data_2K5Z # _entry.id 2K5Z # _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 2K5Z pdb_00002k5z 10.2210/pdb2k5z/pdb RCSB RCSB100718 ? ? WWPDB D_1000100718 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 2OJ7 PDB 'UGUU tetraloop' unspecified 2OJ8 PDB 'UGUU tetraloop chemical shift refined' unspecified 2k5y PDB 'structure before rdc refinement' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2K5Z _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-07-01 _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 'Ampt, K.A.M.' 1 'Tessari, M.' 2 'Wijmenga, S.S.' 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 ;The unstable part of the apical stem of duck hepatitis B virus epsilon shows enhanced base pair opening but not pico- to nanosecond dynamics and is essential for reverse transcriptase binding. ; Biochemistry 48 10499 10508 2009 BICHAW US 0006-2960 0033 ? 19817488 10.1021/bi9011385 1 '1H, 13C and 15N NMR assignments of Duck HBV apical stem loop of the epsilon encapsidation signal' 'To be Published' ? ? ? ? ? ? ? 0353 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ampt, K.A.' 1 ? primary 'van der Werf, R.M.' 2 ? primary 'Nelissen, F.H.' 3 ? primary 'Tessari, M.' 4 ? primary 'Wijmenga, S.S.' 5 ? 1 'Ampt, K.A.M.' 6 ? 1 'Ottink, O.M.' 7 ? 1 'Girard, F.C.' 8 ? 1 'Nelissen, F.H.T.' 9 ? 1 'Tessari, M.' 10 ? 1 'Wijmenga, S.S.' 11 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Duck HBV apical loop' _entity.formula_weight 9248.428 _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 no _entity_poly.pdbx_seq_one_letter_code GGUCUACAUUGCUGUUGUCGUGUGUGACC _entity_poly.pdbx_seq_one_letter_code_can GGUCUACAUUGCUGUUGUCGUGUGUGACC _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 G n 1 2 G n 1 3 U n 1 4 C n 1 5 U n 1 6 A n 1 7 C n 1 8 A n 1 9 U n 1 10 U n 1 11 G n 1 12 C n 1 13 U n 1 14 G n 1 15 U n 1 16 U n 1 17 G n 1 18 U n 1 19 C n 1 20 G n 1 21 U n 1 22 G n 1 23 U n 1 24 G n 1 25 U n 1 26 G n 1 27 A n 1 28 C n 1 29 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 'The Sequence of this RNA can be found in Duck Hepatitis B virus' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2K5Z _struct_ref.pdbx_db_accession 2K5Z _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GGUCUACAUUGCUGUUGUCGUGUGUGACC _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2K5Z _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 29 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2K5Z _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 29 _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 29 # 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 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' 3 2 2 '2D 1H-1H NOESY' 2 3 5 '3D 1H-13C NOESY' 1 4 3 '2D 1H-15N HSQC' 2 5 5 '2D 1H-15N HSQC' 3 6 2 '2D 1H-13C HSQC' 3 7 4 '2D 1H-13C HSQC' 2 8 5 '2D 1H-13C HSQC' 3 9 2 '2D DQF-COSY' 2 10 5 '2D 1H-1H COSY' 2 11 5 '3D HCCH-TOCSY' 2 12 5 '3D HCN' # 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 10 6.7 ambient ? 278 K 2 10 6.7 ambient ? 288 K 3 10 6.7 ambient ? 298 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '1.2 mM Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 95% H2O, 5% D2O, 95% H2O/5% D2O' 1 '95% H2O/5% D2O' '1.2 mM Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 100% D2O, 100% D2O' 2 '100% D2O' '1 mM [U-13C; U-15N]-Ura Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 95% H2O/5% D2O' 3 '95% H2O/5% D2O' '1 mM [U-13C; U-15N]-Ura Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 100% D2O, 100% D2O' 4 '100% D2O' '0.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 1 mM DSS, 95% H2O/5% D2O' 5 '95% H2O/5% D2O' ;0.7 mM [U-13C; U-15N] Duck HBV apical loop, 10 mM sodium phosphate buffer, 0.1 mM EDTA, 5% D2O, 95% H2O, 15 mg/mL Pf1 phage, 95% H2O/5% D2O ; 6 '95% H2O/5% 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 Varian INOVA 1 'Varian INOVA' 600 Varian INOVA 2 'Varian INOVA' 800 Varian INOVA 3 'Varian INOVA' # _pdbx_nmr_refine.entry_id 2K5Z _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details 'RDC refinement' _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 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2K5Z _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 2K5Z _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 Goddard 'chemical shift assignment' Sparky ? 1 Goddard 'peak picking' Sparky ? 2 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRDraw ? 3 Brunger 'structure solution' X-PLOR 3.851 4 Brunger refinement X-PLOR 3.851 5 # _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 2K5Z _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2K5Z _struct.title 'Solution structure and dynamics of the apical stem-loop of Duck hepatitis B virus' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2K5Z _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'HBV, Duck, apical loop, epsilon, RNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_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 hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 1 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 1 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 1 A C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 28 N3 ? ? A G 2 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 28 O2 ? ? A G 2 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 28 N4 ? ? A G 2 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 27 N1 ? ? A U 3 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 27 N6 ? ? A U 3 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 26 N1 ? ? A C 4 A G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 26 O6 ? ? A C 4 A G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 26 N2 ? ? A C 4 A G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 5 N3 ? ? ? 1_555 A G 24 O6 ? ? A U 5 A G 24 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog13 hydrog ? ? A U 5 O2 ? ? ? 1_555 A G 24 N1 ? ? A U 5 A G 24 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog14 hydrog ? ? A U 5 O2 ? ? ? 1_555 A G 26 N1 ? ? A U 5 A G 26 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog15 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 23 N3 ? ? A A 6 A U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 23 O4 ? ? A A 6 A U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 7 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 7 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 7 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 21 N3 ? ? A A 8 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 21 O4 ? ? A A 8 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 9 N3 ? ? ? 1_555 A G 20 O6 ? ? A U 9 A G 20 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A U 9 O2 ? ? ? 1_555 A G 20 N1 ? ? A U 9 A G 20 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog24 hydrog ? ? A U 10 O4 ? ? ? 1_555 A C 19 N4 ? ? A U 10 A C 19 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog25 hydrog ? ? A G 11 N1 ? ? ? 1_555 A U 18 O2 ? ? A G 11 A U 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog26 hydrog ? ? A G 11 O6 ? ? ? 1_555 A U 18 N3 ? ? A G 11 A U 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog27 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 12 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 12 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 12 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2K5Z _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 U 3 3 3 U U A . n A 1 4 C 4 4 4 C C A . n A 1 5 U 5 5 5 U U A . n A 1 6 A 6 6 6 A A A . n A 1 7 C 7 7 7 C C A . n A 1 8 A 8 8 8 A A A . n A 1 9 U 9 9 9 U U A . n A 1 10 U 10 10 10 U U 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 G 14 14 14 G G A . n A 1 15 U 15 15 15 U U A . n A 1 16 U 16 16 16 U U A . n A 1 17 G 17 17 17 G G A . n A 1 18 U 18 18 18 U U A . n A 1 19 C 19 19 19 C C A . n A 1 20 G 20 20 20 G G A . n A 1 21 U 21 21 21 U U A . n A 1 22 G 22 22 22 G G A . n A 1 23 U 23 23 23 U U A . n A 1 24 G 24 24 24 G G A . n A 1 25 U 25 25 25 U U A . n A 1 26 G 26 26 26 G G A . n A 1 27 A 27 27 27 A A A . n A 1 28 C 28 28 28 C C A . n A 1 29 C 29 29 29 C C A . n # _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 # 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 2009-07-14 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_struct_assembly 4 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_nmr_software.name' # 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 'Duck HBV apical loop' 1.2 mM ? 1 'sodium phosphate buffer' 10 mM ? 1 EDTA 0.1 mM ? 1 H2O 95 % ? 1 D2O 5 % ? 1 'Duck HBV apical loop' 1.2 mM ? 2 'sodium phosphate buffer' 10 mM ? 2 EDTA 0.1 mM ? 2 D2O 100 % ? 2 'Duck HBV apical loop' 1 mM '[U-13C; U-15N]-Ura' 3 'sodium phosphate buffer' 10 mM ? 3 EDTA 0.1 mM ? 3 D2O 5 % ? 3 H2O 95 % ? 3 'Duck HBV apical loop' 1 mM '[U-13C; U-15N]-Ura' 4 'sodium phosphate buffer' 10 mM ? 4 EDTA 0.1 mM ? 4 D2O 100 % ? 4 'Duck HBV apical loop' 0.7 mM '[U-13C; U-15N]' 5 'sodium phosphate buffer' 10 mM ? 5 EDTA 0.1 mM ? 5 D2O 5 % ? 5 H2O 95 % ? 5 DSS 1 mM ? 5 'Duck HBV apical loop' 0.7 mM '[U-13C; U-15N]' 6 'sodium phosphate buffer' 10 mM ? 6 EDTA 0.1 mM ? 6 D2O 5 % ? 6 H2O 95 % ? 6 'Pf1 phage' 15 mg/mL ? 6 # 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 5 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 112.81 108.50 4.31 0.70 N 2 6 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 112.74 108.50 4.24 0.70 N 3 9 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 113.39 108.50 4.89 0.70 N 4 10 "O4'" A C 7 ? ? "C1'" A C 7 ? ? N1 A C 7 ? ? 112.80 108.50 4.30 0.70 N 5 10 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 113.73 108.50 5.23 0.70 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2K5Z 'double helix' 2K5Z 'a-form double helix' 2K5Z 'hairpin loop' 2K5Z 'bulge loop' 2K5Z '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 A C 29 1_555 -0.038 0.070 -0.054 -3.347 -5.198 -2.714 1 A_G1:C29_A A 1 ? A 29 ? 19 1 1 A G 2 1_555 A C 28 1_555 -0.066 -0.040 0.597 0.953 -13.020 -0.043 2 A_G2:C28_A A 2 ? A 28 ? 19 1 1 A U 3 1_555 A A 27 1_555 0.075 0.067 -0.048 5.621 -8.463 -0.367 3 A_U3:A27_A A 3 ? A 27 ? 20 1 1 A C 4 1_555 A G 26 1_555 0.093 0.007 0.299 1.834 -7.786 -2.096 4 A_C4:G26_A A 4 ? A 26 ? 19 1 1 A U 5 1_555 A G 24 1_555 2.245 -0.342 -0.085 12.138 -26.447 -1.895 5 A_U5:G24_A A 5 ? A 24 ? 28 ? 1 A A 6 1_555 A U 23 1_555 -0.160 -0.009 -0.437 0.377 -12.405 3.888 6 A_A6:U23_A A 6 ? A 23 ? 20 1 1 A C 7 1_555 A G 22 1_555 0.068 0.064 0.208 -6.484 -10.709 -1.497 7 A_C7:G22_A A 7 ? A 22 ? 19 1 1 A A 8 1_555 A U 21 1_555 -0.071 0.004 -0.474 0.256 0.396 -1.581 8 A_A8:U21_A A 8 ? A 21 ? 20 1 1 A U 9 1_555 A G 20 1_555 2.215 -0.362 0.009 1.856 -0.055 -3.502 9 A_U9:G20_A A 9 ? A 20 ? 28 ? 1 A U 10 1_555 A C 19 1_555 -2.092 -0.919 -0.965 3.441 3.662 -22.188 10 A_U10:C19_A A 10 ? A 19 ? ? ? 1 A G 11 1_555 A U 18 1_555 -2.166 -0.450 0.744 -0.968 -14.828 -5.656 11 A_G11:U18_A A 11 ? A 18 ? 28 ? 1 A C 12 1_555 A G 17 1_555 0.235 -0.022 -0.352 4.848 -7.080 4.470 12 A_C12:G17_A A 12 ? A 17 ? 19 1 1 A U 13 1_555 A U 16 1_555 3.391 -2.753 -2.210 24.384 29.335 -2.997 13 A_U13:U16_A A 13 ? A 16 ? 16 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 29 1_555 A G 2 1_555 A C 28 1_555 -0.326 -1.273 3.634 -3.686 7.912 31.736 -3.698 -0.099 3.248 14.136 6.586 32.885 1 AA_G1G2:C28C29_AA A 1 ? A 29 ? A 2 ? A 28 ? 1 A G 2 1_555 A C 28 1_555 A U 3 1_555 A A 27 1_555 -0.331 -0.881 3.789 2.472 8.418 32.301 -3.093 1.034 3.424 14.794 -4.344 33.440 2 AA_G2U3:A27C28_AA A 2 ? A 28 ? A 3 ? A 27 ? 1 A U 3 1_555 A A 27 1_555 A C 4 1_555 A G 26 1_555 0.387 -0.894 4.262 -0.454 5.437 32.758 -2.732 -0.775 4.059 9.558 0.798 33.197 3 AA_U3C4:G26A27_AA A 3 ? A 27 ? A 4 ? A 26 ? 1 A C 4 1_555 A G 26 1_555 A U 5 1_555 A G 24 1_555 1.706 -0.865 4.156 -7.155 18.793 51.178 -2.301 -2.373 3.420 20.858 7.941 54.738 4 AA_C4U5:G24G26_AA A 4 ? A 26 ? A 5 ? A 24 ? 1 A U 5 1_555 A G 24 1_555 A A 6 1_555 A U 23 1_555 -0.112 -0.443 4.401 1.875 11.995 27.605 -4.091 0.721 3.862 23.737 -3.711 30.110 5 AA_U5A6:U23G24_AA A 5 ? A 24 ? A 6 ? A 23 ? 1 A A 6 1_555 A U 23 1_555 A C 7 1_555 A G 22 1_555 -0.191 -1.011 4.444 -3.693 7.506 30.568 -3.692 -0.555 4.082 13.912 6.845 31.666 6 AA_A6C7:G22U23_AA A 6 ? A 23 ? A 7 ? A 22 ? 1 A C 7 1_555 A G 22 1_555 A A 8 1_555 A U 21 1_555 0.050 -0.302 3.973 1.310 11.076 31.251 -2.771 0.178 3.657 19.787 -2.340 33.135 7 AA_C7A8:U21G22_AA A 7 ? A 22 ? A 8 ? A 21 ? 1 A A 8 1_555 A U 21 1_555 A U 9 1_555 A G 20 1_555 -0.227 -0.436 4.556 -1.116 6.603 35.671 -1.979 0.148 4.413 10.663 1.802 36.274 8 AA_A8U9:G20U21_AA A 8 ? A 21 ? A 9 ? A 20 ? 1 A U 9 1_555 A G 20 1_555 A U 10 1_555 A C 19 1_555 -1.568 -1.124 3.838 -0.396 19.647 15.277 -8.654 3.524 1.513 52.482 1.057 24.845 9 AA_U9U10:C19G20_AA A 9 ? A 20 ? A 10 ? A 19 ? 1 A U 10 1_555 A C 19 1_555 A G 11 1_555 A U 18 1_555 0.771 -0.373 4.710 -8.088 1.270 32.259 -0.951 -3.254 4.376 2.241 14.271 33.255 10 AA_U10G11:U18C19_AA A 10 ? A 19 ? A 11 ? A 18 ? 1 A G 11 1_555 A U 18 1_555 A C 12 1_555 A G 17 1_555 0.988 -0.658 3.616 0.726 7.968 35.027 -2.307 -1.490 3.409 13.028 -1.187 35.902 11 AA_G11C12:G17U18_AA A 11 ? A 18 ? A 12 ? A 17 ? 1 A C 12 1_555 A G 17 1_555 A U 13 1_555 A U 16 1_555 0.184 -0.765 3.483 3.072 -13.430 46.387 0.218 0.039 3.566 -16.624 -3.803 48.281 12 AA_C12U13:U16G17_AA A 12 ? A 17 ? A 13 ? A 16 ? #