data_4694 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of two cyclic oligonucleotides. A monomer-dimer equlilibrium between dumbbell and quadruplex structures. ; _BMRB_accession_number 4694 _BMRB_flat_file_name bmr4694.str _Entry_type original _Submission_date 2000-03-20 _Accession_date 2000-03-20 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gonzalez Carlos . . 2 Escaja Nuria . . 3 Rico Manuel . . 4 Pedroso Enrique . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 89 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-16 update BMRB 'update DNA residue label to two-letter code' 2000-06-16 original author 'original release' stop_ _Original_release_date 2000-03-20 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR structure of two cyclic oligonucleotides. A monomer-dimer equlilibrium between dumbbell and quadruplex structures. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gonzalez Carlos . . 2 Escaja Nuria . . 3 Rico Manuel . . 4 Pedroso Enrique . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 120 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2176 _Page_last 2177 _Year 1998 _Details . save_ ################################## # Molecular system description # ################################## save_system_d _Saveframe_category molecular_system _Mol_system_name 'cyclic oligonucleotide d' _Abbreviation_common d _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'd subunit 1' $d 'd subunit 2' $d stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'd subunit 1' 2 'd subunit 2' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_d _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'cyclic oligonucleotide' _Abbreviation_common d _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence ; TGCTCGCT ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DG 3 DC 4 DT 5 DC 6 DG 7 DC 8 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $d . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $d 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $d 5.0 mM 2.0 5.0 . D2O 100 % . . . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $d 5.0 mM 2.0 5.0 . D2O . % . . . H2O . % . . . stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Task 'spectra processing' stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version . loop_ _Task 'peak assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 7.0 0.5 pH temperature 293 1 K stop_ save_ save_sample_conditions_two _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 7.0 0.5 pH temperature 278 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis TSP H 1 methyl ppm 0.0 internal direct . internal . stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_set_d2o _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label TOCSY DQF-COSY NOESY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'd subunit 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 DT H5' H 4.18 . 2 2 . 1 DT H5'' H 4.06 . 2 3 . 1 DT H4' H 4.61 . 1 4 . 1 DT H3' H 4.58 . 1 5 . 1 DT H2' H 2.35 . 1 6 . 1 DT H2'' H 2.53 . 1 7 . 1 DT H1' H 6.48 . 1 8 . 1 DT H71 H 1.92 . 1 9 . 1 DT H72 H 1.92 . 1 10 . 1 DT H73 H 1.92 . 1 11 . 1 DT H6 H 7.85 . 1 12 . 2 DG H5' H 4.25 . 1 13 . 2 DG H5'' H 4.02 . 1 14 . 2 DG H4' H 4.59 . 1 15 . 2 DG H3' H 5.04 . 1 16 . 2 DG H2' H 2.74 . 1 17 . 2 DG H2'' H 3.08 . 1 18 . 2 DG H1' H 6.30 . 1 19 . 2 DG H8 H 8.14 . 1 20 . 3 DC H5' H 4.32 . 2 21 . 3 DC H5'' H 4.00 . 2 22 . 3 DC H4' H 4.52 . 1 23 . 3 DC H3' H 5.03 . 1 24 . 3 DC H2' H 2.35 . 2 25 . 3 DC H2'' H 2.35 . 2 26 . 3 DC H1' H 6.57 . 1 27 . 3 DC H5 H 5.39 . 1 28 . 3 DC H6 H 7.47 . 1 29 . 4 DT H5' H 4.18 . 1 30 . 4 DT H5'' H 4.08 . 1 31 . 4 DT H4' H 3.42 . 1 32 . 4 DT H3' H 4.64 . 1 33 . 4 DT H2' H 1.86 . 1 34 . 4 DT H2'' H 2.37 . 1 35 . 4 DT H1' H 5.93 . 1 36 . 4 DT H71 H 1.8 . 1 37 . 4 DT H72 H 1.8 . 1 38 . 4 DT H73 H 1.8 . 1 39 . 4 DT H6 H 7.38 . 1 40 . 5 DC H5' H 4.19 . 2 41 . 5 DC H5'' H 4.07 . 2 42 . 5 DC H4' H 4.56 . 1 43 . 5 DC H3' H 4.57 . 1 44 . 5 DC H2' H 2.26 . 1 45 . 5 DC H2'' H 2.58 . 1 46 . 5 DC H1' H 6.48 . 1 47 . 5 DC H5 H 6.11 . 1 48 . 5 DC H6 H 8.00 . 1 49 . 6 DG H5' H 4.25 . 1 50 . 6 DG H5'' H 4.02 . 1 51 . 6 DG H4' H 4.59 . 1 52 . 6 DG H3' H 5.04 . 1 53 . 6 DG H2' H 2.74 . 1 54 . 6 DG H2'' H 3.08 . 1 55 . 6 DG H1' H 6.30 . 1 56 . 6 DG H8 H 8.14 . 1 57 . 7 DC H5' H 4.32 . 2 58 . 7 DC H5'' H 4.00 . 2 59 . 7 DC H4' H 4.52 . 1 60 . 7 DC H3' H 5.03 . 1 61 . 7 DC H2' H 2.35 . 2 62 . 7 DC H2'' H 2.35 . 2 63 . 7 DC H1' H 6.57 . 1 64 . 7 DC H5 H 5.39 . 1 65 . 7 DC H6 H 7.47 . 1 66 . 8 DT H5' H 4.18 . 1 67 . 8 DT H5'' H 4.08 . 1 68 . 8 DT H4' H 3.42 . 1 69 . 8 DT H3' H 4.66 . 1 70 . 8 DT H2' H 1.88 . 1 71 . 8 DT H2'' H 2.37 . 1 72 . 8 DT H1' H 5.93 . 1 73 . 8 DT H71 H 1.8 . 1 74 . 8 DT H72 H 1.8 . 1 75 . 8 DT H73 H 1.8 . 1 76 . 8 DT H6 H 7.38 . 1 stop_ save_ save_set_h2o _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label TOCSY DQF-COSY NOESY stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_two _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'd subunit 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 DT H3 H 11.18 . 1 2 . 2 DG H1 H 13.45 . 1 3 . 2 DG H21 H 9.25 . 1 4 . 2 DG H22 H 6.27 . 1 5 . 3 DC H41 H 8.77 . 1 6 . 3 DC H42 H 6.49 . 1 7 . 4 DT H3 H 10.72 . 1 8 . 6 DG H1 H 13.45 . 1 9 . 6 DG H21 H 9.25 . 1 10 . 6 DG H22 H 6.27 . 1 11 . 7 DC H41 H 8.77 . 1 12 . 7 DC H42 H 6.49 . 1 13 . 8 DT H3 H 10.72 . 1 stop_ save_