data_18724 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; FUC_TBA ; _BMRB_accession_number 18724 _BMRB_flat_file_name bmr18724.str _Entry_type original _Submission_date 2012-09-18 _Accession_date 2012-09-18 _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 Gomez-Pinto Irene . . 2 Vengut-Climent Empar . . 3 Lucas Ricardo . . 4 'Avi o' Anna . . 5 Eritja Ramon . . 6 'Gonzalez-Iba ez' Carlos . . 7 Morales 'Juan Carlos' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 183 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-10-18 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Monosaccharide interactions with G-quadruplex DNA: induced-fit effect on thrombin-binding aptamer with sugars at the 5 -end' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gomez-Pinto Irene . . 2 Vengut-Climent Empar . . 3 Lucas Ricardo . . 4 'Avi o' Anna . . 5 Eritja Ramon . . 6 'Gonzalez Iba ez' Carlos . . 7 Morales 'Juan Carlos' . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _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 . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name G-quadruplex_DNA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label G-quadruplex_DNA $G-quadruplex_DNA ALPHA-L-FUCOSE $entity_FUC 1,2-ETHANEDIOL $entity_EDO 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_G-quadruplex_DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common G-quadruplex_DNA _Molecular_mass 4743.092 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence GGTTGGTGTGGTTGG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DG 3 3 DT 4 4 DT 5 5 DG 6 6 DG 7 7 DT 8 8 DG 9 9 DT 10 10 DG 11 11 DG 12 12 DT 13 13 DT 14 14 DG 15 15 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_FUC _Saveframe_category ligand _Mol_type "non-polymer (SACCHARIDE)" _Name_common ALPHA-L-FUCOSE _BMRB_code FUC _PDB_code FUC _Molecular_mass 164.156 _Mol_charge 0 _Mol_paramagnetic no _Mol_aromatic no _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 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H63 H63 H . 0 . ? HO1 HO1 H . 0 . ? HO2 HO2 H . 0 . ? HO3 HO3 H . 0 . ? HO4 HO4 H . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? O5 O5 O . 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 C1 C2 ? ? SING C1 O1 ? ? SING C1 O5 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 O2 ? ? SING C2 H2 ? ? SING C3 C4 ? ? SING C3 O3 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 O4 ? ? SING C4 H4 ? ? SING C5 C6 ? ? SING C5 O5 ? ? SING C5 H5 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING C6 H63 ? ? SING O1 HO1 ? ? SING O2 HO2 ? ? SING O3 HO3 ? ? SING O4 HO4 ? ? stop_ _Mol_thiol_state 'not present' _Sequence_homology_query_date . save_ save_EDO _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 1,2-ETHANEDIOL _BMRB_code EDO _PDB_code EDO _Molecular_mass 62.068 _Mol_charge 0 _Mol_paramagnetic no _Mol_aromatic no _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 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? HO1 HO1 H . 0 . ? HO2 HO2 H . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 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 C1 O1 ? ? SING C1 C2 ? ? SING C1 H11 ? ? SING C1 H12 ? ? SING O1 HO1 ? ? SING C2 O2 ? ? SING C2 H21 ? ? SING C2 H22 ? ? SING O2 HO2 ? ? stop_ _Mol_thiol_state 'not present' _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $G-quadruplex_DNA . . . . . . 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 $G-quadruplex_DNA 'chemical synthesis' . . . . . $entity_FUC '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 $G-quadruplex_DNA 1 mM 'natural abundance' $entity_FUC 1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % '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' . . Goddard . . 'Bruker Biospin' . . stop_ loop_ _Task refinement 'chemical shift assignment' processing 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_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_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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 temperature 279.6 . K pH 7 . pH pressure 1 . atm 'ionic strength' 10 10 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 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-1H COSY' 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 G-quadruplex_DNA _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 12.07 0.000 1 2 1 1 DG H1' H 6.05 0.000 1 3 1 1 DG H2' H 3.48 0.000 1 4 1 1 DG H2'' H 2.90 0.000 1 5 1 1 DG H3' H 0.00 0.000 9 6 1 1 DG H4' H 4.29 0.000 1 7 1 1 DG H5' H 0.00 0.000 9 8 1 1 DG H5'' H 0.00 0.000 9 9 1 1 DG H8 H 7.37 0.000 1 10 1 1 DG H21 H 0.00 0.000 9 11 1 1 DG H22 H 0.00 0.000 9 12 2 2 DG H1 H 12.11 0.000 1 13 2 2 DG H1' H 6.06 0.000 1 14 2 2 DG H2' H 3.07 0.000 1 15 2 2 DG H2'' H 2.34 0.000 1 16 2 2 DG H3' H 5.15 0.000 1 17 2 2 DG H4' H 4.43 0.000 1 18 2 2 DG H5' H 4.28 0.000 2 19 2 2 DG H5'' H 4.28 0.000 2 20 2 2 DG H8 H 8.29 0.000 1 21 2 2 DG H21 H 8.00 0.000 9 22 2 2 DG H22 H 9.00 0.000 9 23 3 3 DT H1' H 6.20 0.000 1 24 3 3 DT H2' H 2.27 0.000 1 25 3 3 DT H2'' H 2.61 0.000 1 26 3 3 DT H3 H 11.33 0.000 1 27 3 3 DT H3' H 4.93 0.000 1 28 3 3 DT H4' H 4.28 0.000 1 29 3 3 DT H5' H 4.23 0.000 2 30 3 3 DT H5'' H 4.23 0.000 2 31 3 3 DT H6 H 7.92 0.000 1 32 3 3 DT H71 H 1.99 0.000 1 33 3 3 DT H72 H 1.99 0.000 1 34 3 3 DT H73 H 1.99 0.000 1 35 4 4 DT H1' H 6.06 0.000 1 36 4 4 DT H2' H 2.03 0.000 1 37 4 4 DT H2'' H 2.70 0.000 1 38 4 4 DT H3 H 11.39 0.000 1 39 4 4 DT H3' H 4.90 0.000 1 40 4 4 DT H4' H 4.29 0.000 1 41 4 4 DT H5' H 3.93 0.000 2 42 4 4 DT H5'' H 3.93 0.000 2 43 4 4 DT H6 H 7.14 0.000 1 44 4 4 DT H71 H 1.01 0.000 1 45 4 4 DT H72 H 1.01 0.000 1 46 4 4 DT H73 H 1.01 0.000 1 47 5 5 DG H1 H 12.20 0.000 1 48 5 5 DG H1' H 6.05 0.000 1 49 5 5 DG H2' H 3.36 0.000 1 50 5 5 DG H2'' H 2.93 0.000 1 51 5 5 DG H3' H 4.88 0.000 1 52 5 5 DG H4' H 4.41 0.000 1 53 5 5 DG H5' H 4.30 0.000 2 54 5 5 DG H5'' H 4.23 0.000 2 55 5 5 DG H8 H 7.44 0.000 1 56 5 5 DG H21 H 0.00 0.000 9 57 5 5 DG H22 H 0.00 0.000 9 58 6 6 DG H1 H 12.11 0.000 1 59 6 6 DG H1' H 5.89 0.000 1 60 6 6 DG H2' H 2.74 0.000 1 61 6 6 DG H2'' H 2.62 0.000 1 62 6 6 DG H3' H 5.11 0.000 1 63 6 6 DG H4' H 4.41 0.000 1 64 6 6 DG H5' H 4.29 0.000 2 65 6 6 DG H5'' H 4.29 0.000 2 66 6 6 DG H8 H 7.61 0.000 1 67 6 6 DG H21 H 0.00 0.000 9 68 6 6 DG H22 H 0.00 0.000 9 69 7 7 DT H1' H 6.54 0.000 1 70 7 7 DT H2' H 2.53 0.000 1 71 7 7 DT H2'' H 2.66 0.000 1 72 7 7 DT H3 H 11.31 0.000 1 73 7 7 DT H3' H 4.86 0.000 1 74 7 7 DT H4' H 4.47 0.000 1 75 7 7 DT H5' H 4.33 0.000 2 76 7 7 DT H5'' H 4.25 0.000 2 77 7 7 DT H6 H 8.00 0.000 1 78 7 7 DT H71 H 1.99 0.000 1 79 7 7 DT H72 H 1.99 0.000 1 80 7 7 DT H73 H 1.99 0.000 1 81 8 8 DG H1 H 0.00 0.000 9 82 8 8 DG H1' H 5.84 0.000 1 83 8 8 DG H2' H 2.09 0.000 1 84 8 8 DG H2'' H 2.35 0.000 1 85 8 8 DG H3' H 4.79 0.000 1 86 8 8 DG H4' H 4.01 0.000 1 87 8 8 DG H5' H 4.14 0.000 2 88 8 8 DG H5'' H 4.08 0.000 2 89 8 8 DG H8 H 7.61 0.000 1 90 8 8 DG H21 H 0.00 0.000 9 91 8 8 DG H22 H 0.00 0.000 9 92 9 9 DT H1' H 5.83 0.000 1 93 9 9 DT H2' H 1.97 0.000 1 94 9 9 DT H2'' H 2.44 0.000 1 95 9 9 DT H3 H 10.32 0.000 1 96 9 9 DT H3' H 4.64 0.000 1 97 9 9 DT H4' H 3.90 0.000 1 98 9 9 DT H5' H 3.56 0.000 2 99 9 9 DT H5'' H 2.98 0.000 2 100 9 9 DT H6 H 7.29 0.000 1 101 9 9 DT H71 H 1.89 0.000 1 102 9 9 DT H72 H 1.89 0.000 1 103 9 9 DT H73 H 1.89 0.000 1 104 10 10 DG H1 H 11.94 0.000 1 105 10 10 DG H1' H 6.07 0.000 1 106 10 10 DG H2' H 3.71 0.000 1 107 10 10 DG H2'' H 2.97 0.000 1 108 10 10 DG H3' H 0.00 0.000 9 109 10 10 DG H4' H 0.00 0.000 9 110 10 10 DG H5' H 0.00 0.000 9 111 10 10 DG H5'' H 0.00 0.000 9 112 10 10 DG H8 H 7.45 0.000 1 113 10 10 DG H21 H 0.00 0.000 9 114 10 10 DG H22 H 0.00 0.000 9 115 11 11 DG H1 H 12.05 0.000 1 116 11 11 DG H1' H 6.02 0.000 1 117 11 11 DG H2' H 2.97 0.000 1 118 11 11 DG H2'' H 2.33 0.000 1 119 11 11 DG H3' H 5.15 0.000 1 120 11 11 DG H4' H 4.40 0.000 1 121 11 11 DG H5' H 4.32 0.000 2 122 11 11 DG H5'' H 4.26 0.000 2 123 11 11 DG H8 H 8.22 0.000 1 124 11 11 DG H21 H 0.00 0.000 9 125 11 11 DG H22 H 0.00 0.000 9 126 12 12 DT H1' H 6.19 0.000 1 127 12 12 DT H2' H 2.24 0.000 1 128 12 12 DT H2'' H 2.60 0.000 1 129 12 12 DT H3 H 11.33 0.000 1 130 12 12 DT H3' H 4.93 0.000 1 131 12 12 DT H4' H 4.28 0.000 1 132 12 12 DT H5' H 4.23 0.000 2 133 12 12 DT H5'' H 4.23 0.000 2 134 12 12 DT H6 H 7.92 0.000 1 135 12 12 DT H71 H 2.00 0.000 1 136 12 12 DT H72 H 2.00 0.000 1 137 12 12 DT H73 H 2.00 0.000 1 138 13 13 DT H1' H 6.12 0.000 1 139 13 13 DT H2' H 2.09 0.000 1 140 13 13 DT H2'' H 2.75 0.000 1 141 13 13 DT H3 H 11.33 0.000 1 142 13 13 DT H3' H 4.91 0.000 1 143 13 13 DT H4' H 4.29 0.000 1 144 13 13 DT H5' H 3.93 0.000 2 145 13 13 DT H5'' H 3.93 0.000 2 146 13 13 DT H6 H 7.25 0.000 1 147 13 13 DT H71 H 0.97 0.000 1 148 13 13 DT H72 H 0.97 0.000 1 149 13 13 DT H73 H 0.97 0.000 1 150 14 14 DG H1 H 12.17 0.000 1 151 14 14 DG H1' H 6.10 0.000 1 152 14 14 DG H2' H 3.52 0.000 1 153 14 14 DG H2'' H 2.99 0.000 1 154 14 14 DG H3' H 4.93 0.000 1 155 14 14 DG H4' H 4.44 0.000 1 156 14 14 DG H5' H 4.28 0.000 2 157 14 14 DG H5'' H 4.28 0.000 2 158 14 14 DG H8 H 7.48 0.000 1 159 14 14 DG H21 H 0.00 0.000 9 160 14 14 DG H22 H 0.00 0.000 9 161 15 15 DG H1 H 12.46 0.000 1 162 15 15 DG H1' H 6.17 0.000 1 163 15 15 DG H2' H 2.69 0.000 1 164 15 15 DG H2'' H 2.44 0.000 1 165 15 15 DG H3' H 4.80 0.000 1 166 15 15 DG H4' H 4.25 0.000 1 167 15 15 DG H5' H 4.18 0.000 2 168 15 15 DG H5'' H 4.18 0.000 2 169 15 15 DG H8 H 8.08 0.000 1 170 15 15 DG H21 H 0.00 0.000 9 171 15 15 DG H22 H 0.00 0.000 9 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-1H COSY' 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 ALPHA-L-FUCOSE _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 1 101 1 FUC H1 H 4.35 0.000 1 2 101 1 FUC H2 H 3.43 0.000 1 3 101 1 FUC H3 H 3.55 0.000 1 4 101 1 FUC H4 H 3.64 0.000 1 5 101 1 FUC H5 H 3.68 0.000 1 6 101 1 FUC H61 H 1.18 0.000 1 7 101 1 FUC H62 H 1.18 0.000 1 8 101 1 FUC H63 H 1.18 0.000 1 stop_ save_ save_assigned_chem_shift_list_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-1H COSY' 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 1,2-ETHANEDIOL _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 1 102 1 EDO H11 H 3.76 0.000 2 2 102 1 EDO H12 H 3.76 0.000 2 3 102 1 EDO H21 H 4.06 0.000 2 4 102 1 EDO H22 H 3.98 0.000 2 stop_ save_