data_34118 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; An i-motif containing the neutral cytidine protonated analogue pseudoisocytidine ; _BMRB_accession_number 34118 _BMRB_flat_file_name bmr34118.str _Entry_type original _Submission_date 2017-03-24 _Accession_date 2017-03-24 _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 Mir B. . . 2 Soles X. . . 3 Gonzalez C. . . 4 Escaja N. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 75 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-06-22 original BMRB . stop_ _Original_release_date 2017-06-07 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28584239 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mir B. . . 2 Soles X. . . 3 Gonzalez C. . . 4 Escaja N. . . stop_ _Journal_abbreviation 'Sci. Rep.' _Journal_volume 7 _Journal_issue . _Journal_ISSN 2045-2322 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2772 _Page_last 2772 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*TP*(DCP)P*CP*GP*TP*TP*TP*CP*(PSC)P*GP*T)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common entity_1 _Molecular_mass 3275.146 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence ; TCCGTTTCXGT ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DC 3 DC 4 DG 5 DT 6 DT 7 DT 8 DC 9 8YN 10 DG 11 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_8YN _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common pseudopisocytidine _BMRB_code 8YN _PDB_code 8YN _Standard_residue_derivative . _Molecular_mass 291.198 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? C1 C1 C . 0 . ? C2 C2 C . 0 . ? C4 C4 C . 0 . ? C6 C6 C . 0 . ? O1P O1P O . 0 . ? O2P O2P O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? N4 N4 N . 0 . ? N5 N5 N . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? H6 H6 H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? 2H5' 2H5' H . 0 . ? 1H5' 1H5' H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? H3 H3 H . 0 . ? 1H4 1H4 H . 0 . ? 2H4 2H4 H . 0 . ? 1H2' 1H2' H . 0 . ? 2H2' 2H2' H . 0 . ? H3' H3' H . 0 . ? H4 H4 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB O2 C2 ? ? SING C2 N3 ? ? SING C2 C1 ? ? SING N3 C4 ? ? SING O3' C3' ? ? SING C1' C1 ? ? SING C1' O4' ? ? SING C1' C2' ? ? DOUB C1 C6 ? ? SING C4 N4 ? ? DOUB C4 N5 ? ? SING O4' C4' ? ? SING C2' C3' ? ? SING C3' C4' ? ? SING C4' C5' ? ? SING C6 N5 ? ? SING O1P P ? ? SING P O5' ? ? SING P O2P ? ? SING C5' O5' ? ? SING C6 H6 ? ? SING O1P H1 ? ? SING O2P H2 ? ? SING C5' 2H5' ? ? SING C5' 1H5' ? ? SING C4' H4' ? ? SING C1' H1' ? ? SING N3 H3 ? ? SING N4 1H4 ? ? SING N4 2H4 ? ? SING C2' 1H2' ? ? SING C2' 2H2' ? ? SING C3' H3' ? ? SING O3' H4 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 . 32630 . . . . 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details "0.8 mM DNA (5'-D(*TP*(DCP)P*CP*GP*TP*TP*TP*CP*(PSC)P*GP*T)-3'), 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM 'natural abundance' NaCl 100 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMAN' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name DYANA _Version . loop_ _Task 'structure solution' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name SPARKY _Version . loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 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' 100 . mM pH 7 . pH pressure 1 . atm temperature 278 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 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 1 DT H6 H 7.62 0.00 1 2 1 1 DT H71 H 1.79 0.00 1 3 1 1 DT H72 H 1.79 0.00 1 4 1 1 DT H73 H 1.79 0.00 1 5 2 2 DC H1' H 6.32 0.00 1 6 2 2 DC H2' H 2.06 0.00 . 7 2 2 DC H2'' H 2.45 0.00 . 8 2 2 DC H3' H 4.71 0.00 1 9 2 2 DC H5 H 5.83 0.00 1 10 2 2 DC H6 H 7.84 0.00 1 11 2 2 DC H41 H 8.09 0.01 . 12 2 2 DC H42 H 9.61 0.00 . 13 3 3 DC H1' H 5.91 0.00 1 14 3 3 DC H2' H 1.43 0.00 . 15 3 3 DC H2'' H 1.96 0.01 . 16 3 3 DC H3' H 4.53 0.00 1 17 3 3 DC H5 H 5.54 0.02 1 18 3 3 DC H6 H 7.83 0.01 1 19 3 3 DC H41 H 7.01 0.01 . 20 3 3 DC H42 H 8.83 0.02 . 21 4 4 DG H1 H 10.39 0.00 1 22 4 4 DG H1' H 5.77 0.01 1 23 4 4 DG H2' H 2.72 0.00 . 24 4 4 DG H2'' H 2.38 0.00 . 25 4 4 DG H8 H 8.03 0.01 1 26 4 4 DG H21 H 6.00 0.00 . 27 4 4 DG H22 H 8.35 0.00 . 28 5 5 DT H1' H 5.84 0.00 1 29 5 5 DT H2' H 2.00 0.00 . 30 5 5 DT H2'' H 2.00 0.00 . 31 5 5 DT H3' H 4.34 0.00 1 32 5 5 DT H6 H 7.50 0.00 1 33 5 5 DT H71 H 1.59 0.00 1 34 5 5 DT H72 H 1.59 0.00 1 35 5 5 DT H73 H 1.59 0.00 1 36 6 6 DT H1' H 5.95 0.00 1 37 6 6 DT H2' H 2.05 0.00 . 38 6 6 DT H2'' H 2.34 0.00 . 39 6 6 DT H3' H 4.57 0.00 1 40 6 6 DT H6 H 7.38 0.00 1 41 6 6 DT H71 H 1.61 0.00 1 42 6 6 DT H72 H 1.61 0.00 1 43 6 6 DT H73 H 1.61 0.00 1 44 7 7 DT H6 H 7.62 0.00 1 45 7 7 DT H71 H 1.79 0.00 1 46 7 7 DT H72 H 1.79 0.00 1 47 7 7 DT H73 H 1.79 0.00 1 48 8 8 DC H1' H 6.34 0.01 1 49 8 8 DC H2' H 1.68 0.01 . 50 8 8 DC H2'' H 2.37 0.01 . 51 8 8 DC H5 H 5.78 0.00 1 52 8 8 DC H6 H 7.66 0.01 1 53 8 8 DC H41 H 7.54 0.00 . 54 8 8 DC H42 H 8.93 0.00 . 55 9 9 8YN H1' H 5.90 0.04 1 56 9 9 8YN H2' H 1.41 0.01 . 57 9 9 8YN H2'' H 1.95 0.00 . 58 9 9 8YN H6 H 7.03 0.04 1 59 9 9 8YN H41 H 6.10 0.00 . 60 9 9 8YN H42 H 8.67 0.06 . 61 10 10 DG H1 H 9.70 0.00 1 62 10 10 DG H1' H 5.70 0.00 1 63 10 10 DG H2' H 2.74 0.00 . 64 10 10 DG H2'' H 2.38 0.00 . 65 10 10 DG H8 H 8.10 0.00 1 66 10 10 DG H21 H 6.49 0.00 . 67 10 10 DG H22 H 8.34 0.00 . 68 11 11 DT H1' H 5.84 0.00 1 69 11 11 DT H2' H 2.00 0.00 . 70 11 11 DT H2'' H 2.00 0.00 . 71 11 11 DT H3' H 4.34 0.00 1 72 11 11 DT H6 H 7.50 0.00 1 73 11 11 DT H71 H 1.59 0.00 1 74 11 11 DT H72 H 1.59 0.00 1 75 11 11 DT H73 H 1.59 0.00 1 stop_ save_