data_19276 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of d[CGCGAAGCATTCGCG] hairpin ; _BMRB_accession_number 19276 _BMRB_flat_file_name bmr19276.str _Entry_type original _Submission_date 2013-05-30 _Accession_date 2013-05-30 _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 Lim 'Kah Wai' . . 2 Phan 'Anh Tuan' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 139 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-10-09 update BMRB 'update entry citation' 2013-07-08 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 19277 'd[GGTTGGCGCGAAGCATTCGCGGGTTGG] duplex-quadruplex hybrid' 19278 'd[GCGCGAAGCATTCGCGGGGAGGTGGGGAAGGG] duplex-quadruplex hybrid' 19279 'd[GGGAAGGGCGCGAAGCATTCGCGAGGTAGG] duplex-quadruplex hybrid' 19280 'd[AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG] duplex-quadruplex hybrid' 19281 'd[TTGGGTGGGCGCGAAGCATTCGCGGGGTGGGT] duplex-quadruplex hybrid' stop_ save_ ############################# # Citation for this entry # ############################# save_Citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural basis of DNA quadruplex-duplex junction formation.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23794476 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lim 'Kah Wai' . . 2 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation 'Angew. Chem. Int. Ed. Engl.' _Journal_name_full 'Angewandte Chemie (International ed. in English)' _Journal_volume 52 _Journal_issue 33 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8566 _Page_last 8569 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'd[CGCGAAGCATTCGCG] hairpin' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3')' $DNA 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-3') _Molecular_mass 4595.023 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence CGCGAAGCATTCGCG loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DG 5 DA 6 DA 7 DG 8 DC 9 DA 10 DT 11 DT 12 DC 13 DG 14 DC 15 DG 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 $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 $DNA 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_DNA-1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA 0.5-2.0 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_DNA-2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA 0.5-2.0 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_DNA-3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA 0.5-2.0 mM '[U-2% 15N]' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_DNA-4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA 0.5-2.0 mM '[U-100% 2H]' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version 2007 loop_ _Vendor _Address _Electronic_address 'Felix NMR, Inc.' . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.29 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 Avance _Field_strength 400 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $DNA-2 save_ save_2D_1H-1H_JR_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H JR NOESY' _Sample_label $DNA-1 save_ save_2D_1H-1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $DNA-2 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $DNA-2 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $DNA-2 save_ save_2D_1H-13C_JR_HMBC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C JR HMBC' _Sample_label $DNA-1 save_ save_2D_1H-31P_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HSQC' _Sample_label $DNA-2 save_ save_H-D_EXCHANGE_8 _Saveframe_category NMR_applied_experiment _Experiment_name 'H-D EXCHANGE' _Sample_label $DNA-2 save_ save_15N-FILTERED_9 _Saveframe_category NMR_applied_experiment _Experiment_name 15N-FILTERED _Sample_label $DNA-3 save_ save_D-LABELED_10 _Saveframe_category NMR_applied_experiment _Experiment_name D-LABELED _Sample_label $DNA-4 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' 40 . mM stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 278 . K pH 7 . pH pressure 1 . atm 'ionic strength' 40 . 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' 15N-FILTERED D-LABELED stop_ loop_ _Sample_label $DNA-2 $DNA-3 $DNA-4 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (5'-D(*CP*GP*CP*GP*AP*AP*GP*CP*AP*TP*TP*CP*GP*CP*G)-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 DC H1' H 5.767 0.010 1 2 1 1 DC H2' H 1.986 0.010 1 3 1 1 DC H2'' H 2.421 0.010 1 4 1 1 DC H3' H 4.709 0.010 1 5 1 1 DC H4' H 4.067 0.010 1 6 1 1 DC H5 H 5.922 0.010 1 7 1 1 DC H5' H 3.723 0.010 2 8 1 1 DC H5'' H 3.723 0.010 2 9 1 1 DC H6 H 7.646 0.010 1 10 2 2 DG H1 H 13.093 0.010 1 11 2 2 DG H1' H 5.907 0.010 1 12 2 2 DG H2' H 2.674 0.010 1 13 2 2 DG H2'' H 2.740 0.010 1 14 2 2 DG H3' H 4.976 0.010 1 15 2 2 DG H4' H 4.350 0.010 1 16 2 2 DG H5' H 4.088 0.010 2 17 2 2 DG H5'' H 3.987 0.010 2 18 2 2 DG H8 H 7.968 0.010 1 19 3 3 DC H1' H 5.664 0.010 1 20 3 3 DC H2' H 1.938 0.010 1 21 3 3 DC H2'' H 2.345 0.010 1 22 3 3 DC H3' H 4.836 0.010 1 23 3 3 DC H4' H 4.164 0.010 1 24 3 3 DC H5 H 5.400 0.010 1 25 3 3 DC H5' H 4.182 0.010 2 26 3 3 DC H5'' H 4.128 0.010 2 27 3 3 DC H6 H 7.314 0.010 1 28 4 4 DG H1 H 12.853 0.010 1 29 4 4 DG H1' H 5.450 0.010 1 30 4 4 DG H2' H 2.646 0.010 1 31 4 4 DG H2'' H 2.729 0.010 1 32 4 4 DG H3' H 4.986 0.010 1 33 4 4 DG H4' H 4.303 0.010 1 34 4 4 DG H5' H 4.094 0.010 2 35 4 4 DG H5'' H 3.996 0.010 2 36 4 4 DG H8 H 7.879 0.010 1 37 5 5 DA H1' H 5.931 0.010 1 38 5 5 DA H2 H 7.623 0.010 1 39 5 5 DA H2' H 2.337 0.010 1 40 5 5 DA H2'' H 2.646 0.010 1 41 5 5 DA H3' H 4.989 0.010 1 42 5 5 DA H4' H 4.335 0.010 1 43 5 5 DA H5' H 4.152 0.010 2 44 5 5 DA H5'' H 4.122 0.010 2 45 5 5 DA H8 H 7.935 0.010 1 46 6 6 DA H1' H 5.905 0.010 1 47 6 6 DA H2 H 7.729 0.010 1 48 6 6 DA H2' H 2.081 0.010 1 49 6 6 DA H2'' H 2.442 0.010 1 50 6 6 DA H3' H 4.901 0.010 1 51 6 6 DA H4' H 4.379 0.010 1 52 6 6 DA H5' H 4.119 0.010 2 53 6 6 DA H5'' H 4.119 0.010 2 54 6 6 DA H8 H 7.477 0.010 1 55 7 7 DG H1' H 5.396 0.010 1 56 7 7 DG H2' H 2.646 0.010 1 57 7 7 DG H2'' H 2.358 0.010 1 58 7 7 DG H3' H 4.824 0.010 1 59 7 7 DG H4' H 4.390 0.010 1 60 7 7 DG H5' H 4.105 0.010 2 61 7 7 DG H5'' H 4.063 0.010 2 62 7 7 DG H8 H 8.056 0.010 1 63 8 8 DC H1' H 5.711 0.010 1 64 8 8 DC H2' H 1.603 0.010 1 65 8 8 DC H2'' H 2.052 0.010 1 66 8 8 DC H3' H 4.422 0.010 1 67 8 8 DC H4' H 2.112 0.010 1 68 8 8 DC H5 H 5.223 0.010 1 69 8 8 DC H5' H 3.372 0.010 2 70 8 8 DC H5'' H 3.062 0.010 2 71 8 8 DC H6 H 7.209 0.010 1 72 9 9 DA H1' H 6.327 0.010 1 73 9 9 DA H2 H 8.048 0.010 1 74 9 9 DA H2' H 3.007 0.010 1 75 9 9 DA H2'' H 2.960 0.010 1 76 9 9 DA H3' H 4.822 0.010 1 77 9 9 DA H4' H 4.344 0.010 1 78 9 9 DA H5' H 3.984 0.010 2 79 9 9 DA H5'' H 3.844 0.010 2 80 9 9 DA H8 H 8.098 0.010 1 81 10 10 DT H1' H 5.698 0.010 1 82 10 10 DT H2' H 2.131 0.010 1 83 10 10 DT H2'' H 2.520 0.010 1 84 10 10 DT H3 H 13.356 0.010 1 85 10 10 DT H3' H 4.764 0.010 1 86 10 10 DT H4' H 4.304 0.010 1 87 10 10 DT H5' H 4.346 0.010 2 88 10 10 DT H5'' H 4.101 0.010 2 89 10 10 DT H6 H 7.422 0.010 1 90 10 10 DT H71 H 1.844 0.010 2 91 10 10 DT H72 H 1.844 0.010 2 92 10 10 DT H73 H 1.844 0.010 2 93 11 11 DT H1' H 6.091 0.010 1 94 11 11 DT H2' H 2.235 0.010 1 95 11 11 DT H2'' H 2.526 0.010 1 96 11 11 DT H3 H 13.952 0.010 1 97 11 11 DT H3' H 4.896 0.010 1 98 11 11 DT H4' H 4.252 0.010 1 99 11 11 DT H5' H 4.135 0.010 2 100 11 11 DT H5'' H 4.135 0.010 2 101 11 11 DT H6 H 7.458 0.010 1 102 11 11 DT H71 H 1.649 0.010 2 103 11 11 DT H72 H 1.649 0.010 2 104 11 11 DT H73 H 1.649 0.010 2 105 12 12 DC H1' H 5.666 0.010 1 106 12 12 DC H2' H 2.125 0.010 1 107 12 12 DC H2'' H 2.427 0.010 1 108 12 12 DC H3' H 4.875 0.010 1 109 12 12 DC H4' H 4.173 0.010 1 110 12 12 DC H5 H 5.714 0.010 1 111 12 12 DC H5' H 4.153 0.010 2 112 12 12 DC H5'' H 4.124 0.010 2 113 12 12 DC H6 H 7.546 0.010 1 114 13 13 DG H1 H 12.974 0.010 1 115 13 13 DG H1' H 5.859 0.010 1 116 13 13 DG H2' H 2.637 0.010 1 117 13 13 DG H2'' H 2.696 0.010 1 118 13 13 DG H3' H 4.981 0.010 1 119 13 13 DG H4' H 4.355 0.010 1 120 13 13 DG H5' H 4.119 0.010 2 121 13 13 DG H5'' H 4.049 0.010 2 122 13 13 DG H8 H 7.923 0.010 1 123 14 14 DC H1' H 5.757 0.010 1 124 14 14 DC H2' H 1.889 0.010 1 125 14 14 DC H2'' H 2.326 0.010 1 126 14 14 DC H3' H 4.802 0.010 1 127 14 14 DC H4' H 4.136 0.010 1 128 14 14 DC H5 H 5.446 0.010 1 129 14 14 DC H5' H 4.177 0.010 2 130 14 14 DC H5'' H 4.099 0.010 2 131 14 14 DC H6 H 7.326 0.010 1 132 15 15 DG H1' H 6.149 0.010 1 133 15 15 DG H2' H 2.605 0.010 1 134 15 15 DG H2'' H 2.361 0.010 1 135 15 15 DG H3' H 4.663 0.010 1 136 15 15 DG H4' H 4.160 0.010 1 137 15 15 DG H5' H 4.061 0.010 2 138 15 15 DG H5'' H 4.061 0.010 2 139 15 15 DG H8 H 7.933 0.010 1 stop_ save_