data_25840 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC at acidic pH ; _BMRB_accession_number 25840 _BMRB_flat_file_name bmr25840.str _Entry_type original _Submission_date 2015-10-09 _Accession_date 2015-10-09 _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 Abou-Assi Robert . . 2 Harkness Robert W. . 3 Martin-Pintado Nerea W. . 4 Wilds Christopher J. . 5 Campos-Olivas Ramon . . 6 Mittermaier Anthony K. . 7 Gonzalez Carlos W. . 8 Damha Masad J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 51 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-08-15 original BMRB . stop_ _Original_release_date 2016-08-15 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Stabilization of i-motif structures by 2'-beta-fluorination of DNA ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27166371 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Abou-Assi Hala . . 2 Harkness Robert W. . 3 Martin-Pintado Nerea . . 4 Wilds Christopher J. . 5 Campos-Olivas Ramon . . 6 Mittermaier Anthony K. . 7 Gonzalez Carlos . . 8 Damha Masad J. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 44 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4998 _Page_last 5009 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Tetrameric i-motif structure of dT-dC-dC-CFL-CFL-dC' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_1" $DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') "DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_2" $DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') "DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_3" $DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') "DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_4" $DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-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_DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') _Molecular_mass 1741.139 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 6 _Mol_residue_sequence ; TCCXXC ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DC 3 DC 4 CFL 5 CFL 6 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_CFL _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one _BMRB_code CFL _PDB_code CFL _Standard_residue_derivative . _Molecular_mass 325.188 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O3P O3P O . 0 . ? P P P . 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 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? C1' C1' C . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? N4 N4 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? F F F . 0 . ? HO3P HO3P H . 0 . ? HO1P HO1P H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? H1' H1' H . 0 . ? HN41 HN41 H . 0 . ? HN42 HN42 H . 0 . ? H5 H5 H . 0 . ? H6 H6 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 SING O3P P ? ? SING O3P HO3P ? ? SING P O1P ? ? DOUB P O2P ? ? SING P O5' ? ? SING O1P HO1P ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' F ? ? SING C2' H2' ? ? SING C1' N1 ? ? SING C1' H1' ? ? SING N1 C2 ? ? SING N1 C6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? DOUB N3 C4 ? ? SING C4 N4 ? ? SING C4 C5 ? ? SING N4 HN41 ? ? SING N4 HN42 ? ? DOUB C5 C6 ? ? SING C5 H5 ? ? SING C6 H6 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') . . . . . . 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 $DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') '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 $DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') 1.25 mM 0.5 2.0 'natural abundance' 'sodium chloride' 10 mM . . 'natural abundance' 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 $DNA_(5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3') 1.25 mM 0.5 2.0 'natural abundance' 'sodium chloride' 10 mM . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' 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_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-19F_HOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-19F HOESY' _Sample_label $sample_2 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' 10 . mM pH 5.0 . pH pressure 1 . atm temperature 278 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 10 . mM pH 5.0 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 19F 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 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 '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name "DNA (5'-D(*TP*CP*CP*(CFL)P*(CFL)P*C)-3')_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 H1' H 6.338 0.005 . 2 1 1 DT H2' H 2.164 0.004 . 3 1 1 DT H2'' H 2.660 0.006 . 4 1 1 DT H3 H 11.465 0.000 . 5 1 1 DT H3' H 4.832 0.000 . 6 1 1 DT H4' H 4.032 0.001 . 7 1 1 DT H6 H 7.638 0.001 . 8 1 1 DT H71 H 1.751 0.002 . 9 1 1 DT H72 H 1.751 0.002 . 10 1 1 DT H73 H 1.751 0.002 . 11 2 2 DC H1' H 6.575 0.007 . 12 2 2 DC H2' H 2.057 0.002 . 13 2 2 DC H2'' H 2.412 0.004 . 14 2 2 DC H3' H 4.822 0.001 . 15 2 2 DC H4' H 4.186 0.000 . 16 2 2 DC H5 H 5.905 0.006 . 17 2 2 DC H6 H 7.946 0.007 . 18 2 2 DC H41 H 8.338 0.006 . 19 2 2 DC H42 H 9.343 0.011 . 20 3 3 DC H1' H 6.398 0.020 . 21 3 3 DC H2' H 2.183 0.002 . 22 3 3 DC H2'' H 2.654 0.004 . 23 3 3 DC H3' H 4.892 0.000 . 24 3 3 DC H4' H 4.200 0.000 . 25 3 3 DC H5 H 5.886 0.005 . 26 3 3 DC H6 H 7.733 0.005 . 27 3 3 DC H41 H 8.492 0.014 . 28 3 3 DC H42 H 9.253 0.005 . 29 4 4 CFL H1' H 6.347 0.008 . 30 4 4 CFL H2' H 5.363 0.001 . 31 4 4 CFL H3' H 4.755 0.005 . 32 4 4 CFL H41 H 8.515 0.013 . 33 4 4 CFL H42 H 9.262 0.008 . 34 4 4 CFL H5 H 5.953 0.004 . 35 4 4 CFL H6 H 7.617 0.004 . 36 5 5 CFL H1' H 6.348 0.007 . 37 5 5 CFL H2' H 5.157 0.005 . 38 5 5 CFL H3' H 4.583 0.006 . 39 5 5 CFL H41 H 8.612 0.008 . 40 5 5 CFL H42 H 9.367 0.006 . 41 5 5 CFL H5 H 5.832 0.008 . 42 5 5 CFL H6 H 7.707 0.004 . 43 6 6 DC H1' H 6.156 0.010 . 44 6 6 DC H2' H 2.199 0.004 . 45 6 6 DC H2'' H 2.454 0.000 . 46 6 6 DC H3' H 4.304 0.007 . 47 6 6 DC H4' H 3.987 0.006 . 48 6 6 DC H5 H 5.920 0.008 . 49 6 6 DC H6 H 7.752 0.004 . 50 6 6 DC H41 H 8.270 0.009 . 51 6 6 DC H42 H 9.221 0.005 . stop_ save_