data_2K7E # _entry.id 2K7E # _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 2K7E pdb_00002k7e 10.2210/pdb2k7e/pdb RCSB RCSB100769 ? ? WWPDB D_1000100769 ? ? # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2K7E _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-08-09 _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 'Bilbille, Y.' 1 'Vendeix, F.P.A.' 2 'Guenther, R.' 3 'Malkiewicz, A.' 4 'Ariza, X.' 5 'Vilarrasa, J.' 6 'Agris, P.' 7 # _citation.id primary _citation.title ;The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 37 _citation.page_first 3342 _citation.page_last 3353 _citation.year 2009 _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 19324888 _citation.pdbx_database_id_DOI 10.1093/nar/gkp187 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bilbille, Y.' 1 ? primary 'Vendeix, F.A.' 2 ? primary 'Guenther, R.' 3 ? primary 'Malkiewicz, A.' 4 ? primary 'Ariza, X.' 5 ? primary 'Vilarrasa, J.' 6 ? primary 'Agris, P.F.' 7 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') ; 3915.408 1 ? ? ? 'HIV A-loop' 2 polymer syn ;RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') ; 3727.266 1 ? ? ? 'tRNALys3 ASL' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GCGGUGUAAAAG GCGGUGUAAAAG A ? 2 polyribonucleotide no yes 'CU(SUR)UUAA(PSU)CUGC' CUUUUAAUCUGC B ? # 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 C n 1 3 G n 1 4 G n 1 5 U n 1 6 G n 1 7 U n 1 8 A n 1 9 A n 1 10 A n 1 11 A n 1 12 G n 2 1 C n 2 2 U n 2 3 SUR n 2 4 U n 2 5 U n 2 6 A n 2 7 A n 2 8 PSU n 2 9 C n 2 10 U n 2 11 G n 2 12 C n # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 2K7E 2K7E 1 1 GCGGUGUAAAAG ? 2 PDB 2K7E 2K7E 2 1 CUUUUAAUCUGC ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2K7E A 1 ? 12 ? 2K7E 1 ? 12 ? 1 12 2 2 2K7E B 1 ? 12 ? 2K7E 1 ? 12 ? 1 12 # 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 PSU 'RNA linking' n "PSEUDOURIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 SUR 'RNA linking' n "1-(BETA-D-RIBOFURANOSYL)-2-THIO-URACIL-5'-PHOSPHATE" ? 'C9 H13 N2 O8 P S' 340.247 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 1 '2D 1H-1H NOESY' 2 3 2 '2D 1H-13C HSQC' 2 4 2 '2D DQF-COSY' 2 5 2 '2D 1H-1H NOESY' 1 6 1 '2D 1H-15N 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 0.1 6.5 ambient ? 276 K 2 0.1 6.5 ambient ? 293 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;0.3 mM RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'), 0.3 mM T-RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O ; 1 '90% H2O/10% D2O' ;0.3 mM RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'), 0.3 mM T-RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 100% D2O ; 2 '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 500 Bruker AVANCE 1 'Bruker Avance' 600 Varian INOVA 2 'Varian INOVA' # _pdbx_nmr_refine.entry_id 2K7E _pdbx_nmr_refine.method 'simulated annealing' _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 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2K7E _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 2K7E _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 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.1 1 Goddard 'chemical shift assignment' Sparky ? 2 'Koradi, Billeter and Wuthrich' 'data analysis' MOLMOL ? 3 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 'data analysis' NMRDraw ? 4 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRPipe ? 5 'Johnson, One Moon Scientific' 'data analysis' NMRView ? 6 'Bruker Biospin' collection XwinNMR ? 7 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNS 1.1 8 # _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 ;NMR structure of the human tRNALys3 bound to the HIV genome Loop I containing 2 modified nucleosides: pseudouridine and 2-thiouridine in position 39 and 34 respectively ; _exptl.entry_id 2K7E _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2K7E _struct.title 'NMR structure of the human tRNALys3 bound to the HIV genome Loop I' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2K7E _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, tRNALys3, pseudouridine, HIV, 2-thiouridine, S2U, PSU, modifications' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _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 ? B U 2 "O3'" ? ? ? 1_555 B SUR 3 P ? ? B U 2 B SUR 3 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale both ? B SUR 3 "O3'" ? ? ? 1_555 B U 4 P ? ? B SUR 3 B U 4 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale3 covale both ? B A 7 "O3'" ? ? ? 1_555 B PSU 8 P ? ? B A 7 B PSU 8 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale4 covale both ? B PSU 8 "O3'" ? ? ? 1_555 B C 9 P ? ? B PSU 8 B C 9 1_555 ? ? ? ? ? ? ? 1.608 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 2 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 2 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 2 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B U 10 O2 ? ? A G 3 B U 10 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 B U 10 N3 ? ? A G 3 B U 10 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 4 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 4 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 4 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 N1 ? ? ? 1_555 B A 7 N1 ? ? A G 6 B A 7 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog13 hydrog ? ? A G 6 O6 ? ? ? 1_555 B A 7 N6 ? ? A G 6 B A 7 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog14 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 6 N1 ? ? A U 7 B A 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 6 N6 ? ? A U 7 B A 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 8 N1 ? ? ? 1_555 B U 5 N3 ? ? A A 8 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 8 N6 ? ? ? 1_555 B U 5 O4 ? ? A A 8 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 9 B U 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 9 B U 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N1 ? ? ? 1_555 B SUR 3 N3 ? ? A A 10 B SUR 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 10 N6 ? ? ? 1_555 B SUR 3 O4 ? ? A A 10 B SUR 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 11 N1 ? ? ? 1_555 B U 2 N3 ? ? A A 11 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 11 N6 ? ? ? 1_555 B U 2 O4 ? ? A A 11 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 12 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 12 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 12 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2K7E _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_ _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 C 2 2 2 C C A . n A 1 3 G 3 3 3 G G A . n A 1 4 G 4 4 4 G G A . n A 1 5 U 5 5 5 U U 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 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 A 11 11 11 A A A . n A 1 12 G 12 12 12 G G A . n B 2 1 C 1 1 1 C C B . n B 2 2 U 2 2 2 U U B . n B 2 3 SUR 3 3 3 SUR SUR B . n B 2 4 U 4 4 4 U U B . n B 2 5 U 5 5 5 U U B . n B 2 6 A 6 6 6 A A B . n B 2 7 A 7 7 7 A A B . n B 2 8 PSU 8 8 8 PSU PSU B . n B 2 9 C 9 9 9 C C B . n B 2 10 U 10 10 10 U U B . n B 2 11 G 11 11 11 G G B . n B 2 12 C 12 12 12 C C B . n # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 B SUR 3 B SUR 3 ? U ? 2 B PSU 8 B PSU 8 ? U "PSEUDOURIDINE-5'-MONOPHOSPHATE" # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 2008-10-07 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_nmr_spectrometer 4 3 'Structure model' pdbx_struct_assembly 5 3 'Structure model' pdbx_struct_oper_list 6 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_nmr_software.name' 4 3 'Structure model' '_pdbx_nmr_spectrometer.model' 5 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_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id ;RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') ; 0.3 mM ? 1 ;T-RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') ; 0.3 mM ? 1 'sodium phosphate' 10 mM ? 1 'sodium chloride' 100 mM ? 1 ;RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3') ; 0.3 mM ? 2 ;T-RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3') ; 0.3 mM ? 2 'sodium phosphate' 10 mM ? 2 'sodium chloride' 100 mM ? 2 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2K7E _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _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 292 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 115 _pdbx_nmr_constraints.NOE_long_range_total_count 0 _pdbx_nmr_constraints.NOE_medium_range_total_count 0 _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count 139 _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 H61 A A 10 ? ? O4 B SUR 3 ? ? 1.60 2 6 H61 A A 11 ? ? O4 B U 2 ? ? 1.60 3 7 H61 A A 10 ? ? O4 B SUR 3 ? ? 1.60 4 8 H61 A A 10 ? ? O4 B SUR 3 ? ? 1.59 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2K7E 'double helix' 2K7E 'a-form double helix' 2K7E '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 B C 12 1_555 -0.625 -0.287 0.086 -12.317 -3.536 0.271 1 A_G1:C12_B A 1 ? B 12 ? 19 1 1 A C 2 1_555 B G 11 1_555 0.461 -0.312 0.058 -3.400 -7.777 -0.636 2 A_C2:G11_B A 2 ? B 11 ? 19 1 1 A G 3 1_555 B U 10 1_555 -1.877 -0.257 0.080 -1.952 -7.565 -2.988 3 A_G3:U10_B A 3 ? B 10 ? 28 ? 1 A G 4 1_555 B C 9 1_555 -0.670 -0.359 0.103 2.937 -7.520 -4.150 4 A_G4:C9_B A 4 ? B 9 ? 19 1 1 A G 6 1_555 B A 7 1_555 -0.430 1.169 -0.568 -1.660 -14.902 -12.977 5 A_G6:A7_B A 6 ? B 7 ? 8 ? 1 A U 7 1_555 B A 6 1_555 -0.087 -0.270 0.102 0.264 -19.198 -1.198 6 A_U7:A6_B A 7 ? B 6 ? 20 1 1 A A 8 1_555 B U 5 1_555 -0.501 -0.408 -0.045 -3.974 -10.238 2.590 7 A_A8:U5_B A 8 ? B 5 ? 20 1 1 A A 9 1_555 B U 4 1_555 0.009 -0.257 0.219 -3.119 -14.330 4.209 8 A_A9:U4_B A 9 ? B 4 ? 20 1 1 A A 10 1_555 B SUR 3 1_555 0.185 -0.303 0.261 4.304 -10.693 -6.343 9 A_A10:SUR3_B A 10 ? B 3 ? 20 1 1 A A 11 1_555 B U 2 1_555 -0.001 -0.288 -0.020 -1.539 -2.265 -3.536 10 A_A11:U2_B A 11 ? B 2 ? 20 1 1 A G 12 1_555 B C 1 1_555 -0.435 -0.311 0.273 11.845 -9.447 -0.627 11 A_G12:C1_B A 12 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 12 1_555 A C 2 1_555 B G 11 1_555 -0.704 -0.335 3.195 1.042 11.933 35.270 -2.052 1.237 2.913 19.029 -1.662 37.187 1 AA_G1C2:G11C12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A C 2 1_555 B G 11 1_555 A G 3 1_555 B U 10 1_555 -0.269 -0.749 3.262 -1.903 17.323 26.348 -4.415 0.163 2.349 33.718 3.704 31.504 2 AA_C2G3:U10G11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A G 3 1_555 B U 10 1_555 A G 4 1_555 B C 9 1_555 -0.131 -0.350 3.391 -3.186 7.467 34.563 -1.699 -0.266 3.246 12.358 5.272 35.475 3 AA_G3G4:C9U10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A G 4 1_555 B C 9 1_555 A G 6 1_555 B A 7 1_555 -1.345 -1.093 6.622 -2.948 15.659 71.698 -1.932 0.937 6.348 13.208 2.486 73.215 4 AA_G4G6:A7C9_BB A 4 ? B 9 ? A 6 ? B 7 ? 1 A G 6 1_555 B A 7 1_555 A U 7 1_555 B A 6 1_555 1.539 -0.528 3.127 -5.225 1.974 33.357 -1.200 -3.420 2.826 3.410 9.025 33.808 5 AA_G6U7:A6A7_BB A 6 ? B 7 ? A 7 ? B 6 ? 1 A U 7 1_555 B A 6 1_555 A A 8 1_555 B U 5 1_555 -0.663 -0.878 3.389 -4.319 4.276 37.397 -1.920 0.450 3.325 6.616 6.682 37.870 6 AA_U7A8:U5A6_BB A 7 ? B 6 ? A 8 ? B 5 ? 1 A A 8 1_555 B U 5 1_555 A A 9 1_555 B U 4 1_555 0.134 -0.862 3.142 -1.545 5.330 35.449 -2.119 -0.426 2.977 8.688 2.518 35.866 7 AA_A8A9:U4U5_BB A 8 ? B 5 ? A 9 ? B 4 ? 1 A A 9 1_555 B U 4 1_555 A A 10 1_555 B SUR 3 1_555 -1.238 -0.338 2.975 -1.319 4.569 38.898 -1.001 1.703 2.956 6.830 1.972 39.177 8 AA_A9A10:SUR3U4_BB A 9 ? B 4 ? A 10 ? B 3 ? 1 A A 10 1_555 B SUR 3 1_555 A A 11 1_555 B U 2 1_555 0.279 -0.706 3.958 0.555 8.996 29.061 -3.477 -0.400 3.588 17.407 -1.075 30.397 9 AA_A10A11:U2SUR3_BB A 10 ? B 3 ? A 11 ? B 2 ? 1 A A 11 1_555 B U 2 1_555 A G 12 1_555 B C 1 1_555 0.518 -0.507 3.114 -1.345 7.858 28.118 -2.593 -1.299 2.844 15.776 2.700 29.205 10 AA_A11G12:C1U2_BB A 11 ? B 2 ? A 12 ? B 1 ? #