data_18452 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of a mini i-motif ; _BMRB_accession_number 18452 _BMRB_flat_file_name bmr18452.str _Entry_type original _Submission_date 2012-05-09 _Accession_date 2012-05-09 _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 Escaja N. . . 2 Viladoms J. . . 3 Villasante A. . . 4 Pedroso E. . . 5 Gonzalez C. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 116 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-08 update BMRB 'update entry citation' 2012-10-15 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'A minimal i-motif stabilized by minor groove G:T:G:T tetrads.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23042679 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Escaja Nuria . . 2 Viladoms Julia . . 3 Garavis Miguel . . 4 Villasante Alfredo . . 5 Pedroso Enrique . . 6 Gonzalez Carlos . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 40 _Journal_issue 22 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11737 _Page_last 11747 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Synthetic cyclic oligonucleotide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Synthetic cyclic oligonucleotide' $Synthetic_cyclic_oligonucleotide DNA_1 $DNA_1 entity_3_1 $entity_3 entity_3_2 $entity_3 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Synthetic_cyclic_oligonucleotide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common Synthetic_cyclic_oligonucleotide _Molecular_mass 3017.002 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence TCGTTTCGTT loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DC 3 3 DG 4 4 DT 5 5 DT 6 6 DT 7 7 DC 8 8 DG 9 9 DT 10 10 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_1 _Molecular_mass 3321.197 _Mol_thiol_state 'not present' _Details . _Residue_count 10 _Mol_residue_sequence TCGTTTCGTT loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DC 3 3 DG 4 4 DT 5 5 DT 6 6 DT 7 7 DC 8 8 DG 9 9 DT 10 10 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_3 _Molecular_mass 945.025 _Mol_thiol_state . _Details . _Residue_count 10 _Mol_residue_sequence TCGTTTCGTT loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 THR 2 2 CYS 3 3 GLY 4 4 THR 5 5 THR 6 6 THR 7 7 CYS 8 8 GLY 9 9 THR 10 10 THR 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 $Synthetic_cyclic_oligonucleotide . . . . . . 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 $Synthetic_cyclic_oligonucleotide 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details '120 mM NACl; 90% H2O, 10% D2O pH 5.0' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Synthetic_cyclic_oligonucleotide 0.5 mM 'natural abundance' NaCl 150 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 7.0 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 125 . mM pH 5.0 . pH pressure 1 . atm temperature 279 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _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 _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NOESY stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Synthetic cyclic oligonucleotide' _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 1 DT H1' H 6.49 . 1 2 1 1 DT H2' H 2.55 . 1 3 1 1 DT H2'' H 2.55 . 1 4 1 1 DT H3 H 11.85 . 1 5 1 1 DT H3' H 4.97 . 1 6 1 1 DT H4' H 4.38 . 1 7 1 1 DT H5' H 4.12 . 1 8 1 1 DT H5'' H 4.12 . 1 9 1 1 DT H6 H 7.85 . 1 10 1 1 DT H71 H 1.99 . 1 11 1 1 DT H72 H 1.99 . 1 12 1 1 DT H73 H 1.99 . 1 13 2 2 DC H1' H 6.35 . 1 14 2 2 DC H2' H 1.06 . 1 15 2 2 DC H2'' H 2.15 . 1 16 2 2 DC H3' H 4.82 . 1 17 2 2 DC H4' H 4.56 . 1 18 2 2 DC H5 H 6.31 . 1 19 2 2 DC H5' H 4.10 . 1 20 2 2 DC H5'' H 4.10 . 1 21 2 2 DC H6 H 7.49 . 1 22 2 2 DC H41 H 7.58 . 1 23 2 2 DC H42 H 9.52 . 1 24 3 3 DG H1 H 10.85 . 1 25 3 3 DG H1' H 5.95 . 1 26 3 3 DG H2' H 3.00 . 1 27 3 3 DG H2'' H 2.68 . 1 28 3 3 DG H3' H 5.15 . 1 29 3 3 DG H4' H 4.41 . 1 30 3 3 DG H5' H 3.90 . 2 31 3 3 DG H5'' H 4.11 . 2 32 3 3 DG H8 H 8.38 . 1 33 3 3 DG H21 H 5.69 . 1 34 3 3 DG H22 H 8.83 . 1 35 4 4 DT H1' H 6.08 . 1 36 4 4 DT H2' H 2.07 . 1 37 4 4 DT H2'' H 2.33 . 1 38 4 4 DT H3 H 11.5 . 1 39 4 4 DT H3' H 4.81 . 1 40 4 4 DT H4' H 3.99 . 1 41 4 4 DT H5' H 3.99 . 2 42 4 4 DT H5'' H 3.99 . 2 43 4 4 DT H6 H 7.63 . 1 44 4 4 DT H71 H 1.76 . 1 45 4 4 DT H72 H 1.76 . 1 46 4 4 DT H73 H 1.76 . 1 47 5 5 DT H1' H 6.43 . 1 48 5 5 DT H2' H 2.28 . 1 49 5 5 DT H2'' H 2.55 . 1 50 5 5 DT H3 H 10.47 . 1 51 5 5 DT H3' H 4.63 . 1 52 5 5 DT H4' H 4.47 . 1 53 5 5 DT H5' H 3.98 . 2 54 5 5 DT H5'' H 4.13 . 2 55 5 5 DT H6 H 7.77 . 1 56 5 5 DT H71 H 1.92 . 1 57 5 5 DT H72 H 1.92 . 1 58 5 5 DT H73 H 1.92 . 1 59 6 6 DT H1' H 6.49 . 1 60 6 6 DT H2' H 2.55 . 1 61 6 6 DT H2'' H 2.55 . 1 62 6 6 DT H3 H 11.85 . 1 63 6 6 DT H3' H 4.97 . 1 64 6 6 DT H4' H 4.38 . 1 65 6 6 DT H5' H 4.12 . 1 66 6 6 DT H5'' H 4.12 . 1 67 6 6 DT H6 H 7.85 . 1 68 6 6 DT H71 H 1.99 . 1 69 6 6 DT H72 H 1.99 . 1 70 6 6 DT H73 H 1.99 . 1 71 7 7 DC H1' H 6.35 . 1 72 7 7 DC H2' H 1.06 . 1 73 7 7 DC H2'' H 2.15 . 1 74 7 7 DC H3' H 4.82 . 1 75 7 7 DC H4' H 4.56 . 1 76 7 7 DC H5 H 6.31 . 1 77 7 7 DC H5' H 4.10 . 1 78 7 7 DC H5'' H 4.10 . 1 79 7 7 DC H6 H 7.49 . 1 80 7 7 DC H41 H 7.58 . 1 81 7 7 DC H42 H 9.52 . 1 82 8 8 DG H1 H 10.85 . 1 83 8 8 DG H1' H 5.95 . 1 84 8 8 DG H2' H 3.00 . 1 85 8 8 DG H2'' H 2.68 . 1 86 8 8 DG H3' H 5.15 . 1 87 8 8 DG H4' H 4.41 . 1 88 8 8 DG H5' H 3.90 . 2 89 8 8 DG H5'' H 4.11 . 2 90 8 8 DG H8 H 8.38 . 1 91 8 8 DG H21 H 5.69 . 1 92 8 8 DG H22 H 8.83 . 1 93 9 9 DT H1' H 6.08 . 1 94 9 9 DT H2' H 2.07 . 1 95 9 9 DT H2'' H 2.33 . 1 96 9 9 DT H3 H 11.5 . 1 97 9 9 DT H3' H 4.81 . 1 98 9 9 DT H4' H 3.99 . 1 99 9 9 DT H5' H 3.99 . 2 100 9 9 DT H5'' H 3.99 . 2 101 9 9 DT H6 H 7.63 . 1 102 9 9 DT H71 H 1.76 . 1 103 9 9 DT H72 H 1.76 . 1 104 9 9 DT H73 H 1.76 . 1 105 10 10 DT H1' H 6.43 . 1 106 10 10 DT H2' H 2.28 . 1 107 10 10 DT H2'' H 2.55 . 1 108 10 10 DT H3 H 10.47 . 1 109 10 10 DT H3' H 4.63 . 1 110 10 10 DT H4' H 4.47 . 1 111 10 10 DT H5' H 3.98 . 2 112 10 10 DT H5'' H 4.13 . 2 113 10 10 DT H6 H 7.77 . 1 114 10 10 DT H71 H 1.92 . 1 115 10 10 DT H72 H 1.92 . 1 116 10 10 DT H73 H 1.92 . 1 stop_ save_