data_19890 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; MINOR GROOVE RECOGNITION OF DNA BY THIAZOTROPSIN ANALOGUES ; _BMRB_accession_number 19890 _BMRB_flat_file_name bmr19890.str _Entry_type original _Submission_date 2014-04-03 _Accession_date 2014-04-03 _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 Alniss H. Y. . 2 Salvia M. -V. . 3 Sadikov M. . . 4 Golovchenko I. . . 5 Anthony N. G. . 6 Khalaf A. I. . 7 Mackay S. P. . 8 Suckling C. J. . 9 Parkinson J. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 82 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-07-28 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 19888 'CGACGCGTCG with 5,6,7,8-TETRAHYDROBIOPTERIN' 19889 'CGACTAGTCG with AIK-18/51-1' stop_ _Original_release_date 2014-07-17 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title ; Minor Groove Recognition of DNA by Thiazotropsin Analogues ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Alniss H. Y. . 2 Salvia M. -V. . 3 Sadikov M. . . 4 Golovchenko I. . . 5 Anthony N. G. . 6 Khalaf A. I. . 7 Mackay S. P. . 8 Suckling C. J. . 9 Parkinson J. A. . stop_ _Journal_abbreviation 'To be Published' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'CGACTAGTCG dimer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3'_1 $5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3' 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3'_2 $5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3' 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_5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3' _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3' _Molecular_mass 3045.029 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; CGACTAGTCG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DA 4 4 DC 5 5 DT 6 6 DA 7 7 DG 8 8 DT 9 9 DC 10 10 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 $5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3' . . . . . . 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 $5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3' 'obtained from a vendor' . . . . . 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 $5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3' 2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_SYBYL _Saveframe_category software _Name SYBYL _Version . loop_ _Vendor _Address _Electronic_address Tripos . . stop_ loop_ _Task 'geometry optimization' 'structure building' 'structure solution' stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address Tripos . . stop_ loop_ _Task 'NOE to distance restraint conversion' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'data analysis' 'geometry optimization' 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _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 'ionic strength' 0.05 . M pH 7.4 . pH pressure 1 . atm temperature 298 . K 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 TSP H 1 'methyl protons' ppm 0 internal 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H COSY' '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 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*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 DC H1' H 5.610 . . 2 1 1 DC H2' H 1.750 . . 3 1 1 DC H3' H 4.580 . . 4 1 1 DC H4' H 3.960 . . 5 1 1 DC H5 H 5.788 . . 6 1 1 DC H5' H 3.620 . . 7 1 1 DC H6 H 7.511 . . 8 2 2 DG H1 H 12.800 . . 9 2 2 DG H1' H 5.400 . . 10 2 2 DG H2' H 2.620 . . 11 2 2 DG H3' H 4.910 . . 12 2 2 DG H4' H 4.230 . . 13 2 2 DG H5' H 3.990 . . 14 2 2 DG H8 H 7.862 . . 15 3 3 DA H1' H 6.170 . . 16 3 3 DA H2 H 7.792 . . 17 3 3 DA H2' H 2.650 . . 18 3 3 DA H3' H 4.960 . . 19 3 3 DA H4' H 4.400 . . 20 3 3 DA H5' H 4.150 . . 21 3 3 DA H8 H 8.131 . . 22 4 4 DC H1' H 5.680 . . 23 4 4 DC H2' H 1.830 . . 24 4 4 DC H3' H 4.580 . . 25 4 4 DC H4' H 4.100 . . 26 4 4 DC H5 H 5.100 . . 27 4 4 DC H5' H 3.970 . . 28 4 4 DC H6 H 7.155 . . 29 4 4 DC H41 H 7.880 . . 30 4 4 DC H42 H 6.530 . . 31 5 5 DT H1' H 5.550 . . 32 5 5 DT H2' H 2.000 . . 33 5 5 DT H2'' H 2.360 . . 34 5 5 DT H3 H 13.500 . . 35 5 5 DT H3' H 4.770 . . 36 5 5 DT H4' H 4.020 . . 37 5 5 DT H5' H 3.990 . . 38 5 5 DT H5'' H 3.970 . . 39 5 5 DT H6 H 7.235 . . 40 5 5 DT H71 H 1.490 . . 41 5 5 DT H72 H 1.490 . . 42 5 5 DT H73 H 1.490 . . 43 6 6 DA H1' H 5.940 . . 44 6 6 DA H2 H 7.081 . . 45 6 6 DA H2' H 2.660 . . 46 6 6 DA H3' H 4.950 . . 47 6 6 DA H4' H 4.330 . . 48 6 6 DA H5' H 3.980 . . 49 6 6 DA H8 H 8.130 . . 50 7 7 DG H1 H 12.600 . . 51 7 7 DG H1' H 5.760 . . 52 7 7 DG H2' H 2.360 . . 53 7 7 DG H3' H 4.770 . . 54 7 7 DG H4' H 4.310 . . 55 7 7 DG H5' H 4.120 . . 56 7 7 DG H8 H 7.511 . . 57 8 8 DT H1' H 5.920 . . 58 8 8 DT H2' H 1.950 . . 59 8 8 DT H2'' H 2.350 . . 60 8 8 DT H3 H 13.600 . . 61 8 8 DT H3' H 4.750 . . 62 8 8 DT H4' H 4.120 . . 63 8 8 DT H5'' H 4.110 . . 64 8 8 DT H6 H 7.144 . . 65 8 8 DT H71 H 1.160 . . 66 8 8 DT H72 H 1.160 . . 67 8 8 DT H73 H 1.160 . . 68 9 9 DC H1' H 5.630 . . 69 9 9 DC H2' H 1.920 . . 70 9 9 DC H3' H 4.740 . . 71 9 9 DC H4' H 4.010 . . 72 9 9 DC H5 H 5.574 . . 73 9 9 DC H5' H 3.990 . . 74 9 9 DC H6 H 7.385 . . 75 9 9 DC H41 H 8.480 . . 76 9 9 DC H42 H 6.900 . . 77 10 10 DG H1' H 6.060 . . 78 10 10 DG H2' H 2.520 . . 79 10 10 DG H3' H 4.590 . . 80 10 10 DG H4' H 4.080 . . 81 10 10 DG H5' H 3.990 . . 82 10 10 DG H8 H 7.839 . . stop_ save_