data_19728 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A tetrahelical DNA fold adopted by alternating GGG and GCG tracts ; _BMRB_accession_number 19728 _BMRB_flat_file_name bmr19728.str _Entry_type original _Submission_date 2014-01-10 _Accession_date 2014-01-10 _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 Kocman Vojc . . 2 Plavec Janez . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 112 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-12-22 original author . stop_ _Original_release_date 2014-12-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'A tetrahelical DNA fold adopted by tandem repeats of alternating GGG and GCG tracts' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25500730 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kocman Vojc . . 2 Plavec Janez . . stop_ _Journal_abbreviation 'Nat. Commun.' _Journal_volume 5 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5831 _Page_last 5831 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'A tetrahelical DNA fold adopted by alternating GGG and GCG tracts' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*G)-3')_1' $d(GGGAGCG)n 'DNA (5'-D(*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*G)-3')_2' $d(GGGAGCG)n 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_d(GGGAGCG)n _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common d(GGGAGCG)n _Molecular_mass 4765.122 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence GGGAGCGAGGGAGCG loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DA 5 DG 6 DC 7 DG 8 DA 9 DG 10 DG 11 DG 12 DA 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 $d(GGGAGCG)n 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 $d(GGGAGCG)n 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_VK1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $d(GGGAGCG)n 2.8 mM 'natural abundance' $d(GGGAGCG)n 1 mM 'partial residue specific 15N' $d(GGGAGCG)n 1 mM 'residue specific 2H' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' LiCl 100 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 11 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model VNMRS _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model VNMRS _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model DD2 _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 $VK1 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $VK1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $VK1 save_ save_2D_1H-31P_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P COSY' _Sample_label $VK1 save_ save_2D_1H-15N_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $VK1 save_ ####################### # Sample conditions # ####################### save_VK1_sample_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 100 . mM pH 6 . pH pressure 1 . atm temperature 273 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_VK1_chemical_shift_reference _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 TMSPA H 1 'methyl protons' ppm 0 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_VK_chemical_shift_list_label _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $VK1 stop_ _Sample_conditions_label $VK1_sample_conditions _Chem_shift_reference_set_label $VK1_chemical_shift_reference _Mol_system_component_name 'DNA (5'-D(*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*G)-3')_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 11.118 0.003 1 2 1 1 DG H1' H 5.857 0.004 1 3 1 1 DG H2' H 2.117 0.001 1 4 1 1 DG H2'' H 2.263 0.001 1 5 1 1 DG H3' H 4.683 0.003 1 6 1 1 DG H4' H 4.059 0.000 1 7 1 1 DG H5' H 3.578 0.004 2 8 1 1 DG H5'' H 3.555 0.011 2 9 1 1 DG H8 H 7.657 0.001 1 10 2 2 DG H1 H 10.781 0.008 1 11 2 2 DG H1' H 5.627 0.003 1 12 2 2 DG H2' H 2.106 0.002 1 13 2 2 DG H2'' H 2.217 0.002 1 14 2 2 DG H3' H 4.817 0.004 1 15 2 2 DG H4' H 4.109 0.000 1 16 2 2 DG H5' H 3.945 0.000 2 17 2 2 DG H8 H 7.675 0.000 1 18 3 3 DG H1 H 10.403 0.007 1 19 3 3 DG H1' H 5.757 0.002 1 20 3 3 DG H2' H 2.424 0.005 1 21 3 3 DG H2'' H 2.525 0.003 1 22 3 3 DG H3' H 4.869 0.002 1 23 3 3 DG H4' H 3.902 0.000 1 24 3 3 DG H5' H 3.797 0.000 2 25 3 3 DG H8 H 7.691 0.001 1 26 4 4 DA H1' H 6.190 0.003 1 27 4 4 DA H2 H 8.011 0.000 1 28 4 4 DA H2' H 2.402 0.003 1 29 4 4 DA H2'' H 2.747 0.003 1 30 4 4 DA H3' H 4.948 0.005 1 31 4 4 DA H4' H 4.355 0.000 1 32 4 4 DA H8 H 7.929 0.001 1 33 5 5 DG H1 H 12.951 0.003 1 34 5 5 DG H1' H 5.349 0.003 1 35 5 5 DG H2' H 2.551 0.004 1 36 5 5 DG H2'' H 2.455 0.007 1 37 5 5 DG H3' H 4.912 0.001 1 38 5 5 DG H4' H 4.343 0.000 1 39 5 5 DG H8 H 8.015 0.002 1 40 6 6 DC H1' H 6.079 0.002 1 41 6 6 DC H2' H 2.247 0.005 1 42 6 6 DC H2'' H 1.475 0.002 1 43 6 6 DC H3' H 4.834 0.004 1 44 6 6 DC H4' H 4.247 0.000 1 45 6 6 DC H5 H 8.234 0.003 1 46 6 6 DC H6 H 6.628 0.002 1 47 6 6 DC H41 H 4.918 0.000 1 48 6 6 DC H42 H 6.948 0.001 1 49 7 7 DG H1 H 10.343 0.002 1 50 7 7 DG H1' H 6.015 0.003 1 51 7 7 DG H2' H 2.785 0.004 1 52 7 7 DG H2'' H 2.862 0.003 1 53 7 7 DG H3' H 5.128 0.002 1 54 7 7 DG H4' H 4.524 0.002 1 55 7 7 DG H8 H 8.238 0.004 1 56 8 8 DA H1' H 5.398 0.003 1 57 8 8 DA H2 H 7.667 0.001 1 58 8 8 DA H2' H 2.209 0.004 1 59 8 8 DA H2'' H 0.575 0.006 1 60 8 8 DA H3' H 4.771 0.002 1 61 8 8 DA H4' H 4.354 0.000 1 62 8 8 DA H8 H 7.479 0.004 1 63 9 9 DG H1 H 10.490 0.002 1 64 9 9 DG H1' H 5.660 0.003 1 65 9 9 DG H2' H 2.446 0.003 1 66 9 9 DG H2'' H 2.938 0.002 1 67 9 9 DG H3' H 4.741 0.003 1 68 9 9 DG H4' H 4.204 0.001 1 69 9 9 DG H8 H 6.929 0.002 1 70 10 10 DG H1 H 10.948 0.007 1 71 10 10 DG H1' H 5.676 0.007 1 72 10 10 DG H2' H 2.086 0.004 1 73 10 10 DG H2'' H 1.963 0.002 1 74 10 10 DG H3' H 4.867 0.003 1 75 10 10 DG H4' H 4.298 0.000 1 76 10 10 DG H8 H 7.390 0.002 1 77 11 11 DG H1 H 10.429 0.001 1 78 11 11 DG H1' H 5.911 0.001 1 79 11 11 DG H2' H 2.888 0.003 1 80 11 11 DG H2'' H 2.626 0.002 1 81 11 11 DG H3' H 5.028 0.007 1 82 11 11 DG H4' H 4.490 0.000 1 83 11 11 DG H8 H 8.121 0.002 1 84 12 12 DA H1' H 5.539 0.002 1 85 12 12 DA H2 H 7.905 0.001 1 86 12 12 DA H2' H 2.356 0.003 1 87 12 12 DA H2'' H 1.058 0.004 1 88 12 12 DA H3' H 4.768 0.004 1 89 12 12 DA H4' H 4.309 0.001 1 90 12 12 DA H8 H 7.285 0.001 1 91 13 13 DG H1 H 12.820 0.005 1 92 13 13 DG H1' H 5.421 0.003 1 93 13 13 DG H2' H 2.476 0.002 1 94 13 13 DG H2'' H 2.514 0.007 1 95 13 13 DG H3' H 5.011 0.002 1 96 13 13 DG H8 H 7.869 0.002 1 97 14 14 DC H1' H 5.914 0.004 1 98 14 14 DC H2' H 1.533 0.002 1 99 14 14 DC H2'' H 2.118 0.002 1 100 14 14 DC H3' H 4.744 0.001 1 101 14 14 DC H4' H 4.181 0.000 1 102 14 14 DC H5 H 8.253 0.003 1 103 14 14 DC H6 H 6.739 0.003 1 104 14 14 DC H41 H 5.013 0.004 1 105 14 14 DC H42 H 6.980 0.001 1 106 15 15 DG H1 H 10.790 0.002 1 107 15 15 DG H1' H 5.507 0.003 1 108 15 15 DG H2' H 2.285 0.004 1 109 15 15 DG H2'' H 2.601 0.002 1 110 15 15 DG H3' H 4.590 0.001 1 111 15 15 DG H4' H 4.214 0.001 1 112 15 15 DG H8 H 7.970 0.001 1 stop_ save_