data_16356 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution ; _BMRB_accession_number 16356 _BMRB_flat_file_name bmr16356.str _Entry_type original _Submission_date 2009-06-16 _Accession_date 2009-06-16 _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 Zhang Zhengjiang . . 2 Dai Jixun . . 3 Yang Danzhou . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 210 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2010-05-28 update BMRB 'edit entity name' 2010-02-10 update BMRB 'completed entry citation' 2009-12-11 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution: insights into the interconversion of human telomeric G-quadruplex structures.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19946019 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhang Zhenjiang . . 2 Dai Jixun . . 3 Veliath Elizabeth . . 4 Jones Roger A. . 5 Yang Danzhou . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 38 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1009 _Page_last 1021 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*(INO)P*GP*GP*TP*TP*AP*GP*GP*GP*T)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA(5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*(INO)P*GP*GP*TP*TP*AP*GP*GP*GP*T)-3') $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA(5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*(INO)P*GP*GP*TP*TP*AP*GP*GP*GP*T)-3') _Molecular_mass 7095.636 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 23 _Mol_residue_sequence ; AGGGTTAGGGTTAXGGTTAG GGT ; loop_ _Residue_seq_code _Residue_label 1 DA 2 DG 3 DG 4 DG 5 DT 6 DT 7 DA 8 DG 9 DG 10 DG 11 DT 12 DT 13 DA 14 INO 15 DG 16 DG 17 DT 18 DT 19 DA 20 DG 21 DG 22 DG 23 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_INO _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common '2-HYDROXYISONICOTINIC ACID N-OXIDE' _BMRB_code . _PDB_code INO _Standard_residue_derivative . _Molecular_mass 155.108 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Nov 18 19:33:54 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N . 1 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . -1 . ? H3 H3 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? HO2 HO2 H . 0 . ? HO3 HO3 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 N1 C2 ? ? DOUB N1 C6 ? ? SING N1 O4 ? ? DOUB C2 C3 ? ? SING C2 O3 ? ? SING C3 C4 ? ? SING C3 H3 ? ? DOUB C4 C5 ? ? SING C4 C7 ? ? SING C5 C6 ? ? SING C5 H5 ? ? SING C6 H6 ? ? DOUB C7 O1 ? ? SING C7 O2 ? ? SING O2 HO2 ? ? SING O3 HO3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity 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 $entity '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 $entity 1 mM 'natural abundance' 'potassium chloride' 60 mM 'natural abundance' 'potassium phosphate' 30 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 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_ ####################### # 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 7 . pH pressure 1 . atm 'ionic strength' 90 . 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 0.00 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(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*(INO)P*GP*GP*TP*TP*AP*GP*GP*GP*T)-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 DA H1' H 5.488 . . 2 1 1 DA H2 H 8.159 . 1 3 1 1 DA H2' H 1.901 . . 4 1 1 DA H2'' H 2.702 . . 5 1 1 DA H3' H 4.526 . . 6 1 1 DA H4' H 3.968 . . 7 1 1 DA H5' H 3.924 . . 8 1 1 DA H5'' H 3.784 . . 9 1 1 DA H8 H 7.969 . 1 10 2 2 DG H1' H 5.360 . . 11 2 2 DG H2' H 2.928 . . 12 2 2 DG H2'' H 2.705 . . 13 2 2 DG H3' H 4.802 . . 14 2 2 DG H4' H 4.360 . . 15 2 2 DG H5' H 4.289 . . 16 2 2 DG H5'' H 4.289 . . 17 2 2 DG H8 H 6.796 . 1 18 3 3 DG H1' H 5.760 . . 19 3 3 DG H2' H 2.114 . . 20 3 3 DG H2'' H 2.339 . . 21 3 3 DG H3' H 4.909 . . 22 3 3 DG H4' H 4.384 . . 23 3 3 DG H5' H 4.161 . . 24 3 3 DG H5'' H 3.937 . . 25 3 3 DG H8 H 7.625 . 1 26 4 4 DG H1' H 5.802 . . 27 4 4 DG H2' H 2.417 . . 28 4 4 DG H2'' H 2.763 . . 29 4 4 DG H3' H 4.942 . . 30 4 4 DG H4' H 4.608 . . 31 4 4 DG H5' H 4.234 . . 32 4 4 DG H5'' H 4.155 . . 33 4 4 DG H8 H 7.970 . 1 34 5 5 DT H1' H 5.794 . . 35 5 5 DT H2' H 1.666 . . 36 5 5 DT H2'' H 1.406 . . 37 5 5 DT H3' H 4.368 . . 38 5 5 DT H4' H 3.782 . . 39 5 5 DT H5' H 3.825 . . 40 5 5 DT H5'' H 3.544 . . 41 5 5 DT H6 H 7.443 . 1 42 5 5 DT H71 H 1.773 . . 43 5 5 DT H72 H 1.773 . . 44 5 5 DT H73 H 1.773 . . 45 6 6 DT H1' H 5.378 . . 46 6 6 DT H2' H 1.636 . . 47 6 6 DT H2'' H 1.957 . . 48 6 6 DT H3' H 4.360 . . 49 6 6 DT H4' H 3.719 . . 50 6 6 DT H5' H 3.296 . . 51 6 6 DT H5'' H 2.966 . . 52 6 6 DT H6 H 6.985 . 1 53 6 6 DT H71 H 1.188 . . 54 6 6 DT H72 H 1.188 . . 55 6 6 DT H73 H 1.188 . . 56 7 7 DA H1' H 6.114 . . 57 7 7 DA H2 H 7.834 . 1 58 7 7 DA H2' H 2.108 . . 59 7 7 DA H2'' H 3.056 . . 60 7 7 DA H3' H 4.642 . . 61 7 7 DA H4' H 4.183 . . 62 7 7 DA H5' H 3.801 . . 63 7 7 DA H5'' H 3.653 . . 64 7 7 DA H8 H 8.022 . 1 65 8 8 DG H1' H 5.540 . . 66 8 8 DG H2' H 2.988 . . 67 8 8 DG H2'' H 2.709 . . 68 8 8 DG H3' H 4.797 . . 69 8 8 DG H4' H 4.255 . . 70 8 8 DG H5' H 4.210 . . 71 8 8 DG H5'' H 4.154 . . 72 8 8 DG H8 H 6.588 . 1 73 9 9 DG H1' H 5.576 . . 74 9 9 DG H2' H 2.492 . . 75 9 9 DG H2'' H 2.452 . . 76 9 9 DG H3' H 4.937 . . 77 9 9 DG H4' H 4.300 . . 78 9 9 DG H5' H 4.139 . . 79 9 9 DG H5'' H 4.099 . . 80 9 9 DG H8 H 7.940 . 1 81 10 10 DG H1' H 6.031 . . 82 10 10 DG H2' H 2.523 . . 83 10 10 DG H2'' H 2.523 . . 84 10 10 DG H3' H 4.956 . . 85 10 10 DG H4' H 4.445 . . 86 10 10 DG H5' H 4.167 . . 87 10 10 DG H5'' H 4.167 . . 88 10 10 DG H8 H 7.655 . 1 89 11 11 DT H1' H 5.955 . . 90 11 11 DT H2' H 2.086 . . 91 11 11 DT H2'' H 2.445 . . 92 11 11 DT H3' H 4.596 . . 93 11 11 DT H4' H 4.182 . . 94 11 11 DT H5' H 4.010 . . 95 11 11 DT H5'' H 3.938 . . 96 11 11 DT H6 H 7.507 . 1 97 11 11 DT H71 H 1.832 . . 98 11 11 DT H72 H 1.832 . . 99 11 11 DT H73 H 1.832 . . 100 12 12 DT H1' H 5.171 . . 101 12 12 DT H2' H 0.908 . . 102 12 12 DT H2'' H 1.496 . . 103 12 12 DT H3' H 4.331 . . 104 12 12 DT H4' H 3.738 . . 105 12 12 DT H5' H 3.877 . . 106 12 12 DT H5'' H 3.839 . . 107 12 12 DT H6 H 7.041 . 1 108 12 12 DT H71 H 1.270 . . 109 12 12 DT H72 H 1.270 . . 110 12 12 DT H73 H 1.270 . . 111 13 13 DA H1' H 5.847 . . 112 13 13 DA H2 H 7.403 . 1 113 13 13 DA H2' H 2.433 . . 114 13 13 DA H2'' H 2.113 . . 115 13 13 DA H3' H 4.507 . . 116 13 13 DA H4' H 3.668 . . 117 13 13 DA H5' H 3.151 . . 118 13 13 DA H5'' H 3.151 . . 119 13 13 DA H8 H 7.883 . 1 120 14 14 INO H1' H 6.358 . . 121 14 14 INO H2 H 8.024 . . 122 14 14 INO H2' H 2.811 . . 123 14 14 INO H2'' H 2.766 . . 124 14 14 INO H3' H 4.733 . . 125 14 14 INO H4' H 4.234 . . 126 14 14 INO H5' H 4.359 . . 127 14 14 INO H5'' H 3.888 . . 128 14 14 INO H8 H 8.492 . . 129 15 15 DG H1' H 5.699 . . 130 15 15 DG H2' H 3.018 . . 131 15 15 DG H2'' H 2.658 . . 132 15 15 DG H3' H 4.734 . . 133 15 15 DG H4' H 4.488 . . 134 15 15 DG H5' H 4.367 . . 135 15 15 DG H5'' H 4.125 . . 136 15 15 DG H8 H 7.004 . 1 137 16 16 DG H1' H 5.753 . . 138 16 16 DG H2' H 2.478 . . 139 16 16 DG H2'' H 2.478 . . 140 16 16 DG H3' H 5.078 . . 141 16 16 DG H4' H 4.240 . . 142 16 16 DG H5' H 4.150 . . 143 16 16 DG H5'' H 4.102 . . 144 16 16 DG H8 H 7.191 . 1 145 17 17 DT H1' H 6.284 . . 146 17 17 DT H2' H 2.274 . . 147 17 17 DT H2'' H 2.371 . . 148 17 17 DT H3' H 4.886 . . 149 17 17 DT H4' H 4.429 . . 150 17 17 DT H5' H 4.264 . . 151 17 17 DT H5'' H 4.098 . . 152 17 17 DT H6 H 7.855 . 1 153 17 17 DT H71 H 1.953 . . 154 17 17 DT H72 H 1.953 . . 155 17 17 DT H73 H 1.953 . . 156 18 18 DT H1' H 5.795 . . 157 18 18 DT H2' H 1.439 . . 158 18 18 DT H2'' H 1.984 . . 159 18 18 DT H3' H 4.736 . . 160 18 18 DT H4' H 4.172 . . 161 18 18 DT H5' H 3.937 . . 162 18 18 DT H5'' H 3.786 . . 163 18 18 DT H6 H 7.415 . 1 164 18 18 DT H71 H 1.610 . . 165 18 18 DT H72 H 1.610 . . 166 18 18 DT H73 H 1.610 . . 167 19 19 DA H1' H 6.120 . . 168 19 19 DA H2 H 8.186 . 1 169 19 19 DA H2' H 2.770 . . 170 19 19 DA H2'' H 2.681 . . 171 19 19 DA H3' H 4.946 . . 172 19 19 DA H4' H 4.299 . . 173 19 19 DA H5' H 3.963 . . 174 19 19 DA H5'' H 3.785 . . 175 19 19 DA H8 H 8.141 . 1 176 20 20 DG H1' H 5.998 . . 177 20 20 DG H2' H 3.360 . . 178 20 20 DG H2'' H 2.871 . . 179 20 20 DG H3' H 4.893 . . 180 20 20 DG H4' H 4.383 . . 181 20 20 DG H5' H 4.316 . . 182 20 20 DG H5'' H 4.162 . . 183 20 20 DG H8 H 7.334 . 1 184 21 21 DG H1' H 5.883 . . 185 21 21 DG H2' H 2.644 . . 186 21 21 DG H2'' H 2.644 . . 187 21 21 DG H3' H 4.984 . . 188 21 21 DG H4' H 4.385 . . 189 21 21 DG H5' H 4.226 . . 190 21 21 DG H5'' H 4.152 . . 191 21 21 DG H8 H 8.147 . 1 192 22 22 DG H1' H 6.119 . . 193 22 22 DG H2' H 2.342 . . 194 22 22 DG H2'' H 2.552 . . 195 22 22 DG H3' H 4.905 . . 196 22 22 DG H4' H 4.380 . . 197 22 22 DG H5' H 4.234 . . 198 22 22 DG H5'' H 4.205 . . 199 22 22 DG H8 H 7.496 . 1 200 23 23 DT H1' H 6.197 . . 201 23 23 DT H2' H 2.245 . . 202 23 23 DT H2'' H 2.183 . . 203 23 23 DT H3' H 4.445 . . 204 23 23 DT H4' H 4.005 . . 205 23 23 DT H5' H 4.096 . . 206 23 23 DT H5'' H 3.991 . . 207 23 23 DT H6 H 7.383 . 1 208 23 23 DT H71 H 1.304 . . 209 23 23 DT H72 H 1.304 . . 210 23 23 DT H73 H 1.304 . . stop_ save_