data_19888 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; MINOR GROOVE RECOGNITION OF DNA BY THIAZOTROPSIN ANALOGUES ; _BMRB_accession_number 19888 _BMRB_flat_file_name bmr19888.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 author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19889 'CGACTAGTCG with AIK-18/51-1' 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 submitted _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 'CGACGCGTCG with 5,6,7,8-TETRAHYDROBIOPTERIN' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3'_1 $5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3' 5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3'_2 $5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3' 5,6,7,8-TETRAHYDROBIOPTERIN_1 $entity_3BF 5,6,7,8-TETRAHYDROBIOPTERIN_2 $entity_3BF 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*GP*CP*GP*TP*CP*G)-3' _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3' _Molecular_mass 3046.017 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence CGACGCGTCG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DA 4 4 DC 5 5 DG 6 6 DC 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_3BF _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'thiazotropsin B' _BMRB_code 3BF _PDB_code 3BF _Molecular_mass 558.676 _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 N2 N2 N . 0 . ? C4 C4 C . 0 . ? N5 N5 N . 0 . ? N8 N8 N . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C9 C9 C . 0 . ? C10 C10 C . 0 . ? C11 C11 C . 0 . ? O1' O1' O . 0 . ? C1' C1' C . 0 . ? C1 C1 C . 0 . ? C3 C3 C . 0 . ? C5 C5 C . 0 . ? N6 N6 N . 0 . ? O7 O7 O . 0 . ? N11 N11 N . 0 . ? C13 C13 C . 0 . ? C12 C12 C . 0 . ? C14 C14 C . 0 . ? O12 O12 O . 0 . ? N14 N14 N . 0 . ? C15 C15 C . 0 . ? S16 S16 S . 0 . ? C17 C17 C . 0 . ? C20 C20 C . 0 . ? C21 C21 C . 0 . ? C28 C28 C . 0 . ? N19 N19 N . 0 . ? C18 C18 C . 0 . ? C22 C22 C . 0 . ? O22 O22 O . 0 . ? N22 N22 N . 0 . ? C23 C23 C . 0 . ? C24 C24 C . 0 . ? C25 C25 C . 0 . ? N26 N26 N . 1 . ? C29 C29 C . 0 . ? C27 C27 C . 0 . ? H2 H2 H . 0 . ? H4 H4 H . 0 . ? H8 H8 H . 0 . ? H10 H10 H . 0 . ? H111 H111 H . 0 . ? H112 H112 H . 0 . ? H113 H113 H . 0 . ? H102 H102 H . 0 . ? H101 H101 H . 0 . ? H103 H103 H . 0 . ? H53 H53 H . 0 . ? H51 H51 H . 0 . ? H52 H52 H . 0 . ? H13 H13 H . 0 . ? H14 H14 H . 0 . ? H20 H20 H . 0 . ? H212 H212 H . 0 . ? H211 H211 H . 0 . ? H213 H213 H . 0 . ? H283 H283 H . 0 . ? H281 H281 H . 0 . ? H282 H282 H . 0 . ? H22 H22 H . 0 . ? H232 H232 H . 0 . ? H231 H231 H . 0 . ? H242 H242 H . 0 . ? H241 H241 H . 0 . ? H251 H251 H . 0 . ? H252 H252 H . 0 . ? H291 H291 H . 0 . ? H293 H293 H . 0 . ? H292 H292 H . 0 . ? H273 H273 H . 0 . ? H272 H272 H . 0 . ? H271 H271 H . 0 . ? H26 H26 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 C21 C20 ? ? SING C28 C20 ? ? SING C20 C17 ? ? SING C11 N11 ? ? SING S16 C17 ? ? SING S16 C15 ? ? DOUB O12 C14 ? ? DOUB C17 C18 ? ? SING N11 C10 ? ? SING N11 C12 ? ? SING C29 N26 ? ? SING C14 C12 ? ? SING C14 N14 ? ? DOUB O22 C22 ? ? SING C18 C22 ? ? SING C18 N19 ? ? SING C15 N14 ? ? DOUB C15 N19 ? ? DOUB C10 C9 ? ? DOUB C12 C13 ? ? SING C22 N22 ? ? SING N26 C27 ? ? SING N26 C25 ? ? SING C9 C13 ? ? SING C9 N8 ? ? SING C25 C24 ? ? DOUB O7 C7 ? ? SING N22 C23 ? ? SING N8 C7 ? ? SING C7 C6 ? ? SING C23 C24 ? ? SING C5 N5 ? ? SING C6 N5 ? ? DOUB C6 N6 ? ? SING N5 C4 ? ? SING N6 C3 ? ? DOUB C4 C3 ? ? SING C3 N2 ? ? SING N2 C1' ? ? DOUB O1' C1' ? ? SING C1' C1 ? ? SING N2 H2 ? ? SING C4 H4 ? ? SING N8 H8 ? ? SING C10 H10 ? ? SING C11 H111 ? ? SING C11 H112 ? ? SING C11 H113 ? ? SING C1 H102 ? ? SING C1 H101 ? ? SING C1 H103 ? ? SING C5 H53 ? ? SING C5 H51 ? ? SING C5 H52 ? ? SING C13 H13 ? ? SING N14 H14 ? ? SING C20 H20 ? ? SING C21 H212 ? ? SING C21 H211 ? ? SING C21 H213 ? ? SING C28 H283 ? ? SING C28 H281 ? ? SING C28 H282 ? ? SING N22 H22 ? ? SING C23 H232 ? ? SING C23 H231 ? ? SING C24 H242 ? ? SING C24 H241 ? ? SING C25 H251 ? ? SING C25 H252 ? ? SING C29 H291 ? ? SING C29 H293 ? ? SING C29 H292 ? ? SING C27 H273 ? ? SING C27 H272 ? ? SING C27 H271 ? ? SING N26 H26 ? ? 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*GP*CP*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*GP*CP*GP*TP*CP*G)-3' 'obtained from a vendor' . . . . . $entity_3BF '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_3BF 2 mM 'natural abundance' $5'-D(*CP*GP*AP*CP*GP*CP*GP*TP*CP*G)-3' 2 mM '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 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' 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 'geometry optimization' refinement 'structure solution' stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address Tripos . . stop_ loop_ _Task '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 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 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*GP*CP*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 5.795 . . 2 1 1 DC H2' H 1.926 . . 3 1 1 DC H3' H 4.745 . . 4 1 1 DC H4' H 4.103 . . 5 1 1 DC H5 H 5.951 . . 6 1 1 DC H5' H 3.755 . . 7 1 1 DC H6 H 7.660 . . 8 2 2 DG H1 H 12.950 . . 9 2 2 DG H1' H 5.624 . . 10 2 2 DG H2' H 2.769 . . 11 2 2 DG H3' H 5.063 . . 12 2 2 DG H4' H 4.366 . . 13 2 2 DG H5' H 4.012 . . 14 2 2 DG H8 H 8.008 . . 15 3 3 DA H1' H 6.093 . . 16 3 3 DA H2 H 7.937 . . 17 3 3 DA H2' H 2.684 . . 18 3 3 DA H3' H 5.094 . . 19 3 3 DA H4' H 4.465 . . 20 3 3 DA H5' H 4.231 . . 21 3 3 DA H8 H 8.312 . . 22 4 4 DC H1' H 5.909 . . 23 4 4 DC H2' H 1.893 . . 24 4 4 DC H3' H 4.944 . . 25 4 4 DC H4' H 4.187 . . 26 4 4 DC H5 H 5.322 . . 27 4 4 DC H5' H 4.190 . . 28 4 4 DC H6 H 7.387 . . 29 4 4 DC H41 H 7.725 . . 30 4 4 DC H42 H 6.119 . . 31 5 5 DG H1 H 13.200 . . 32 5 5 DG H1' H 5.390 . . 33 5 5 DG H2' H 2.458 . . 34 5 5 DG H3' H 4.677 . . 35 5 5 DG H4' H 2.247 . . 36 5 5 DG H5' H 3.847 . . 37 5 5 DG H8 H 7.920 . . 38 5 5 DG H21 H 8.022 . . 39 5 5 DG H22 H 8.497 . . 40 6 6 DC H1' H 5.469 . . 41 6 6 DC H2' H 1.555 . . 42 6 6 DC H3' H 4.642 . . 43 6 6 DC H4' H 2.214 . . 44 6 6 DC H5 H 5.659 . . 45 6 6 DC H5' H 3.810 . . 46 6 6 DC H6 H 7.065 . . 47 6 6 DC H41 H 8.465 . . 48 6 6 DC H42 H 6.295 . . 49 7 7 DG H1 H 13.360 . . 50 7 7 DG H1' H 5.304 . . 51 7 7 DG H2' H 2.180 . . 52 7 7 DG H3' H 4.688 . . 53 7 7 DG H4' H 3.845 . . 54 7 7 DG H5' H 3.502 . . 55 7 7 DG H8 H 7.847 . . 56 7 7 DG H21 H 8.031 . . 57 7 7 DG H22 H 8.499 . . 58 8 8 DT H1' H 5.528 . . 59 8 8 DT H2' H 1.721 . . 60 8 8 DT H3 H 13.900 . . 61 8 8 DT H3' H 4.579 . . 62 8 8 DT H4' H 2.262 . . 63 8 8 DT H5' H 3.886 . . 64 8 8 DT H6 H 6.931 . . 65 8 8 DT H71 H 1.678 . . 66 8 8 DT H72 H 1.678 . . 67 8 8 DT H73 H 1.678 . . 68 9 9 DC H1' H 5.676 . . 69 9 9 DC H2' H 2.165 . . 70 9 9 DC H3' H 4.899 . . 71 9 9 DC H4' H 4.174 . . 72 9 9 DC H5 H 5.726 . . 73 9 9 DC H5' H 4.021 . . 74 9 9 DC H6 H 7.459 . . 75 9 9 DC H41 H 8.808 . . 76 9 9 DC H42 H 6.962 . . 77 10 10 DG H1' H 6.223 . . 78 10 10 DG H2' H 2.439 . . 79 10 10 DG H3' H 5.064 . . 80 10 10 DG H4' H 4.136 . . 81 10 10 DG H5' H 4.136 . . 82 10 10 DG H8 H 8.006 . . stop_ save_