data_1RME # _entry.id 1RME # _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 1RME pdb_00001rme 10.2210/pdb1rme/pdb WWPDB D_1000176118 ? ? # 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 1997-01-11 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-03-14 5 'Structure model' 1 4 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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Experimental preparation' 6 4 'Structure model' Other 7 4 'Structure model' 'Source and taxonomy' 8 5 'Structure model' 'Data collection' 9 5 'Structure model' 'Database references' 10 5 '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' ndb_struct_conf_na 2 4 'Structure model' ndb_struct_na_base_pair 3 4 'Structure model' ndb_struct_na_base_pair_step 4 4 'Structure model' pdbx_database_status 5 4 'Structure model' pdbx_entity_src_syn 6 4 'Structure model' pdbx_nmr_ensemble 7 4 'Structure model' pdbx_nmr_exptl 8 4 'Structure model' pdbx_nmr_exptl_sample 9 4 'Structure model' pdbx_nmr_sample_details 10 4 'Structure model' pdbx_nmr_software 11 4 'Structure model' pdbx_nmr_spectrometer 12 4 'Structure model' pdbx_struct_assembly 13 4 'Structure model' pdbx_struct_assembly_prop 14 4 'Structure model' pdbx_struct_oper_list 15 4 'Structure model' struct_conn 16 5 'Structure model' chem_comp_atom 17 5 'Structure model' chem_comp_bond 18 5 'Structure model' database_2 19 5 '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' '_ndb_struct_na_base_pair.hbond_type_28' 2 4 'Structure model' '_ndb_struct_na_base_pair_step.tilt' 3 4 'Structure model' '_ndb_struct_na_base_pair_step.twist' 4 4 'Structure model' '_pdbx_database_status.process_site' 5 4 'Structure model' '_pdbx_nmr_ensemble.conformer_selection_criteria' 6 4 'Structure model' '_pdbx_nmr_software.authors' 7 4 'Structure model' '_struct_conn.details' 8 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 9 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 10 5 'Structure model' '_database_2.pdbx_DOI' 11 5 'Structure model' '_database_2.pdbx_database_accession' 12 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1RME _pdbx_database_status.recvd_initial_deposition_date 1996-07-12 _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nonin, S.' 1 'Leroy, J.-L.' 2 # 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 'Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.' J.Mol.Biol. 261 399 414 1996 JMOBAK UK 0022-2836 0070 ? 8780782 10.1006/jmbi.1996.0472 1 ;Solution Structures of the I-Motif Tetramers of D(Tcc), D(5Methylcct) and D(T5Methylcc): Novel Noe Connections between Amino Protons and Sugar Protons ; Structure 3 101 ? 1995 STRUE6 UK 0969-2126 2005 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nonin, S.' 1 ? primary 'Leroy, J.L.' 2 ? 1 'Leroy, J.L.' 3 ? 1 'Gueron, M.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*(MCY)P*CP*TP*CP*C)-3') ; _entity.formula_weight 1350.010 _entity.pdbx_number_of_molecules 4 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details 'TETRAMER FORMED BY FOUR 5MCCTCC STRANDS' # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(MCY)(DC)(DT)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can CCTCC _entity_poly.pdbx_strand_id A,B,C,D _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 MCY n 1 2 DC n 1 3 DT n 1 4 DC n 1 5 DC 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 MCY 'DNA linking' n "5-METHYL-2'-DEOXYCYTIDINE" ? 'C10 H15 N3 O4' 241.244 # 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 MCY 1 1 1 MCY MCY A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DC 5 5 5 DC DC A . n B 1 1 MCY 1 1 1 MCY MCY B . n B 1 2 DC 2 2 2 DC DC B . n B 1 3 DT 3 3 3 DT DT B . n B 1 4 DC 4 4 4 DC DC B . n B 1 5 DC 5 5 5 DC DC B . n C 1 1 MCY 1 1 1 MCY MCY C . n C 1 2 DC 2 2 2 DC DC C . n C 1 3 DT 3 3 3 DT DT C . n C 1 4 DC 4 4 4 DC DC C . n C 1 5 DC 5 5 5 DC DC C . n D 1 1 MCY 1 1 1 MCY MCY D . n D 1 2 DC 2 2 2 DC DC D . n D 1 3 DT 3 3 3 DT DT D . n D 1 4 DC 4 4 4 DC DC D . n D 1 5 DC 5 5 5 DC DC D . n # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing 3.1 ? 3 # _cell.entry_id 1RME _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 1RME _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 1RME _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 1RME _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 1RME _struct.title ;DNA (5'-D(MCYP*CP*TP*CP*C)-3') tetramer, NMR, 1 structure ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1RME _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DEOXYRIBONUCLEIC ACID, I-MOTIF, TETRAMER, DNA' # 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 ? C N N 1 ? D N N 1 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1RME _struct_ref.pdbx_db_accession 1RME _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 1RME A 1 ? 5 ? 1RME 1 ? 5 ? 1 5 2 1 1RME B 1 ? 5 ? 1RME 1 ? 5 ? 1 5 3 1 1RME C 1 ? 5 ? 1RME 1 ? 5 ? 1 5 4 1 1RME D 1 ? 5 ? 1RME 1 ? 5 ? 1 5 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3880 ? 1 MORE -0 ? 1 'SSA (A^2)' 2070 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 ? _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 covale1 covale both ? A MCY 1 "O3'" ? ? ? 1_555 A DC 2 P ? ? A MCY 1 A DC 2 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale2 covale both ? B MCY 1 "O3'" ? ? ? 1_555 B DC 2 P ? ? B MCY 1 B DC 2 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale3 covale both ? C MCY 1 "O3'" ? ? ? 1_555 C DC 2 P ? ? C MCY 1 C DC 2 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale4 covale both ? D MCY 1 "O3'" ? ? ? 1_555 D DC 2 P ? ? D MCY 1 D DC 2 1_555 ? ? ? ? ? ? ? 1.613 ? ? hydrog1 hydrog ? ? A MCY 1 N4 ? ? ? 1_555 C MCY 1 O2 ? ? A MCY 1 C MCY 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog2 hydrog ? ? A MCY 1 O2 ? ? ? 1_555 C MCY 1 N4 ? ? A MCY 1 C MCY 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog3 hydrog ? ? A DC 2 N4 ? ? ? 1_555 C DC 2 O2 ? ? A DC 2 C DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog4 hydrog ? ? A DC 2 O2 ? ? ? 1_555 C DC 2 N4 ? ? A DC 2 C DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog5 hydrog ? ? A DT 3 N3 ? ? ? 1_555 C DT 3 O4 ? ? A DT 3 C DT 3 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog6 hydrog ? ? A DT 3 O4 ? ? ? 1_555 C DT 3 N3 ? ? A DT 3 C DT 3 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog7 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DC 4 O2 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog8 hydrog ? ? A DC 4 O2 ? ? ? 1_555 C DC 4 N4 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog9 hydrog ? ? A DC 5 N4 ? ? ? 1_555 C DC 5 O2 ? ? A DC 5 C DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog10 hydrog ? ? A DC 5 O2 ? ? ? 1_555 C DC 5 N4 ? ? A DC 5 C DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog11 hydrog ? ? B MCY 1 N4 ? ? ? 1_555 D MCY 1 O2 ? ? B MCY 1 D MCY 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog12 hydrog ? ? B MCY 1 O2 ? ? ? 1_555 D MCY 1 N4 ? ? B MCY 1 D MCY 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog13 hydrog ? ? B DC 2 N4 ? ? ? 1_555 D DC 2 O2 ? ? B DC 2 D DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog14 hydrog ? ? B DC 2 O2 ? ? ? 1_555 D DC 2 N4 ? ? B DC 2 D DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog15 hydrog ? ? B DC 4 N4 ? ? ? 1_555 D DC 4 O2 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog16 hydrog ? ? B DC 4 O2 ? ? ? 1_555 D DC 4 N4 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog17 hydrog ? ? B DC 5 N4 ? ? ? 1_555 D DC 5 O2 ? ? B DC 5 D DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog18 hydrog ? ? B DC 5 O2 ? ? ? 1_555 D DC 5 N4 ? ? B DC 5 D DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.03 108.30 2.73 0.30 N 2 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.53 108.30 2.23 0.30 N 3 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 110.60 108.30 2.30 0.30 N 4 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 111.08 108.30 2.78 0.30 N 5 1 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? N1 B DC 2 ? ? 111.14 108.30 2.84 0.30 N 6 1 "O4'" B DT 3 ? ? "C1'" B DT 3 ? ? N1 B DT 3 ? ? 110.58 108.30 2.28 0.30 N 7 1 "O4'" B DC 4 ? ? "C1'" B DC 4 ? ? N1 B DC 4 ? ? 110.69 108.30 2.39 0.30 N 8 1 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 110.91 108.30 2.61 0.30 N 9 1 "O4'" C DC 2 ? ? "C1'" C DC 2 ? ? N1 C DC 2 ? ? 111.22 108.30 2.92 0.30 N 10 1 C2 C DC 2 ? ? N3 C DC 2 ? ? C4 C DC 2 ? ? 123.18 119.90 3.28 0.50 N 11 1 N1 C DC 2 ? ? C2 C DC 2 ? ? O2 C DC 2 ? ? 122.59 118.90 3.69 0.60 N 12 1 "O4'" C DT 3 ? ? "C1'" C DT 3 ? ? N1 C DT 3 ? ? 110.89 108.30 2.59 0.30 N 13 1 "O4'" C DC 4 ? ? "C1'" C DC 4 ? ? N1 C DC 4 ? ? 111.50 108.30 3.20 0.30 N 14 1 C2 C DC 4 ? ? N3 C DC 4 ? ? C4 C DC 4 ? ? 123.12 119.90 3.22 0.50 N 15 1 "O4'" C DC 5 ? ? "C1'" C DC 5 ? ? N1 C DC 5 ? ? 110.97 108.30 2.67 0.30 N 16 1 C2 C DC 5 ? ? N3 C DC 5 ? ? C4 C DC 5 ? ? 123.08 119.90 3.18 0.50 N 17 1 "O4'" D DC 2 ? ? "C1'" D DC 2 ? ? N1 D DC 2 ? ? 111.36 108.30 3.06 0.30 N 18 1 C2 D DC 2 ? ? N3 D DC 2 ? ? C4 D DC 2 ? ? 123.10 119.90 3.20 0.50 N 19 1 "O4'" D DT 3 ? ? "C1'" D DT 3 ? ? N1 D DT 3 ? ? 110.69 108.30 2.39 0.30 N 20 1 "O4'" D DC 4 ? ? "C1'" D DC 4 ? ? N1 D DC 4 ? ? 110.89 108.30 2.59 0.30 N 21 1 C2 D DC 4 ? ? N3 D DC 4 ? ? C4 D DC 4 ? ? 123.03 119.90 3.13 0.50 N 22 1 N1 D DC 4 ? ? C2 D DC 4 ? ? O2 D DC 4 ? ? 122.53 118.90 3.63 0.60 N 23 1 "O4'" D DC 5 ? ? "C1'" D DC 5 ? ? N1 D DC 5 ? ? 110.84 108.30 2.54 0.30 N 24 1 C2 D DC 5 ? ? N3 D DC 5 ? ? C4 D DC 5 ? ? 123.11 119.90 3.21 0.50 N # 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 MCY 1 A MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 2 B MCY 1 B MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 3 C MCY 1 C MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 4 D MCY 1 D MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" # _pdbx_nmr_ensemble.entry_id 1RME _pdbx_nmr_ensemble.conformers_calculated_total_number 24 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.details _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.type '8 mM d(5mCCTCC), 90% H20/10% D2O' ? sample_1 1 '90% H2O/10% D2O' solution '8 mM d(5mCCTCC), 100% D2O' ? sample_2 2 '100% D2O' solution # 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 'd(5mCCTCC)' 8 ? mM ? 1 'd(5mCCTCC)' 8 ? mM ? 2 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature ? _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 4.6 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K _pdbx_nmr_exptl_sample_conditions.label ? _pdbx_nmr_exptl_sample_conditions.pH_units ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ? # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 TOCSY 1 3 1 '1H EXCHANGE' 1 4 1 NOESY-ROESY 1 5 1 TOCSY 2 6 1 NOESY 2 # _pdbx_nmr_refine.entry_id 1RME _pdbx_nmr_refine.method 'simulated annealing' _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 X-PLOR 3.1 BRUNGER 1 'structure solution' X-PLOR 3.1 BRUNGER 2 # 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DT OP3 O N N 35 DT P P N N 36 DT OP1 O N N 37 DT OP2 O N N 38 DT "O5'" O N N 39 DT "C5'" C N N 40 DT "C4'" C N R 41 DT "O4'" O N N 42 DT "C3'" C N S 43 DT "O3'" O N N 44 DT "C2'" C N N 45 DT "C1'" C N R 46 DT N1 N N N 47 DT C2 C N N 48 DT O2 O N N 49 DT N3 N N N 50 DT C4 C N N 51 DT O4 O N N 52 DT C5 C N N 53 DT C7 C N N 54 DT C6 C N N 55 DT HOP3 H N N 56 DT HOP2 H N N 57 DT "H5'" H N N 58 DT "H5''" H N N 59 DT "H4'" H N N 60 DT "H3'" H N N 61 DT "HO3'" H N N 62 DT "H2'" H N N 63 DT "H2''" H N N 64 DT "H1'" H N N 65 DT H3 H N N 66 DT H71 H N N 67 DT H72 H N N 68 DT H73 H N N 69 DT H6 H N N 70 MCY N1 N N N 71 MCY C2 C N N 72 MCY N3 N N N 73 MCY C4 C N N 74 MCY C5 C N N 75 MCY C6 C N N 76 MCY O2 O N N 77 MCY N4 N N N 78 MCY "C1'" C N R 79 MCY "C2'" C N N 80 MCY "C3'" C N S 81 MCY "C4'" C N R 82 MCY "O4'" O N N 83 MCY "O3'" O N N 84 MCY "C5'" C N N 85 MCY "O5'" O N N 86 MCY C5A C N N 87 MCY H6 H N N 88 MCY HN41 H N N 89 MCY HN42 H N N 90 MCY "H1'" H N N 91 MCY "H2'" H N N 92 MCY "H2''" H N N 93 MCY "H3'" H N N 94 MCY "H4'" H N N 95 MCY "HO3'" H N N 96 MCY "H5'" H N N 97 MCY "H5''" H N N 98 MCY "HO5'" H N N 99 MCY H5A1 H N N 100 MCY H5A2 H N N 101 MCY H5A3 H N N 102 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DT OP3 P sing N N 36 DT OP3 HOP3 sing N N 37 DT P OP1 doub N N 38 DT P OP2 sing N N 39 DT P "O5'" sing N N 40 DT OP2 HOP2 sing N N 41 DT "O5'" "C5'" sing N N 42 DT "C5'" "C4'" sing N N 43 DT "C5'" "H5'" sing N N 44 DT "C5'" "H5''" sing N N 45 DT "C4'" "O4'" sing N N 46 DT "C4'" "C3'" sing N N 47 DT "C4'" "H4'" sing N N 48 DT "O4'" "C1'" sing N N 49 DT "C3'" "O3'" sing N N 50 DT "C3'" "C2'" sing N N 51 DT "C3'" "H3'" sing N N 52 DT "O3'" "HO3'" sing N N 53 DT "C2'" "C1'" sing N N 54 DT "C2'" "H2'" sing N N 55 DT "C2'" "H2''" sing N N 56 DT "C1'" N1 sing N N 57 DT "C1'" "H1'" sing N N 58 DT N1 C2 sing N N 59 DT N1 C6 sing N N 60 DT C2 O2 doub N N 61 DT C2 N3 sing N N 62 DT N3 C4 sing N N 63 DT N3 H3 sing N N 64 DT C4 O4 doub N N 65 DT C4 C5 sing N N 66 DT C5 C7 sing N N 67 DT C5 C6 doub N N 68 DT C7 H71 sing N N 69 DT C7 H72 sing N N 70 DT C7 H73 sing N N 71 DT C6 H6 sing N N 72 MCY N1 C2 sing N N 73 MCY N1 C6 sing N N 74 MCY N1 "C1'" sing N N 75 MCY C2 N3 sing N N 76 MCY C2 O2 doub N N 77 MCY N3 C4 doub N N 78 MCY C4 C5 sing N N 79 MCY C4 N4 sing N N 80 MCY C5 C6 doub N N 81 MCY C5 C5A sing N N 82 MCY C6 H6 sing N N 83 MCY N4 HN41 sing N N 84 MCY N4 HN42 sing N N 85 MCY "C1'" "C2'" sing N N 86 MCY "C1'" "O4'" sing N N 87 MCY "C1'" "H1'" sing N N 88 MCY "C2'" "C3'" sing N N 89 MCY "C2'" "H2'" sing N N 90 MCY "C2'" "H2''" sing N N 91 MCY "C3'" "C4'" sing N N 92 MCY "C3'" "O3'" sing N N 93 MCY "C3'" "H3'" sing N N 94 MCY "C4'" "O4'" sing N N 95 MCY "C4'" "C5'" sing N N 96 MCY "C4'" "H4'" sing N N 97 MCY "O3'" "HO3'" sing N N 98 MCY "C5'" "O5'" sing N N 99 MCY "C5'" "H5'" sing N N 100 MCY "C5'" "H5''" sing N N 101 MCY "O5'" "HO5'" sing N N 102 MCY C5A H5A1 sing N N 103 MCY C5A H5A2 sing N N 104 MCY C5A H5A3 sing N N 105 # _ndb_struct_conf_na.entry_id 1RME _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 DC 5 1_555 C DC 5 1_555 2.131 1.905 0.097 5.052 5.304 179.503 1 A_DC5:DC5_C A 5 ? C 5 ? 15 2 1 D MCY 1 1_555 B MCY 1 1_555 -2.114 -1.433 -0.016 11.703 -10.633 -179.624 2 D_MCY1:MCY1_B D 1 ? B 1 ? 15 2 1 A DC 4 1_555 C DC 4 1_555 1.969 1.583 -0.001 -4.456 13.085 179.268 3 A_DC4:DC4_C A 4 ? C 4 ? 15 2 1 D DC 2 1_555 B DC 2 1_555 -1.914 -0.496 -0.023 7.670 3.374 -179.915 4 D_DC2:DC2_B D 2 ? B 2 ? 15 2 1 A DT 3 1_555 C DT 3 1_555 -1.351 0.449 -0.267 11.701 -27.670 -172.580 5 A_DT3:DT3_C A 3 ? C 3 ? 12 2 1 C DC 2 1_555 A DC 2 1_555 1.977 0.360 0.087 -13.523 -12.093 179.060 6 C_DC2:DC2_A C 2 ? A 2 ? 15 2 1 B DC 4 1_555 D DC 4 1_555 1.991 1.857 0.023 17.272 27.118 179.676 7 B_DC4:DC4_D B 4 ? D 4 ? 15 2 1 C MCY 1 1_555 A MCY 1 1_555 2.143 1.649 -0.034 -11.908 -5.909 179.963 8 C_MCY1:MCY1_A C 1 ? A 1 ? 15 2 1 B DC 5 1_555 D DC 5 1_555 1.972 1.860 -0.223 -28.101 -38.403 178.027 9 B_DC5:DC5_D B 5 ? D 5 ? 15 2 # 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 DC 5 1_555 C DC 5 1_555 D MCY 1 1_555 B MCY 1 1_555 -2.058 -1.481 0.070 112.825 -138.535 -154.972 0.748 -1.023 0.101 69.280 56.422 -179.711 1 AD_DC5MCY1:MCY1DC5_BC A 5 ? C 5 ? D 1 ? B 1 ? 1 D MCY 1 1_555 B MCY 1 1_555 A DC 4 1_555 C DC 4 1_555 2.443 2.492 -0.038 129.021 -125.019 -76.148 -1.259 1.208 -0.039 62.556 64.558 -179.729 2 DA_MCY1DC4:DC4MCY1_CB D 1 ? B 1 ? A 4 ? C 4 ? 1 A DC 4 1_555 C DC 4 1_555 D DC 2 1_555 B DC 2 1_555 2.170 1.631 -0.012 -111.870 139.448 38.615 0.842 -1.063 -0.085 70.044 56.191 178.844 3 AD_DC4DC2:DC2DC4_BC A 4 ? C 4 ? D 2 ? B 2 ? 1 D DC 2 1_555 B DC 2 1_555 A DT 3 1_555 C DT 3 1_555 -3.052 2.024 -0.110 105.353 142.525 -111.356 -1.000 -1.535 0.014 -71.456 52.819 -178.442 4 DA_DC2DT3:DT3DC2_CB D 2 ? B 2 ? A 3 ? C 3 ? 1 A DT 3 1_555 C DT 3 1_555 C DC 2 1_555 A DC 2 1_555 -0.177 0.178 -2.070 -0.665 1.989 -15.902 0.281 -0.325 -2.082 -7.150 -2.391 -16.039 5 AC_DT3DC2:DC2DT3_AC A 3 ? C 3 ? C 2 ? A 2 ? 1 C DC 2 1_555 A DC 2 1_555 B DC 4 1_555 D DC 4 1_555 -1.988 2.072 0.036 -129.011 -123.922 -51.581 -1.025 -1.006 0.017 62.179 -64.732 -178.998 6 CB_DC2DC4:DC4DC2_DA C 2 ? A 2 ? B 4 ? D 4 ? 1 B DC 4 1_555 D DC 4 1_555 C MCY 1 1_555 A MCY 1 1_555 3.081 -2.361 -0.075 -112.360 -139.601 -157.415 1.175 1.545 -0.056 69.807 -56.185 -179.844 7 BC_DC4MCY1:MCY1DC4_AD B 4 ? D 4 ? C 1 ? A 1 ? 1 C MCY 1 1_555 A MCY 1 1_555 B DC 5 1_555 D DC 5 1_555 -3.516 4.478 0.097 -138.813 -109.077 2.816 2.269 1.721 0.000 -55.581 70.733 176.542 8 CB_MCY1DC5:DC5MCY1_DA C 1 ? A 1 ? B 5 ? D 5 ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 'HOME-MADE SPECTROMETER' Home-built 360 ? 2 AMX Bruker 600 ? # _atom_sites.entry_id 1RME _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_