data_1PBL # _entry.id 1PBL # _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 1PBL pdb_00001pbl 10.2210/pdb1pbl/pdb WWPDB D_1000175588 ? ? # 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 1997-07-07 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 5 'Structure model' 1 4 2024-05-22 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' Other 7 5 'Structure model' 'Data collection' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_nmr_software 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 4 'Structure model' struct_conn 7 5 'Structure model' chem_comp_atom 8 5 'Structure model' chem_comp_bond # 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_database_status.process_site' 4 4 'Structure model' '_pdbx_nmr_software.name' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1PBL _pdbx_database_status.recvd_initial_deposition_date 1996-08-05 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1PBM _pdbx_database_related.details '1 STRUCTURE' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Popenda, M.' 1 'Biala, E.' 2 'Milecki, J.' 3 'Adamiak, R.W.' 4 # 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 ;Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions. ; 'Nucleic Acids Res.' 25 4589 4598 1997 NARHAD UK 0305-1048 0389 ? 9358170 10.1093/nar/25.22.4589 1 ;Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA ; 'NUCLEIC ACIDS RES.' 25 4599 4607 1997 NARHAD UK 0305-1048 0389 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Popenda, M.' 1 ? primary 'Biala, E.' 2 ? primary 'Milecki, J.' 3 ? primary 'Adamiak, R.W.' 4 ? 1 'Adamiak, D.A.' 5 ? 1 'Milecki, J.' 6 ? 1 'Popenda, M.' 7 ? 1 'Adamiak, R.W.' 8 ? 1 'Dauter, Z.' 9 ? 1 'Rypniewski, W.R.' 10 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*OMCP*OMGP*OMCP*OMGP*OMCP*OMG)-3') ; _entity.formula_weight 1990.361 _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 yes _entity_poly.pdbx_seq_one_letter_code '(OMC)(OMG)(OMC)(OMG)(OMC)(OMG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _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 OMC n 1 2 OMG n 1 3 OMC n 1 4 OMG n 1 5 OMC n 1 6 OMG 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 OMC 'RNA linking' n "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O8 P' 337.223 OMG 'RNA linking' n "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" ? 'C11 H16 N5 O8 P' 377.247 # 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 OMC 1 1 1 OMC OMC A . n A 1 2 OMG 2 2 2 OMG OMG A . n A 1 3 OMC 3 3 3 OMC OMC A . n A 1 4 OMG 4 4 4 OMG OMG A . n A 1 5 OMC 5 5 5 OMC OMC A . n A 1 6 OMG 6 6 6 OMG OMG A . n B 1 1 OMC 1 7 7 OMC OMC B . n B 1 2 OMG 2 8 8 OMG OMG B . n B 1 3 OMC 3 9 9 OMC OMC B . n B 1 4 OMG 4 10 10 OMG OMG B . n B 1 5 OMC 5 11 11 OMC OMC B . n B 1 6 OMG 6 12 12 OMG OMG B . n # _cell.entry_id 1PBL _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PBL _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 1PBL _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 1PBL _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1PBL _struct.title 'STRUCTURE OF RIBONUCLEIC ACID, NMR, 1 STRUCTURE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1PBL _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RIBONUCLEIC ACID, RNA DUPLEX, 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.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1PBL _struct_ref.pdbx_db_accession 1PBL _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1PBL A 1 ? 6 ? 1PBL 1 ? 6 ? 1 6 2 1 1PBL B 1 ? 6 ? 1PBL 7 ? 12 ? 7 12 # _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 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A OMC 1 "O3'" ? ? ? 1_555 A OMG 2 P ? ? A OMC 1 A OMG 2 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale2 covale both ? A OMG 2 "O3'" ? ? ? 1_555 A OMC 3 P ? ? A OMG 2 A OMC 3 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale3 covale both ? A OMC 3 "O3'" ? ? ? 1_555 A OMG 4 P ? ? A OMC 3 A OMG 4 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale4 covale both ? A OMG 4 "O3'" ? ? ? 1_555 A OMC 5 P ? ? A OMG 4 A OMC 5 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale5 covale both ? A OMC 5 "O3'" ? ? ? 1_555 A OMG 6 P ? ? A OMC 5 A OMG 6 1_555 ? ? ? ? ? ? ? 1.618 ? ? covale6 covale both ? B OMC 1 "O3'" ? ? ? 1_555 B OMG 2 P ? ? B OMC 7 B OMG 8 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale7 covale both ? B OMG 2 "O3'" ? ? ? 1_555 B OMC 3 P ? ? B OMG 8 B OMC 9 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale8 covale both ? B OMC 3 "O3'" ? ? ? 1_555 B OMG 4 P ? ? B OMC 9 B OMG 10 1_555 ? ? ? ? ? ? ? 1.618 ? ? covale9 covale both ? B OMG 4 "O3'" ? ? ? 1_555 B OMC 5 P ? ? B OMG 10 B OMC 11 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale10 covale both ? B OMC 5 "O3'" ? ? ? 1_555 B OMG 6 P ? ? B OMC 11 B OMG 12 1_555 ? ? ? ? ? ? ? 1.620 ? ? hydrog1 hydrog ? ? A OMC 1 N3 ? ? ? 1_555 B OMG 6 N1 ? ? A OMC 1 B OMG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A OMC 1 N4 ? ? ? 1_555 B OMG 6 O6 ? ? A OMC 1 B OMG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A OMC 1 O2 ? ? ? 1_555 B OMG 6 N2 ? ? A OMC 1 B OMG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A OMG 2 N1 ? ? ? 1_555 B OMC 5 N3 ? ? A OMG 2 B OMC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A OMG 2 N2 ? ? ? 1_555 B OMC 5 O2 ? ? A OMG 2 B OMC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A OMG 2 O6 ? ? ? 1_555 B OMC 5 N4 ? ? A OMG 2 B OMC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A OMC 3 N3 ? ? ? 1_555 B OMG 4 N1 ? ? A OMC 3 B OMG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A OMC 3 N4 ? ? ? 1_555 B OMG 4 O6 ? ? A OMC 3 B OMG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A OMC 3 O2 ? ? ? 1_555 B OMG 4 N2 ? ? A OMC 3 B OMG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A OMG 4 N1 ? ? ? 1_555 B OMC 3 N3 ? ? A OMG 4 B OMC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A OMG 4 N2 ? ? ? 1_555 B OMC 3 O2 ? ? A OMG 4 B OMC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A OMG 4 O6 ? ? ? 1_555 B OMC 3 N4 ? ? A OMG 4 B OMC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A OMC 5 N3 ? ? ? 1_555 B OMG 2 N1 ? ? A OMC 5 B OMG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A OMC 5 N4 ? ? ? 1_555 B OMG 2 O6 ? ? A OMC 5 B OMG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A OMC 5 O2 ? ? ? 1_555 B OMG 2 N2 ? ? A OMC 5 B OMG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A OMG 6 N1 ? ? ? 1_555 B OMC 1 N3 ? ? A OMG 6 B OMC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A OMG 6 N2 ? ? ? 1_555 B OMC 1 O2 ? ? A OMG 6 B OMC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A OMG 6 O6 ? ? ? 1_555 B OMC 1 N4 ? ? A OMG 6 B OMC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "C3'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 OMC _pdbx_validate_rmsd_angle.auth_seq_id_1 5 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "O3'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 OMC _pdbx_validate_rmsd_angle.auth_seq_id_2 5 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 P _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 OMG _pdbx_validate_rmsd_angle.auth_seq_id_3 6 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 112.45 _pdbx_validate_rmsd_angle.angle_target_value 119.70 _pdbx_validate_rmsd_angle.angle_deviation -7.25 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.20 _pdbx_validate_rmsd_angle.linker_flag Y # 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 OMC 1 A OMC 1 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 2 A OMG 2 A OMG 2 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 3 A OMC 3 A OMC 3 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 4 A OMG 4 A OMG 4 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 5 A OMC 5 A OMC 5 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 6 A OMG 6 A OMG 6 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 7 B OMC 1 B OMC 7 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 8 B OMG 2 B OMG 8 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 9 B OMC 3 B OMC 9 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 10 B OMG 4 B OMG 10 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 11 B OMC 5 B OMC 11 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 12 B OMG 6 B OMG 12 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" # _pdbx_nmr_ensemble.entry_id 1PBL _pdbx_nmr_ensemble.conformers_calculated_total_number 106 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'R 1/6 VALUE' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 300 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 6.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_refine.entry_id 1PBL _pdbx_nmr_refine.method 'IRMA, RMD' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement Discover ? BIOSYM 1 'structure solution' NMRCHITECT ? ? 2 'structure solution' Discover ? ? 3 # 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 OMC N1 N N N 1 OMC C2 C N N 2 OMC N3 N N N 3 OMC C4 C N N 4 OMC C5 C N N 5 OMC C6 C N N 6 OMC O2 O N N 7 OMC N4 N N N 8 OMC "C1'" C N R 9 OMC "C2'" C N R 10 OMC "O2'" O N N 11 OMC CM2 C N N 12 OMC "C3'" C N R 13 OMC "C4'" C N R 14 OMC "O4'" O N N 15 OMC "O3'" O N N 16 OMC "C5'" C N N 17 OMC "O5'" O N N 18 OMC P P N N 19 OMC OP1 O N N 20 OMC OP2 O N N 21 OMC OP3 O N N 22 OMC H5 H N N 23 OMC H6 H N N 24 OMC HN41 H N N 25 OMC HN42 H N N 26 OMC "H1'" H N N 27 OMC "H2'" H N N 28 OMC HM21 H N N 29 OMC HM22 H N N 30 OMC HM23 H N N 31 OMC "H3'" H N N 32 OMC "H4'" H N N 33 OMC "HO3'" H N N 34 OMC "H5'" H N N 35 OMC "H5''" H N N 36 OMC HOP2 H N N 37 OMC HOP3 H N N 38 OMG P P N N 39 OMG OP1 O N N 40 OMG OP2 O N N 41 OMG OP3 O N N 42 OMG "O5'" O N N 43 OMG "C5'" C N N 44 OMG "C4'" C N R 45 OMG "O4'" O N N 46 OMG "C3'" C N R 47 OMG "O3'" O N N 48 OMG "C2'" C N R 49 OMG "O2'" O N N 50 OMG CM2 C N N 51 OMG "C1'" C N R 52 OMG N9 N Y N 53 OMG C8 C Y N 54 OMG N7 N Y N 55 OMG C5 C Y N 56 OMG C6 C N N 57 OMG O6 O N N 58 OMG N1 N N N 59 OMG C2 C N N 60 OMG N2 N N N 61 OMG N3 N N N 62 OMG C4 C Y N 63 OMG HOP2 H N N 64 OMG HOP3 H N N 65 OMG "H5'" H N N 66 OMG "H5''" H N N 67 OMG "H4'" H N N 68 OMG "H3'" H N N 69 OMG "HO3'" H N N 70 OMG "H2'" H N N 71 OMG HM21 H N N 72 OMG HM22 H N N 73 OMG HM23 H N N 74 OMG "H1'" H N N 75 OMG H8 H N N 76 OMG HN1 H N N 77 OMG HN21 H N N 78 OMG HN22 H N N 79 # 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 OMC N1 C2 sing N N 1 OMC N1 C6 sing N N 2 OMC N1 "C1'" sing N N 3 OMC C2 N3 sing N N 4 OMC C2 O2 doub N N 5 OMC N3 C4 doub N N 6 OMC C4 C5 sing N N 7 OMC C4 N4 sing N N 8 OMC C5 C6 doub N N 9 OMC C5 H5 sing N N 10 OMC C6 H6 sing N N 11 OMC N4 HN41 sing N N 12 OMC N4 HN42 sing N N 13 OMC "C1'" "C2'" sing N N 14 OMC "C1'" "O4'" sing N N 15 OMC "C1'" "H1'" sing N N 16 OMC "C2'" "O2'" sing N N 17 OMC "C2'" "C3'" sing N N 18 OMC "C2'" "H2'" sing N N 19 OMC "O2'" CM2 sing N N 20 OMC CM2 HM21 sing N N 21 OMC CM2 HM22 sing N N 22 OMC CM2 HM23 sing N N 23 OMC "C3'" "C4'" sing N N 24 OMC "C3'" "O3'" sing N N 25 OMC "C3'" "H3'" sing N N 26 OMC "C4'" "O4'" sing N N 27 OMC "C4'" "C5'" sing N N 28 OMC "C4'" "H4'" sing N N 29 OMC "O3'" "HO3'" sing N N 30 OMC "C5'" "O5'" sing N N 31 OMC "C5'" "H5'" sing N N 32 OMC "C5'" "H5''" sing N N 33 OMC "O5'" P sing N N 34 OMC P OP1 doub N N 35 OMC P OP2 sing N N 36 OMC P OP3 sing N N 37 OMC OP2 HOP2 sing N N 38 OMC OP3 HOP3 sing N N 39 OMG P OP1 doub N N 40 OMG P OP2 sing N N 41 OMG P OP3 sing N N 42 OMG P "O5'" sing N N 43 OMG OP2 HOP2 sing N N 44 OMG OP3 HOP3 sing N N 45 OMG "O5'" "C5'" sing N N 46 OMG "C5'" "C4'" sing N N 47 OMG "C5'" "H5'" sing N N 48 OMG "C5'" "H5''" sing N N 49 OMG "C4'" "O4'" sing N N 50 OMG "C4'" "C3'" sing N N 51 OMG "C4'" "H4'" sing N N 52 OMG "O4'" "C1'" sing N N 53 OMG "C3'" "O3'" sing N N 54 OMG "C3'" "C2'" sing N N 55 OMG "C3'" "H3'" sing N N 56 OMG "O3'" "HO3'" sing N N 57 OMG "C2'" "O2'" sing N N 58 OMG "C2'" "C1'" sing N N 59 OMG "C2'" "H2'" sing N N 60 OMG "O2'" CM2 sing N N 61 OMG CM2 HM21 sing N N 62 OMG CM2 HM22 sing N N 63 OMG CM2 HM23 sing N N 64 OMG "C1'" N9 sing N N 65 OMG "C1'" "H1'" sing N N 66 OMG N9 C8 sing Y N 67 OMG N9 C4 sing Y N 68 OMG C8 N7 doub Y N 69 OMG C8 H8 sing N N 70 OMG N7 C5 sing Y N 71 OMG C5 C6 sing N N 72 OMG C5 C4 doub Y N 73 OMG C6 O6 doub N N 74 OMG C6 N1 sing N N 75 OMG N1 C2 sing N N 76 OMG N1 HN1 sing N N 77 OMG C2 N2 sing N N 78 OMG C2 N3 doub N N 79 OMG N2 HN21 sing N N 80 OMG N2 HN22 sing N N 81 OMG N3 C4 sing N N 82 # _ndb_struct_conf_na.entry_id 1PBL _ndb_struct_conf_na.feature 'double helix' # 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 OMC 1 1_555 B OMG 6 1_555 0.843 -0.285 0.200 -25.627 -8.137 0.104 1 A_OMC1:OMG12_B A 1 ? B 12 ? 19 1 1 A OMG 2 1_555 B OMC 5 1_555 0.123 -0.049 -0.195 -17.859 -16.110 -0.299 2 A_OMG2:OMC11_B A 2 ? B 11 ? 19 1 1 A OMC 3 1_555 B OMG 4 1_555 0.537 -0.245 0.013 -2.263 -18.364 -0.949 3 A_OMC3:OMG10_B A 3 ? B 10 ? 19 1 1 A OMG 4 1_555 B OMC 3 1_555 -0.352 -0.181 -0.491 -16.899 -30.917 2.424 4 A_OMG4:OMC9_B A 4 ? B 9 ? 19 1 1 A OMC 5 1_555 B OMG 2 1_555 0.685 -0.300 -0.133 -0.082 -15.957 -0.870 5 A_OMC5:OMG8_B A 5 ? B 8 ? 19 1 1 A OMG 6 1_555 B OMC 1 1_555 -0.572 -0.266 0.207 -8.236 -26.762 -0.545 6 A_OMG6:OMC7_B A 6 ? B 7 ? 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 OMC 1 1_555 B OMG 6 1_555 A OMG 2 1_555 B OMC 5 1_555 0.103 -1.278 2.922 6.373 17.687 31.275 -4.027 0.548 1.936 29.689 -10.696 36.370 1 AA_OMC1OMG2:OMC11OMG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A OMG 2 1_555 B OMC 5 1_555 A OMC 3 1_555 B OMG 4 1_555 -0.332 -0.311 2.848 -0.526 12.469 33.748 -2.032 0.473 2.581 20.623 0.870 35.919 2 AA_OMG2OMC3:OMG10OMC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A OMC 3 1_555 B OMG 4 1_555 A OMG 4 1_555 B OMC 3 1_555 0.308 0.054 3.505 4.533 24.672 32.832 -2.865 0.102 2.886 37.582 -6.905 41.107 3 AA_OMC3OMG4:OMC9OMG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A OMG 4 1_555 B OMC 3 1_555 A OMC 5 1_555 B OMG 2 1_555 0.438 0.254 2.739 -2.599 9.746 37.516 -0.623 -0.927 2.684 14.827 3.954 38.801 4 AA_OMG4OMC5:OMG8OMC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A OMC 5 1_555 B OMG 2 1_555 A OMG 6 1_555 B OMC 1 1_555 1.041 -1.066 3.152 0.935 18.995 31.598 -3.989 -1.538 2.211 31.564 -1.554 36.754 5 AA_OMC5OMG6:OMC7OMG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model UNITYPLUS _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 500 # _atom_sites.entry_id 1PBL _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_