data_2LBR # _entry.id 2LBR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 2LBR pdb_00002lbr 10.2210/pdb2lbr/pdb RCSB RCSB102201 ? ? BMRB 17573 ? 10.13018/BMR17573 WWPDB D_1000102201 ? ? # 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 2011-08-03 2 'Structure model' 1 1 2011-09-14 3 'Structure model' 1 2 2023-06-14 4 'Structure model' 1 3 2024-05-15 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' Other 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Database references' # 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_database_status 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' struct_conn 5 4 'Structure model' chem_comp_atom 6 4 'Structure model' chem_comp_bond 7 4 'Structure model' database_2 # 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_database_status.status_code_nmr_data' 4 3 'Structure model' '_pdbx_nmr_software.name' 5 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 4 'Structure model' '_database_2.pdbx_DOI' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LBR _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-04-05 _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.status_code_cs REL _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 17573 BMRB unspecified . 2LBQ PDB unspecified . 2LA9 PDB unspecified . 2LAC PDB unspecified . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Denmon, A.P.' 1 'Wang, J.' 2 'Nikonowicz, E.P.' 3 # _citation.id primary _citation.title 'Conformation Effects of Base Modification on the Anticodon Stem-Loop of Bacillus subtilis tRNA(Tyr).' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 412 _citation.page_first 285 _citation.page_last 303 _citation.year 2011 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21782828 _citation.pdbx_database_id_DOI 10.1016/j.jmb.2011.07.010 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Denmon, A.P.' 1 ? primary 'Wang, J.' 2 ? primary 'Nikonowicz, E.P.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*UP*AP*(6IA)P*AP*(PSU)P*CP*CP*CP*C)-3') ; _entity.formula_weight 5512.433 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GGGGACUGUA(6IA)A(PSU)CCCC' _entity_poly.pdbx_seq_one_letter_code_can GGGGACUGUAAAUCCCC _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 G n 1 4 G n 1 5 A n 1 6 C n 1 7 U n 1 8 G n 1 9 U n 1 10 A n 1 11 6IA n 1 12 A n 1 13 PSU n 1 14 C n 1 15 C n 1 16 C n 1 17 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 'molecule was made using T7 polymerase and primers' # 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 6IA 'RNA linking' n "N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE" ? 'C15 H24 N5 O7 P' 417.354 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G 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 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C 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 6IA 11 11 11 6IA 6IA A . n A 1 12 A 12 12 12 A A A . n A 1 13 PSU 13 13 13 PSU PSU A . n A 1 14 C 14 14 14 C C A . n A 1 15 C 15 15 15 C C A . n A 1 16 C 16 16 16 C C A . n A 1 17 C 17 17 17 C C A . n # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2LBR _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LBR _struct.title 'Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR' _struct.pdbx_model_details 'closest to the average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LBR _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Tyrosyl-tRNA, 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_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2LBR _struct_ref.pdbx_db_accession 2LBR _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2LBR _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 17 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2LBR _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 17 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 17 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A A 10 "O3'" ? ? ? 1_555 A 6IA 11 P ? ? A A 10 A 6IA 11 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale2 covale both ? A 6IA 11 "O3'" ? ? ? 1_555 A A 12 P ? ? A 6IA 11 A A 12 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale3 covale both ? A A 12 "O3'" ? ? ? 1_555 A PSU 13 P ? ? A A 12 A PSU 13 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale4 covale both ? A PSU 13 "O3'" ? ? ? 1_555 A C 14 P ? ? A PSU 13 A C 14 1_555 ? ? ? ? ? ? ? 1.609 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 1 A C 17 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog2 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 2 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 2 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 2 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 3 A C 15 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog6 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 4 A C 14 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog7 hydrog ? ? A A 5 N1 ? ? ? 1_555 A PSU 13 N3 ? ? A A 5 A PSU 13 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog8 hydrog ? ? A A 5 N6 ? ? ? 1_555 A PSU 13 O2 ? ? A A 5 A PSU 13 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O6 A G 3 ? ? H41 A C 15 ? ? 1.56 2 2 O6 A G 3 ? ? H41 A C 15 ? ? 1.57 3 3 O6 A G 3 ? ? H41 A C 15 ? ? 1.58 4 4 O6 A G 3 ? ? H41 A C 15 ? ? 1.57 5 5 "HO2'" A U 7 ? ? "O5'" A G 8 ? ? 1.44 6 5 O6 A G 2 ? ? H41 A C 16 ? ? 1.57 7 6 O6 A G 2 ? ? H41 A C 16 ? ? 1.57 8 6 "H2'" A U 7 ? ? "O4'" A G 8 ? ? 1.59 9 7 O6 A G 3 ? ? H41 A C 15 ? ? 1.56 10 8 O6 A G 3 ? ? H41 A C 15 ? ? 1.57 # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 5 _pdbx_validate_planes.auth_comp_id G _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 3 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.046 _pdbx_validate_planes.type 'SIDE CHAIN' # 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 A 6IA 11 A 6IA 11 ? A ? 2 A PSU 13 A PSU 13 ? U "PSEUDOURIDINE-5'-MONOPHOSPHATE" # _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 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 8 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LBR _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 2LBR _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_sample_details.contents '2.0 mM i6A,PSU-ASL, 10 mM potassium chloride, 0.02 mM EDTA, 10 mM potassium phosphate, 100% D2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '100% D2O' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id i6A,PSU-ASL-1 2.0 ? mM ? 1 'potassium chloride-2' 10 ? mM . 1 EDTA-3 0.02 ? mM . 1 'potassium phosphate-4' 10 ? mM . 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH 6.3 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 'Natural abundance 2D 1H-13C HSQC' 1 2 1 '2D 1H-1H NOESY' # _pdbx_nmr_refine.entry_id 2LBR _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Accelrys Software Inc.' processing Felix ? 1 'Accelrys Software Inc.' 'data analysis' Felix ? 2 'Accelrys Software Inc.' 'data analysis' 'Insight II' ? 3 'Schwieters, Kuszewski, Tjandra and Clore' refinement 'X-PLOR NIH' ? 4 'Schwieters, Kuszewski, Tjandra and Clore' 'structure calculation' 'X-PLOR NIH' ? 5 Varian collection VnmrJ ? 6 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 6IA OP3 O N N 1 6IA P P N N 2 6IA OP1 O N N 3 6IA OP2 O N N 4 6IA "O5'" O N N 5 6IA "C5'" C N N 6 6IA "C4'" C N R 7 6IA "O4'" O N N 8 6IA "C3'" C N S 9 6IA "O3'" O N N 10 6IA "C2'" C N R 11 6IA "O2'" O N N 12 6IA "C1'" C N R 13 6IA N9 N Y N 14 6IA C8 C Y N 15 6IA N7 N Y N 16 6IA C5 C Y N 17 6IA C6 C Y N 18 6IA N6 N N N 19 6IA N1 N Y N 20 6IA C2 C Y N 21 6IA N3 N Y N 22 6IA C4 C Y N 23 6IA C12 C N N 24 6IA C13 C N N 25 6IA C14 C N N 26 6IA C15 C N N 27 6IA C16 C N N 28 6IA HOP3 H N N 29 6IA HOP2 H N N 30 6IA "H5'" H N N 31 6IA "H5''" H N N 32 6IA "H4'" H N N 33 6IA "H3'" H N N 34 6IA "HO3'" H N N 35 6IA "H2'" H N N 36 6IA "HO2'" H N N 37 6IA "H1'" H N N 38 6IA H8 H N N 39 6IA HN6 H N N 40 6IA H2 H N N 41 6IA H121 H N N 42 6IA H122 H N N 43 6IA H131 H N N 44 6IA H132 H N N 45 6IA H14 H N N 46 6IA H151 H N N 47 6IA H152 H N N 48 6IA H153 H N N 49 6IA H161 H N N 50 6IA H162 H N N 51 6IA H163 H N N 52 A OP3 O N N 53 A P P N N 54 A OP1 O N N 55 A OP2 O N N 56 A "O5'" O N N 57 A "C5'" C N N 58 A "C4'" C N R 59 A "O4'" O N N 60 A "C3'" C N S 61 A "O3'" O N N 62 A "C2'" C N R 63 A "O2'" O N N 64 A "C1'" C N R 65 A N9 N Y N 66 A C8 C Y N 67 A N7 N Y N 68 A C5 C Y N 69 A C6 C Y N 70 A N6 N N N 71 A N1 N Y N 72 A C2 C Y N 73 A N3 N Y N 74 A C4 C Y N 75 A HOP3 H N N 76 A HOP2 H N N 77 A "H5'" H N N 78 A "H5''" H N N 79 A "H4'" H N N 80 A "H3'" H N N 81 A "HO3'" H N N 82 A "H2'" H N N 83 A "HO2'" H N N 84 A "H1'" H N N 85 A H8 H N N 86 A H61 H N N 87 A H62 H N N 88 A H2 H N N 89 C OP3 O N N 90 C P P N N 91 C OP1 O N N 92 C OP2 O N N 93 C "O5'" O N N 94 C "C5'" C N N 95 C "C4'" C N R 96 C "O4'" O N N 97 C "C3'" C N S 98 C "O3'" O N N 99 C "C2'" C N R 100 C "O2'" O N N 101 C "C1'" C N R 102 C N1 N N N 103 C C2 C N N 104 C O2 O N N 105 C N3 N N N 106 C C4 C N N 107 C N4 N N N 108 C C5 C N N 109 C C6 C N N 110 C HOP3 H N N 111 C HOP2 H N N 112 C "H5'" H N N 113 C "H5''" H N N 114 C "H4'" H N N 115 C "H3'" H N N 116 C "HO3'" H N N 117 C "H2'" H N N 118 C "HO2'" H N N 119 C "H1'" H N N 120 C H41 H N N 121 C H42 H N N 122 C H5 H N N 123 C H6 H N N 124 G OP3 O N N 125 G P P N N 126 G OP1 O N N 127 G OP2 O N N 128 G "O5'" O N N 129 G "C5'" C N N 130 G "C4'" C N R 131 G "O4'" O N N 132 G "C3'" C N S 133 G "O3'" O N N 134 G "C2'" C N R 135 G "O2'" O N N 136 G "C1'" C N R 137 G N9 N Y N 138 G C8 C Y N 139 G N7 N Y N 140 G C5 C Y N 141 G C6 C N N 142 G O6 O N N 143 G N1 N N N 144 G C2 C N N 145 G N2 N N N 146 G N3 N N N 147 G C4 C Y N 148 G HOP3 H N N 149 G HOP2 H N N 150 G "H5'" H N N 151 G "H5''" H N N 152 G "H4'" H N N 153 G "H3'" H N N 154 G "HO3'" H N N 155 G "H2'" H N N 156 G "HO2'" H N N 157 G "H1'" H N N 158 G H8 H N N 159 G H1 H N N 160 G H21 H N N 161 G H22 H N N 162 PSU N1 N N N 163 PSU C2 C N N 164 PSU N3 N N N 165 PSU C4 C N N 166 PSU C5 C N N 167 PSU C6 C N N 168 PSU O2 O N N 169 PSU O4 O N N 170 PSU "C1'" C N S 171 PSU "C2'" C N R 172 PSU "O2'" O N N 173 PSU "C3'" C N S 174 PSU "C4'" C N R 175 PSU "O3'" O N N 176 PSU "O4'" O N N 177 PSU "C5'" C N N 178 PSU "O5'" O N N 179 PSU P P N N 180 PSU OP1 O N N 181 PSU OP2 O N N 182 PSU OP3 O N N 183 PSU HN1 H N N 184 PSU HN3 H N N 185 PSU H6 H N N 186 PSU "H1'" H N N 187 PSU "H2'" H N N 188 PSU "HO2'" H N N 189 PSU "H3'" H N N 190 PSU "H4'" H N N 191 PSU "HO3'" H N N 192 PSU "H5'" H N N 193 PSU "H5''" H N N 194 PSU HOP2 H N N 195 PSU HOP3 H N N 196 U OP3 O N N 197 U P P N N 198 U OP1 O N N 199 U OP2 O N N 200 U "O5'" O N N 201 U "C5'" C N N 202 U "C4'" C N R 203 U "O4'" O N N 204 U "C3'" C N S 205 U "O3'" O N N 206 U "C2'" C N R 207 U "O2'" O N N 208 U "C1'" C N R 209 U N1 N N N 210 U C2 C N N 211 U O2 O N N 212 U N3 N N N 213 U C4 C N N 214 U O4 O N N 215 U C5 C N N 216 U C6 C N N 217 U HOP3 H N N 218 U HOP2 H N N 219 U "H5'" H N N 220 U "H5''" H N N 221 U "H4'" H N N 222 U "H3'" H N N 223 U "HO3'" H N N 224 U "H2'" H N N 225 U "HO2'" H N N 226 U "H1'" H N N 227 U H3 H N N 228 U H5 H N N 229 U H6 H N N 230 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 6IA OP3 P sing N N 1 6IA OP3 HOP3 sing N N 2 6IA P OP1 doub N N 3 6IA P OP2 sing N N 4 6IA P "O5'" sing N N 5 6IA OP2 HOP2 sing N N 6 6IA "O5'" "C5'" sing N N 7 6IA "C5'" "C4'" sing N N 8 6IA "C5'" "H5'" sing N N 9 6IA "C5'" "H5''" sing N N 10 6IA "C4'" "O4'" sing N N 11 6IA "C4'" "C3'" sing N N 12 6IA "C4'" "H4'" sing N N 13 6IA "O4'" "C1'" sing N N 14 6IA "C3'" "O3'" sing N N 15 6IA "C3'" "C2'" sing N N 16 6IA "C3'" "H3'" sing N N 17 6IA "O3'" "HO3'" sing N N 18 6IA "C2'" "O2'" sing N N 19 6IA "C2'" "C1'" sing N N 20 6IA "C2'" "H2'" sing N N 21 6IA "O2'" "HO2'" sing N N 22 6IA "C1'" N9 sing N N 23 6IA "C1'" "H1'" sing N N 24 6IA N9 C8 sing Y N 25 6IA N9 C4 sing Y N 26 6IA C8 N7 doub Y N 27 6IA C8 H8 sing N N 28 6IA N7 C5 sing Y N 29 6IA C5 C6 sing Y N 30 6IA C5 C4 doub Y N 31 6IA C6 N6 sing N N 32 6IA C6 N1 doub Y N 33 6IA N6 C12 sing N N 34 6IA N6 HN6 sing N N 35 6IA N1 C2 sing Y N 36 6IA C2 N3 doub Y N 37 6IA C2 H2 sing N N 38 6IA N3 C4 sing Y N 39 6IA C12 C13 sing N N 40 6IA C12 H121 sing N N 41 6IA C12 H122 sing N N 42 6IA C13 C14 sing N N 43 6IA C13 H131 sing N N 44 6IA C13 H132 sing N N 45 6IA C14 C15 sing N N 46 6IA C14 C16 sing N N 47 6IA C14 H14 sing N N 48 6IA C15 H151 sing N N 49 6IA C15 H152 sing N N 50 6IA C15 H153 sing N N 51 6IA C16 H161 sing N N 52 6IA C16 H162 sing N N 53 6IA C16 H163 sing N N 54 A OP3 P sing N N 55 A OP3 HOP3 sing N N 56 A P OP1 doub N N 57 A P OP2 sing N N 58 A P "O5'" sing N N 59 A OP2 HOP2 sing N N 60 A "O5'" "C5'" sing N N 61 A "C5'" "C4'" sing N N 62 A "C5'" "H5'" sing N N 63 A "C5'" "H5''" sing N N 64 A "C4'" "O4'" sing N N 65 A "C4'" "C3'" sing N N 66 A "C4'" "H4'" sing N N 67 A "O4'" "C1'" sing N N 68 A "C3'" "O3'" sing N N 69 A "C3'" "C2'" sing N N 70 A "C3'" "H3'" sing N N 71 A "O3'" "HO3'" sing N N 72 A "C2'" "O2'" sing N N 73 A "C2'" "C1'" sing N N 74 A "C2'" "H2'" sing N N 75 A "O2'" "HO2'" sing N N 76 A "C1'" N9 sing N N 77 A "C1'" "H1'" sing N N 78 A N9 C8 sing Y N 79 A N9 C4 sing Y N 80 A C8 N7 doub Y N 81 A C8 H8 sing N N 82 A N7 C5 sing Y N 83 A C5 C6 sing Y N 84 A C5 C4 doub Y N 85 A C6 N6 sing N N 86 A C6 N1 doub Y N 87 A N6 H61 sing N N 88 A N6 H62 sing N N 89 A N1 C2 sing Y N 90 A C2 N3 doub Y N 91 A C2 H2 sing N N 92 A N3 C4 sing Y N 93 C OP3 P sing N N 94 C OP3 HOP3 sing N N 95 C P OP1 doub N N 96 C P OP2 sing N N 97 C P "O5'" sing N N 98 C OP2 HOP2 sing N N 99 C "O5'" "C5'" sing N N 100 C "C5'" "C4'" sing N N 101 C "C5'" "H5'" sing N N 102 C "C5'" "H5''" sing N N 103 C "C4'" "O4'" sing N N 104 C "C4'" "C3'" sing N N 105 C "C4'" "H4'" sing N N 106 C "O4'" "C1'" sing N N 107 C "C3'" "O3'" sing N N 108 C "C3'" "C2'" sing N N 109 C "C3'" "H3'" sing N N 110 C "O3'" "HO3'" sing N N 111 C "C2'" "O2'" sing N N 112 C "C2'" "C1'" sing N N 113 C "C2'" "H2'" sing N N 114 C "O2'" "HO2'" sing N N 115 C "C1'" N1 sing N N 116 C "C1'" "H1'" sing N N 117 C N1 C2 sing N N 118 C N1 C6 sing N N 119 C C2 O2 doub N N 120 C C2 N3 sing N N 121 C N3 C4 doub N N 122 C C4 N4 sing N N 123 C C4 C5 sing N N 124 C N4 H41 sing N N 125 C N4 H42 sing N N 126 C C5 C6 doub N N 127 C C5 H5 sing N N 128 C C6 H6 sing N N 129 G OP3 P sing N N 130 G OP3 HOP3 sing N N 131 G P OP1 doub N N 132 G P OP2 sing N N 133 G P "O5'" sing N N 134 G OP2 HOP2 sing N N 135 G "O5'" "C5'" sing N N 136 G "C5'" "C4'" sing N N 137 G "C5'" "H5'" sing N N 138 G "C5'" "H5''" sing N N 139 G "C4'" "O4'" sing N N 140 G "C4'" "C3'" sing N N 141 G "C4'" "H4'" sing N N 142 G "O4'" "C1'" sing N N 143 G "C3'" "O3'" sing N N 144 G "C3'" "C2'" sing N N 145 G "C3'" "H3'" sing N N 146 G "O3'" "HO3'" sing N N 147 G "C2'" "O2'" sing N N 148 G "C2'" "C1'" sing N N 149 G "C2'" "H2'" sing N N 150 G "O2'" "HO2'" sing N N 151 G "C1'" N9 sing N N 152 G "C1'" "H1'" sing N N 153 G N9 C8 sing Y N 154 G N9 C4 sing Y N 155 G C8 N7 doub Y N 156 G C8 H8 sing N N 157 G N7 C5 sing Y N 158 G C5 C6 sing N N 159 G C5 C4 doub Y N 160 G C6 O6 doub N N 161 G C6 N1 sing N N 162 G N1 C2 sing N N 163 G N1 H1 sing N N 164 G C2 N2 sing N N 165 G C2 N3 doub N N 166 G N2 H21 sing N N 167 G N2 H22 sing N N 168 G N3 C4 sing N N 169 PSU N1 C2 sing N N 170 PSU N1 C6 sing N N 171 PSU N1 HN1 sing N N 172 PSU C2 N3 sing N N 173 PSU C2 O2 doub N N 174 PSU N3 C4 sing N N 175 PSU N3 HN3 sing N N 176 PSU C4 C5 sing N N 177 PSU C4 O4 doub N N 178 PSU C5 C6 doub N N 179 PSU C5 "C1'" sing N N 180 PSU C6 H6 sing N N 181 PSU "C1'" "C2'" sing N N 182 PSU "C1'" "O4'" sing N N 183 PSU "C1'" "H1'" sing N N 184 PSU "C2'" "O2'" sing N N 185 PSU "C2'" "C3'" sing N N 186 PSU "C2'" "H2'" sing N N 187 PSU "O2'" "HO2'" sing N N 188 PSU "C3'" "C4'" sing N N 189 PSU "C3'" "O3'" sing N N 190 PSU "C3'" "H3'" sing N N 191 PSU "C4'" "O4'" sing N N 192 PSU "C4'" "C5'" sing N N 193 PSU "C4'" "H4'" sing N N 194 PSU "O3'" "HO3'" sing N N 195 PSU "C5'" "O5'" sing N N 196 PSU "C5'" "H5'" sing N N 197 PSU "C5'" "H5''" sing N N 198 PSU "O5'" P sing N N 199 PSU P OP1 doub N N 200 PSU P OP2 sing N N 201 PSU P OP3 sing N N 202 PSU OP2 HOP2 sing N N 203 PSU OP3 HOP3 sing N N 204 U OP3 P sing N N 205 U OP3 HOP3 sing N N 206 U P OP1 doub N N 207 U P OP2 sing N N 208 U P "O5'" sing N N 209 U OP2 HOP2 sing N N 210 U "O5'" "C5'" sing N N 211 U "C5'" "C4'" sing N N 212 U "C5'" "H5'" sing N N 213 U "C5'" "H5''" sing N N 214 U "C4'" "O4'" sing N N 215 U "C4'" "C3'" sing N N 216 U "C4'" "H4'" sing N N 217 U "O4'" "C1'" sing N N 218 U "C3'" "O3'" sing N N 219 U "C3'" "C2'" sing N N 220 U "C3'" "H3'" sing N N 221 U "O3'" "HO3'" sing N N 222 U "C2'" "O2'" sing N N 223 U "C2'" "C1'" sing N N 224 U "C2'" "H2'" sing N N 225 U "O2'" "HO2'" sing N N 226 U "C1'" N1 sing N N 227 U "C1'" "H1'" sing N N 228 U N1 C2 sing N N 229 U N1 C6 sing N N 230 U C2 O2 doub N N 231 U C2 N3 sing N N 232 U N3 C4 sing N N 233 U N3 H3 sing N N 234 U C4 O4 doub N N 235 U C4 C5 sing N N 236 U C5 C6 doub N N 237 U C5 H5 sing N N 238 U C6 H6 sing N N 239 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LBR 'double helix' 2LBR 'a-form double helix' 2LBR 'hairpin loop' 2LBR '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 17 1_555 0.563 0.031 -0.291 9.789 38.560 16.271 1 A_G1:C17_A A 1 ? A 17 ? ? 1 1 A G 2 1_555 A C 16 1_555 -0.152 -0.292 -0.161 2.358 -2.182 -2.140 2 A_G2:C16_A A 2 ? A 16 ? 19 1 1 A G 3 1_555 A C 15 1_555 0.637 -0.115 -0.288 0.707 -22.122 -14.583 3 A_G3:C15_A A 3 ? A 15 ? ? 1 1 A G 4 1_555 A C 14 1_555 0.743 -0.011 -0.376 2.806 -19.318 -13.436 4 A_G4:C14_A A 4 ? A 14 ? ? 1 1 A A 5 1_555 A PSU 13 1_555 0.431 0.427 -0.053 -2.864 -21.217 -6.033 5 A_A5:PSU13_A A 5 ? A 13 ? 21 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 17 1_555 A G 2 1_555 A C 16 1_555 -1.147 -0.039 4.159 5.462 24.904 20.065 -5.573 3.266 2.380 51.187 -11.227 32.342 1 AA_G1G2:C16C17_AA A 1 ? A 17 ? A 2 ? A 16 ? 1 A G 2 1_555 A C 16 1_555 A G 3 1_555 A C 15 1_555 -0.614 0.002 3.755 0.426 2.486 40.020 -0.322 0.952 3.742 3.629 -0.622 40.097 2 AA_G2G3:C15C16_AA A 2 ? A 16 ? A 3 ? A 15 ? 1 A G 3 1_555 A C 15 1_555 A G 4 1_555 A C 14 1_555 0.732 -0.158 3.150 3.678 25.875 37.182 -2.458 -0.633 2.585 35.698 -5.074 45.181 3 AA_G3G4:C14C15_AA A 3 ? A 15 ? A 4 ? A 14 ? 1 A G 4 1_555 A C 14 1_555 A A 5 1_555 A PSU 13 1_555 0.930 -0.536 3.437 2.498 25.196 36.668 -3.115 -0.994 2.623 35.357 -3.505 44.312 4 AA_G4A5:PSU13C14_AA A 4 ? A 14 ? A 5 ? A 13 ? # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 500 Varian INOVA 1 'Varian INOVA' 600 Varian INOVA 2 'Varian INOVA' # _atom_sites.entry_id 2LBR _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_