data_19784 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the G-triplex truncated-TBA ; _BMRB_accession_number 19784 _BMRB_flat_file_name bmr19784.str _Entry_type original _Submission_date 2014-02-10 _Accession_date 2014-02-10 _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 Cerofolini Linda . . 2 Fragai Marco . . 3 Giachetti Andrea . . 4 Limongelli Vittorio . . 5 Luchinat Claudio . . 6 Novellino Ettore . . 7 Parrinello Michele . . 8 Randazzo Antonio . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 119 "13C chemical shifts" 66 "31P chemical shifts" 9 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-11-17 original author . stop_ _Original_release_date 2014-11-17 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'G-triplex structure and formation propensity' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25378342 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cerofolini Linda . . 2 Fragai Marco . . 3 Giachetti Andrea . . 4 Limongelli Vittorio . . 5 Luchinat Claudio . . 6 Novellino Ettore . . 7 Parrinello Michele . . 8 Randazzo Antonio . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'G-triplex truncated-TBA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3')' $DNA_(5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-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(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3') _Molecular_mass 3476.284 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence GGTTGGTGTGG loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DT 4 DT 5 DG 6 DG 7 DT 8 DG 9 DT 10 DG 11 DG 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 $DNA_(5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-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(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-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(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3') 0.7 mM 'natural abundance' 'potassium chloride' 70 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' EDTA 0.2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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 'structure solution' stop_ _Details . save_ 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 refinement stop_ _Details . save_ save_CARA _Saveframe_category software _Name CARA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _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_ save_spectrometer_4 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_5 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ save_spectrometer_6 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 950 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_ROESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_1 save_ save_2D_JR-HMBC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D JR-HMBC' _Sample_label $sample_1 save_ save_E.COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name E.COSY _Sample_label $sample_1 save_ save_2D_31P-1H_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 31P-1H HSQC' _Sample_label $sample_1 save_ save_2D_31P-1H_COSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 31P-1H COSY' _Sample_label $sample_1 save_ save_2D_13C-1H_HSQC_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-1H HSQC' _Sample_label $sample_1 save_ save_IPAP_10 _Saveframe_category NMR_applied_experiment _Experiment_name IPAP _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' 0.08 . M pH 7 . pH pressure 1 . atm temperature 274 . 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 C 13 'methyl protons' ppm 0.00 external indirect . . . 0.251449853 DSS H 1 'methyl protons' ppm 0.00 external direct . . . 1.000000000 'phosphoric acid (85%)' P 31 phosphorus ppm 0.00 external direct . . . 0.404808636 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_ _Software_label $CARA stop_ loop_ _Experiment_label '2D DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-1H ROESY' '2D JR-HMBC' '2D 31P-1H HSQC' '2D 31P-1H COSY' '2D 13C-1H HSQC' 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(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3')' _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 DG H1 H 11.998 0.04 1 2 1 1 DG H1' H 5.623 0.04 1 3 1 1 DG H2' H 2.677 0.04 2 4 1 1 DG H2'' H 1.809 0.04 2 5 1 1 DG H3' H 4.666 0.04 1 6 1 1 DG H4' H 3.599 0.04 1 7 1 1 DG H5' H 3.385 0.04 2 8 1 1 DG H5'' H 2.863 0.04 2 9 1 1 DG H8 H 7.401 0.04 1 10 1 1 DG H21 H 9.716 0.04 2 11 1 1 DG H22 H 6.145 0.04 2 12 1 1 DG C1' C 90.26 0.30 1 13 1 1 DG C2' C 40.793 0.30 1 14 1 1 DG C3' C 81.407 0.30 1 15 1 1 DG C4' C 88.932 0.30 1 16 1 1 DG C5' C 64.008 0.30 1 17 1 1 DG C8 C 141.157 0.30 1 18 2 2 DG H1 H 12.421 0.04 1 19 2 2 DG H1' H 6.159 0.04 1 20 2 2 DG H2' H 2.437 0.04 2 21 2 2 DG H2'' H 2.752 0.04 2 22 2 2 DG H3' H 4.911 0.04 1 23 2 2 DG H4' H 4.412 0.04 1 24 2 2 DG H5' H 4.083 0.04 2 25 2 2 DG H5'' H 4.022 0.04 2 26 2 2 DG H8 H 8.042 0.04 1 27 2 2 DG H22 H 6.901 0.04 2 28 2 2 DG C1' C 83.892 0.30 1 29 2 2 DG C2' C 37.823 0.30 1 30 2 2 DG C3' C 80.03 0.30 1 31 2 2 DG C4' C 87.095 0.30 1 32 2 2 DG C5' C 67.759 0.30 1 33 2 2 DG C8 C 139.365 0.30 1 34 2 2 DG P P -0.622 0.30 1 35 3 3 DT H1' H 5.04 0.04 1 36 3 3 DT H2' H 1.25 0.04 2 37 3 3 DT H2'' H 2.044 0.04 2 38 3 3 DT H3' H 4.413 0.04 1 39 3 3 DT H4' H 4.289 0.04 1 40 3 3 DT H5' H 4.229 0.04 2 41 3 3 DT H5'' H 3.827 0.04 2 42 3 3 DT H6 H 7.087 0.04 1 43 3 3 DT H71 H 1.652 0.04 1 44 3 3 DT H72 H 1.652 0.04 1 45 3 3 DT H73 H 1.652 0.04 1 46 3 3 DT C2' C 39.69 0.30 1 47 3 3 DT C3' C 78.278 0.30 1 48 3 3 DT C4' C 86.103 0.30 1 49 3 3 DT C5' C 67.688 0.30 1 50 3 3 DT C6 C 137.727 0.30 1 51 3 3 DT C7 C 13.699 0.30 1 52 3 3 DT P P -2.152 0.30 1 53 4 4 DT H1' H 6.051 0.04 1 54 4 4 DT H2' H 2.234 0.04 2 55 4 4 DT H2'' H 2.289 0.04 2 56 4 4 DT H3 H 10.343 0.04 1 57 4 4 DT H3' H 4.45 0.04 1 58 4 4 DT H4' H 2.59 0.04 1 59 4 4 DT H5' H 3.01 0.04 2 60 4 4 DT H5'' H 2.813 0.04 2 61 4 4 DT H6 H 7.413 0.04 1 62 4 4 DT H71 H 1.605 0.04 1 63 4 4 DT H72 H 1.605 0.04 1 64 4 4 DT H73 H 1.605 0.04 1 65 4 4 DT C1' C 86.751 0.30 1 66 4 4 DT C2' C 38.995 0.30 1 67 4 4 DT C3' C 77.757 0.30 1 68 4 4 DT C4' C 86.067 0.30 1 69 4 4 DT C5' C 66.658 0.30 1 70 4 4 DT C6 C 140.307 0.30 1 71 4 4 DT C7 C 13.68 0.30 1 72 4 4 DT P P -1.576 0.30 1 73 5 5 DG H1 H 12.231 0.04 1 74 5 5 DG H1' H 6.129 0.04 1 75 5 5 DG H2' H 3.641 0.04 2 76 5 5 DG H2'' H 2.843 0.04 2 77 5 5 DG H3' H 4.866 0.04 1 78 5 5 DG H4' H 4.372 0.04 1 79 5 5 DG H5' H 4.528 0.04 2 80 5 5 DG H5'' H 3.963 0.04 2 81 5 5 DG H8 H 7.44 0.04 1 82 5 5 DG H22 H 7.17 0.04 2 83 5 5 DG C1' C 88.321 0.30 1 84 5 5 DG C2' C 34.086 0.30 1 85 5 5 DG C3' C 80.367 0.30 1 86 5 5 DG C4' C 88.987 0.30 1 87 5 5 DG C5' C 69.471 0.30 1 88 5 5 DG C8 C 142.928 0.30 1 89 5 5 DG P P -0.538 0.30 1 90 6 6 DG H1 H 12.505 0.04 1 91 6 6 DG H1' H 6.14 0.04 1 92 6 6 DG H2' H 2.672 0.04 2 93 6 6 DG H2'' H 2.997 0.04 2 94 6 6 DG H3' H 5.014 0.04 1 95 6 6 DG H4' H 4.569 0.04 1 96 6 6 DG H5' H 4.252 0.04 2 97 6 6 DG H5'' H 4.159 0.04 2 98 6 6 DG H8 H 8.264 0.04 1 99 6 6 DG H22 H 6.91 0.04 2 100 6 6 DG C1' C 83.768 0.30 1 101 6 6 DG C2' C 39.406 0.30 1 102 6 6 DG C4' C 87.164 0.30 1 103 6 6 DG C5' C 68.069 0.30 1 104 6 6 DG C8 C 138.624 0.30 1 105 6 6 DG P P -0.901 0.30 1 106 7 7 DT H1' H 5.5 0.04 1 107 7 7 DT H2' H 0.504 0.04 2 108 7 7 DT H2'' H 1.789 0.04 2 109 7 7 DT H3 H 11.762 0.04 1 110 7 7 DT H3' H 4.647 0.04 1 111 7 7 DT H4' H 4.003 0.04 1 112 7 7 DT H5' H 4.487 0.04 2 113 7 7 DT H5'' H 4.176 0.04 2 114 7 7 DT H6 H 6.839 0.04 1 115 7 7 DT H71 H 1.916 0.04 1 116 7 7 DT H72 H 1.916 0.04 1 117 7 7 DT H73 H 1.916 0.04 1 118 7 7 DT C1' C 84.551 0.30 1 119 7 7 DT C2' C 39.011 0.30 1 120 7 7 DT C3' C 74.404 0.30 1 121 7 7 DT C4' C 84.14 0.30 1 122 7 7 DT C5' C 64.57 0.30 1 123 7 7 DT C6 C 136.08 0.30 1 124 7 7 DT C7 C 14.693 0.30 1 125 7 7 DT P P -1.146 0.30 1 126 8 8 DG H1 H 10.62 0.04 1 127 8 8 DG H1' H 6.031 0.04 1 128 8 8 DG H2' H 2.538 0.04 2 129 8 8 DG H2'' H 2.975 0.04 2 130 8 8 DG H3' H 4.983 0.04 1 131 8 8 DG H4' H 4.182 0.04 1 132 8 8 DG H5' H 4.149 0.04 2 133 8 8 DG H5'' H 4.054 0.04 2 134 8 8 DG H8 H 8.107 0.04 1 135 8 8 DG H22 H 5.899 0.04 2 136 8 8 DG C1' C 85.665 0.30 1 137 8 8 DG C2' C 39.885 0.30 1 138 8 8 DG C3' C 79.54 0.30 1 139 8 8 DG C4' C 88.647 0.30 1 140 8 8 DG C5' C 68.33 0.30 1 141 8 8 DG C8 C 139.237 0.30 1 142 8 8 DG P P -1.376 0.30 1 143 9 9 DT H1' H 5.912 0.04 1 144 9 9 DT H2' H 1.724 0.04 2 145 9 9 DT H2'' H 2.218 0.04 2 146 9 9 DT H3 H 12.437 0.04 1 147 9 9 DT H3' H 4.515 0.04 1 148 9 9 DT H4' H 3.618 0.04 1 149 9 9 DT H5' H 3.439 0.04 2 150 9 9 DT H5'' H 2.536 0.04 2 151 9 9 DT H6 H 7.251 0.04 1 152 9 9 DT H71 H 1.541 0.04 1 153 9 9 DT H72 H 1.541 0.04 1 154 9 9 DT H73 H 1.541 0.04 1 155 9 9 DT C1' C 88.617 0.30 1 156 9 9 DT C2' C 42.958 0.30 1 157 9 9 DT C4' C 89.313 0.30 1 158 9 9 DT C5' C 67.742 0.30 1 159 9 9 DT C6 C 137.803 0.30 1 160 9 9 DT C7 C 14.062 0.30 1 161 10 10 DG H1 H 11.549 0.04 1 162 10 10 DG H1' H 5.976 0.04 1 163 10 10 DG H2' H 2.835 0.04 2 164 10 10 DG H2'' H 2.533 0.04 2 165 10 10 DG H3' H 4.721 0.04 1 166 10 10 DG H4' H 4.302 0.04 1 167 10 10 DG H5' H 3.952 0.04 2 168 10 10 DG H5'' H 3.837 0.04 2 169 10 10 DG H8 H 7.623 0.04 1 170 10 10 DG H22 H 6.483 0.04 2 171 10 10 DG C1' C 89.425 0.30 1 172 10 10 DG C2' C 39.676 0.30 1 173 10 10 DG C3' C 80.099 0.30 1 174 10 10 DG C4' C 88.532 0.30 1 175 10 10 DG C8 C 142.468 0.30 1 176 10 10 DG P P -0.049 0.30 1 177 11 11 DG H1 H 12.082 0.04 1 178 11 11 DG H1' H 5.744 0.04 1 179 11 11 DG H2' H 2.381 0.04 2 180 11 11 DG H2'' H 2.648 0.04 2 181 11 11 DG H3' H 4.78 0.04 1 182 11 11 DG H4' H 4.152 0.04 1 183 11 11 DG H5' H 4.104 0.04 2 184 11 11 DG H5'' H 3.586 0.04 2 185 11 11 DG H8 H 8.022 0.04 1 186 11 11 DG H21 H 10.124 0.04 2 187 11 11 DG H22 H 6.905 0.04 2 188 11 11 DG C1' C 83.604 0.30 1 189 11 11 DG C2' C 41.63 0.30 1 190 11 11 DG C3' C 72.038 0.30 1 191 11 11 DG C4' C 86.87 0.30 1 192 11 11 DG C5' C 63.781 0.30 1 193 11 11 DG C8 C 139.035 0.30 1 194 11 11 DG P P -0.862 0.30 1 stop_ save_