data_34053 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of a stable G-hairpin ; _BMRB_accession_number 34053 _BMRB_flat_file_name bmr34053.str _Entry_type original _Submission_date 2016-10-11 _Accession_date 2016-10-11 _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 Gajarsky M. . . 2 Zivkovic M. L. . 3 Stadlbauer P. . . 4 Pagano B. . . 5 Fiala R. . . 6 Amato J. . . 7 Tomaska L. . . 8 Sponer J. . . 9 Plavec J. . . 10 Trantirek L. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 109 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-06-27 update BMRB 'update entry citation' 2017-02-23 original author 'original release' stop_ _Original_release_date 2016-11-11 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of a stable G-hairpin ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28217994 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gajarsky M. . . 2 Zivkovic M. L. . 3 Stadlbauer P. . . 4 Pagano B. . . 5 Fiala R. . . 6 Amato J. . . 7 Tomaska L. . . 8 Sponer J. . . 9 Plavec J. . . 10 Trantirek L. . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 139 _Journal_issue 10 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3591 _Page_last 3594 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common entity_1 _Molecular_mass 3476.254 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence ; GTGTGGGTGTG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DT 3 DG 4 DT 5 DG 6 DG 7 DG 8 DT 9 DG 10 DT 11 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 $entity_1 "baker's yeast" 4932 Eukaryota Fungi Saccharomyces cerevisiae 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_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.2 mM / SC11, 10 mM / potassium phosphate, 100 mM / potassium chloride, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.2 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.2 mM / SC11, 10 mM / potassium phosphate, 100 mM / potassium chloride, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling SC11 0.2 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details ; 0.2 mM partial (12%) 15N, 13C residue-specific labelling SC11, 10 mM / potassium phosphate, 100 mM / potassium chloride, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling SC11 0.2 mM 'partial (12%) 15N, 13C residue-specific labelling' 'potassium chloride' 100 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version 14.0 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version 3.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_4 _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task 'chemical shift assignment' processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 700 _Details 'room temperature inverse (1H-BB) probe' save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 850 _Details 'triple-resonance (1H-13C-15N) cryogenic probe' save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 950 _Details 'triple-resonance (1H-13C-15N) cryogenic probe' save_ save_NMR_spectrometer_4 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Uniform NMR System' _Field_strength 600 _Details 'DD2 console' save_ save_NMR_spectrometer_5 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 700 _Details 'triple-resonance (1H-13C-15N) cryogenic probe' 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_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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_2D_1H-1H_ROESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_1 save_ save_2D_1H-1H_ROESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_2 save_ save_1D_15N-edited_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 15N-edited HSQC' _Sample_label $sample_3 save_ save_1D_13C-edited_HSQC_8 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 13C-edited HSQC' _Sample_label $sample_3 save_ save_diffusion_experiment_9 _Saveframe_category NMR_applied_experiment _Experiment_name 'diffusion experiment' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 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 7.0 . pH pressure 1 . atm temperature 283 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 100 . mM pH 7.4 . pD pressure 1 . atm temperature 283 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 100 . mM pH 7.0 . pH pressure 1 . atm temperature 283 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 0.000 external direct . . . 1.0 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D DQF-COSY' '2D 1H-1H ROESY' '1D 15N-edited HSQC' '1D 13C-edited HSQC' 'diffusion experiment' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_3 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 1 1 DG H1 H 11.196 0.003 1 2 1 1 DG H1' H 5.41 0.003 1 3 1 1 DG H2' H 2.264 0.003 1 4 1 1 DG H2'' H 2.312 0.003 1 5 1 1 DG H3' H 4.96 0.003 1 6 1 1 DG H4' H 4.377 0.001 1 7 1 1 DG H5' H 3.83 0.005 1 8 1 1 DG H5'' H 3.82 0.005 1 9 1 1 DG H8 H 7.205 0.001 1 10 1 1 DG H21 H 9.463 0.003 1 11 1 1 DG H22 H 6.127 0 1 12 2 2 DT H1' H 6.395 0.002 1 13 2 2 DT H2' H 1.9 0.003 1 14 2 2 DT H2'' H 2.873 0.004 1 15 2 2 DT H3 H 11.989 0.001 1 16 2 2 DT H3' H 5.042 0.002 1 17 2 2 DT H4' H 4.665 0.002 1 18 2 2 DT H5' H 4.26 0.004 1 19 2 2 DT H5'' H 4.192 0.002 1 20 2 2 DT H6 H 8.097 0.001 1 21 2 2 DT H71 H 2.085 0.004 1 22 2 2 DT H72 H 2.085 0.004 1 23 2 2 DT H73 H 2.085 0.004 1 24 3 3 DG H1' H 5.847 0.002 1 25 3 3 DG H2' H 2.137 0.002 1 26 3 3 DG H2'' H 2.271 0.002 1 27 3 3 DG H3' H 4.738 0.001 1 28 3 3 DG H4' H 4.192 0.004 1 29 3 3 DG H8 H 7.74 0.006 1 30 4 4 DT H1' H 6.138 0.002 1 31 4 4 DT H2' H 2.06 0.004 1 32 4 4 DT H2'' H 2.2 0.001 1 33 4 4 DT H3' H 4.722 0.002 1 34 4 4 DT H4' H 4.262 0.002 1 35 4 4 DT H5' H 3.678 0.002 1 36 4 4 DT H5'' H 2.824 0.001 1 37 4 4 DT H6 H 7.355 0 1 38 4 4 DT H71 H 1.527 0.005 1 39 4 4 DT H72 H 1.527 0.005 1 40 4 4 DT H73 H 1.527 0.005 1 41 5 5 DG H1 H 12.239 0.001 1 42 5 5 DG H1' H 6.346 0.002 1 43 5 5 DG H2' H 2.589 0.002 1 44 5 5 DG H2'' H 3.094 0.002 1 45 5 5 DG H3' H 5.654 0.003 1 46 5 5 DG H4' H 4.302 0.006 1 47 5 5 DG H5' H 4.198 0.002 1 48 5 5 DG H8 H 7.691 0.004 1 49 6 6 DG H1 H 12.39 0.001 1 50 6 6 DG H1' H 5.87 0.001 1 51 6 6 DG H2' H 2.576 0.001 1 52 6 6 DG H2'' H 2.769 0.002 1 53 6 6 DG H3' H 4.873 0.001 1 54 6 6 DG H4' H 5.196 0.001 1 55 6 6 DG H5' H 4.58 0.001 1 56 6 6 DG H5'' H 4.082 0.003 1 57 6 6 DG H8 H 7.976 0.008 1 58 6 6 DG H21 H 9.499 0.001 1 59 6 6 DG H22 H 5.164 0.001 1 60 7 7 DG H1 H 11.512 0.001 1 61 7 7 DG H1' H 6.375 0.004 1 62 7 7 DG H2' H 2.045 0.001 1 63 7 7 DG H2'' H 2.835 0.003 1 64 7 7 DG H3' H 5.143 0 1 65 7 7 DG H4' H 4.63 0.001 1 66 7 7 DG H5' H 4.496 0.001 1 67 7 7 DG H5'' H 4.2 0.003 1 68 7 7 DG H8 H 7.245 0.004 1 69 7 7 DG H21 H 9.226 0.003 1 70 7 7 DG H22 H 6.894 0.003 1 71 8 8 DT H1' H 6.558 0.005 1 72 8 8 DT H2' H 2.433 0.003 1 73 8 8 DT H2'' H 2.627 0.002 1 74 8 8 DT H3' H 5.019 0.003 1 75 8 8 DT H4' H 4.716 0.005 1 76 8 8 DT H5' H 4.305 0.007 1 77 8 8 DT H5'' H 4.206 0.003 1 78 8 8 DT H6 H 7.979 0.004 1 79 8 8 DT H71 H 2.112 0.002 1 80 8 8 DT H72 H 2.112 0.002 1 81 8 8 DT H73 H 2.112 0.002 1 82 9 9 DG H1 H 11.656 0.002 1 83 9 9 DG H1' H 6.244 0.004 1 84 9 9 DG H2' H 2.294 0.001 1 85 9 9 DG H2'' H 2.667 0.003 1 86 9 9 DG H3' H 5.065 0.001 1 87 9 9 DG H4' H 4.615 0.001 1 88 9 9 DG H8 H 8.098 0.003 1 89 10 10 DT H1' H 6.396 0.002 1 90 10 10 DT H2' H 2.407 0.002 1 91 10 10 DT H2'' H 2.605 0.002 1 92 10 10 DT H3' H 5.007 0.001 1 93 10 10 DT H4' H 4.662 0.003 1 94 10 10 DT H5' H 4.321 0.005 1 95 10 10 DT H6 H 7.866 0 1 96 10 10 DT H71 H 1.921 0.004 1 97 10 10 DT H72 H 1.921 0.004 1 98 10 10 DT H73 H 1.921 0.004 1 99 11 11 DG H1 H 11.468 0.001 1 100 11 11 DG H1' H 6.239 0.003 1 101 11 11 DG H2' H 2.953 0.005 1 102 11 11 DG H2'' H 2.724 0.001 1 103 11 11 DG H3' H 5.249 0.002 1 104 11 11 DG H4' H 4.333 0.006 1 105 11 11 DG H5' H 4.412 0.007 1 106 11 11 DG H5'' H 4.305 0.003 1 107 11 11 DG H8 H 7.281 0.006 1 108 11 11 DG H21 H 9.039 0.001 1 109 11 11 DG H22 H 4.783 0.002 1 stop_ save_