59 # _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 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KRV _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 2KRV _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;0.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-1, 90% H2O/10% D2O ; 1 '90% H2O/10% D2O' ;0.8 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-2, 100% D2O ; 2 '100% D2O' # 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(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-1 ; 0.8 ? mM ? 1 ;RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*IP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-2 ; 0.8 ? mM ? 2 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 20 _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # 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 2 '2D 1H-1H NOESY' 1 3 2 '2D DQF-COSY' 1 4 1 '2D 1H-1H COSY' 1 5 1 '2D 1H-1H TOCSY' 1 6 2 '2D 1H-13C HSQC' 1 7 2 '2D 1H-31P HETCOR' # _pdbx_nmr_refine.entry_id 2KRV _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _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 'Bruker Biospin' collection TopSpin ? 2 Varian collection VnmrJ ? 3 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRPipe ? 4 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRDraw ? 5 Goddard 'chemical shift assignment' Sparky ? 6 Goddard 'data analysis' Sparky ? 7 Goddard 'peak picking' Sparky ? 8 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.21 9 'Koradi, Billeter and Wuthrich' 'data analysis' MOLMOL ? 10 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNS 1.21 11 # 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 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 I OP3 O N N 111 I P P N N 112 I OP1 O N N 113 I OP2 O N N 114 I "O5'" O N N 115 I "C5'" C N N 116 I "C4'" C N R 117 I "O4'" O N N 118 I "C3'" C N S 119 I "O3'" O N N 120 I "C2'" C N R 121 I "O2'" O N N 122 I "C1'" C N R 123 I N9 N Y N 124 I C8 C Y N 125 I N7 N Y N 126 I C5 C Y N 127 I C6 C N N 128 I O6 O N N 129 I N1 N N N 130 I C2 C N N 131 I N3 N N N 132 I C4 C Y N 133 I HOP3 H N N 134 I HOP2 H N N 135 I "H5'" H N N 136 I "H5''" H N N 137 I "H4'" H N N 138 I "H3'" H N N 139 I "HO3'" H N N 140 I "H2'" H N N 141 I "HO2'" H N N 142 I "H1'" H N N 143 I H8 H N N 144 I H1 H N N 145 I H2 H N N 146 RSP P P N N 147 RSP N1 N N N 148 RSP C2 C N N 149 RSP S2 S N N 150 RSP N3 N N N 151 RSP C4 C N N 152 RSP N4 N N N 153 RSP C5 C N N 154 RSP C6 C N N 155 RSP "C1'" C N R 156 RSP "C2'" C N R 157 RSP "O2'" O N N 158 RSP "C3'" C N S 159 RSP "O3'" O N N 160 RSP "C4'" C N R 161 RSP "O4'" O N N 162 RSP "C5'" C N N 163 RSP "O5'" O N N 164 RSP OP1 O N N 165 RSP OP2 O N N 166 RSP OP3 O N N 167 RSP H5 H N N 168 RSP H6 H N N 169 RSP "H5'" H N N 170 RSP "H1'" H N N 171 RSP "H2'" H N N 172 RSP "HO2'" H N N 173 RSP "H3'" H N N 174 RSP "H4'" H N N 175 RSP HN4 H N N 176 RSP HN4A H N N 177 RSP "H5'A" H N N 178 RSP "HO3'" H N N 179 RSP HOP2 H N N 180 RSP HOP3 H N N 181 U OP3 O N N 182 U P P N N 183 U OP1 O N N 184 U OP2 O N N 185 U "O5'" O N N 186 U "C5'" C N N 187 U "C4'" C N R 188 U "O4'" O N N 189 U "C3'" C N S 190 U "O3'" O N N 191 U "C2'" C N R 192 U "O2'" O N N 193 U "C1'" C N R 194 U N1 N N N 195 U C2 C N N 196 U O2 O N N 197 U N3 N N N 198 U C4 C N N 199 U O4 O N N 200 U C5 C N N 201 U C6 C N N 202 U HOP3 H N N 203 U HOP2 H N N 204 U "H5'" H N N 205 U "H5''" H N N 206 U "H4'" H N N 207 U "H3'" H N N 208 U "HO3'" H N N 209 U "H2'" H N N 210 U "HO2'" H N N 211 U "H1'" H N N 212 U H3 H N N 213 U H5 H N N 214 U H6 H N N 215 # 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 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 I OP3 P sing N N 116 I OP3 HOP3 sing N N 117 I P OP1 doub N N 118 I P OP2 sing N N 119 I P "O5'" sing N N 120 I OP2 HOP2 sing N N 121 I "O5'" "C5'" sing N N 122 I "C5'" "C4'" sing N N 123 I "C5'" "H5'" sing N N 124 I "C5'" "H5''" sing N N 125 I "C4'" "O4'" sing N N 126 I "C4'" "C3'" sing N N 127 I "C4'" "H4'" sing N N 128 I "O4'" "C1'" sing N N 129 I "C3'" "O3'" sing N N 130 I "C3'" "C2'" sing N N 131 I "C3'" "H3'" sing N N 132 I "O3'" "HO3'" sing N N 133 I "C2'" "O2'" sing N N 134 I "C2'" "C1'" sing N N 135 I "C2'" "H2'" sing N N 136 I "O2'" "HO2'" sing N N 137 I "C1'" N9 sing N N 138 I "C1'" "H1'" sing N N 139 I N9 C8 sing Y N 140 I N9 C4 sing Y N 141 I C8 N7 doub Y N 142 I C8 H8 sing N N 143 I N7 C5 sing Y N 144 I C5 C6 sing N N 145 I C5 C4 doub Y N 146 I C6 O6 doub N N 147 I C6 N1 sing N N 148 I N1 C2 sing N N 149 I N1 H1 sing N N 150 I C2 N3 doub N N 151 I C2 H2 sing N N 152 I N3 C4 sing N N 153 RSP OP1 P doub N N 154 RSP OP3 P sing N N 155 RSP P OP2 sing N N 156 RSP P "O5'" sing N N 157 RSP C6 N1 sing N N 158 RSP N1 C2 sing N N 159 RSP N1 "C1'" sing N N 160 RSP N3 C2 sing N N 161 RSP C2 S2 doub N N 162 RSP C4 N3 doub N N 163 RSP N4 C4 sing N N 164 RSP C5 C4 sing N N 165 RSP HN4 N4 sing N N 166 RSP N4 HN4A sing N N 167 RSP H5 C5 sing N N 168 RSP C5 C6 doub N N 169 RSP H6 C6 sing N N 170 RSP "O4'" "C1'" sing N N 171 RSP "C1'" "H1'" sing N N 172 RSP "C1'" "C2'" sing N N 173 RSP "C3'" "C2'" sing N N 174 RSP "C2'" "H2'" sing N N 175 RSP "C2'" "O2'" sing N N 176 RSP "O2'" "HO2'" sing N N 177 RSP "C4'" "C3'" sing N N 178 RSP "H3'" "C3'" sing N N 179 RSP "C3'" "O3'" sing N N 180 RSP "O3'" "HO3'" sing N N 181 RSP "C5'" "C4'" sing N N 182 RSP "O4'" "C4'" sing N N 183 RSP "C4'" "H4'" sing N N 184 RSP "O5'" "C5'" sing N N 185 RSP "H5'A" "C5'" sing N N 186 RSP "C5'" "H5'" sing N N 187 RSP OP2 HOP2 sing N N 188 RSP OP3 HOP3 sing N N 189 U OP3 P sing N N 190 U OP3 HOP3 sing N N 191 U P OP1 doub N N 192 U P OP2 sing N N 193 U P "O5'" sing N N 194 U OP2 HOP2 sing N N 195 U "O5'" "C5'" sing N N 196 U "C5'" "C4'" sing N N 197 U "C5'" "H5'" sing N N 198 U "C5'" "H5''" sing N N 199 U "C4'" "O4'" sing N N 200 U "C4'" "C3'" sing N N 201 U "C4'" "H4'" sing N N 202 U "O4'" "C1'" sing N N 203 U "C3'" "O3'" sing N N 204 U "C3'" "C2'" sing N N 205 U "C3'" "H3'" sing N N 206 U "O3'" "HO3'" sing N N 207 U "C2'" "O2'" sing N N 208 U "C2'" "C1'" sing N N 209 U "C2'" "H2'" sing N N 210 U "O2'" "HO2'" sing N N 211 U "C1'" N1 sing N N 212 U "C1'" "H1'" sing N N 213 U N1 C2 sing N N 214 U N1 C6 sing N N 215 U C2 O2 doub N N 216 U C2 N3 sing N N 217 U N3 C4 sing N N 218 U N3 H3 sing N N 219 U C4 O4 doub N N 220 U C4 C5 sing N N 221 U C5 C6 doub N N 222 U C5 H5 sing N N 223 U C6 H6 sing N N 224 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2KRV 'a-form double helix' 2KRV 'hairpin 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 C 1 1_555 A G 17 1_555 0.092 -0.162 0.609 -4.563 -5.841 -3.356 1 A_C1:G17_A A 1 ? A 17 ? 19 1 1 A U 2 1_555 A A 16 1_555 -0.330 -0.025 -0.221 8.287 -20.093 -2.097 2 A_U2:A16_A A 2 ? A 16 ? 20 1 1 A C 3 1_555 A G 15 1_555 0.773 -0.235 -0.338 25.203 -12.216 -1.799 3 A_C3:G15_A A 3 ? A 15 ? 19 1 1 A G 4 1_555 A C 14 1_555 -0.374 -0.165 -0.345 10.083 2.004 -1.362 4 A_G4:C14_A A 4 ? A 14 ? 19 1 1 A G 5 1_555 A C 13 1_555 -0.197 -0.167 0.033 -10.681 -22.053 -2.686 5 A_G5:C13_A A 5 ? A 13 ? 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 C 1 1_555 A G 17 1_555 A U 2 1_555 A A 16 1_555 -0.569 -0.892 2.884 7.576 4.391 29.007 -2.455 2.378 2.500 8.524 -14.707 30.273 1 AA_C1U2:A16G17_AA A 1 ? A 17 ? A 2 ? A 16 ? 1 A U 2 1_555 A A 16 1_555 A C 3 1_555 A G 15 1_555 0.653 -0.103 3.110 -0.127 3.019 37.501 -0.532 -1.028 3.091 4.686 0.197 37.619 2 AA_U2C3:G15A16_AA A 2 ? A 16 ? A 3 ? A 15 ? 1 A C 3 1_555 A G 15 1_555 A G 4 1_555 A C 14 1_555 0.416 -1.868 3.795 1.630 11.138 26.104 -6.508 -0.453 2.798 23.328 -3.413 28.389 3 AA_C3G4:C14G15_AA A 3 ? A 15 ? A 4 ? A 14 ? 1 A G 4 1_555 A C 14 1_555 A G 5 1_555 A C 13 1_555 -0.160 -0.943 5.282 3.360 -7.612 35.119 0.251 1.042 5.326 -12.400 -5.475 36.061 4 AA_G4G5:C13C14_AA A 4 ? A 14 ? A 5 ? A 13 ? # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 600 Varian INOVA 1 'Varian INOVA' 500 Bruker AVANCE 2 'Bruker Avance' # _atom_sites.entry_id 2KRV _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 S # loop_