data_2KD4 # _entry.id 2KD4 # _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 2KD4 pdb_00002kd4 10.2210/pdb2kd4/pdb RCSB RCSB100971 ? ? WWPDB D_1000100971 ? ? # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KD4 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-01-02 _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 'Horowitz, E.D.' 1 'Lilavivat, S.' 2 'Holladay, B.W.' 3 'Germann, M.W.' 4 'Hud, N.V.' 5 # _citation.id primary _citation.title ;Solution structure and thermodynamics of 2',5' RNA intercalation. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 131 _citation.page_first 5831 _citation.page_last 5838 _citation.year 2009 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19309071 _citation.pdbx_database_id_DOI 10.1021/ja810068e # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Horowitz, E.D.' 1 ? primary 'Lilavivat, S.' 2 ? primary 'Holladay, B.W.' 3 ? primary 'Germann, M.W.' 4 ? primary 'Hud, N.V.' 5 ? # 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 "5'-R(*GP*CP*CP*GP*CP*GP*GP*C)-2'" 2556.593 2 ? ? ? ? 2 non-polymer syn PROFLAVIN 209.247 2 ? ? ? ? # _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 GCCGCGGC _entity_poly.pdbx_seq_one_letter_code_can GCCGCGGC _entity_poly.pdbx_strand_id A,B _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 C n 1 3 C n 1 4 G n 1 5 C n 1 6 G n 1 7 G n 1 8 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details ;Synthetic 2',5' RNA ; # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2KD4 _struct_ref.pdbx_db_accession 2KD4 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code GCCGCGGC _struct_ref.pdbx_db_isoform ? # 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 2KD4 A 1 ? 8 ? 2KD4 1 ? 8 ? 1 8 2 1 2KD4 B 1 ? 8 ? 2KD4 1 ? 8 ? 1 8 # 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 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 PRL non-polymer . PROFLAVIN ? 'C13 H11 N3' 209.247 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '1H-1H NOESY' 1 2 1 '31P-1H HETCOR' 1 3 1 '1H-1H TOCSY' 1 4 1 '31P-decoupled 1H-1H COSY' 2 5 1 '1H-1H NOESY with WATERGATE water suppression' # 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 1 260 6.5 1 atm 282 K 2 130 ? 1 atm 282 K # _pdbx_nmr_sample_details.contents ;2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4, 99.9% D2O ; _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '99.9% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 600 Bruker DRX 1 'Bruker DRX' 500 Bruker DRX 2 'Bruker DRX' # _pdbx_nmr_refine.entry_id 2KD4 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details '300 random structures were generated and annealed. The lowest 10 energy structures were then re-annealed' _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 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KD4 _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 2KD4 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Bruker Biospin' collection XwinNMR ? 1 'Bruker Biospin' 'data analysis' XwinNMR ? 2 'Bruker Biospin' processing XwinNMR ? 3 Goddard 'chemical shift assignment' Sparky ? 4 Goddard 'data analysis' Sparky ? 5 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' 'structure solution' Amber ? 6 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' refinement Amber ? 7 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2KD4 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KD4 _struct.title ;Solution structure and thermodynamics of 2',5' RNA intercalation ; _struct.pdbx_model_details 'lowest energy, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KD4 _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;proflavine, intercalation, 2', 5' RNA, RNA, nearest-neighbor exclusion ; # 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 1 ? C N N 2 ? D 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 one ? A G 1 "O2'" ? ? ? 1_555 A C 2 P ? ? A G 1 A C 2 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale one ? A C 2 "O2'" ? ? ? 1_555 A C 3 P ? ? A C 2 A C 3 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale3 covale one ? A C 3 "O2'" ? ? ? 1_555 A G 4 P ? ? A C 3 A G 4 1_555 ? ? ? ? ? ? ? 1.625 ? ? covale4 covale one ? A G 4 "O2'" ? ? ? 1_555 A C 5 P ? ? A G 4 A C 5 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale5 covale one ? A C 5 "O2'" ? ? ? 1_555 A G 6 P ? ? A C 5 A G 6 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale6 covale one ? A G 6 "O2'" ? ? ? 1_555 A G 7 P ? ? A G 6 A G 7 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale7 covale one ? A G 7 "O2'" ? ? ? 1_555 A C 8 P ? ? A G 7 A C 8 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale8 covale one ? B G 1 "O2'" ? ? ? 1_555 B C 2 P ? ? B G 1 B C 2 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale9 covale one ? B C 2 "O2'" ? ? ? 1_555 B C 3 P ? ? B C 2 B C 3 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale10 covale one ? B C 3 "O2'" ? ? ? 1_555 B G 4 P ? ? B C 3 B G 4 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale11 covale one ? B G 4 "O2'" ? ? ? 1_555 B C 5 P ? ? B G 4 B C 5 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale12 covale one ? B C 5 "O2'" ? ? ? 1_555 B G 6 P ? ? B C 5 B G 6 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale13 covale one ? B G 6 "O2'" ? ? ? 1_555 B G 7 P ? ? B G 6 B G 7 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale14 covale one ? B G 7 "O2'" ? ? ? 1_555 B C 8 P ? ? B G 7 B C 8 1_555 ? ? ? ? ? ? ? 1.601 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 1 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 1 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 1 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 2 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 2 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 2 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 3 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 3 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 3 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 4 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 4 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 4 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 5 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 5 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 5 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 6 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 6 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 6 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 8 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 8 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 8 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B PRL 17 ? 5 'BINDING SITE FOR RESIDUE PRL B 17' AC2 Software A PRL 17 ? 5 'BINDING SITE FOR RESIDUE PRL A 17' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 5 G A 4 ? G A 4 . ? 1_555 ? 2 AC1 5 C A 5 ? C A 5 . ? 1_555 ? 3 AC1 5 G A 6 ? G A 6 . ? 1_555 ? 4 AC1 5 C B 3 ? C B 3 . ? 1_555 ? 5 AC1 5 G B 4 ? G B 4 . ? 1_555 ? 6 AC2 5 C A 2 ? C A 2 . ? 1_555 ? 7 AC2 5 C A 3 ? C A 3 . ? 1_555 ? 8 AC2 5 G A 4 ? G A 4 . ? 1_555 ? 9 AC2 5 C B 5 ? C B 5 . ? 1_555 ? 10 AC2 5 G B 6 ? G B 6 . ? 1_555 ? # _atom_sites.entry_id 2KD4 _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 C 2 2 2 C C 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 C 5 5 5 C C A . n A 1 6 G 6 6 6 G G A . n A 1 7 G 7 7 7 G G A . n A 1 8 C 8 8 8 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 C 2 2 2 C C B . n B 1 3 C 3 3 3 C C B . n B 1 4 G 4 4 4 G G B . n B 1 5 C 5 5 5 C C B . n B 1 6 G 6 6 6 G G B . n B 1 7 G 7 7 7 G G B . n B 1 8 C 8 8 8 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 PRL 1 17 17 PRL PRL A . D 2 PRL 1 17 17 PRL PRL B . # _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,C,D # _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 2009-04-07 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' Advisory 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 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 5 3 'Structure model' pdbx_validate_polymer_linkage 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site # 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' '_struct_conn.pdbx_leaving_atom_flag' 5 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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 ;2',5' RNA-1 ; 2 ? mM ? 1 PROFLAVINE-2 4 ? mM ? 1 'Sodium phosphate-3' 60 ? mM ? 1 'sodium chloride-4' 200 ? mM ? 1 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2KD4 _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count 14 _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 14 _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total 378 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 258 _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count 378 _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count 258 _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_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 "O4'" A G 1 ? ? "C4'" A G 1 ? ? "C3'" A G 1 ? ? 113.38 106.10 7.28 0.80 N 2 1 "C5'" A G 1 ? ? "C4'" A G 1 ? ? "O4'" A G 1 ? ? 115.29 109.80 5.49 0.90 N 3 1 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 116.29 113.10 3.19 0.50 N 4 1 "O4'" A C 2 ? ? "C4'" A C 2 ? ? "C3'" A C 2 ? ? 113.20 106.10 7.10 0.80 N 5 1 "C3'" A C 2 ? ? "C2'" A C 2 ? ? "C1'" A C 2 ? ? 107.62 101.50 6.12 0.80 N 6 1 "O4'" A C 2 ? ? "C1'" A C 2 ? ? N1 A C 2 ? ? 102.80 108.20 -5.40 0.80 N 7 1 N1 A C 2 ? ? C2 A C 2 ? ? O2 A C 2 ? ? 122.66 118.90 3.76 0.60 N 8 1 N3 A C 5 ? ? C2 A C 5 ? ? O2 A C 5 ? ? 117.58 121.90 -4.32 0.70 N 9 1 C8 A G 6 ? ? N9 A G 6 ? ? C4 A G 6 ? ? 103.85 106.40 -2.55 0.40 N 10 1 "O5'" A G 7 ? ? "C5'" A G 7 ? ? "C4'" A G 7 ? ? 125.35 111.70 13.65 1.90 N 11 1 "C5'" A G 7 ? ? "C4'" A G 7 ? ? "C3'" A G 7 ? ? 104.82 115.20 -10.38 1.40 N 12 1 "O4'" A G 7 ? ? "C1'" A G 7 ? ? N9 A G 7 ? ? 102.52 108.20 -5.68 0.80 N 13 1 "O4'" A C 8 ? ? "C4'" A C 8 ? ? "C3'" A C 8 ? ? 111.10 106.10 5.00 0.80 N 14 1 "C5'" A C 8 ? ? "C4'" A C 8 ? ? "O4'" A C 8 ? ? 115.81 109.80 6.01 0.90 N 15 1 "C3'" A C 8 ? ? "C2'" A C 8 ? ? "C1'" A C 8 ? ? 106.94 101.50 5.44 0.80 N 16 1 C6 A C 8 ? ? N1 A C 8 ? ? "C1'" A C 8 ? ? 113.21 120.80 -7.59 1.20 N 17 1 C2 A C 8 ? ? N1 A C 8 ? ? "C1'" A C 8 ? ? 126.86 118.80 8.06 1.10 N 18 1 "O4'" B G 1 ? ? "C4'" B G 1 ? ? "C3'" B G 1 ? ? 112.98 106.10 6.88 0.80 N 19 1 "C5'" B G 1 ? ? "C4'" B G 1 ? ? "O4'" B G 1 ? ? 115.77 109.80 5.97 0.90 N 20 1 "O4'" B C 2 ? ? "C4'" B C 2 ? ? "C3'" B C 2 ? ? 112.98 106.10 6.88 0.80 N 21 1 "C3'" B C 2 ? ? "C2'" B C 2 ? ? "C1'" B C 2 ? ? 106.91 101.50 5.41 0.80 N 22 1 "O4'" B C 2 ? ? "C1'" B C 2 ? ? N1 B C 2 ? ? 102.74 108.20 -5.46 0.80 N 23 1 N3 B C 2 ? ? C2 B C 2 ? ? O2 B C 2 ? ? 117.70 121.90 -4.20 0.70 N 24 1 "C3'" B G 6 ? ? "C2'" B G 6 ? ? "C1'" B G 6 ? ? 106.50 101.50 5.00 0.80 N 25 1 "O4'" B G 7 ? ? "C1'" B G 7 ? ? N9 B G 7 ? ? 102.17 108.20 -6.03 0.80 N 26 1 "C5'" B C 8 ? ? "C4'" B C 8 ? ? "O4'" B C 8 ? ? 116.33 109.80 6.53 0.90 N 27 1 "C3'" B C 8 ? ? "C2'" B C 8 ? ? "C1'" B C 8 ? ? 106.35 101.50 4.85 0.80 N 28 1 C6 B C 8 ? ? N1 B C 8 ? ? "C1'" B C 8 ? ? 113.01 120.80 -7.79 1.20 N 29 1 C2 B C 8 ? ? N1 B C 8 ? ? "C1'" B C 8 ? ? 126.83 118.80 8.03 1.10 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 G A 1 ? ? 0.077 'SIDE CHAIN' 2 1 C A 2 ? ? 0.120 'SIDE CHAIN' 3 1 G A 4 ? ? 0.127 'SIDE CHAIN' 4 1 G A 6 ? ? 0.149 'SIDE CHAIN' 5 1 G A 7 ? ? 0.089 'SIDE CHAIN' 6 1 G B 1 ? ? 0.065 'SIDE CHAIN' 7 1 C B 2 ? ? 0.117 'SIDE CHAIN' 8 1 G B 4 ? ? 0.115 'SIDE CHAIN' 9 1 G B 6 ? ? 0.115 'SIDE CHAIN' 10 1 G B 7 ? ? 0.129 'SIDE CHAIN' # _ndb_struct_conf_na.entry_id 2KD4 _ndb_struct_conf_na.feature 'double helix' # 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 8 1_555 -0.240 0.023 -0.546 -23.280 -29.530 3.603 1 A_G1:C8_B A 1 ? B 8 ? 19 1 1 A C 2 1_555 B G 7 1_555 0.359 -0.210 0.406 15.650 -39.027 -6.304 2 A_C2:G7_B A 2 ? B 7 ? 19 1 1 A C 3 1_555 B G 6 1_555 0.880 -0.276 -0.198 15.018 -8.216 2.153 3 A_C3:G6_B A 3 ? B 6 ? 19 1 1 A G 4 1_555 B C 5 1_555 -1.083 -0.463 0.560 7.428 -13.834 0.727 4 A_G4:C5_B A 4 ? B 5 ? 19 1 1 A C 5 1_555 B G 4 1_555 1.049 -0.424 0.501 -3.789 -13.446 1.215 5 A_C5:G4_B A 5 ? B 4 ? 19 1 1 A G 6 1_555 B C 3 1_555 -0.958 -0.413 0.166 -13.600 -12.364 -1.714 6 A_G6:C3_B A 6 ? B 3 ? 19 1 1 A G 7 1_555 B C 2 1_555 -0.206 -0.074 -0.102 -15.672 -30.999 -1.036 7 A_G7:C2_B A 7 ? B 2 ? 19 1 1 A C 8 1_555 B G 1 1_555 0.152 -0.029 -0.262 12.867 -26.131 1.480 8 A_C8:G1_B A 8 ? 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 8 1_555 A C 2 1_555 B G 7 1_555 3.746 -0.499 -1.209 13.000 162.562 -36.680 0.761 1.851 -0.195 -87.043 6.961 -163.946 1 AA_G1C2:G7C8_BB A 1 ? B 8 ? A 2 ? B 7 ? 1 A C 2 1_555 B G 7 1_555 A C 3 1_555 B G 6 1_555 0.421 -1.821 4.093 -13.222 0.061 37.792 -2.674 -2.493 3.743 0.091 19.691 39.958 2 AA_C2C3:G6G7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A C 3 1_555 B G 6 1_555 A G 4 1_555 B C 5 1_555 -0.083 -1.167 6.681 -7.874 -11.950 20.278 5.069 -4.936 6.065 -29.639 19.528 24.776 3 AA_C3G4:C5G6_BB A 3 ? B 6 ? A 4 ? B 5 ? 1 A G 4 1_555 B C 5 1_555 A C 5 1_555 B G 4 1_555 0.069 -0.188 3.397 0.222 -0.565 49.800 -0.180 -0.065 3.399 -0.671 -0.263 49.803 4 AA_G4C5:G4C5_BB A 4 ? B 5 ? A 5 ? B 4 ? 1 A C 5 1_555 B G 4 1_555 A G 6 1_555 B C 3 1_555 -0.135 -1.180 6.619 3.496 -6.875 21.724 2.057 2.887 6.574 -17.545 -8.922 23.037 5 AA_C5G6:C3G4_BB A 5 ? B 4 ? A 6 ? B 3 ? 1 A G 6 1_555 B C 3 1_555 A G 7 1_555 B C 2 1_555 0.164 -1.822 3.686 14.100 12.693 39.303 -3.763 1.227 2.887 17.677 -19.636 43.478 6 AA_G6G7:C2C3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A G 7 1_555 B C 2 1_555 A C 8 1_555 B G 1 1_555 -3.411 -0.634 -1.268 -10.038 164.474 -49.960 0.773 -1.690 -0.154 -86.610 -5.286 -166.211 7 AA_G7C8:G1C2_BB A 7 ? B 2 ? A 8 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name PROFLAVIN _pdbx_entity_nonpoly.comp_id PRL #