data_17397 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of all parallel G-quadruplex formed by the oncogene RET promoter sequence ; _BMRB_accession_number 17397 _BMRB_flat_file_name bmr17397.str _Entry_type original _Submission_date 2011-01-06 _Accession_date 2011-01-06 _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 Tong Xiaotian . . 2 Cao Chunyang . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 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' 2011-05-12 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of all parallel G-quadruplex formed by the oncogene RET promoter sequence.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21540209 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tong Xiaotian . . 2 Lan Wenxian . . 3 Zhang Xu . . 4 Wu Houming . . 5 Liu Maili . . 6 Cao Chunyang . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 39 _Journal_issue 15 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6753 _Page_last 6763 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name RET_oncogene _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label RET_oncogene $RET_oncogene 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_RET_oncogene _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common RET_oncogene _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence GGGGCGGGGCGGGGCGGGGT loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DG 5 DC 6 DG 7 DG 8 DG 9 DG 10 DC 11 DG 12 DG 13 DG 14 DG 15 DC 16 DG 17 DG 18 DG 19 DG 20 DT 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 $RET_oncogene . . . . . . 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 $RET_oncogene 'chemical synthesis' . Escherichia coli . 'not applicable' 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RET_oncogene . mM 0.2 3 'natural abundance' 'potassium phosphate' . mM 0.2 0.3 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RET_oncogene . mM 0.2 3 'natural abundance' 'potassium phosphate' . mM 0.2 0.3 'natural abundance' D2O 100 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.17 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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 298 . K pH 6.8 . pH pressure 1 . atm 'ionic strength' 0.1 . 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 protons ppm 0.00 external direct . . . 1 $entry_citation $entry_citation 'phosphoric acid (85%)' P 31 phosphorus ppm 0.00 external direct . . . 1 $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_RET_chemical_shifts _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 RET_oncogene _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 11.74 . 1 2 1 1 DG H1' H 5.89 . 1 3 1 1 DG H2' H 2.43 . 1 4 1 1 DG H2'' H 2.62 . 1 5 1 1 DG H3' H 4.89 . 1 6 1 1 DG H4' H 4.36 . 1 7 1 1 DG H5' H 4.05 . 1 8 1 1 DG H5'' H 4.05 . 1 9 1 1 DG H8 H 7.31 . 1 10 1 1 DG H21 H 5.34 . 1 11 1 1 DG H22 H 8.45 . 1 12 2 2 DG H1 H 11.82 . 1 13 2 2 DG H1' H 5.78 . 1 14 2 2 DG H2' H 1.67 . 1 15 2 2 DG H2'' H 2.18 . 1 16 2 2 DG H3' H 4.79 . 1 17 2 2 DG H4' H 4.34 . 1 18 2 2 DG H5' H 3.99 . 1 19 2 2 DG H5'' H 3.99 . 1 20 2 2 DG H8 H 7.23 . 1 21 2 2 DG H21 H 6.22 . 1 22 2 2 DG H22 H 9.38 . 1 23 3 3 DG H1 H 11.09 . 1 24 3 3 DG H1' H 5.22 . 1 25 3 3 DG H2' H 2.54 . 1 26 3 3 DG H2'' H 2.29 . 1 27 3 3 DG H3' H 4.79 . 1 28 3 3 DG H4' H 4.34 . 1 29 3 3 DG H5' H 3.98 . 1 30 3 3 DG H5'' H 3.76 . 1 31 3 3 DG H8 H 7.76 . 1 32 3 3 DG H21 H 6.30 . 1 33 3 3 DG H22 H 9.22 . 1 34 4 4 DG H1' H 5.86 . 1 35 4 4 DG H2' H 2.12 . 1 36 4 4 DG H2'' H 2.31 . 1 37 4 4 DG H3' H 4.56 . 1 38 4 4 DG H4' H 3.76 . 1 39 4 4 DG H5' H 3.13 . 1 40 4 4 DG H5'' H 3.70 . 1 41 4 4 DG H8 H 7.72 . 1 42 4 4 DG H21 H 5.44 . 1 43 4 4 DG H22 H 5.44 . 1 44 5 5 DC H1' H 5.03 . 1 45 5 5 DC H2' H 2.30 . 1 46 5 5 DC H2'' H 3.00 . 1 47 5 5 DC H3' H 4.66 . 1 48 5 5 DC H4' H 4.04 . 1 49 5 5 DC H5 H 5.28 . 1 50 5 5 DC H5' H 3.92 . 1 51 5 5 DC H5'' H 3.68 . 1 52 5 5 DC H6 H 6.28 . 1 53 5 5 DC H41 H 5.84 . 1 54 5 5 DC H42 H 7.61 . 1 55 6 6 DG H1' H 6.04 . 1 56 6 6 DG H2' H 2.20 . 1 57 6 6 DG H2'' H 1.66 . 1 58 6 6 DG H3' H 4.58 . 1 59 6 6 DG H4' H 4.08 . 1 60 6 6 DG H5' H 3.89 . 1 61 6 6 DG H5'' H 3.49 . 1 62 6 6 DG H8 H 7.41 . 1 63 7 7 DG H1 H 11.85 . 1 64 7 7 DG H1' H 6.04 . 1 65 7 7 DG H2' H 3.66 . 1 66 7 7 DG H2'' H 3.00 . 1 67 7 7 DG H3' H 4.83 . 1 68 7 7 DG H4' H 4.46 . 1 69 7 7 DG H5' H 4.22 . 1 70 7 7 DG H5'' H 4.30 . 1 71 7 7 DG H8 H 7.47 . 1 72 7 7 DG H21 H 6.47 . 1 73 7 7 DG H22 H 9.40 . 1 74 8 8 DG H1 H 11.72 . 1 75 8 8 DG H1' H 6.00 . 1 76 8 8 DG H2' H 2.61 . 1 77 8 8 DG H2'' H 2.85 . 1 78 8 8 DG H3' H 5.05 . 1 79 8 8 DG H4' H 4.47 . 1 80 8 8 DG H5' H 4.39 . 1 81 8 8 DG H5'' H 4.31 . 1 82 8 8 DG H8 H 8.13 . 1 83 8 8 DG H21 H 6.65 . 1 84 8 8 DG H22 H 9.33 . 1 85 9 9 DG H1 H 10.92 . 1 86 9 9 DG H1' H 6.43 . 1 87 9 9 DG H2' H 2.74 . 1 88 9 9 DG H2'' H 2.64 . 1 89 9 9 DG H3' H 5.08 . 1 90 9 9 DG H4' H 4.64 . 1 91 9 9 DG H5' H 4.24 . 1 92 9 9 DG H5'' H 4.36 . 1 93 9 9 DG H8 H 7.69 . 1 94 9 9 DG H21 H 6.10 . 1 95 9 9 DG H22 H 9.01 . 1 96 10 10 DC H1' H 6.41 . 1 97 10 10 DC H2' H 2.28 . 1 98 10 10 DC H2'' H 2.74 . 1 99 10 10 DC H3' H 5.01 . 1 100 10 10 DC H4' H 4.78 . 1 101 10 10 DC H5 H 6.11 . 1 102 10 10 DC H5' H 4.25 . 1 103 10 10 DC H5'' H 4.31 . 1 104 10 10 DC H6 H 7.95 . 1 105 11 11 DG H1 H 11.86 . 1 106 11 11 DG H1' H 5.91 . 1 107 11 11 DG H2' H 2.56 . 1 108 11 11 DG H2'' H 2.84 . 1 109 11 11 DG H3' H 5.02 . 1 110 11 11 DG H4' H 4.51 . 1 111 11 11 DG H5' H 4.23 . 1 112 11 11 DG H5'' H 4.11 . 1 113 11 11 DG H8 H 7.24 . 1 114 11 11 DG H21 H 6.32 . 1 115 11 11 DG H22 H 9.41 . 1 116 12 12 DG H1 H 11.88 . 1 117 12 12 DG H1' H 5.66 . 1 118 12 12 DG H2' H 2.60 . 1 119 12 12 DG H2'' H 2.47 . 1 120 12 12 DG H3' H 5.00 . 1 121 12 12 DG H4' H 4.37 . 1 122 12 12 DG H5' H 4.15 . 1 123 12 12 DG H5'' H 4.08 . 1 124 12 12 DG H8 H 8.15 . 1 125 12 12 DG H21 H 6.06 . 1 126 12 12 DG H22 H 10.10 . 1 127 13 13 DG H1 H 11.43 . 1 128 13 13 DG H1' H 6.15 . 1 129 13 13 DG H2' H 2.62 . 1 130 13 13 DG H2'' H 2.83 . 1 131 13 13 DG H3' H 4.79 . 1 132 13 13 DG H4' H 4.42 . 1 133 13 13 DG H5' H 4.15 . 1 134 13 13 DG H5'' H 4.00 . 1 135 13 13 DG H8 H 7.40 . 1 136 13 13 DG H21 H 6.14 . 1 137 13 13 DG H22 H 8.42 . 1 138 14 14 DG H1' H 4.92 . 1 139 14 14 DG H2' H 1.56 . 1 140 14 14 DG H2'' H 2.11 . 1 141 14 14 DG H3' H 4.33 . 1 142 14 14 DG H4' H 4.09 . 1 143 14 14 DG H5' H 4.10 . 1 144 14 14 DG H5'' H 3.88 . 1 145 14 14 DG H8 H 7.40 . 1 146 14 14 DG H21 H 5.39 . 1 147 14 14 DG H22 H 5.39 . 1 148 15 15 DC H1' H 5.75 . 1 149 15 15 DC H2' H 1.73 . 1 150 15 15 DC H2'' H 2.00 . 1 151 15 15 DC H3' H 4.39 . 1 152 15 15 DC H4' H 3.17 . 1 153 15 15 DC H5 H 4.60 . 1 154 15 15 DC H5' H 3.02 . 1 155 15 15 DC H5'' H 2.83 . 1 156 15 15 DC H6 H 7.03 . 1 157 16 16 DG H1 H 11.23 . 1 158 16 16 DG H1' H 6.09 . 1 159 16 16 DG H2' H 2.69 . 1 160 16 16 DG H2'' H 2.90 . 1 161 16 16 DG H3' H 5.90 . 1 162 16 16 DG H4' H 4.16 . 1 163 16 16 DG H5' H 3.93 . 1 164 16 16 DG H5'' H 3.98 . 1 165 16 16 DG H8 H 7.26 . 1 166 17 17 DG H1 H 11.37 . 1 167 17 17 DG H1' H 5.96 . 1 168 17 17 DG H2' H 2.95 . 1 169 17 17 DG H2'' H 2.68 . 1 170 17 17 DG H3' H 4.90 . 1 171 17 17 DG H4' H 4.53 . 1 172 17 17 DG H5' H 4.36 . 1 173 17 17 DG H5'' H 4.05 . 1 174 17 17 DG H8 H 7.22 . 1 175 17 17 DG H21 H 6.23 . 1 176 17 17 DG H22 H 9.34 . 1 177 18 18 DG H1 H 11.74 . 1 178 18 18 DG H1' H 6.03 . 1 179 18 18 DG H2' H 3.06 . 1 180 18 18 DG H2'' H 2.51 . 1 181 18 18 DG H3' H 4.80 . 1 182 18 18 DG H4' H 4.54 . 1 183 18 18 DG H5' H 4.29 . 1 184 18 18 DG H5'' H 4.04 . 1 185 18 18 DG H8 H 7.69 . 1 186 18 18 DG H21 H 6.11 . 1 187 18 18 DG H22 H 9.98 . 1 188 19 19 DG H1 H 11.48 . 1 189 19 19 DG H1' H 6.32 . 1 190 19 19 DG H2' H 2.55 . 1 191 19 19 DG H2'' H 2.66 . 1 192 19 19 DG H3' H 4.87 . 1 193 19 19 DG H4' H 4.52 . 1 194 19 19 DG H5' H 4.25 . 1 195 19 19 DG H5'' H 4.25 . 1 196 19 19 DG H8 H 7.88 . 1 197 19 19 DG H21 H 6.30 . 1 198 19 19 DG H22 H 8.48 . 1 199 20 20 DT H1' H 6.13 . 1 200 20 20 DT H2' H 2.17 . 1 201 20 20 DT H2'' H 2.17 . 1 202 20 20 DT H3' H 4.44 . 1 203 20 20 DT H4' H 4.07 . 1 204 20 20 DT H5' H 4.14 . 1 205 20 20 DT H5'' H 4.14 . 1 206 20 20 DT H6 H 7.30 . 1 207 20 20 DT H71 H 1.28 . 1 208 20 20 DT H72 H 1.28 . 1 209 20 20 DT H73 H 1.28 . 1 stop_ save_