data_18862 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Parallel human telomeric quadruplex containing 2'F-ANA substitutions ; _BMRB_accession_number 18862 _BMRB_flat_file_name bmr18862.str _Entry_type original _Submission_date 2012-11-27 _Accession_date 2012-11-27 _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 Martin-Pintado Nerea . . 2 Yahyaee-Anzahaee Maryam . . 3 Portella Guillem . . 4 Orozco Modesto . . 5 Damha Masad J. . 6 Gonzalez Carlos . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 111 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-05-06 original author . stop_ _Original_release_date 2013-05-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title "Dramatic effect of furanose c2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom" _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23521511 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Martin-Pintado Nerea . . 2 Yahyaee-Anzahaee Maryam . . 3 Deleavey Glen F. . 4 Portella Guillem . . 5 Orozco Modesto . . 6 Damha Masad J. . 7 Gonzalez Carlos . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 135 _Journal_issue 14 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5344 _Page_last 5347 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Parallel human telomeric quadruplex containing 2'F-ANA substitutions' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3')_1' $DNA_(5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3') 'DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3')_2' $DNA_(5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-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*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3') _Molecular_mass 3791.484 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence TAGGGTTAXGGT loop_ _Residue_seq_code _Residue_label 1 DT 2 DA 3 DG 4 DG 5 DG 6 DT 7 DT 8 DA 9 GFL 10 DG 11 DG 12 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_GFL _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE _BMRB_code GFL _PDB_code GFL _Standard_residue_derivative . _Molecular_mass 365.212 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1' C1' C . 0 . ? C2 C2 C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4 C4 C . 0 . ? C4' C4' C . 0 . ? C5 C5 C . 0 . ? C5' C5' C . 0 . ? C6 C6 C . 0 . ? C8 C8 C . 0 . ? F F F . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H8 H8 H . 0 . ? HN1 HN1 H . 0 . ? HN21 HN21 H . 0 . ? HN22 HN22 H . 0 . ? HO2P HO2P H . 0 . ? HO3' HO3' H . 0 . ? HO3P HO3P H . 0 . ? N1 N1 N . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? N7 N7 N . 0 . ? N9 N9 N . 0 . ? O1P O1P O . 0 . ? O2P O2P O . 0 . ? O3' O3' O . 0 . ? O3P O3P O . 0 . ? O4' O4' O . 0 . ? O5' O5' O . 0 . ? O6 O6 O . 0 . ? P P P . 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 ? ? DOUB P O1P ? ? SING P O2P ? ? SING P O5' ? ? SING O2P HO2P ? ? 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' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING N1 C2 ? ? SING N1 HN1 ? ? SING C2 N2 ? ? DOUB C2 N3 ? ? SING N2 HN21 ? ? SING N2 HN22 ? ? SING N3 C4 ? ? 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*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-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*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-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 _Isotopic_labeling $DNA_(5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3') 0.7 mM 'natural abundance' 'potassium chloride' 5 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3') 0.7 mM 'natural abundance' 'potassium chloride' 10 mM 'natural abundance' 'potassium phosphate' 5 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 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 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_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'geometry optimization' 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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 15 . mM 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 0.00 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 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-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 6.234 . . 2 1 1 DT H2' H 1.992 . . 3 1 1 DT H2'' H 2.413 . . 4 1 1 DT H3' H 4.791 . . 5 1 1 DT H4' H 4.159 . . 6 1 1 DT H5' H 3.744 . . 7 1 1 DT H6 H 7.381 . . 8 1 1 DT H71 H 1.783 . . 9 1 1 DT H72 H 1.783 . . 10 1 1 DT H73 H 1.783 . . 11 2 2 DA H1' H 6.109 . . 12 2 2 DA H2 H 8.158 . . 13 2 2 DA H2' H 2.811 . . 14 2 2 DA H2'' H 3.003 . . 15 2 2 DA H3' H 5.178 . . 16 2 2 DA H4' H 4.506 . . 17 2 2 DA H5' H 4.061 . . 18 2 2 DA H5'' H 4.194 . . 19 2 2 DA H8 H 8.218 . . 20 3 3 DG H1 H 11.952 . . 21 3 3 DG H1' H 6.321 . . 22 3 3 DG H2' H 2.991 . . 23 3 3 DG H2'' H 3.249 . . 24 3 3 DG H3' H 5.301 . . 25 3 3 DG H4' H 4.755 . . 26 3 3 DG H5'' H 4.418 . . 27 3 3 DG H8 H 8.219 . . 28 4 4 DG H1 H 11.603 . . 29 4 4 DG H1' H 6.280 . . 30 4 4 DG H2' H 2.833 . . 31 4 4 DG H2'' H 3.006 . . 32 4 4 DG H3' H 5.248 . . 33 4 4 DG H4' H 4.674 . . 34 4 4 DG H5' H 4.200 . . 35 4 4 DG H5'' H 4.374 . . 36 4 4 DG H8 H 7.910 . . 37 5 5 DG H1 H 11.331 . . 38 5 5 DG H1' H 6.448 . . 39 5 5 DG H2' H 2.729 . . 40 5 5 DG H3' H 5.168 . . 41 5 5 DG H4' H 4.563 . . 42 5 5 DG H5' H 4.188 . . 43 5 5 DG H8 H 7.888 . . 44 6 6 DT H1' H 6.512 . . 45 6 6 DT H2' H 2.561 . . 46 6 6 DT H2'' H 2.659 . . 47 6 6 DT H3' H 5.019 . . 48 6 6 DT H4' H 4.606 . . 49 6 6 DT H5' H 4.191 . . 50 6 6 DT H5'' H 4.305 . . 51 6 6 DT H6 H 7.735 . . 52 6 6 DT H71 H 1.989 . . 53 6 6 DT H72 H 1.989 . . 54 6 6 DT H73 H 1.989 . . 55 7 7 DT H1' H 6.499 . . 56 7 7 DT H2' H 2.461 . . 57 7 7 DT H2'' H 2.714 . . 58 7 7 DT H3' H 5.000 . . 59 7 7 DT H4' H 4.550 . . 60 7 7 DT H5' H 4.281 . . 61 7 7 DT H5'' H 4.134 . . 62 7 7 DT H6 H 7.888 . . 63 7 7 DT H71 H 2.194 . . 64 7 7 DT H72 H 2.194 . . 65 7 7 DT H73 H 2.194 . . 66 8 8 DA H1' H 6.767 . . 67 8 8 DA H2 H 8.640 . . 68 8 8 DA H2' H 2.746 . . 69 8 8 DA H2'' H 3.176 . . 70 8 8 DA H3' H 5.369 . . 71 8 8 DA H4' H 4.737 . . 72 8 8 DA H5' H 4.310 . . 73 8 8 DA H5'' H 4.494 . . 74 8 8 DA H8 H 8.681 . . 75 9 9 GFL H1' H 6.272 . . 76 9 9 GFL H2' H 5.464 . . 77 9 9 GFL H3' H 5.145 . . 78 9 9 GFL H4' H 4.709 . . 79 9 9 GFL H5'1 H 4.490 . . 80 9 9 GFL H5'2 H 4.541 . . 81 9 9 GFL H8 H 8.032 . . 82 9 9 GFL HN1 H 11.739 . . 83 10 10 DG H1 H 11.643 . . 84 10 10 DG H1' H 6.201 . . 85 10 10 DG H2' H 2.678 . . 86 10 10 DG H2'' H 2.916 . . 87 10 10 DG H3' H 5.244 . . 88 10 10 DG H4' H 4.731 . . 89 10 10 DG H5' H 4.500 . . 90 10 10 DG H5'' H 4.209 . . 91 10 10 DG H8 H 7.650 . . 92 11 11 DG H1 H 11.431 . . 93 11 11 DG H1' H 6.393 . . 94 11 11 DG H2' H 2.845 . . 95 11 11 DG H2'' H 2.996 . . 96 11 11 DG H3' H 5.111 . . 97 11 11 DG H4' H 4.715 . . 98 11 11 DG H5' H 4.316 . . 99 11 11 DG H5'' H 4.519 . . 100 11 11 DG H8 H 7.972 . . 101 12 12 DT H1' H 6.097 . . 102 12 12 DT H2' H 2.167 . . 103 12 12 DT H2'' H 2.288 . . 104 12 12 DT H3' H 4.636 . . 105 12 12 DT H4' H 4.164 . . 106 12 12 DT H5' H 4.250 . . 107 12 12 DT H5'' H 4.516 . . 108 12 12 DT H6 H 7.281 . . 109 12 12 DT H71 H 1.743 . . 110 12 12 DT H72 H 1.743 . . 111 12 12 DT H73 H 1.743 . . stop_ save_