data_2M39 # _entry.id 2M39 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 2M39 pdb_00002m39 10.2210/pdb2m39/pdb RCSB RCSB103153 ? ? BMRB 18950 ? ? WWPDB D_1000103153 ? ? # _pdbx_database_related.db_id 18950 _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2M39 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-01-15 _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 REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Plevnik, M.' 1 'Cevec, M.' 2 'Plavec, J.' 3 # _citation.id primary _citation.title ;NMR structure of 2'-O-(2-methoxyethyl) modified and C5-methylated RNA dodecamer duplex. ; _citation.journal_abbrev Biochimie _citation.journal_volume 95 _citation.page_first 2385 _citation.page_last 2391 _citation.year 2013 _citation.journal_id_ASTM BICMBE _citation.country FR _citation.journal_id_ISSN 0300-9084 _citation.journal_id_CSD 0466 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24012551 _citation.pdbx_database_id_DOI 10.1016/j.biochi.2013.08.025 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Plevnik, M.' 1 ? primary 'Cevec, M.' 2 ? primary 'Plavec, J.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L)P*DG)-3') ; _entity.formula_weight 4534.364 _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 '(C5L)(G48)(C5L)(G48)(A44)(A44)(T39)(T39)(C5L)(G48)(C5L)(DG)' _entity_poly.pdbx_seq_one_letter_code_can XGXGAATTXGXG _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 C5L n 1 2 G48 n 1 3 C5L n 1 4 G48 n 1 5 A44 n 1 6 A44 n 1 7 T39 n 1 8 T39 n 1 9 C5L n 1 10 G48 n 1 11 C5L n 1 12 DG 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 _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details 'SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE CHEMISTRY' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2M39 _struct_ref.pdbx_db_accession 2M39 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code XGXGAATTXGXG _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 2M39 A 1 ? 12 ? 2M39 1 ? 12 ? 1 12 2 1 2M39 B 1 ? 12 ? 2M39 13 ? 24 ? 13 24 # 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 A44 'RNA linking' n ;2'-O-METHYOXYETHYL-ADENOSINE 5'-MONOPHOSPHATE ; ? 'C13 H20 N5 O8 P' 405.300 C5L 'RNA linking' n ;2'-O-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate) ; ? 'C13 H22 N3 O9 P' 395.302 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 G48 'RNA linking' n "2'-O-METHYOXYETHYL-GUANOSINE-5'-MONOPHOSPHATE" ? 'C13 H20 N5 O9 P' 421.300 T39 'RNA linking' n ;2'-O-METHOXYETHYLENE THYMIDINE 5'-MONOPHOSPHATE ; ? 'C13 H21 N2 O10 P' 396.287 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 2 1 1 '2D NOESY' 1 2 2 '2D NOESY' 1 3 2 '2D DQF-COSY' # 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 1 100 7.0 ambient ? 303 K 2 100 7.0 ambient ? 278 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;2.5 mM 5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3', 100 mM potassium chloride, 90% H2O/10% D2O ; 1 '90% H2O/10% D2O' ;2.5 mM 5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3', 100 mM potassium chloride, 100% D2O ; 2 '100% D2O' # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model 'Unity Inova' _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Varian Unity Inova' # _pdbx_nmr_refine.entry_id 2M39 _pdbx_nmr_refine.method 'simulated annealing, energy minimization' _pdbx_nmr_refine.details ;STRUCTURES WERE REFINED BY NMR RESTRAINED MOLECULAR DYNAMICS IN TWO STAGES USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL. THE RESULTING STRUCTURES WERE SUBJECTED TO ENERGY MINIMIZATION. 3',5'-PHOSPHODIESTER LINKAGES BETWEEN RESIDUES, O2' OF EACH RIBOSE MODIFIED BY METHOXYETHYL. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2M39 _pdbx_nmr_details.text 'STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND HETERONUCLEAR TECHNIQUES.' # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 9 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2M39 _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 2M39 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal Varian collection VNMR 6.1B 1 Varian processing VNMR 6.1B 2 'Accelrys Software Inc.' processing Felix 2000 3 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollman' 'structure solution' Amber 7 4 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollman' refinement Amber 7 5 # _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 2M39 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2M39 _struct.title ;The solution structure of 3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA DUPLEX ; _struct.pdbx_model_details 'lowest energy, model7' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2M39 _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;DUPLEX, (3', 5')-RNA, 2'-O-(2-METHOXYETHYL) RIBOSE, 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_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 G48 2 "O3'" ? ? ? 1_555 A C5L 3 P ? ? A G48 2 A C5L 3 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A G48 4 "O3'" ? ? ? 1_555 A A44 5 P ? ? A G48 4 A A44 5 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale3 covale both ? A A44 5 "O3'" ? ? ? 1_555 A A44 6 P ? ? A A44 5 A A44 6 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale4 covale both ? A A44 6 "O3'" ? ? ? 1_555 A T39 7 P ? ? A A44 6 A T39 7 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale5 covale both ? A T39 7 "O3'" ? ? ? 1_555 A T39 8 P ? ? A T39 7 A T39 8 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale6 covale both ? A T39 8 "O3'" ? ? ? 1_555 A C5L 9 P ? ? A T39 8 A C5L 9 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale7 covale both ? A G48 10 "O3'" ? ? ? 1_555 A C5L 11 P ? ? A G48 10 A C5L 11 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale8 covale both ? B G48 2 "O3'" ? ? ? 1_555 B C5L 3 P ? ? B G48 14 B C5L 15 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale9 covale both ? B G48 4 "O3'" ? ? ? 1_555 B A44 5 P ? ? B G48 16 B A44 17 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale10 covale both ? B A44 5 "O3'" ? ? ? 1_555 B A44 6 P ? ? B A44 17 B A44 18 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale11 covale both ? B A44 6 "O3'" ? ? ? 1_555 B T39 7 P ? ? B A44 18 B T39 19 1_555 ? ? ? ? ? ? ? 1.594 ? ? covale12 covale both ? B T39 7 "O3'" ? ? ? 1_555 B T39 8 P ? ? B T39 19 B T39 20 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale13 covale both ? B T39 8 "O3'" ? ? ? 1_555 B C5L 9 P ? ? B T39 20 B C5L 21 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale14 covale both ? B G48 10 "O3'" ? ? ? 1_555 B C5L 11 P ? ? B G48 22 B C5L 23 1_555 ? ? ? ? ? ? ? 1.607 ? ? hydrog1 hydrog ? ? A A44 5 N1 ? ? ? 1_555 B T39 8 N3 ? ? A A44 5 B T39 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A44 5 N6 ? ? ? 1_555 B T39 8 O4 ? ? A A44 5 B T39 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A A44 6 N1 ? ? ? 1_555 B T39 7 N3 ? ? A A44 6 B T39 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A44 6 N6 ? ? ? 1_555 B T39 7 O4 ? ? A A44 6 B T39 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A T39 7 N3 ? ? ? 1_555 B A44 6 N1 ? ? A T39 7 B A44 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A T39 7 O4 ? ? ? 1_555 B A44 6 N6 ? ? A T39 7 B A44 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A T39 8 N3 ? ? ? 1_555 B A44 5 N1 ? ? A T39 8 B A44 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A T39 8 O4 ? ? ? 1_555 B A44 5 N6 ? ? A T39 8 B A44 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2M39 _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 HO N O P # 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 C5L 1 1 1 C5L C5L A . n A 1 2 G48 2 2 2 G48 G48 A . n A 1 3 C5L 3 3 3 C5L C5L A . n A 1 4 G48 4 4 4 G48 G48 A . n A 1 5 A44 5 5 5 A44 A44 A . n A 1 6 A44 6 6 6 A44 A44 A . n A 1 7 T39 7 7 7 T39 T39 A . n A 1 8 T39 8 8 8 T39 T39 A . n A 1 9 C5L 9 9 9 C5L C5L A . n A 1 10 G48 10 10 10 G48 G48 A . n A 1 11 C5L 11 11 11 C5L C5L A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 C5L 1 13 13 C5L C5L B . n B 1 2 G48 2 14 14 G48 G48 B . n B 1 3 C5L 3 15 15 C5L C5L B . n B 1 4 G48 4 16 16 G48 G48 B . n B 1 5 A44 5 17 17 A44 A44 B . n B 1 6 A44 6 18 18 A44 A44 B . n B 1 7 T39 7 19 19 T39 T39 B . n B 1 8 T39 8 20 20 T39 T39 B . n B 1 9 C5L 9 21 21 C5L C5L B . n B 1 10 G48 10 22 22 G48 G48 B . n B 1 11 C5L 11 23 23 C5L C5L B . n B 1 12 DG 12 24 24 DG DG B . 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 C5L 1 A C5L 1 ? C ? 2 A G48 2 A G48 2 ? G ? 3 A C5L 3 A C5L 3 ? C ? 4 A G48 4 A G48 4 ? G ? 5 A A44 5 A A44 5 ? A ? 6 A A44 6 A A44 6 ? A ? 7 A T39 7 A T39 7 ? DT ? 8 A T39 8 A T39 8 ? DT ? 9 A C5L 9 A C5L 9 ? C ? 10 A G48 10 A G48 10 ? G ? 11 A C5L 11 A C5L 11 ? C ? 12 B C5L 1 B C5L 13 ? C ? 13 B G48 2 B G48 14 ? G ? 14 B C5L 3 B C5L 15 ? C ? 15 B G48 4 B G48 16 ? G ? 16 B A44 5 B A44 17 ? A ? 17 B A44 6 B A44 18 ? A ? 18 B T39 7 B T39 19 ? DT ? 19 B T39 8 B T39 20 ? DT ? 20 B C5L 9 B C5L 21 ? C ? 21 B G48 10 B G48 22 ? G ? 22 B C5L 11 B C5L 23 ? C ? # _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_ _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 2013-11-27 2 'Structure model' 1 1 2023-06-14 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 'Structure model' Other # 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 2 'Structure model' database_2 2 2 'Structure model' pdbx_database_status 3 2 'Structure model' pdbx_nmr_software 4 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 2 'Structure model' '_pdbx_nmr_software.name' 5 2 'Structure model' '_struct_conn.pdbx_dist_value' 6 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 2 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 2 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 2 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 2 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 2 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 2 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 2 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 2 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 2 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 2 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 2 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 2 'Structure model' '_struct_conn.ptnr2_label_seq_id' # 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 "5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3'-1" 2.5 ? mM ? 1 'potassium chloride-2' 100 ? mM ? 1 "5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3'-3" 2.5 ? mM ? 2 'potassium chloride-4' 100 ? mM ? 2 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2M39 _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total 394 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count ? _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # 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 DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 110.55 108.30 2.25 0.30 N 2 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.80 108.30 4.50 0.30 N 3 2 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 111.07 108.30 2.77 0.30 N 4 2 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.68 108.30 4.38 0.30 N 5 3 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.57 108.30 4.27 0.30 N 6 3 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.56 108.30 4.26 0.30 N 7 4 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 110.73 108.30 2.43 0.30 N 8 4 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.38 108.30 4.08 0.30 N 9 5 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.31 108.30 4.01 0.30 N 10 5 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 110.20 108.30 1.90 0.30 N 11 6 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 111.21 108.30 2.91 0.30 N 12 6 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.75 108.30 4.45 0.30 N 13 7 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 110.57 108.30 2.27 0.30 N 14 7 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 113.41 108.30 5.11 0.30 N 15 8 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.10 108.30 3.80 0.30 N 16 8 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.54 108.30 4.24 0.30 N 17 9 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.18 108.30 3.88 0.30 N 18 9 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 110.49 108.30 2.19 0.30 N # _ndb_struct_conf_na.entry_id 2M39 _ndb_struct_conf_na.feature 'a-form 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 A44 5 1_555 B T39 8 1_555 -0.006 -0.075 -0.316 -9.894 -15.860 -5.992 1 A_A445:T3920_B A 5 ? B 20 ? 20 1 1 A A44 6 1_555 B T39 7 1_555 -0.554 -0.170 0.796 8.068 -7.899 8.582 2 A_A446:T3919_B A 6 ? B 19 ? 20 1 1 A T39 7 1_555 B A44 6 1_555 0.501 -0.127 0.729 -10.581 -8.856 8.548 3 A_T397:A4418_B A 7 ? B 18 ? 20 1 1 A T39 8 1_555 B A44 5 1_555 0.060 -0.140 -0.202 3.833 -19.200 0.611 4 A_T398:A4417_B A 8 ? B 17 ? 20 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 A44 5 1_555 B T39 8 1_555 A A44 6 1_555 B T39 7 1_555 0.555 -1.712 2.490 -5.779 1.519 28.623 -3.633 -2.016 2.245 3.030 11.530 29.227 1 AA_A445A446:T3919T3920_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A A44 6 1_555 B T39 7 1_555 A T39 7 1_555 B A44 6 1_555 0.032 -1.007 3.780 0.498 12.060 33.079 -3.658 0.029 3.228 20.356 -0.841 35.155 2 AA_A446T397:A4418T3919_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A T39 7 1_555 B A44 6 1_555 A T39 8 1_555 B A44 5 1_555 -0.340 -1.769 2.574 4.933 3.762 27.935 -4.216 1.519 2.230 7.673 -10.062 28.602 3 AA_T397T398:A4417A4418_BB A 7 ? B 18 ? A 8 ? B 17 ? #