data_19889 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; MINOR GROOVE RECOGNITION OF DNA BY THIAZOTROPSIN ANALOGUES ; _BMRB_accession_number 19889 _BMRB_flat_file_name bmr19889.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" 96 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-07-28 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19888 'CGACGCGTCG with 5,6,7,8-TETRAHYDROBIOPTERIN' 19890 'CGACTAGTCG dimer' stop_ _Original_release_date 2014-07-28 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 with AIK-18/51-1' _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' 'AIK-18/51, 1' $entity_3B5 'AIK-18/51, 2' $entity_3B5 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 'not present' _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_ ############# # Ligands # ############# save_3B5 _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common AIK-18/51 _BMRB_code 3B5 _PDB_code 3B5 _Molecular_mass 620.746 _Mol_charge 1 _Mol_paramagnetic . _Mol_aromatic yes _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C10 C10 C . 0 . ? C8 C8 C . 0 . ? C6 C6 C . 0 . ? C3 C3 C . 0 . ? C1 C1 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C11 C11 C . 0 . ? N12 N12 N . 0 . ? C12 C12 C . 0 . ? C13 C13 C . 0 . ? C15 C15 C . 0 . ? C17 C17 C . 0 . ? N21 N21 N . 0 . ? C20 C20 C . 0 . ? C25 C25 C . 0 . ? C27 C27 C . 0 . ? C28 C28 C . 0 . ? C32 C32 C . 0 . ? C31 C31 C . 0 . ? C19 C19 C . 0 . ? C22 C22 C . 0 . ? C23 C23 C . 0 . ? C24 C24 C . 0 . ? C34 C34 C . 0 . ? N33 N33 N . 1 . ? C35 C35 C . 0 . ? C30 C30 C . 0 . ? N29 N29 N . 0 . ? O28 O28 O . 0 . ? N22 N22 N . 0 . ? C26 C26 C . 0 . ? S22 S22 S . 0 . ? O20 O20 O . 0 . ? N19 N19 N . 0 . ? C18 C18 C . 0 . ? C16 C16 C . 0 . ? N14 N14 N . 0 . ? O13 O13 O . 0 . ? C9 C9 C . 0 . ? N7 N7 N . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? H3 H3 H . 0 . ? H1 H1 H . 0 . ? H5 H5 H . 0 . ? H11 H11 H . 0 . ? H123 H123 H . 0 . ? H121 H121 H . 0 . ? H122 H122 H . 0 . ? H21 H21 H . 0 . ? H25 H25 H . 0 . ? H273 H273 H . 0 . ? H271 H271 H . 0 . ? H272 H272 H . 0 . ? H322 H322 H . 0 . ? H321 H321 H . 0 . ? H312 H312 H . 0 . ? H311 H311 H . 0 . ? H193 H193 H . 0 . ? H192 H192 H . 0 . ? H191 H191 H . 0 . ? H341 H341 H . 0 . ? H342 H342 H . 0 . ? H343 H343 H . 0 . ? H353 H353 H . 0 . ? H352 H352 H . 0 . ? H351 H351 H . 0 . ? H302 H302 H . 0 . ? H301 H301 H . 0 . ? H29 H29 H . 0 . ? H263 H263 H . 0 . ? H261 H261 H . 0 . ? H262 H262 H . 0 . ? H18 H18 H . 0 . ? H16 H16 H . 0 . ? H14 H14 H . 0 . ? H9 H9 H . 0 . ? H7 H7 H . 0 . ? H2 H2 H . 0 . ? H33 H33 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 C34 N33 ? ? SING C27 C25 ? ? SING C35 N33 ? ? SING C32 N33 ? ? SING C32 C31 ? ? DOUB O28 C28 ? ? SING C25 C26 ? ? SING C25 C24 ? ? SING C31 C30 ? ? SING C30 N29 ? ? SING C28 N29 ? ? SING C28 C23 ? ? DOUB C24 C23 ? ? SING C24 S22 ? ? SING C23 N22 ? ? SING S22 C22 ? ? DOUB N22 C22 ? ? SING C22 N21 ? ? DOUB O20 C20 ? ? SING N21 C20 ? ? SING C20 C17 ? ? SING C19 N19 ? ? SING C17 N19 ? ? DOUB C17 C16 ? ? SING N19 C18 ? ? SING C16 C15 ? ? DOUB C18 C15 ? ? SING C15 N14 ? ? SING N14 C13 ? ? DOUB C13 O13 ? ? SING C13 C10 ? ? DOUB C10 C9 ? ? SING C10 N12 ? ? SING C9 C8 ? ? SING N12 C12 ? ? SING N12 C11 ? ? DOUB C8 C11 ? ? SING C8 N7 ? ? SING N7 C6 ? ? DOUB C6 O6 ? ? SING C6 C4 ? ? DOUB C5 C4 ? ? SING C5 N1 ? ? SING C4 C3 ? ? DOUB N1 C1 ? ? DOUB C3 C2 ? ? SING C1 C2 ? ? SING C3 H3 ? ? SING C1 H1 ? ? SING C5 H5 ? ? SING C11 H11 ? ? SING C12 H123 ? ? SING C12 H121 ? ? SING C12 H122 ? ? SING N21 H21 ? ? SING C25 H25 ? ? SING C27 H273 ? ? SING C27 H271 ? ? SING C27 H272 ? ? SING C32 H322 ? ? SING C32 H321 ? ? SING C31 H312 ? ? SING C31 H311 ? ? SING C19 H193 ? ? SING C19 H192 ? ? SING C19 H191 ? ? SING C34 H341 ? ? SING C34 H342 ? ? SING C34 H343 ? ? SING C35 H353 ? ? SING C35 H352 ? ? SING C35 H351 ? ? SING C30 H302 ? ? SING C30 H301 ? ? SING N29 H29 ? ? SING C26 H263 ? ? SING C26 H261 ? ? SING C26 H262 ? ? SING C18 H18 ? ? SING C16 H16 ? ? SING N14 H14 ? ? SING C9 H9 ? ? SING N7 H7 ? ? SING C2 H2 ? ? SING N33 H33 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_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' . . . . . $entity_3B5 '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_3B5 2 mM 'natural abundance' $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 solution' 'data analysis' 'structure generation' stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address Tripos . . stop_ loop_ _Task 'data analysis' 'structure solution' 'NOE conversion to distances' 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 'structure solution' refinement 'geometry optimization' 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_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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 7.4 . pH pressure 1 . atm 'ionic strength' 0.05 . M 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 NOESY' '2D 1H-1H COSY' 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 5.772 . . 2 1 1 DC H2' H 1.887 . . 3 1 1 DC H2'' H 2.386 . . 4 1 1 DC H3' H 4.724 . . 5 1 1 DC H4' H 4.075 . . 6 1 1 DC H5 H 5.927 . . 7 1 1 DC H5' H 3.275 . . 8 1 1 DC H5'' H 3.250 . . 9 1 1 DC H6 H 7.630 . . 10 2 2 DG H1 H 13.001 . . 11 2 2 DG H1' H 5.567 . . 12 2 2 DG H2' H 2.816 . . 13 2 2 DG H2'' H 2.740 . . 14 2 2 DG H3' H 5.047 . . 15 2 2 DG H4' H 4.340 . . 16 2 2 DG H5' H 3.984 . . 17 2 2 DG H5'' H 4.104 . . 18 2 2 DG H8 H 7.987 . . 19 3 3 DA H1' H 5.983 . . 20 3 3 DA H2 H 8.005 . . 21 3 3 DA H2' H 2.927 . . 22 3 3 DA H2'' H 2.617 . . 23 3 3 DA H3' H 5.111 . . 24 3 3 DA H4' H 4.505 . . 25 3 3 DA H5' H 4.178 . . 26 3 3 DA H5'' H 4.260 . . 27 3 3 DA H8 H 8.395 . . 28 4 4 DC H1' H 6.283 . . 29 4 4 DC H2' H 2.249 . . 30 4 4 DC H2'' H 1.868 . . 31 4 4 DC H3' H 4.635 . . 32 4 4 DC H4' H 4.268 . . 33 4 4 DC H5 H 5.466 . . 34 4 4 DC H5' H 3.853 . . 35 4 4 DC H5'' H 3.319 . . 36 4 4 DC H6 H 7.677 . . 37 4 4 DC H41 H 7.498 . . 38 4 4 DC H42 H 6.500 . . 39 5 5 DT H1' H 4.535 . . 40 5 5 DT H2' H 1.902 . . 41 5 5 DT H2'' H 2.198 . . 42 5 5 DT H3 H 13.120 . . 43 5 5 DT H3' H 4.721 . . 44 5 5 DT H4' H 2.771 . . 45 5 5 DT H5' H 3.711 . . 46 5 5 DT H5'' H 3.558 . . 47 5 5 DT H6 H 7.268 . . 48 5 5 DT H71 H 1.725 . . 49 5 5 DT H72 H 1.725 . . 50 5 5 DT H73 H 1.725 . . 51 6 6 DA H1' H 5.406 . . 52 6 6 DA H2 H 7.906 . . 53 6 6 DA H2' H 2.752 . . 54 6 6 DA H2'' H 2.257 . . 55 6 6 DA H3' H 4.707 . . 56 6 6 DA H4' H 2.692 . . 57 6 6 DA H5' H 3.259 . . 58 6 6 DA H5'' H 3.848 . . 59 6 6 DA H8 H 8.045 . . 60 7 7 DG H1 H 12.790 . . 61 7 7 DG H1' H 5.260 . . 62 7 7 DG H2' H 2.612 . . 63 7 7 DG H2'' H 2.105 . . 64 7 7 DG H3' H 4.678 . . 65 7 7 DG H4' H 2.580 . . 66 7 7 DG H5' H 3.552 . . 67 7 7 DG H5'' H 3.882 . . 68 7 7 DG H8 H 7.686 . . 69 7 7 DG H21 H 8.515 . . 70 7 7 DG H22 H 6.127 . . 71 8 8 DT H1' H 5.452 . . 72 8 8 DT H2' H 1.630 . . 73 8 8 DT H2'' H 1.716 . . 74 8 8 DT H3 H 13.850 . . 75 8 8 DT H3' H 4.469 . . 76 8 8 DT H4' H 2.166 . . 77 8 8 DT H5' H 3.661 . . 78 8 8 DT H5'' H 3.529 . . 79 8 8 DT H6 H 6.834 . . 80 8 8 DT H71 H 1.566 . . 81 8 8 DT H72 H 1.566 . . 82 8 8 DT H73 H 1.566 . . 83 9 9 DC H1' H 5.553 . . 84 9 9 DC H2' H 2.308 . . 85 9 9 DC H2'' H 2.120 . . 86 9 9 DC H4' H 4.014 . . 87 9 9 DC H5 H 5.638 . . 88 9 9 DC H6 H 7.394 . . 89 10 10 DG H1' H 6.203 . . 90 10 10 DG H2' H 2.410 . . 91 10 10 DG H2'' H 2.640 . . 92 10 10 DG H3' H 4.699 . . 93 10 10 DG H4' H 4.216 . . 94 10 10 DG H5' H 4.069 . . 95 10 10 DG H5'' H 4.069 . . 96 10 10 DG H8 H 7.964 . . stop_ save_