data_2L8U # _entry.id 2L8U # _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 2L8U pdb_00002l8u 10.2210/pdb2l8u/pdb RCSB RCSB102101 ? ? BMRB 17401 ? 10.13018/BMR17401 WWPDB D_1000102101 ? ? # 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 2011-02-23 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-02-15 4 'Structure model' 1 3 2023-06-14 5 'Structure model' 1 4 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' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Source and taxonomy' 5 4 'Structure model' Other 6 5 'Structure model' 'Data collection' 7 5 '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_entity_src_syn 3 3 'Structure model' pdbx_nmr_software 4 4 'Structure model' pdbx_database_status 5 5 'Structure model' chem_comp_atom 6 5 'Structure model' chem_comp_bond 7 5 '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_nmr_software.name' 4 4 'Structure model' '_pdbx_database_status.status_code_nmr_data' 5 5 'Structure model' '_database_2.pdbx_DOI' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2L8U _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-01-25 _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.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 17401 BMRB . unspecified 2L8C PDB 'UU pair with zero hydrogen bond pairs' unspecified 2L8W PDB 'UU pair with two hydrogen bond pairs' # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Parkesh, R.' 1 'Fountain, M.A.' 2 'Disney, M.D.' 3 # _citation.id primary _citation.title ;NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)(2) Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 50 _citation.page_first 599 _citation.page_last 601 _citation.year 2011 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21204525 _citation.pdbx_database_id_DOI 10.1021/bi101896j # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Parkesh, R.' 1 ? primary 'Fountain, M.' 2 ? primary 'Disney, M.D.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3') ; _entity.formula_weight 2862.759 _entity.pdbx_number_of_molecules 2 _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 CCGCUGCGG _entity_poly.pdbx_seq_one_letter_code_can CCGCUGCGG _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 C n 1 2 C n 1 3 G n 1 4 C n 1 5 U n 1 6 G n 1 7 C n 1 8 G n 1 9 G 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 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 C 1 1 1 C C A . n A 1 2 C 2 2 2 C C A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 U 5 5 5 U U A . n A 1 6 G 6 6 6 G G A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G A . n A 1 9 G 9 9 9 G G A . n B 1 1 C 1 10 10 C C B . n B 1 2 C 2 11 11 C C B . n B 1 3 G 3 12 12 G G B . n B 1 4 C 4 13 13 C C B . n B 1 5 U 5 14 14 U U B . n B 1 6 G 6 15 15 G G B . n B 1 7 C 7 16 16 C C B . n B 1 8 G 8 17 17 G G B . n B 1 9 G 9 18 18 G G B . 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 'duplex with UU Internal Loop Found in Myotonic Dystrophy Type 1' _exptl.entry_id 2L8U _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2L8U _struct.title ;NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1 - UU pair with one hydrogen bond pair ; _struct.pdbx_model_details 'fewest violations, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2L8U _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'UU mismatch, RNA' # 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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2L8U _struct_ref.pdbx_db_accession 2L8U _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _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 2L8U A 1 ? 9 ? 2L8U 1 ? 9 ? 1 9 2 1 2L8U B 1 ? 9 ? 2L8U 10 ? 18 ? 10 18 # _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_ _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 C 1 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 1 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 1 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 1 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 2 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 2 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 2 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 3 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 3 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 3 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 4 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 4 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 4 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 5 N3 ? ? ? 1_555 B U 5 O4 ? ? A U 5 B U 14 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog14 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 6 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 6 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 6 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 8 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 8 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 8 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 8 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 9 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 9 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 9 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 C 1 ? ? "C1'" A C 1 ? ? N1 A C 1 ? ? 114.34 108.50 5.84 0.70 N 2 1 N1 A C 1 ? ? C2 A C 1 ? ? O2 A C 1 ? ? 122.74 118.90 3.84 0.60 N 3 1 N3 A C 1 ? ? C2 A C 1 ? ? O2 A C 1 ? ? 116.27 121.90 -5.63 0.70 N 4 1 N3 A C 2 ? ? C2 A C 2 ? ? O2 A C 2 ? ? 116.97 121.90 -4.93 0.70 N 5 1 N3 A C 4 ? ? C2 A C 4 ? ? O2 A C 4 ? ? 116.36 121.90 -5.54 0.70 N 6 1 N3 A U 5 ? ? C2 A U 5 ? ? O2 A U 5 ? ? 117.42 122.20 -4.78 0.70 N 7 1 N3 A C 7 ? ? C2 A C 7 ? ? O2 A C 7 ? ? 116.99 121.90 -4.91 0.70 N 8 1 N3 B C 10 ? ? C2 B C 10 ? ? O2 B C 10 ? ? 116.95 121.90 -4.95 0.70 N 9 1 N3 B C 11 ? ? C2 B C 11 ? ? O2 B C 11 ? ? 116.69 121.90 -5.21 0.70 N 10 1 "O4'" B C 13 ? ? "C1'" B C 13 ? ? N1 B C 13 ? ? 113.24 108.50 4.74 0.70 N 11 1 N1 B C 13 ? ? C2 B C 13 ? ? O2 B C 13 ? ? 122.54 118.90 3.64 0.60 N 12 1 N3 B C 13 ? ? C2 B C 13 ? ? O2 B C 13 ? ? 116.62 121.90 -5.28 0.70 N 13 1 N3 B C 16 ? ? C2 B C 16 ? ? O2 B C 16 ? ? 116.80 121.90 -5.10 0.70 N 14 1 N1 B G 18 ? ? C6 B G 18 ? ? O6 B G 18 ? ? 116.12 119.90 -3.78 0.60 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 U B 14 ? ? 0.073 'SIDE CHAIN' 2 1 G B 15 ? ? 0.068 'SIDE CHAIN' # _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 acceptable covalent geometry' _pdbx_nmr_ensemble.conformers_calculated_total_number 25 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2L8U _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 2L8U _pdbx_nmr_representative.selection_criteria 'fewest violations' # _pdbx_nmr_sample_details.contents ;1.5 mM RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3'), 100% D2O ; _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '100% D2O' # _pdbx_nmr_exptl_sample.component ;RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')-1 ; _pdbx_nmr_exptl_sample.concentration 1.5 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling ? _pdbx_nmr_exptl_sample.solution_id 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.1 _pdbx_nmr_exptl_sample_conditions.pH 7.2 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 313 _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 '2D DQF-COSY' 1 2 1 '2D 1H-1H NOESY' 1 3 1 '2D 1H-1H TOCSY' # _pdbx_nmr_refine.entry_id 2L8U _pdbx_nmr_refine.method 'molecular dynamics' _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 'Guntert, Mumenthaler and Wuthrich' 'geometry optimization' CYANA 2.1 1 Goddard 'chemical shift assignment' Sparky 3.111 2 Goddard 'data analysis' Sparky 3.111 3 Goddard 'peak picking' Sparky 3.111 4 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' refinement Amber 11 5 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' 'structure solution' Amber 11 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 G OP3 O N N 36 G P P N N 37 G OP1 O N N 38 G OP2 O N N 39 G "O5'" O N N 40 G "C5'" C N N 41 G "C4'" C N R 42 G "O4'" O N N 43 G "C3'" C N S 44 G "O3'" O N N 45 G "C2'" C N R 46 G "O2'" O N N 47 G "C1'" C N R 48 G N9 N Y N 49 G C8 C Y N 50 G N7 N Y N 51 G C5 C Y N 52 G C6 C N N 53 G O6 O N N 54 G N1 N N N 55 G C2 C N N 56 G N2 N N N 57 G N3 N N N 58 G C4 C Y N 59 G HOP3 H N N 60 G HOP2 H N N 61 G "H5'" H N N 62 G "H5''" H N N 63 G "H4'" H N N 64 G "H3'" H N N 65 G "HO3'" H N N 66 G "H2'" H N N 67 G "HO2'" H N N 68 G "H1'" H N N 69 G H8 H N N 70 G H1 H N N 71 G H21 H N N 72 G H22 H N N 73 U OP3 O N N 74 U P P N N 75 U OP1 O N N 76 U OP2 O N N 77 U "O5'" O N N 78 U "C5'" C N N 79 U "C4'" C N R 80 U "O4'" O N N 81 U "C3'" C N S 82 U "O3'" O N N 83 U "C2'" C N R 84 U "O2'" O N N 85 U "C1'" C N R 86 U N1 N N N 87 U C2 C N N 88 U O2 O N N 89 U N3 N N N 90 U C4 C N N 91 U O4 O N N 92 U C5 C N N 93 U C6 C N N 94 U HOP3 H N N 95 U HOP2 H N N 96 U "H5'" H N N 97 U "H5''" H N N 98 U "H4'" H N N 99 U "H3'" H N N 100 U "HO3'" H N N 101 U "H2'" H N N 102 U "HO2'" H N N 103 U "H1'" H N N 104 U H3 H N N 105 U H5 H N N 106 U H6 H N N 107 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 G OP3 P sing N N 37 G OP3 HOP3 sing N N 38 G P OP1 doub N N 39 G P OP2 sing N N 40 G P "O5'" sing N N 41 G OP2 HOP2 sing N N 42 G "O5'" "C5'" sing N N 43 G "C5'" "C4'" sing N N 44 G "C5'" "H5'" sing N N 45 G "C5'" "H5''" sing N N 46 G "C4'" "O4'" sing N N 47 G "C4'" "C3'" sing N N 48 G "C4'" "H4'" sing N N 49 G "O4'" "C1'" sing N N 50 G "C3'" "O3'" sing N N 51 G "C3'" "C2'" sing N N 52 G "C3'" "H3'" sing N N 53 G "O3'" "HO3'" sing N N 54 G "C2'" "O2'" sing N N 55 G "C2'" "C1'" sing N N 56 G "C2'" "H2'" sing N N 57 G "O2'" "HO2'" sing N N 58 G "C1'" N9 sing N N 59 G "C1'" "H1'" sing N N 60 G N9 C8 sing Y N 61 G N9 C4 sing Y N 62 G C8 N7 doub Y N 63 G C8 H8 sing N N 64 G N7 C5 sing Y N 65 G C5 C6 sing N N 66 G C5 C4 doub Y N 67 G C6 O6 doub N N 68 G C6 N1 sing N N 69 G N1 C2 sing N N 70 G N1 H1 sing N N 71 G C2 N2 sing N N 72 G C2 N3 doub N N 73 G N2 H21 sing N N 74 G N2 H22 sing N N 75 G N3 C4 sing N N 76 U OP3 P sing N N 77 U OP3 HOP3 sing N N 78 U P OP1 doub N N 79 U P OP2 sing N N 80 U P "O5'" sing N N 81 U OP2 HOP2 sing N N 82 U "O5'" "C5'" sing N N 83 U "C5'" "C4'" sing N N 84 U "C5'" "H5'" sing N N 85 U "C5'" "H5''" sing N N 86 U "C4'" "O4'" sing N N 87 U "C4'" "C3'" sing N N 88 U "C4'" "H4'" sing N N 89 U "O4'" "C1'" sing N N 90 U "C3'" "O3'" sing N N 91 U "C3'" "C2'" sing N N 92 U "C3'" "H3'" sing N N 93 U "O3'" "HO3'" sing N N 94 U "C2'" "O2'" sing N N 95 U "C2'" "C1'" sing N N 96 U "C2'" "H2'" sing N N 97 U "O2'" "HO2'" sing N N 98 U "C1'" N1 sing N N 99 U "C1'" "H1'" sing N N 100 U N1 C2 sing N N 101 U N1 C6 sing N N 102 U C2 O2 doub N N 103 U C2 N3 sing N N 104 U N3 C4 sing N N 105 U N3 H3 sing N N 106 U C4 O4 doub N N 107 U C4 C5 sing N N 108 U C5 C6 doub N N 109 U C5 H5 sing N N 110 U C6 H6 sing N N 111 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2L8U 'double helix' 2L8U 'a-form double helix' 2L8U '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 C 1 1_555 B G 9 1_555 0.490 -0.042 -0.488 20.753 -21.208 3.126 1 A_C1:G18_B A 1 ? B 18 ? 19 1 1 A C 2 1_555 B G 8 1_555 0.277 -0.077 -0.129 11.236 -7.460 -1.854 2 A_C2:G17_B A 2 ? B 17 ? 19 1 1 A G 3 1_555 B C 7 1_555 -0.283 -0.071 0.405 15.860 6.333 -1.361 3 A_G3:C16_B A 3 ? B 16 ? 19 1 1 A C 4 1_555 B G 6 1_555 0.348 -0.144 -0.559 -2.641 -18.794 3.647 4 A_C4:G15_B A 4 ? B 15 ? 19 1 1 A U 5 1_555 B U 5 1_555 3.035 -1.143 -0.087 -22.070 -6.465 -24.295 5 A_U5:U14_B A 5 ? B 14 ? ? ? 1 A G 6 1_555 B C 4 1_555 -0.291 -0.066 -0.206 -12.841 -20.740 2.278 6 A_G6:C13_B A 6 ? B 13 ? 19 1 1 A C 7 1_555 B G 3 1_555 0.027 -0.070 0.425 -12.733 -3.513 -3.915 7 A_C7:G12_B A 7 ? B 12 ? 19 1 1 A G 8 1_555 B C 2 1_555 -0.196 -0.057 -0.108 -10.387 -8.849 -0.444 8 A_G8:C11_B A 8 ? B 11 ? 19 1 1 A G 9 1_555 B C 1 1_555 -0.477 -0.055 -0.238 -14.445 -19.077 2.042 9 A_G9:C10_B A 9 ? B 10 ? 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 C 1 1_555 B G 9 1_555 A C 2 1_555 B G 8 1_555 -0.518 -1.759 3.537 -5.773 13.336 32.107 -4.892 -0.001 2.671 22.715 9.834 35.164 1 AA_C1C2:G17G18_BB A 1 ? B 18 ? A 2 ? B 17 ? 1 A C 2 1_555 B G 8 1_555 A G 3 1_555 B C 7 1_555 -0.187 -2.573 3.170 -7.878 2.197 25.676 -6.059 -1.509 2.873 4.792 17.181 26.926 2 AA_C2G3:C16G17_BB A 2 ? B 17 ? A 3 ? B 16 ? 1 A G 3 1_555 B C 7 1_555 A C 4 1_555 B G 6 1_555 1.232 -2.181 3.677 11.405 10.536 39.367 -4.217 -0.424 3.237 14.953 -16.186 42.205 3 AA_G3C4:G15C16_BB A 3 ? B 16 ? A 4 ? B 15 ? 1 A C 4 1_555 B G 6 1_555 A U 5 1_555 B U 5 1_555 -1.298 -2.217 4.069 1.970 16.457 40.297 -4.773 1.966 2.926 22.759 -2.724 43.441 4 AA_C4U5:U14G15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A U 5 1_555 B U 5 1_555 A G 6 1_555 B C 4 1_555 0.935 -2.130 3.012 8.179 18.858 4.247 -10.102 -0.722 -0.937 71.972 -31.217 20.985 5 AA_U5G6:C13U14_BB A 5 ? B 14 ? A 6 ? B 13 ? 1 A G 6 1_555 B C 4 1_555 A C 7 1_555 B G 3 1_555 -1.105 -1.373 3.251 -7.586 6.899 35.757 -3.068 0.731 3.104 10.961 12.053 37.152 6 AA_G6C7:G12C13_BB A 6 ? B 13 ? A 7 ? B 12 ? 1 A C 7 1_555 B G 3 1_555 A G 8 1_555 B C 2 1_555 0.691 -1.758 3.162 5.536 8.528 30.253 -4.622 -0.335 2.662 15.789 -10.251 31.878 7 AA_C7G8:C11G12_BB A 7 ? B 12 ? A 8 ? B 11 ? 1 A G 8 1_555 B C 2 1_555 A G 9 1_555 B C 1 1_555 0.703 -1.750 3.354 4.188 13.857 31.053 -5.018 -0.579 2.447 24.297 -7.344 34.186 8 AA_G8G9:C10C11_BB A 8 ? B 11 ? A 9 ? B 10 ? # _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Varian INOVA' # _atom_sites.entry_id 2L8U _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_