data_25759 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure for quercetin complexed with c-myc G-quadruplex DNA ; _BMRB_accession_number 25759 _BMRB_flat_file_name bmr25759.str _Entry_type original _Submission_date 2015-08-18 _Accession_date 2015-09-03 _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 Kumar Amit . . 2 Tawani Arpita . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 57 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-09-12 original BMRB . stop_ _Original_release_date 2016-09-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution structure for quercetin complexed with c-myc G-quadruplex DNA ; _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 Kumar Amit . . 2 Tawani Arpita . . stop_ _Journal_abbreviation 'Not known' _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 'Quercetin complexed with c-myc G-quadruplex DNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*(DN)P*(DN))-3')" $DNA_(5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*(DN)P*(DN))-3') entity_QUE $entity_QUE 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*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*(DN)P*(DN))-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*(DN)P*(DN))-3') _Molecular_mass 7862.206 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 26 _Mol_residue_sequence ; TGAGGGTGGTGAGGGTGGGG AAGGXX ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DG 3 3 DA 4 4 DG 5 5 DG 6 6 DG 7 7 DT 8 8 DG 9 9 DG 10 10 DT 11 11 DG 12 12 DA 13 13 DG 14 14 DG 15 15 DG 16 16 DT 17 17 DG 18 18 DG 19 19 DG 20 20 DG 21 21 DA 22 22 DA 23 23 DG 24 24 DG 25 25 DN 26 26 DN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DN _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common "UNKNOWN 2'-DEOXYNUCLEOTIDE" _BMRB_code DN _PDB_code DN _Standard_residue_derivative . _Molecular_mass 198.111 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons OP3 OP3 O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 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 . ? HOP3 HOP3 H . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? H1' H1' H . 0 . ? H1'2 H1'2 H . 0 . ? H2'2 H2'2 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 OP3 P ? ? SING OP3 HOP3 ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? 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' H2'2 ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING C1' H1' ? ? SING C1' H1'2 ? ? stop_ save_ ############# # Ligands # ############# save_QUE _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_QUE (3,5,7,3',4'-PENTAHYDROXYFLAVONE)" _BMRB_code QUE _PDB_code QUE _Molecular_mass 302.236 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _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 . ? C9 C9 C . 0 . ? C10 C10 C . 0 . ? C11 C11 C . 0 . ? C14 C14 C . 0 . ? C15 C15 C . 0 . ? C16 C16 C . 0 . ? C17 C17 C . 0 . ? C18 C18 C . 0 . ? C19 C19 C . 0 . ? O12 O12 O . 0 . ? O13 O13 O . 0 . ? O23 O23 O . 0 . ? O24 O24 O . 0 . ? O27 O27 O . 0 . ? O29 O29 O . 0 . ? O30 O30 O . 0 . ? H1 H1 H . 0 . ? H5 H5 H . 0 . ? H15 H15 H . 0 . ? H16 H16 H . 0 . ? H19 H19 H . 0 . ? HO3 HO3 H . 0 . ? HO4 HO4 H . 0 . ? HO7 HO7 H . 0 . ? HO9 HO9 H . 0 . ? HO0 HO0 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 C1 C2 ? ? SING C1 C6 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 O30 ? ? DOUB C3 C4 ? ? SING C3 C9 ? ? SING C4 C5 ? ? SING C4 O12 ? ? DOUB C5 C6 ? ? SING C5 H5 ? ? SING C6 O29 ? ? SING C9 C10 ? ? DOUB C9 O13 ? ? DOUB C10 C11 ? ? SING C10 O27 ? ? SING C11 C14 ? ? SING C11 O12 ? ? DOUB C14 C15 ? ? SING C14 C19 ? ? SING C15 C16 ? ? SING C15 H15 ? ? DOUB C16 C17 ? ? SING C16 H16 ? ? SING C17 C18 ? ? SING C17 O24 ? ? DOUB C18 C19 ? ? SING C18 O23 ? ? SING C19 H19 ? ? SING O23 HO3 ? ? SING O24 HO4 ? ? SING O27 HO7 ? ? SING O29 HO9 ? ? SING O30 HO0 ? ? stop_ _Mol_thiol_state . _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 $DNA_(5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*(DN)P*(DN))-3') . . . . . . $entity_QUE . . . . . . 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*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*(DN)P*(DN))-3') 'chemical synthesis' . . . . . $entity_QUE '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*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*(DN)P*(DN))-3') 2.3 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger A. T. et.al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 400 _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 7.1 . pH pressure 1 . atm temperature 295 . 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 H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*(DN)P*(DN))-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 2 2 DG H8 H 8.057 0.005 . 2 3 3 DA H1' H 6.471 0.000 . 3 3 3 DA H8 H 7.684 0.029 . 4 4 4 DG H1 H 11.758 0.003 . 5 4 4 DG H8 H 8.014 0.042 . 6 5 5 DG H1 H 11.206 0.014 . 7 5 5 DG H1' H 5.861 0.000 . 8 5 5 DG H8 H 7.957 0.013 . 9 6 6 DG H1 H 10.920 0.019 . 10 6 6 DG H1' H 5.761 0.378 . 11 6 6 DG H8 H 7.894 0.006 . 12 7 7 DT H1' H 5.508 0.000 . 13 7 7 DT H6 H 7.915 0.005 . 14 8 8 DG H1 H 11.510 0.005 . 15 8 8 DG H1' H 6.328 0.000 . 16 8 8 DG H8 H 7.718 0.029 . 17 9 9 DG H1 H 11.529 0.032 . 18 9 9 DG H1' H 5.891 0.000 . 19 9 9 DG H8 H 7.212 0.015 . 20 10 10 DT H6 H 7.392 0.036 . 21 10 10 DT H71 H 1.837 0.000 . 22 10 10 DT H72 H 1.837 0.000 . 23 10 10 DT H73 H 1.837 0.000 . 24 11 11 DG H1' H 5.463 0.000 . 25 11 11 DG H8 H 7.502 0.006 . 26 12 12 DA H1' H 6.150 0.000 . 27 12 12 DA H8 H 7.555 0.161 . 28 13 13 DG H1 H 11.675 0.032 . 29 13 13 DG H1' H 6.549 0.008 . 30 13 13 DG H8 H 7.930 0.020 . 31 14 14 DG H1 H 11.212 0.013 . 32 14 14 DG H1' H 5.887 0.000 . 33 14 14 DG H8 H 7.760 0.033 . 34 15 15 DG H1 H 11.161 0.019 . 35 15 15 DG H1' H 5.946 0.000 . 36 15 15 DG H8 H 7.232 0.016 . 37 17 17 DG H1 H 11.133 0.009 . 38 17 17 DG H1' H 5.704 0.000 . 39 17 17 DG H8 H 7.861 0.026 . 40 18 18 DG H1 H 11.422 0.020 . 41 18 18 DG H1' H 5.955 0.000 . 42 18 18 DG H8 H 7.646 0.011 . 43 19 19 DG H1 H 10.731 0.018 . 44 19 19 DG H1' H 5.596 0.000 . 45 19 19 DG H8 H 7.464 0.021 . 46 20 20 DG H1 H 10.852 0.033 . 47 20 20 DG H1' H 5.786 0.000 . 48 20 20 DG H8 H 7.182 0.016 . 49 21 21 DA H1' H 6.381 0.000 . 50 21 21 DA H8 H 8.122 0.003 . 51 22 22 DA H1' H 6.205 0.000 . 52 22 22 DA H8 H 8.151 0.013 . 53 23 23 DG H1' H 5.712 0.000 . 54 23 23 DG H8 H 7.539 0.008 . 55 24 24 DG H1 H 11.506 0.022 . 56 24 24 DG H1' H 5.930 0.010 . 57 24 24 DG H8 H 7.561 0.019 . stop_ save_