data_2MER # _entry.id 2MER # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 2MER pdb_00002mer 10.2210/pdb2mer/pdb RCSB RCSB103540 ? ? BMRB 18974 ? 10.13018/BMR18974 WWPDB D_1000103540 ? ? # 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 2014-01-01 2 'Structure model' 1 1 2014-01-15 3 'Structure model' 1 2 2014-04-16 4 'Structure model' 1 3 2024-05-01 # _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' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_nmr_software 5 4 'Structure model' pdbx_nmr_spectrometer 6 4 'Structure model' struct_conn # 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' 3 4 'Structure model' '_pdbx_nmr_software.name' 4 4 'Structure model' '_pdbx_nmr_spectrometer.model' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2MER _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-09-26 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_id 18974 _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Jiang, J.' 1 'Aduri, R.' 2 'Chow, C.S.' 3 'Santalucia, J.' 4 # _citation.id primary _citation.title 'Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 42 _citation.page_first 3971 _citation.page_last 3981 _citation.year 2014 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24371282 _citation.pdbx_database_id_DOI 10.1093/nar/gkt1329 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Jiang, J.' 1 ? primary 'Aduri, R.' 2 ? primary 'Chow, C.S.' 3 ? primary 'Santalucia, J.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "RNA_(5'-R(P*GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3')" _entity.formula_weight 6077.673 _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 'GGCCG(PSU)AAC(PSU)A(PSU)AACGGUC' _entity_poly.pdbx_seq_one_letter_code_can GGCCGUAACUAUAACGGUC _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 C n 1 4 C n 1 5 G n 1 6 PSU n 1 7 A n 1 8 A n 1 9 C n 1 10 PSU n 1 11 A n 1 12 PSU n 1 13 A n 1 14 A n 1 15 C n 1 16 G n 1 17 G n 1 18 U n 1 19 C n # 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 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 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 PSU 6 6 6 PSU PSU A . n A 1 7 A 7 7 7 A A A . n A 1 8 A 8 8 8 A A A . n A 1 9 C 9 9 9 C C A . n A 1 10 PSU 10 10 10 PSU PSU A . n A 1 11 A 11 11 11 A A A . n A 1 12 PSU 12 12 12 PSU PSU A . n A 1 13 A 13 13 13 A A A . n A 1 14 A 14 14 14 A A A . n A 1 15 C 15 15 15 C C A . n A 1 16 G 16 16 16 G G 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 # _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 2MER _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2MER _struct.title 'Structure of helix 69 from escherichia coli 23s ribosomal rna' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2MER _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Pseudouridine, Helix 69, Ribosomal, 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 2MER _struct_ref.pdbx_db_accession 2MER _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GGCCGUAACUAUAACGGUC _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2MER _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 19 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2MER _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 19 _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 19 # _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 G 5 "O3'" ? ? ? 1_555 A PSU 6 P ? ? A G 5 A PSU 6 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale2 covale both ? A PSU 6 "O3'" ? ? ? 1_555 A A 7 P ? ? A PSU 6 A A 7 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale3 covale both ? A C 9 "O3'" ? ? ? 1_555 A PSU 10 P ? ? A C 9 A PSU 10 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale4 covale both ? A PSU 10 "O3'" ? ? ? 1_555 A A 11 P ? ? A PSU 10 A A 11 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale5 covale both ? A A 11 "O3'" ? ? ? 1_555 A PSU 12 P ? ? A A 11 A PSU 12 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale6 covale both ? A PSU 12 "O3'" ? ? ? 1_555 A A 13 P ? ? A PSU 12 A A 13 1_555 ? ? ? ? ? ? ? 1.609 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 19 N3 ? ? A G 1 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 19 O2 ? ? A G 1 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 19 N4 ? ? A G 1 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 18 O2 ? ? A G 2 A U 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 18 N3 ? ? A G 2 A U 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 3 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 3 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 3 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 4 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 4 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 4 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 5 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 5 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 5 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A PSU 6 N3 ? ? ? 1_555 A A 14 N1 ? ? A PSU 6 A A 14 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog16 hydrog ? ? A PSU 6 O2 ? ? ? 1_555 A A 14 N6 ? ? A PSU 6 A A 14 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog17 hydrog ? ? A A 8 N1 ? ? ? 1_555 A PSU 12 N3 ? ? A A 8 A PSU 12 1_555 ? ? ? ? ? ? 'A-PSU MISPAIR' ? ? ? # 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 O2 A PSU 6 ? ? H61 A A 14 ? ? 1.49 2 1 O6 A G 1 ? ? H41 A C 19 ? ? 1.52 3 1 O2 A C 4 ? ? H21 A G 16 ? ? 1.60 4 2 O6 A G 1 ? ? H41 A C 19 ? ? 1.51 5 3 O6 A G 1 ? ? H41 A C 19 ? ? 1.49 6 4 O6 A G 1 ? ? H41 A C 19 ? ? 1.51 7 5 O2 A PSU 6 ? ? H61 A A 14 ? ? 1.49 8 5 "O2'" A A 11 ? ? "O4'" A PSU 12 ? ? 1.79 9 6 O2 A PSU 6 ? ? H61 A A 14 ? ? 1.50 10 6 O6 A G 1 ? ? H41 A C 19 ? ? 1.51 11 6 "O2'" A A 11 ? ? "O4'" A PSU 12 ? ? 1.77 12 7 O6 A G 1 ? ? H41 A C 19 ? ? 1.52 13 8 O2 A PSU 6 ? ? H61 A A 14 ? ? 1.49 14 8 O6 A G 1 ? ? H41 A C 19 ? ? 1.51 15 8 O2 A C 4 ? ? H21 A G 16 ? ? 1.60 16 8 "O2'" A A 11 ? ? "O4'" A PSU 12 ? ? 1.79 17 9 O6 A G 1 ? ? H41 A C 19 ? ? 1.51 18 10 O2 A PSU 6 ? ? H61 A A 14 ? ? 1.51 19 10 O6 A G 1 ? ? H41 A C 19 ? ? 1.52 20 10 O2 A C 4 ? ? H21 A G 16 ? ? 1.60 # 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 PSU 6 A PSU 6 ? U "PSEUDOURIDINE-5'-MONOPHOSPHATE" 2 A PSU 10 A PSU 10 ? U "PSEUDOURIDINE-5'-MONOPHOSPHATE" 3 A PSU 12 A PSU 12 ? 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 'CONVERGED LOWEST ENERGY STRUCTURES' _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 2MER _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 2MER _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;1.0 mM RNA (5'-P(GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 100% D2O ; 1 '100% D2O' ;1.0 mM RNA (5'-P(GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 90% H2O/10% D2O ; 2 '90% H2O/10% 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 ;RNA (5'-P(GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3')-1 ; 1.0 ? mM ? 1 'Potassium Phosphate-2' 10 ? mM ? 1 'Potassium Chloride-3' 50 ? mM ? 1 EDTA-4 0.1 ? mM ? 1 ;RNA (5'-P(GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3')-5 ; 1.0 ? mM ? 2 'Potassium Phosphate-6' 10 ? mM ? 2 'Potassium Chloride-7' 50 ? mM ? 2 EDTA-8 0.1 ? mM ? 2 # 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 70 7.3 ambient ? 310.2 K 2 70 7.3 ambient ? 283.2 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 1H-13C NATURAL ABUNDANCE HMQC' 1 2 1 '2D 1H-1H NOESY' 1 3 1 '2D DQF-COSY' 1 4 1 '3D 1H-1H-1H TOCSY-NOESY' 1 5 1 '2D 1H-31P HETCOR' 1 6 1 '1D 31P' 2 7 2 '2D 1H-1H NOESY' # _pdbx_nmr_refine.entry_id 2MER _pdbx_nmr_refine.method 'simulated annealing, molecular dynamics, torsion angle 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 Goddard 'chemical shift assignment' Sparky ? 1 Goddard 'data analysis' Sparky ? 2 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.2 3 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNS 1.2 4 'Bruker Biospin' collection TopSpin ? 5 'Bruker Biospin' processing TopSpin ? 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 PSU N1 N N N 111 PSU C2 C N N 112 PSU N3 N N N 113 PSU C4 C N N 114 PSU C5 C N N 115 PSU C6 C N N 116 PSU O2 O N N 117 PSU O4 O N N 118 PSU "C1'" C N S 119 PSU "C2'" C N R 120 PSU "O2'" O N N 121 PSU "C3'" C N S 122 PSU "C4'" C N R 123 PSU "O3'" O N N 124 PSU "O4'" O N N 125 PSU "C5'" C N N 126 PSU "O5'" O N N 127 PSU P P N N 128 PSU OP1 O N N 129 PSU OP2 O N N 130 PSU OP3 O N N 131 PSU HN1 H N N 132 PSU HN3 H N N 133 PSU H6 H N N 134 PSU "H1'" H N N 135 PSU "H2'" H N N 136 PSU "HO2'" H N N 137 PSU "H3'" H N N 138 PSU "H4'" H N N 139 PSU "HO3'" H N N 140 PSU "H5'" H N N 141 PSU "H5''" H N N 142 PSU HOP2 H N N 143 PSU HOP3 H N N 144 U OP3 O N N 145 U P P N N 146 U OP1 O N N 147 U OP2 O N N 148 U "O5'" O N N 149 U "C5'" C N N 150 U "C4'" C N R 151 U "O4'" O N N 152 U "C3'" C N S 153 U "O3'" O N N 154 U "C2'" C N R 155 U "O2'" O N N 156 U "C1'" C N R 157 U N1 N N N 158 U C2 C N N 159 U O2 O N N 160 U N3 N N N 161 U C4 C N N 162 U O4 O N N 163 U C5 C N N 164 U C6 C N N 165 U HOP3 H N N 166 U HOP2 H N N 167 U "H5'" H N N 168 U "H5''" H N N 169 U "H4'" H N N 170 U "H3'" H N N 171 U "HO3'" H N N 172 U "H2'" H N N 173 U "HO2'" H N N 174 U "H1'" H N N 175 U H3 H N N 176 U H5 H N N 177 U H6 H N N 178 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 PSU N1 C2 sing N N 116 PSU N1 C6 sing N N 117 PSU N1 HN1 sing N N 118 PSU C2 N3 sing N N 119 PSU C2 O2 doub N N 120 PSU N3 C4 sing N N 121 PSU N3 HN3 sing N N 122 PSU C4 C5 sing N N 123 PSU C4 O4 doub N N 124 PSU C5 C6 doub N N 125 PSU C5 "C1'" sing N N 126 PSU C6 H6 sing N N 127 PSU "C1'" "C2'" sing N N 128 PSU "C1'" "O4'" sing N N 129 PSU "C1'" "H1'" sing N N 130 PSU "C2'" "O2'" sing N N 131 PSU "C2'" "C3'" sing N N 132 PSU "C2'" "H2'" sing N N 133 PSU "O2'" "HO2'" sing N N 134 PSU "C3'" "C4'" sing N N 135 PSU "C3'" "O3'" sing N N 136 PSU "C3'" "H3'" sing N N 137 PSU "C4'" "O4'" sing N N 138 PSU "C4'" "C5'" sing N N 139 PSU "C4'" "H4'" sing N N 140 PSU "O3'" "HO3'" sing N N 141 PSU "C5'" "O5'" sing N N 142 PSU "C5'" "H5'" sing N N 143 PSU "C5'" "H5''" sing N N 144 PSU "O5'" P sing N N 145 PSU P OP1 doub N N 146 PSU P OP2 sing N N 147 PSU P OP3 sing N N 148 PSU OP2 HOP2 sing N N 149 PSU OP3 HOP3 sing N N 150 U OP3 P sing N N 151 U OP3 HOP3 sing N N 152 U P OP1 doub N N 153 U P OP2 sing N N 154 U P "O5'" sing N N 155 U OP2 HOP2 sing N N 156 U "O5'" "C5'" sing N N 157 U "C5'" "C4'" sing N N 158 U "C5'" "H5'" sing N N 159 U "C5'" "H5''" sing N N 160 U "C4'" "O4'" sing N N 161 U "C4'" "C3'" sing N N 162 U "C4'" "H4'" sing N N 163 U "O4'" "C1'" sing N N 164 U "C3'" "O3'" sing N N 165 U "C3'" "C2'" sing N N 166 U "C3'" "H3'" sing N N 167 U "O3'" "HO3'" sing N N 168 U "C2'" "O2'" sing N N 169 U "C2'" "C1'" sing N N 170 U "C2'" "H2'" sing N N 171 U "O2'" "HO2'" sing N N 172 U "C1'" N1 sing N N 173 U "C1'" "H1'" sing N N 174 U N1 C2 sing N N 175 U N1 C6 sing N N 176 U C2 O2 doub N N 177 U C2 N3 sing N N 178 U N3 C4 sing N N 179 U N3 H3 sing N N 180 U C4 O4 doub N N 181 U C4 C5 sing N N 182 U C5 C6 doub N N 183 U C5 H5 sing N N 184 U C6 H6 sing N N 185 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2MER 'double helix' 2MER 'a-form double helix' 2MER 'hairpin loop' 2MER '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 19 1_555 0.290 -0.242 0.015 2.359 1.988 -8.118 1 A_G1:C19_A A 1 ? A 19 ? 19 1 1 A G 2 1_555 A U 18 1_555 -2.020 -0.292 -0.076 1.806 -1.428 -1.392 2 A_G2:U18_A A 2 ? A 18 ? 28 1 1 A C 3 1_555 A G 17 1_555 -0.232 -0.121 -0.047 1.759 -2.505 1.839 3 A_C3:G17_A A 3 ? A 17 ? 19 1 1 A C 4 1_555 A G 16 1_555 0.016 -0.244 -0.321 6.787 4.416 0.669 4 A_C4:G16_A A 4 ? A 16 ? 19 1 1 A G 5 1_555 A C 15 1_555 -0.225 -0.176 -0.193 -1.109 0.386 -5.546 5 A_G5:C15_A A 5 ? A 15 ? 19 1 1 A PSU 6 1_555 A A 14 1_555 -0.271 -0.265 0.036 -0.458 -4.209 -12.254 6 A_PSU6:A14_A A 6 ? A 14 ? 21 1 1 A A 8 1_555 A PSU 12 1_555 0.064 0.660 2.091 30.204 -3.382 37.321 7 A_A8:PSU12_A A 8 ? A 12 ? ? 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 19 1_555 A G 2 1_555 A U 18 1_555 0.276 -2.111 3.498 0.200 -3.361 20.820 -4.190 -0.660 3.789 -9.222 -0.549 21.088 1 AA_G1G2:U18C19_AA A 1 ? A 19 ? A 2 ? A 18 ? 1 A G 2 1_555 A U 18 1_555 A C 3 1_555 A G 17 1_555 0.134 -1.200 4.051 0.486 -7.174 36.445 -0.664 -0.129 4.205 -11.336 -0.767 37.124 2 AA_G2C3:G17U18_AA A 2 ? A 18 ? A 3 ? A 17 ? 1 A C 3 1_555 A G 17 1_555 A C 4 1_555 A G 16 1_555 0.800 -0.673 3.965 3.198 -7.731 35.313 0.269 -0.728 4.072 -12.528 -5.182 36.259 3 AA_C3C4:G16G17_AA A 3 ? A 17 ? A 4 ? A 16 ? 1 A C 4 1_555 A G 16 1_555 A G 5 1_555 A C 15 1_555 -1.166 -1.168 4.460 1.172 -8.494 26.353 0.466 2.838 4.552 -18.033 -2.489 27.689 4 AA_C4G5:C15G16_AA A 4 ? A 16 ? A 5 ? A 15 ? 1 A G 5 1_555 A C 15 1_555 A PSU 6 1_555 A A 14 1_555 0.042 -1.839 3.767 -3.938 -0.914 24.737 -3.923 -1.451 3.778 -2.115 9.113 25.060 5 AA_G5PSU6:A14C15_AA A 5 ? A 15 ? A 6 ? A 14 ? # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 700 Bruker AVANCE 1 'Bruker Avance' 400 Varian Mercury 2 'Varian Mercury' # _atom_sites.entry_id 2MER _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_