data_17379 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; QUI/G-quadruplex complex ; _BMRB_accession_number 17379 _BMRB_flat_file_name bmr17379.str _Entry_type original _Submission_date 2010-12-23 _Accession_date 2010-12-23 _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 Dai Jixun . . 2 Carver Megan . . 3 Mathad Ravi . . 4 Yang Danzhou . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 209 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-03-09 update BMRB 'update entry citation' 2011-10-12 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of a 2:1 quindoline-c-MYC G-quadruplex: insights into G-quadruplex-interactive small molecule drug design.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21967482 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dai Jixun . . 2 Carver Megan . . 3 Hurley Laurence H. . 4 Yang Danzhou . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 133 _Journal_issue 44 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 17673 _Page_last 17680 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name '5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3', 2-CARBOXYQUINOXALINE' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_(5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3') $DNA_(5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3') 2-CARBOXYQUINOXALINE_1 $QUI 2-CARBOXYQUINOXALINE_2 $QUI 'POTASSIUM ION_1' $K 'POTASSIUM ION_2' $K 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*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-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*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3')_ _Molecular_mass 7008.566 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; TGAGGGTGGGTAGGGTGGGT AA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 4 DT 2 5 DG 3 6 DA 4 7 DG 5 8 DG 6 9 DG 7 10 DT 8 11 DG 9 12 DG 10 13 DG 11 14 DT 12 15 DA 13 16 DG 14 17 DG 15 18 DG 16 19 DT 17 20 DG 18 21 DG 19 22 DG 20 23 DT 21 24 DA 22 25 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_QUI _Saveframe_category ligand _Mol_type non-polymer _Name_common "QUI (2-CARBOXYQUINOXALINE)" _BMRB_code . _PDB_code QUI _Molecular_mass 174.156 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Dec 9 11:04:28 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? N4 N4 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? C9 C9 C . 0 . ? C10 C10 C . 0 . ? C C C . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? H3 H3 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? HO2 HO2 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 N1 C2 ? ? SING N1 C9 ? ? SING C2 C3 ? ? SING C2 C ? ? DOUB C3 N4 ? ? SING C3 H3 ? ? SING N4 C10 ? ? DOUB C5 C6 ? ? SING C5 C10 ? ? SING C5 H5 ? ? SING C6 C7 ? ? SING C6 H6 ? ? DOUB C7 C8 ? ? SING C7 H7 ? ? SING C8 C9 ? ? SING C8 H8 ? ? DOUB C9 C10 ? ? DOUB C O1 ? ? SING C O2 ? ? SING O2 HO2 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ save_K _Saveframe_category ligand _Mol_type non-polymer _Name_common "K (POTASSIUM ION)" _BMRB_code . _PDB_code K _Molecular_mass 39.098 _Mol_charge 1 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Dec 9 11:05:05 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons K K K . 1 . ? 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*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3') human 9606 Eukaryota Metazoa Homo sapiens 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*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3') 'chemical synthesis' . . . . . $QUI '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*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3') 1 mM 'natural abundance' $QUI 2 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' DSS 0.1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_InsightII _Saveframe_category software _Name InsightII _Version 2003 loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _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_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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_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 308 . K pH 6 . pH pressure 1 . atm 'ionic strength' 0.01 . M 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 $entry_citation $entry_citation 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_2 _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 2-CARBOXYQUINOXALINE_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 0 1 QUI H1' H 4.093 . 2 2 0 1 QUI H10 H 6.703 . 2 3 0 1 QUI H11 H 7.590 . 2 4 0 1 QUI H2 H 7.276 . 2 5 0 1 QUI H2' H 3.462 . 2 6 0 1 QUI H3 H 7.217 . 2 7 0 1 QUI H4 H 6.948 . 2 8 0 1 QUI H4' H 3.244 . 2 9 0 1 QUI H5 H 7.599 . 2 10 0 1 QUI H5' H 1.236 . 2 11 0 1 QUI H8 H 7.000 . 2 12 0 1 QUI H9 H 7.053 . 2 stop_ save_ save_assigned_chem_shift_list_1_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*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-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 4 1 DT H1' H 5.643 . 2 2 4 1 DT H2' H 1.325 . 2 3 4 1 DT H2'' H 1.800 . 2 4 4 1 DT H3' H 4.293 . 2 5 4 1 DT H4' H 3.672 . 2 6 4 1 DT H5'' H 3.340 . 2 7 4 1 DT H6 H 7.061 . 1 8 5 2 DG H1' H 5.263 . 2 9 5 2 DG H2' H 2.033 . 2 10 5 2 DG H2'' H 1.866 . 2 11 5 2 DG H3' H 4.536 . 2 12 5 2 DG H4' H 3.924 . 2 13 5 2 DG H5' H 3.567 . 2 14 5 2 DG H5'' H 3.651 . 2 15 5 2 DG H8 H 7.056 . 1 16 6 3 DA H1' H 6.301 . 2 17 6 3 DA H2 H 8.059 . 1 18 6 3 DA H2' H 2.685 . 2 19 6 3 DA H2'' H 2.784 . 2 20 6 3 DA H3' H 4.961 . 2 21 6 3 DA H4' H 4.234 . 2 22 6 3 DA H5' H 3.873 . 2 23 6 3 DA H5'' H 3.933 . 2 24 6 3 DA H8 H 8.144 . 1 25 7 4 DG H1 H 11.411 . 1 26 7 4 DG H1' H 6.050 . 2 27 7 4 DG H2' H 2.751 . 2 28 7 4 DG H2'' H 2.992 . 2 29 7 4 DG H3' H 4.998 . 2 30 7 4 DG H4' H 4.497 . 2 31 7 4 DG H5' H 4.169 . 2 32 7 4 DG H5'' H 4.228 . 2 33 7 4 DG H8 H 8.070 . 1 34 8 5 DG H1 H 10.894 . 1 35 8 5 DG H1' H 6.086 . 2 36 8 5 DG H2' H 2.617 . 2 37 8 5 DG H2'' H 2.906 . 2 38 8 5 DG H3' H 5.010 . 2 39 8 5 DG H4' H 4.513 . 2 40 8 5 DG H5' H 4.310 . 2 41 8 5 DG H5'' H 4.290 . 2 42 8 5 DG H8 H 7.657 . 1 43 9 6 DG H1 H 10.509 . 1 44 9 6 DG H1' H 6.309 . 2 45 9 6 DG H2' H 2.773 . 2 46 9 6 DG H2'' H 2.688 . 2 47 9 6 DG H3' H 5.169 . 2 48 9 6 DG H4' H 4.596 . 2 49 9 6 DG H5' H 4.310 . 2 50 9 6 DG H5'' H 4.361 . 2 51 9 6 DG H8 H 7.643 . 1 52 10 7 DT H1' H 6.513 . 2 53 10 7 DT H2' H 2.470 . 2 54 10 7 DT H2'' H 2.669 . 2 55 10 7 DT H3' H 5.099 . 2 56 10 7 DT H4' H 4.585 . 2 57 10 7 DT H5' H 4.277 . 2 58 10 7 DT H5'' H 4.345 . 2 59 10 7 DT H6 H 7.870 . 1 60 10 7 DT H71 H 2.002 . 2 61 10 7 DT H72 H 2.002 . 2 62 10 7 DT H73 H 2.002 . 2 63 11 8 DG H1 H 11.021 . 1 64 11 8 DG H1' H 6.020 . 2 65 11 8 DG H2' H 2.378 . 2 66 11 8 DG H2'' H 2.835 . 2 67 11 8 DG H3' H 5.060 . 2 68 11 8 DG H4' H 4.470 . 2 69 11 8 DG H5'' H 4.310 . 2 70 11 8 DG H8 H 7.864 . 1 71 12 9 DG H1 H 11.082 . 1 72 12 9 DG H1' H 6.004 . 2 73 12 9 DG H2' H 2.562 . 2 74 12 9 DG H2'' H 2.772 . 2 75 12 9 DG H3' H 5.015 . 2 76 12 9 DG H4' H 4.427 . 2 77 12 9 DG H5' H 4.186 . 2 78 12 9 DG H5'' H 4.243 . 2 79 12 9 DG H8 H 7.722 . 1 80 13 10 DG H1 H 10.878 . 1 81 13 10 DG H1' H 6.325 . 2 82 13 10 DG H2' H 2.754 . 2 83 13 10 DG H2'' H 2.684 . 2 84 13 10 DG H3' H 5.075 . 2 85 13 10 DG H4' H 4.470 . 2 86 13 10 DG H5'' H 4.265 . 2 87 13 10 DG H8 H 7.684 . 1 88 14 11 DT H1' H 6.255 . 2 89 14 11 DT H2' H 2.243 . 2 90 14 11 DT H2'' H 2.482 . 2 91 14 11 DT H4' H 3.960 . 2 92 14 11 DT H5'' H 3.821 . 2 93 14 11 DT H6 H 7.674 . 1 94 14 11 DT H71 H 1.954 . 2 95 14 11 DT H72 H 1.954 . 2 96 14 11 DT H73 H 1.954 . 2 97 15 12 DA H1' H 6.665 . 2 98 15 12 DA H2 H 8.361 . 1 99 15 12 DA H2' H 3.069 . 2 100 15 12 DA H2'' H 2.950 . 2 101 15 12 DA H3' H 5.193 . 2 102 15 12 DA H4' H 4.592 . 2 103 15 12 DA H5' H 4.199 . 2 104 15 12 DA H5'' H 4.291 . 2 105 15 12 DA H8 H 8.552 . 1 106 16 13 DG H1 H 11.080 . 1 107 16 13 DG H1' H 6.076 . 2 108 16 13 DG H2' H 2.552 . 2 109 16 13 DG H2'' H 2.900 . 2 110 16 13 DG H3' H 5.013 . 2 111 16 13 DG H4' H 4.513 . 2 112 16 13 DG H5' H 4.229 . 2 113 16 13 DG H5'' H 4.294 . 2 114 16 13 DG H8 H 7.973 . 1 115 17 14 DG H1 H 10.902 . 1 116 17 14 DG H1' H 6.097 . 2 117 17 14 DG H2' H 2.598 . 2 118 17 14 DG H2'' H 2.918 . 2 119 17 14 DG H3' H 4.987 . 2 120 17 14 DG H4' H 4.526 . 2 121 17 14 DG H5' H 4.199 . 2 122 17 14 DG H5'' H 4.251 . 2 123 17 14 DG H8 H 7.609 . 1 124 18 15 DG H1 H 10.562 . 1 125 18 15 DG H1' H 6.357 . 2 126 18 15 DG H2' H 2.759 . 2 127 18 15 DG H2'' H 2.691 . 2 128 18 15 DG H3' H 5.165 . 2 129 18 15 DG H4' H 4.598 . 2 130 18 15 DG H5'' H 4.345 . 2 131 18 15 DG H8 H 7.705 . 1 132 19 16 DT H1' H 6.523 . 2 133 19 16 DT H2' H 2.483 . 2 134 19 16 DT H2'' H 2.683 . 2 135 19 16 DT H3' H 5.112 . 2 136 19 16 DT H4' H 4.598 . 2 137 19 16 DT H5' H 4.281 . 2 138 19 16 DT H5'' H 4.351 . 2 139 19 16 DT H6 H 7.880 . 1 140 19 16 DT H71 H 2.007 . 2 141 19 16 DT H72 H 2.007 . 2 142 19 16 DT H73 H 2.007 . 2 143 20 17 DG H1 H 11.092 . 1 144 20 17 DG H1' H 6.002 . 2 145 20 17 DG H2' H 2.342 . 2 146 20 17 DG H2'' H 2.790 . 2 147 20 17 DG H3' H 5.074 . 2 148 20 17 DG H4' H 4.484 . 2 149 20 17 DG H5' H 4.285 . 2 150 20 17 DG H5'' H 4.332 . 2 151 20 17 DG H8 H 7.829 . 1 152 21 18 DG H1 H 11.132 . 1 153 21 18 DG H1' H 5.984 . 2 154 21 18 DG H2' H 2.645 . 2 155 21 18 DG H2'' H 2.715 . 2 156 21 18 DG H3' H 5.059 . 2 157 21 18 DG H4' H 4.520 . 2 158 21 18 DG H5' H 4.205 . 2 159 21 18 DG H5'' H 4.275 . 2 160 21 18 DG H8 H 7.794 . 1 161 22 19 DG H1 H 10.669 . 1 162 22 19 DG H1' H 6.219 . 2 163 22 19 DG H2' H 2.658 . 2 164 22 19 DG H2'' H 2.730 . 2 165 22 19 DG H3' H 5.086 . 2 166 22 19 DG H4' H 4.543 . 2 167 22 19 DG H5' H 4.266 . 2 168 22 19 DG H5'' H 4.321 . 2 169 22 19 DG H8 H 7.597 . 1 170 23 20 DT H1' H 6.012 . 2 171 23 20 DT H2' H 2.002 . 2 172 23 20 DT H2'' H 2.324 . 2 173 23 20 DT H3' H 4.809 . 2 174 23 20 DT H4' H 4.276 . 2 175 23 20 DT H5' H 4.117 . 2 176 23 20 DT H5'' H 4.240 . 2 177 23 20 DT H6 H 7.520 . 1 178 23 20 DT H71 H 1.854 . 2 179 23 20 DT H72 H 1.854 . 2 180 23 20 DT H73 H 1.854 . 2 181 24 21 DA H1' H 5.519 . 2 182 24 21 DA H2 H 7.428 . 2 183 24 21 DA H2' H 2.039 . 2 184 24 21 DA H2'' H 2.203 . 2 185 24 21 DA H3' H 4.559 . 2 186 24 21 DA H4' H 3.810 . 2 187 24 21 DA H5'' H 3.818 . 2 188 24 21 DA H8 H 7.792 . 1 189 25 22 DA H1' H 5.776 . 2 190 25 22 DA H2 H 7.584 . 2 191 25 22 DA H2' H 2.270 . 2 192 25 22 DA H2'' H 2.173 . 2 193 25 22 DA H3' H 4.390 . 2 194 25 22 DA H4' H 3.852 . 2 195 25 22 DA H5' H 3.686 . 2 196 25 22 DA H5'' H 3.766 . 2 197 25 22 DA H8 H 7.778 . 1 stop_ save_