data_1ZBN # _entry.id 1ZBN # _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 1ZBN pdb_00001zbn 10.2210/pdb1zbn/pdb RCSB RCSB032536 ? ? WWPDB D_1000032536 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1BIV 'The same RNA complexed with BIV Tat (65-81) arginine-rich domain' unspecified PDB 1MNB 'The same RNA complexed with BIV Tat (68-81) arginine-rich domain' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1ZBN _pdbx_database_status.recvd_initial_deposition_date 2005-04-08 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _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 'Calabro, V.' 1 'Daugherty, M.D.' 2 'Frankel, A.D.' 3 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'A single intermolecular contact mediates intramolecular stabilization of both RNA and protein.' Proc.Natl.Acad.Sci.Usa 102 6849 6854 2005 PNASA6 US 0027-8424 0040 ? 15857951 10.1073/pnas.0409282102 1 'An RNA-binding chameleon' Mol.Cell 6 1067 1076 2000 MOCEFL US 1097-2765 2168 ? ? ? 2 'Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex' Science 270 1200 1203 1995 SCIEAS US 0036-8075 0038 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Calabro, V.' 1 ? primary 'Daugherty, M.D.' 2 ? primary 'Frankel, A.D.' 3 ? 1 'Smith, C.A.' 4 ? 1 'Calabro, V.' 5 ? 1 'Frankel, A.D.' 6 ? 2 'Puglisi, J.D.' 7 ? 2 'Chen, L.' 8 ? 2 'Blanchard, S.' 9 ? 2 'Frankel, A.D.' 10 ? # 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 'BIV mRNA' 8923.310 1 ? 'A4G, U31C' ? 'A4G, U31C' 2 polymer syn 'JDV tat protein' 2064.493 1 ? ? 'Arginine-rich domain' ? # 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 GGCUCGUGUAGCUCAUUAGCUCCGAGCC GGCUCGUGUAGCUCAUUAGCUCCGAGCC A ? 2 'polypeptide(L)' no no GRRKKRGTRGKGRKIHY GRRKKRGTRGKGRKIHY 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 G n 1 3 C n 1 4 U n 1 5 C n 1 6 G n 1 7 U n 1 8 G n 1 9 U n 1 10 A n 1 11 G n 1 12 C n 1 13 U n 1 14 C n 1 15 A n 1 16 U n 1 17 U n 1 18 A n 1 19 G n 1 20 C n 1 21 U n 1 22 C n 1 23 C n 1 24 G n 1 25 A n 1 26 G n 1 27 C n 1 28 C n 2 1 GLY n 2 2 ARG n 2 3 ARG n 2 4 LYS n 2 5 LYS n 2 6 ARG n 2 7 GLY n 2 8 THR n 2 9 ARG n 2 10 GLY n 2 11 LYS n 2 12 GLY n 2 13 ARG n 2 14 LYS n 2 15 ILE n 2 16 HIS n 2 17 TYR n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'This sequence occurs naturally in Bovine immunodeficiency virus (BIV).' 2 1 sample ? ? ? ? ? 'This sequence occurs naturally in Jembrana disease virus (JDV).' # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1ZBN 1ZBN ? ? ? 2 2 PDB 1ZBN 1ZBN ? ? ? # 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 1ZBN A 1 ? 28 ? 1ZBN 1 ? 28 ? 1 28 2 2 1ZBN B 1 ? 17 ? 1ZBN 1 ? 17 ? 1 17 # 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 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 DQF-COSY 2 2 1 '2D TOCSY' 2 3 1 '2D NOESY' 2 4 3 '2D NOESY' 2 5 2 '2D NOESY' 1 6 1 '2D TOCSY' 1 7 1 DQF-COSY 1 # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 290 ambient 6.5 '50mM NaCl, 10mM sodium phosphate' . K 2 285 ambient 6.5 '50mM NaCl, 10mM sodium phosphate' . K 3 300 ambient 6.5 '50mM NaCl, 10mM sodium phosphate' . K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1.5mM RNA, 1.5mM peptide, 90% H2O, 10% D2O' '90% H2O/10% D2O' 2 '1.5mM RNA, 1.5mM peptide, 100% D2O' '100% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model UNITY _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 1ZBN _pdbx_nmr_refine.method 'distance geometry and restrained molecular dynamics' _pdbx_nmr_refine.details ;Structures were calculated beginning with 1,000 random structures and incrementally adding distance constraints in four iterations. The final 30 structures with the lowest number of violations were subjected to RMD. The structures are based on a total of 700 distance constraints, 61 dihedral angle restraints. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1ZBN _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear techniques.' # _pdbx_nmr_ensemble.entry_id 1ZBN _pdbx_nmr_ensemble.conformers_calculated_total_number 30 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1ZBN _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal 'structure solution' CYANA 1.x Guentert 1 refinement CNS 1.1 Brunger 2 processing NMRPipe NA Delaglio 3 'data analysis' Sparky 3 Goddard 4 # _exptl.entry_id 1ZBN _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.density_Matthews ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1ZBN _struct.title 'Solution structure of BIV TAR hairpin complexed to JDV Tat arginine-rich motif' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1ZBN _struct_keywords.pdbx_keywords 'RNA binding protein/RNA' _struct_keywords.text 'RNA-peptide complex, RNA binding protein-RNA COMPLEX' # 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 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 28 N3 ? ? A G 1 A C 28 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog2 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 27 N3 ? ? A G 2 A C 27 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog3 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 26 N1 ? ? A C 3 A G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 26 O6 ? ? A C 3 A G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 26 N2 ? ? A C 3 A G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 25 N1 ? ? A U 4 A A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 25 N6 ? ? A U 4 A A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 24 O6 ? ? A C 5 A G 24 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog9 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 6 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 6 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 6 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 10 N6 ? ? A U 7 A A 10 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog13 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 8 A C 22 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog14 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 21 N3 ? ? A A 10 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 21 O4 ? ? A A 10 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog17 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 19 N1 ? ? A C 12 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 19 O6 ? ? A C 12 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 19 N2 ? ? A C 12 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 13 N3 ? ? ? 1_555 A A 18 N1 ? ? A U 13 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 13 O4 ? ? ? 1_555 A A 18 N6 ? ? A U 13 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1ZBN _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1ZBN _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 U 4 4 4 U U A . n A 1 5 C 5 5 5 C C A . n A 1 6 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 G 8 8 8 G G A . n A 1 9 U 9 9 9 U U A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 C 12 12 12 C C A . n A 1 13 U 13 13 13 U U A . n A 1 14 C 14 14 14 C C A . n A 1 15 A 15 15 15 A A A . n A 1 16 U 16 16 16 U U A . n A 1 17 U 17 17 17 U U A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 C 20 20 20 C C A . n A 1 21 U 21 21 21 U U A . n A 1 22 C 22 22 22 C C A . n A 1 23 C 23 23 23 C C A . n A 1 24 G 24 24 24 G G A . n A 1 25 A 25 25 25 A A A . n A 1 26 G 26 26 26 G G A . n A 1 27 C 27 27 27 C C A . n A 1 28 C 28 28 28 C C A . n B 2 1 GLY 1 1 1 GLY GLY B . n B 2 2 ARG 2 2 2 ARG ARG B . n B 2 3 ARG 3 3 3 ARG ARG B . n B 2 4 LYS 4 4 4 LYS LYS B . n B 2 5 LYS 5 5 5 LYS LYS B . n B 2 6 ARG 6 6 6 ARG ARG B . n B 2 7 GLY 7 7 7 GLY GLY B . n B 2 8 THR 8 8 8 THR THR B . n B 2 9 ARG 9 9 9 ARG ARG B . n B 2 10 GLY 10 10 10 GLY GLY B . n B 2 11 LYS 11 11 11 LYS LYS B . n B 2 12 GLY 12 12 12 GLY GLY B . n B 2 13 ARG 13 13 13 ARG ARG B . n B 2 14 LYS 14 14 14 LYS LYS B . n B 2 15 ILE 15 15 15 ILE ILE B . n B 2 16 HIS 16 16 16 HIS HIS B . n B 2 17 TYR 17 17 17 TYR TYR B . n # _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 2005-04-19 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _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' 'Database references' 4 4 '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 4 'Structure model' database_2 2 4 'Structure model' pdbx_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' # 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 O4 A U 13 ? ? H61 A A 18 ? ? 1.44 2 1 H61 A A 10 ? ? O4 A U 21 ? ? 1.45 3 1 "H1'" A U 7 ? ? "O5'" A G 8 ? ? 1.50 4 1 "O2'" A C 23 ? ? H8 A G 24 ? ? 1.57 5 2 O4 A U 13 ? ? H61 A A 18 ? ? 1.47 6 2 "HO2'" A G 1 ? ? "O5'" A G 2 ? ? 1.50 7 2 O B GLY 7 ? ? H B ILE 15 ? ? 1.50 8 2 O6 A G 11 ? ? H41 A C 20 ? ? 1.56 9 2 O B GLY 7 ? ? N B ILE 15 ? ? 2.08 10 3 O4 A U 13 ? ? H61 A A 18 ? ? 1.48 11 3 H21 A G 6 ? ? O2 A C 23 ? ? 1.57 12 4 O4 A U 13 ? ? H61 A A 18 ? ? 1.43 13 4 O4 A U 4 ? ? H61 A A 25 ? ? 1.53 14 4 "O2'" A C 23 ? ? H8 A G 24 ? ? 1.54 15 4 "H1'" A U 7 ? ? "O5'" A G 8 ? ? 1.54 16 4 "HO2'" A C 5 ? ? "O5'" A G 6 ? ? 1.59 17 5 O4 A U 13 ? ? H61 A A 18 ? ? 1.39 18 5 "H1'" A U 7 ? ? "O5'" A G 8 ? ? 1.50 19 5 O4 A U 4 ? ? H61 A A 25 ? ? 1.56 20 6 O4 A U 13 ? ? H61 A A 18 ? ? 1.52 21 6 O4 A U 4 ? ? H61 A A 25 ? ? 1.59 22 6 O B GLY 7 ? ? N B ILE 15 ? ? 2.19 23 7 O4 A U 13 ? ? H61 A A 18 ? ? 1.37 24 7 O4 A U 4 ? ? H61 A A 25 ? ? 1.57 25 7 "O2'" A C 23 ? ? H8 A G 24 ? ? 1.58 26 7 O B GLY 7 ? ? N B ILE 15 ? ? 2.15 27 8 O4 A U 13 ? ? H61 A A 18 ? ? 1.42 28 8 "HO2'" A C 23 ? ? "O5'" A G 24 ? ? 1.51 29 8 H61 A A 10 ? ? O4 A U 21 ? ? 1.52 30 8 H21 A G 2 ? ? O2 A C 27 ? ? 1.59 31 9 O4 A U 13 ? ? H61 A A 18 ? ? 1.45 32 9 O4 A U 4 ? ? H61 A A 25 ? ? 1.57 33 9 H21 A G 2 ? ? O2 A C 27 ? ? 1.60 34 10 O4 A U 13 ? ? H61 A A 18 ? ? 1.43 35 10 O4 A U 4 ? ? H61 A A 25 ? ? 1.55 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ARG B 2 ? ? -58.29 84.19 2 1 ARG B 3 ? ? -177.04 -178.47 3 1 LYS B 5 ? ? 28.66 100.77 4 1 ARG B 6 ? ? -163.60 -58.01 5 1 LYS B 11 ? ? -163.60 43.30 6 1 LYS B 14 ? ? 64.11 171.91 7 1 HIS B 16 ? ? 35.02 90.56 8 2 ARG B 3 ? ? 62.56 139.63 9 2 LYS B 4 ? ? 34.62 38.24 10 2 ARG B 6 ? ? -151.20 -51.55 11 2 LYS B 11 ? ? 113.68 36.32 12 2 LYS B 14 ? ? -36.27 158.50 13 2 HIS B 16 ? ? -152.31 80.61 14 3 ARG B 3 ? ? 179.96 -174.33 15 3 LYS B 5 ? ? 44.84 -156.11 16 3 ARG B 6 ? ? 76.17 -62.54 17 3 LYS B 11 ? ? 105.95 38.24 18 3 LYS B 14 ? ? 47.31 168.63 19 4 ARG B 2 ? ? 72.56 153.49 20 4 ARG B 3 ? ? 94.65 179.01 21 4 LYS B 5 ? ? 24.50 114.75 22 4 ARG B 6 ? ? -178.43 -50.12 23 4 LYS B 11 ? ? -163.39 45.68 24 4 LYS B 14 ? ? 44.64 170.36 25 4 HIS B 16 ? ? 9.86 86.52 26 5 ARG B 2 ? ? 33.07 113.74 27 5 ARG B 3 ? ? 72.19 147.27 28 5 ARG B 6 ? ? -132.05 -49.79 29 5 LYS B 11 ? ? -166.25 45.76 30 5 LYS B 14 ? ? 45.42 169.63 31 5 HIS B 16 ? ? 11.64 86.11 32 6 ARG B 2 ? ? 50.95 126.54 33 6 ARG B 3 ? ? 70.59 132.35 34 6 ARG B 6 ? ? -176.64 -51.18 35 6 ARG B 9 ? ? -96.72 30.13 36 6 LYS B 11 ? ? 104.09 38.66 37 6 LYS B 14 ? ? 64.28 158.72 38 6 HIS B 16 ? ? 21.07 89.36 39 7 ARG B 2 ? ? -9.16 78.55 40 7 ARG B 3 ? ? 173.19 106.74 41 7 LYS B 4 ? ? 38.22 40.47 42 7 ARG B 6 ? ? 179.09 -48.05 43 7 LYS B 11 ? ? 104.11 38.14 44 7 LYS B 14 ? ? 53.91 163.97 45 7 HIS B 16 ? ? -158.46 83.75 46 8 ARG B 3 ? ? 81.09 -145.11 47 8 LYS B 4 ? ? -23.55 -44.45 48 8 LYS B 5 ? ? 10.66 76.38 49 8 ARG B 6 ? ? -135.66 -54.64 50 8 LYS B 11 ? ? 102.89 38.47 51 8 LYS B 14 ? ? 45.37 164.85 52 8 ILE B 15 ? ? -130.69 -59.68 53 8 HIS B 16 ? ? 29.58 96.42 54 9 ARG B 3 ? ? 83.25 -175.31 55 9 LYS B 5 ? ? 41.82 -141.23 56 9 ARG B 6 ? ? 67.13 -68.36 57 9 ARG B 9 ? ? -95.52 30.10 58 9 LYS B 11 ? ? 108.32 37.61 59 9 LYS B 14 ? ? 54.06 171.05 60 9 ILE B 15 ? ? -130.05 -59.12 61 9 HIS B 16 ? ? 39.56 94.88 62 10 ARG B 2 ? ? 60.47 160.50 63 10 ARG B 3 ? ? 82.90 -174.35 64 10 LYS B 5 ? ? 36.39 -149.76 65 10 ARG B 6 ? ? 75.07 -43.61 66 10 LYS B 11 ? ? -163.88 43.49 67 10 LYS B 14 ? ? 56.04 163.03 68 10 ILE B 15 ? ? -108.61 -70.48 69 10 HIS B 16 ? ? 52.30 94.44 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1ZBN 'double helix' 1ZBN 'a-form double helix' 1ZBN '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 G 1 1_555 A C 28 1_555 0.800 -0.023 0.151 2.895 -1.117 -17.184 1 A_G1:C28_A A 1 ? A 28 ? ? ? 1 A G 2 1_555 A C 27 1_555 0.893 0.068 0.077 1.042 -0.982 -15.296 2 A_G2:C27_A A 2 ? A 27 ? ? ? 1 A C 3 1_555 A G 26 1_555 -0.700 0.141 -0.120 -1.425 -0.670 1.541 3 A_C3:G26_A A 3 ? A 26 ? 19 1 1 A U 4 1_555 A A 25 1_555 0.341 0.204 -0.015 1.308 -1.631 -27.470 4 A_U4:A25_A A 4 ? A 25 ? 20 1 1 A C 5 1_555 A G 24 1_555 1.331 -0.653 -0.004 4.830 1.896 -15.645 5 A_C5:G24_A A 5 ? A 24 ? ? 1 1 A G 6 1_555 A C 23 1_555 0.485 0.070 0.037 0.284 -4.434 4.583 6 A_G6:C23_A A 6 ? A 23 ? 19 1 1 A G 8 1_555 A C 22 1_555 0.077 0.238 -0.059 -0.093 2.062 -10.170 7 A_G8:C22_A A 8 ? A 22 ? ? ? 1 A A 10 1_555 A U 21 1_555 0.603 -0.194 -0.113 3.543 1.785 -11.870 8 A_A10:U21_A A 10 ? A 21 ? 20 1 1 A G 11 1_555 A C 20 1_555 0.787 -0.084 -0.458 -8.171 3.455 -18.634 9 A_G11:C20_A A 11 ? A 20 ? ? ? 1 A C 12 1_555 A G 19 1_555 -0.053 0.271 -0.071 -4.127 -1.346 -6.574 10 A_C12:G19_A A 12 ? A 19 ? 19 1 1 A U 13 1_555 A A 18 1_555 0.012 -0.224 -0.200 3.537 3.086 -13.646 11 A_U13:A18_A A 13 ? A 18 ? 20 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 A C 28 1_555 A G 2 1_555 A C 27 1_555 3.320 -0.992 1.507 12.612 160.230 54.817 -0.977 -1.641 0.057 85.267 -6.712 162.907 1 AA_G1G2:C27C28_AA A 1 ? A 28 ? A 2 ? A 27 ? 1 A G 2 1_555 A C 27 1_555 A C 3 1_555 A G 26 1_555 0.019 0.358 4.432 -0.484 1.728 13.956 -0.758 -0.701 4.439 7.074 1.983 14.070 2 AA_G2C3:G26C27_AA A 2 ? A 27 ? A 3 ? A 26 ? 1 A C 3 1_555 A G 26 1_555 A U 4 1_555 A A 25 1_555 -0.887 -1.126 3.754 -0.750 9.792 28.101 -4.445 1.556 3.210 19.431 1.488 29.735 3 AA_C3U4:A25G26_AA A 3 ? A 26 ? A 4 ? A 25 ? 1 A U 4 1_555 A A 25 1_555 A C 5 1_555 A G 24 1_555 2.544 -1.376 2.785 8.177 10.044 45.216 -2.455 -2.602 2.829 12.758 -10.385 46.940 4 AA_U4C5:G24A25_AA A 4 ? A 25 ? A 5 ? A 24 ? 1 A C 5 1_555 A G 24 1_555 A G 6 1_555 A C 23 1_555 2.849 -0.340 2.776 19.479 18.285 34.947 -2.294 -1.867 3.330 26.240 -27.952 43.735 5 AA_C5G6:C23G24_AA A 5 ? A 24 ? A 6 ? A 23 ? 1 A G 6 1_555 A C 23 1_555 A G 8 1_555 A C 22 1_555 -3.408 -0.763 2.929 -8.968 42.486 49.862 -2.356 2.815 2.266 42.433 8.957 65.193 6 AA_G6G8:C22C23_AA A 6 ? A 23 ? A 8 ? A 22 ? 1 A G 8 1_555 A C 22 1_555 A A 10 1_555 A U 21 1_555 -1.184 -2.156 4.084 0.185 -27.051 37.013 0.737 1.554 4.578 -37.157 -0.254 45.564 7 AA_G8A10:U21C22_AA A 8 ? A 22 ? A 10 ? A 21 ? 1 A A 10 1_555 A U 21 1_555 A G 11 1_555 A C 20 1_555 -0.951 -2.813 3.868 8.252 39.392 30.873 -5.510 1.580 0.122 52.857 -11.073 50.331 8 AA_A10G11:C20U21_AA A 10 ? A 21 ? A 11 ? A 20 ? 1 A G 11 1_555 A C 20 1_555 A C 12 1_555 A G 19 1_555 -0.478 -1.499 3.949 -5.397 -4.305 29.580 -1.778 -0.446 4.141 -8.290 10.394 30.357 9 AA_G11C12:G19C20_AA A 11 ? A 20 ? A 12 ? A 19 ? 1 A C 12 1_555 A G 19 1_555 A U 13 1_555 A A 18 1_555 -0.371 -0.980 3.224 6.542 30.907 30.550 -3.913 1.048 1.552 46.019 -9.740 43.674 10 AA_C12U13:A18G19_AA A 12 ? A 19 ? A 13 ? A 18 ? #