data_17789 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; structure of the duplex containing (5'S)-8,5'-cyclo-2'-deoxyadenosine ; _BMRB_accession_number 17789 _BMRB_flat_file_name bmr17789.str _Entry_type original _Submission_date 2011-07-18 _Accession_date 2011-07-18 _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 Huang Hai . . 2 Das Rajat S. . 3 Basu Ashis . . 4 Stone Michael P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 171 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-25 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17786 (5'S)-8,5'-cyclo-2'-deoxyguanosine 17787 (5'S)-8,5'-cyclo-2'-deoxyadenosine 17788 'gamma-hydroxy-1,N2-propano-2'-deoxyguanosine adduct' 17790 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' 17791 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of (5'S)-8,5'-cyclo-2'-deoxyguanosine in DNA' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22103478 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huang Hai . . 2 Das Rajat S. . 3 Basu Ashis . . 4 Stone Michael P. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 133 _Journal_issue 50 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 20357 _Page_last 20368 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name (5'S)-8,5'-cyclo-2'-deoxyadenosine _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3') $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-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_DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3')_ _Molecular_mass 2752.830 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GTGCATGTTTGT loop_ _Residue_seq_code _Residue_label 1 DG 2 DT 3 DG 4 DC 5 DA 6 DT 7 DG 8 DT 9 DT 10 DT 11 DG 12 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3')_ _Molecular_mass 3022.044 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence ACAAACATGCAC loop_ _Residue_seq_code _Residue_label 1 DA 2 DC 3 DA 4 DA 5 DA 6 DC 7 DA 8 DT 9 DG 10 DC 11 DA 12 DC 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 $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') . . . . . . $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-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 $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') 'chemical synthesis' . . . . . $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3') '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 $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') 1.0 mM 'natural abundance' $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3') 1.0 mM 'natural abundance' D2O 100 % 'natural abundance' 'phosphate buffer' 10 mM 'natural abundance' NaCl 100 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 10 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . 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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 303 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 100 . mM 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 4.712 internal direct . . . 1.000000000 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '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 DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') _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 6.030 .003 1 2 1 1 DG H2' H 2.659 .003 1 3 1 1 DG H2'' H 2.816 .003 2 4 1 1 DG H3' H 4.841 .003 1 5 1 1 DG H4' H 4.254 .003 1 6 1 1 DG H8 H 7.967 .003 1 7 2 2 DT H1' H 5.976 .003 1 8 2 2 DT H2' H 2.186 .003 1 9 2 2 DT H2'' H 2.551 .003 2 10 2 2 DT H3' H 4.938 .003 1 11 2 2 DT H4' H 4.267 .003 1 12 2 2 DT H6 H 7.364 .003 1 13 2 2 DT H71 H 1.406 .003 1 14 2 2 DT H72 H 1.406 .003 1 15 2 2 DT H73 H 1.406 .003 1 16 3 3 DG H1' H 5.866 .003 1 17 3 3 DG H2' H 2.630 .003 1 18 3 3 DG H2'' H 2.735 .003 2 19 3 3 DG H3' H 5.006 .003 1 20 3 3 DG H4' H 4.387 .003 1 21 3 3 DG H8 H 7.879 .003 1 22 4 4 DC H1' H 6.084 .003 1 23 4 4 DC H2' H 2.276 .003 1 24 4 4 DC H2'' H 3.468 .003 2 25 4 4 DC H3' H 5.032 .003 1 26 4 4 DC H4' H 4.399 .003 1 27 4 4 DC H5 H 5.488 .003 1 28 4 4 DC H5' H 4.229 .003 1 29 4 4 DC H5'' H 4.196 .003 2 30 4 4 DC H6 H 7.598 .003 1 31 5 5 DA H1' H 6.352 .003 1 32 5 5 DA H2' H 2.538 .003 1 33 5 5 DA H2'' H 2.333 .003 1 34 5 5 DA H3' H 4.856 .003 1 35 5 5 DA H4' H 5.200 .003 1 36 5 5 DA H5' H 5.690 .003 1 37 6 6 DT H1' H 5.968 .003 1 38 6 6 DT H2' H 2.264 .003 1 39 6 6 DT H2'' H 2.644 .003 2 40 6 6 DT H3' H 4.879 .003 1 41 6 6 DT H4' H 4.320 .003 1 42 6 6 DT H5' H 4.061 .003 1 43 6 6 DT H6 H 7.465 .003 1 44 6 6 DT H71 H 1.752 .003 1 45 6 6 DT H72 H 1.752 .003 1 46 6 6 DT H73 H 1.752 .003 1 47 7 7 DG H1' H 5.982 .003 1 48 7 7 DG H2' H 2.542 .003 1 49 7 7 DG H2'' H 2.795 .003 2 50 7 7 DG H3' H 4.924 .003 1 51 7 7 DG H4' H 4.366 .003 1 52 7 7 DG H8 H 7.742 .003 1 53 8 8 DT H1' H 6.027 .003 1 54 8 8 DT H2' H 2.143 .003 1 55 8 8 DT H2'' H 2.596 .003 2 56 8 8 DT H3' H 4.882 .003 1 57 8 8 DT H4' H 4.261 .003 1 58 8 8 DT H6 H 7.244 .003 1 59 8 8 DT H71 H 1.314 .003 1 60 8 8 DT H72 H 1.314 .003 1 61 8 8 DT H73 H 1.314 .003 1 62 9 9 DT H1' H 6.151 .003 1 63 9 9 DT H2' H 2.174 .003 1 64 9 9 DT H2'' H 2.617 .003 2 65 9 9 DT H3' H 4.913 .003 1 66 9 9 DT H4' H 4.179 .003 1 67 9 9 DT H6 H 7.453 .003 1 68 9 9 DT H71 H 1.617 .003 1 69 9 9 DT H72 H 1.617 .003 1 70 9 9 DT H73 H 1.617 .003 1 71 10 10 DT H1' H 5.874 .003 1 72 10 10 DT H2' H 2.008 .003 1 73 10 10 DT H2'' H 2.398 .003 2 74 10 10 DT H3' H 4.922 .003 1 75 10 10 DT H4' H 4.155 .003 1 76 10 10 DT H6 H 7.319 .003 1 77 10 10 DT H71 H 1.728 .003 1 78 10 10 DT H72 H 1.728 .003 1 79 10 10 DT H73 H 1.728 .003 1 80 11 11 DG H1' H 6.095 .003 1 81 11 11 DG H2' H 2.734 .003 1 82 11 11 DG H3' H 5.028 .003 1 83 11 11 DG H4' H 4.427 .003 1 84 11 11 DG H8 H 7.988 .003 1 85 12 12 DT H1' H 6.270 .003 1 86 12 12 DT H2' H 2.284 .003 1 87 12 12 DT H3' H 4.568 .003 1 88 12 12 DT H4' H 4.115 .003 1 89 12 12 DT H6 H 7.449 .003 1 90 12 12 DT H71 H 1.653 .003 1 91 12 12 DT H72 H 1.653 .003 1 92 12 12 DT H73 H 1.653 .003 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '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 DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*TP*GP*CP*A)-3') _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 13 1 DA H1' H 6.189 .003 1 2 13 1 DA H2' H 2.599 .003 1 3 13 1 DA H2'' H 2.760 .003 2 4 13 1 DA H3' H 4.842 .003 1 5 13 1 DA H4' H 4.250 .003 1 6 13 1 DA H8 H 8.193 .003 1 7 14 2 DC H1' H 5.169 .003 1 8 14 2 DC H2' H 1.999 .003 1 9 14 2 DC H2'' H 2.232 .003 2 10 14 2 DC H3' H 4.792 .003 1 11 14 2 DC H4' H 4.100 .003 1 12 14 2 DC H5 H 5.513 .003 1 13 14 2 DC H6 H 7.413 .003 1 14 15 3 DA H1' H 5.787 .003 1 15 15 3 DA H2' H 2.750 .003 1 16 15 3 DA H2'' H 2.859 .003 2 17 15 3 DA H3' H 5.060 .003 1 18 15 3 DA H4' H 4.381 .003 1 19 15 3 DA H8 H 8.213 .003 1 20 16 4 DA H1' H 5.909 .003 1 21 16 4 DA H2' H 2.670 .003 1 22 16 4 DA H2'' H 2.877 .003 2 23 16 4 DA H3' H 5.081 .003 1 24 16 4 DA H4' H 4.467 .003 1 25 16 4 DA H8 H 8.125 .003 1 26 17 5 DA H1' H 6.083 .003 1 27 17 5 DA H2' H 2.594 .003 1 28 17 5 DA H2'' H 2.865 .003 2 29 17 5 DA H3' H 5.005 .003 1 30 17 5 DA H4' H 4.468 .003 1 31 17 5 DA H8 H 8.055 .003 1 32 18 6 DC H1' H 5.666 .003 1 33 18 6 DC H2' H 2.010 .003 1 34 18 6 DC H2'' H 2.420 .003 2 35 18 6 DC H3' H 4.771 .003 1 36 18 6 DC H4' H 4.199 .003 1 37 18 6 DC H5 H 5.169 .003 1 38 18 6 DC H6 H 7.165 .003 1 39 19 7 DA H1' H 6.146 .003 1 40 19 7 DA H2' H 2.403 .003 1 41 19 7 DA H2'' H 2.843 .003 2 42 19 7 DA H3' H 4.962 .003 1 43 19 7 DA H4' H 4.325 .003 1 44 19 7 DA H8 H 7.968 .003 1 45 20 8 DT H1' H 5.546 .003 1 46 20 8 DT H2' H 2.063 .003 1 47 20 8 DT H2'' H 2.390 .003 2 48 20 8 DT H3' H 4.854 .003 1 49 20 8 DT H4' H 4.152 .003 1 50 20 8 DT H6 H 7.069 .003 1 51 20 8 DT H71 H 1.393 .003 1 52 20 8 DT H72 H 1.393 .003 1 53 20 8 DT H73 H 1.393 .003 1 54 21 9 DG H1' H 5.801 .003 1 55 21 9 DG H2' H 2.537 .003 1 56 21 9 DG H2'' H 2.671 .003 2 57 21 9 DG H3' H 4.950 .003 1 58 21 9 DG H4' H 4.320 .003 1 59 21 9 DG H8 H 7.820 .003 1 60 22 10 DC H1' H 5.606 .003 1 61 22 10 DC H2' H 2.027 .003 1 62 22 10 DC H2'' H 2.374 .003 2 63 22 10 DC H3' H 4.835 .003 1 64 22 10 DC H4' H 4.159 .003 1 65 22 10 DC H5 H 5.321 .003 1 66 22 10 DC H6 H 7.315 .003 1 67 23 11 DA H1' H 6.262 .003 1 68 23 11 DA H2' H 2.681 .003 1 69 23 11 DA H2'' H 2.877 .003 2 70 23 11 DA H3' H 5.016 .003 1 71 23 11 DA H4' H 4.398 .003 1 72 23 11 DA H8 H 8.242 .003 1 73 24 12 DC H1' H 6.116 .003 1 74 24 12 DC H2' H 2.121 .003 1 75 24 12 DC H2'' H 2.164 .003 2 76 24 12 DC H3' H 4.491 .003 1 77 24 12 DC H4' H 4.045 .003 1 78 24 12 DC H5 H 5.413 .003 1 79 24 12 DC H6 H 7.390 .003 1 stop_ save_