data_18835 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex ; _BMRB_accession_number 18835 _BMRB_flat_file_name bmr18835.str _Entry_type original _Submission_date 2012-11-09 _Accession_date 2012-11-09 _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 Kowal Ewa A. . 2 Lad Rahul . . 3 Pallan Pradeep S. . 4 Muffly Elizabeth . . 5 Wawrzak Zdzislaw . . 6 Egli Martin . . 7 Sturla Shana J. . 8 Stone Michael P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 homonucl_NOEs 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 109 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-17 update BMRB 'update entry citation' 2013-06-10 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23748954 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kowal Ewa A. . 2 Lad Rahul R. . 3 Pallan Pradeep S. . 4 Dhummakupt Elizabeth . . 5 Wawrzak Zdzislaw . . 6 Egli Martin . . 7 Sturla Shana J. . 8 Stone Michael P. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 41 _Journal_issue 15 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 7566 _Page_last 7576 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'dodecamer duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'strand 1' $dodecamer_duplex 'strand 2' $dodecamer_duplex 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_dodecamer_duplex _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3' _Molecular_mass 2755.845 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence CGCGAATTXGCG loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DG 5 DA 6 DA 7 DT 8 DT 9 D3N 10 DG 11 DC 12 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_D3N _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-perimidin-2(3H)-one _BMRB_code D3N _PDB_code D3N _Standard_residue_derivative . _Molecular_mass 380.289 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O1P O1P O . 0 . ? P P P . 0 . ? O2P O2P O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? C1' C1' C . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? C9 C9 C . 0 . ? C10 C10 C . 0 . ? C11 C11 C . 0 . ? C12 C12 C . 0 . ? C13 C13 C . 0 . ? H1 H1 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H9 H9 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H13 H13 H . 0 . ? H14 H14 H . 0 . ? H15 H15 H . 0 . ? H16 H16 H . 0 . ? H17 H17 H . 0 . ? OP3 OP3 O . 0 . ? H2 H2 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 O3' C3' ? ? SING C2' C3' ? ? SING C2' C1' ? ? SING C3' C4' ? ? SING C1' N1 ? ? SING C1' O4' ? ? DOUB O2 C2 ? ? SING N1 C2 ? ? SING N1 C6 ? ? SING C2 N3 ? ? DOUB C7 C6 ? ? SING C7 C8 ? ? SING C6 C5 ? ? SING C4' O4' ? ? SING C4' C5' ? ? DOUB C8 C9 ? ? SING N3 C4 ? ? DOUB C5 C4 ? ? SING C5 C10 ? ? SING C4 C13 ? ? SING C9 C10 ? ? DOUB C10 C11 ? ? DOUB C13 C12 ? ? SING C5' O5' ? ? SING C11 C12 ? ? SING O5' P ? ? DOUB O2P P ? ? SING P O1P ? ? SING O1P H1 ? ? SING C5' H3 ? ? SING C5' H4 ? ? SING C4' H5 ? ? SING C3' H6 ? ? SING O3' H7 ? ? SING C2' H8 ? ? SING C2' H9 ? ? SING C1' H10 ? ? SING N3 H11 ? ? SING C7 H12 ? ? SING C8 H13 ? ? SING C9 H14 ? ? SING C11 H15 ? ? SING C12 H16 ? ? SING C13 H17 ? ? SING P OP3 ? ? SING OP3 H2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $dodecamer_duplex . . . . . . 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 $dodecamer_duplex 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 10 mM NaH2PO4 100 mM NaCl 50 uM Na2EDTA ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $dodecamer_duplex 0.53 mM 'natural abundance' D2O 100 % '[U-100% 2H]' 'sodium chloride' 100 mM 'natural abundance' EDTA 50 uM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details ; 10 mM NaH2PO4 100 mM NaCl 50 uM Na2EDTA ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $dodecamer_duplex 0.53 mM 'natural abundance' D2O 90 % '[U-100% 2H]' H2O 10 % 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 50 uM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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 refinement stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_CORMA _Saveframe_category software _Name CORMA _Version . loop_ _Vendor _Address _Electronic_address 'Thomas L. James' ; Thomas James Department of Pharmaceutical Chemistry University of California San Francisco, CA 94143-0446 ; . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_CURVES _Saveframe_category software _Name CURVES _Version 5.3 loop_ _Vendor _Address _Electronic_address 'Ravishankar, G. et al.' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address 'Thomas L. James' ; Prof. Thomas L. James, Attn: MARDIGRAS license, Box 0446, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco CA 94143-0446 ; . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'chemical shift calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details 'with CPTCI probe' save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details 'with CPTCI 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_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_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 . 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 . pH pressure 1 . atm temperature 278 . 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 water H 1 protons ppm 4.7 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 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 'strand 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 5.547 . . 2 1 1 DC H2' H 2.220 . . 3 1 1 DC H2'' H 1.813 . . 4 1 1 DC H3' H 4.513 . . 5 1 1 DC H4' H 3.782 . . 6 1 1 DC H5 H 5.645 . . 7 1 1 DC H5' H 3.560 . . 8 1 1 DC H5'' H 3.866 . . 9 1 1 DC H6 H 7.421 . . 10 2 2 DG H1' H 5.745 . . 11 2 2 DG H2' H 2.572 . . 12 2 2 DG H2'' H 2.422 . . 13 2 2 DG H3' H 4.799 . . 14 2 2 DG H4' H 4.052 . . 15 2 2 DG H5' H 4.102 . . 16 2 2 DG H5'' H 4.044 . . 17 2 2 DG H8 H 7.757 . . 18 3 3 DC H1' H 5.503 . . 19 3 3 DC H2' H 2.246 . . 20 3 3 DC H2'' H 1.946 . . 21 3 3 DC H3' H 4.652 . . 22 3 3 DC H4' H 4.166 . . 23 3 3 DC H5 H 5.299 . . 24 3 3 DC H5' H 3.953 . . 25 3 3 DC H5'' H 4.050 . . 26 3 3 DC H6 H 7.189 . . 27 4 4 DG H1' H 5.583 . . 28 4 4 DG H2' H 2.607 . . 29 4 4 DG H2'' H 2.407 . . 30 4 4 DG H3' H 4.830 . . 31 4 4 DG H4' H 4.095 . . 32 4 4 DG H5' H 4.103 . . 33 4 4 DG H5'' H 4.040 . . 34 4 4 DG H8 H 7.628 . . 35 5 5 DA H1' H 5.723 . . 36 5 5 DA H2 H 7.092 . . 37 5 5 DA H2' H 2.706 . . 38 5 5 DA H2'' H 2.391 . . 39 5 5 DA H3' H 4.841 . . 40 5 5 DA H5' H 4.039 . . 41 5 5 DA H5'' H 4.232 . . 42 5 5 DA H8 H 7.828 . . 43 6 6 DA H1' H 5.937 . . 44 6 6 DA H2 H 7.391 . . 45 6 6 DA H2' H 2.693 . . 46 6 6 DA H2'' H 2.385 . . 47 6 6 DA H3' H 4.825 . . 48 6 6 DA H4' H 3.933 . . 49 6 6 DA H5' H 4.035 . . 50 6 6 DA H5'' H 4.266 . . 51 6 6 DA H8 H 7.982 . . 52 7 7 DT H1' H 5.596 . . 53 7 7 DT H2' H 2.088 . . 54 7 7 DT H2'' H 1.557 . . 55 7 7 DT H3' H 4.548 . . 56 7 7 DT H4' H 3.955 . . 57 7 7 DT H5' H 4.043 . . 58 7 7 DT H5'' H 3.957 . . 59 7 7 DT H6 H 6.807 . . 60 7 7 DT H71 H 1.056 . . 61 7 7 DT H72 H 1.056 . . 62 7 7 DT H73 H 1.056 . . 63 8 8 DT H1' H 5.762 . . 64 8 8 DT H2' H 2.008 . . 65 8 8 DT H2'' H 1.212 . . 66 8 8 DT H3' H 4.493 . . 67 8 8 DT H4' H 3.798 . . 68 8 8 DT H5' H 3.904 . . 69 8 8 DT H5'' H 3.801 . . 70 8 8 DT H6 H 6.409 . . 71 8 8 DT H71 H 0.784 . . 72 8 8 DT H72 H 0.784 . . 73 8 8 DT H73 H 0.784 . . 74 9 9 D3N H10 H 6.013 . . 75 9 9 D3N H12 H 6.477 . . 76 9 9 D3N H13 H 7.121 . . 77 9 9 D3N H14 H 7.081 . . 78 9 9 D3N H15 H 6.936 . . 79 9 9 D3N H16 H 6.860 . . 80 9 9 D3N H3 H 3.930 . . 81 9 9 D3N H4 H 3.739 . . 82 9 9 D3N H5 H 4.097 . . 83 9 9 D3N H6 H 4.885 . . 84 9 9 D3N H8 H 1.654 . . 85 9 9 D3N H9 H 2.403 . . 86 10 10 DG H1' H 5.579 . . 87 10 10 DG H2' H 2.569 . . 88 10 10 DG H2'' H 2.413 . . 89 10 10 DG H3' H 4.741 . . 90 10 10 DG H4' H 3.801 . . 91 10 10 DG H5' H 4.060 . . 92 10 10 DG H5'' H 3.796 . . 93 10 10 DG H8 H 7.739 . . 94 11 11 DC H1' H 5.612 . . 95 11 11 DC H2' H 2.186 . . 96 11 11 DC H2'' H 1.709 . . 97 11 11 DC H3' H 4.654 . . 98 11 11 DC H4' H 3.870 . . 99 11 11 DC H5 H 5.218 . . 100 11 11 DC H5' H 3.984 . . 101 11 11 DC H5'' H 3.914 . . 102 11 11 DC H6 H 7.146 . . 103 12 12 DG H1' H 5.941 . . 104 12 12 DG H2' H 2.437 . . 105 12 12 DG H2'' H 2.147 . . 106 12 12 DG H3' H 4.476 . . 107 12 12 DG H5' H 4.030 . . 108 12 12 DG H5'' H 3.833 . . 109 12 12 DG H8 H 7.746 . . stop_ save_