data_17746 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine ; _BMRB_accession_number 17746 _BMRB_flat_file_name bmr17746.str _Entry_type original _Submission_date 2011-06-29 _Accession_date 2011-06-29 _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" 160 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-02-17 update BMRB 'update entry citation' 2011-12-12 original author 'original release' 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 K. . 4 Stone Michael P. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _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'-deoxyguanosine in DNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_(5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') $DNA_(5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') $DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-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(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') _Molecular_mass 3386.234 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GTGCXTGTTTGTA loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DT 3 3 DG 4 4 DC 5 5 2LF 6 6 DT 7 7 DG 8 8 DT 9 9 DT 10 10 DT 11 11 DG 12 12 DT 13 13 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') _Molecular_mass 3609.425 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence ACAAACACGCAC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 DA 2 14 DC 3 15 DA 4 16 DA 5 17 DA 6 18 DC 7 19 DA 8 20 DC 9 21 DG 10 22 DC 11 23 DA 12 24 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_2LF _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common '(6S,7S,8S,10R)-2-amino-8-hydroxy-4-oxo-3,6,7,8,9,10-hexahydro-4H-7,10-epoxyazepino[1,2-e]purin-6-yl dihydrogen phosphate' _BMRB_code . _PDB_code 2LF _Standard_residue_derivative . _Molecular_mass 345.205 _Mol_paramagnetic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Jul 22 17:53:53 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N7 N7 N . 0 . ? C8 C8 C . 0 . ? N9 N9 N . 0 . ? C1' C1' C . 0 . ? OP3 OP3 O . 0 . ? C2' C2' C . 0 . ? OP2 OP2 O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 0 . ? HN1 HN1 H . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H'2' H'2' H . 0 . ? HN2 HN2 H . 0 . ? HN2A HN2A H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5' H5' H . 0 . ? HOP3 HOP3 H . 0 . ? HOP2 HOP2 H . 0 . ? HO3' HO3' H . 0 . ? OP1 OP1 O . 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 P OP2 ? ? SING P O5' ? ? SING N1 HN1 ? ? SING N1 C2 ? ? SING C2 N2 ? ? SING N2 HN2A ? ? SING N2 HN2 ? ? DOUB N3 C2 ? ? SING C4 N3 ? ? DOUB C5 C4 ? ? SING C5 C6 ? ? SING C6 N1 ? ? DOUB O6 C6 ? ? SING N7 C5 ? ? DOUB N7 C8 ? ? SING C8 N9 ? ? SING N9 C4 ? ? SING N9 C1' ? ? SING C1' H1' ? ? SING C1' C2' ? ? SING OP3 P ? ? SING OP3 HOP3 ? ? SING C2' H'2' ? ? SING C2' H2' ? ? SING OP2 HOP2 ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING C3' O3' ? ? SING O3' HO3' ? ? SING C4' C3' ? ? SING O4' C1' ? ? SING O4' C4' ? ? SING C5' C8 ? ? SING C5' C4' ? ? SING O5' C5' ? ? SING H4' C4' ? ? SING H5' C5' ? ? DOUB P OP1 ? ? stop_ 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(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') . . . . . . $DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-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(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') 'chemical synthesis' . . . . . $DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-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(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') 1.0 mM 'natural abundance' $DNA_(5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 1.0 mM 'natural abundance' D2O 100 % 'natural abundance' NaCl 100 mM 'natural abundance' 'phosphate buffer' 10 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 298 . 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 4.773 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(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-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 6.058 0.005 . 2 1 1 DG H2' H 2.690 0.005 . 3 1 1 DG H2'' H 2.839 0.005 2 4 1 1 DG H3' H 4.859 0.005 . 5 1 1 DG H4' H 4.272 0.005 . 6 1 1 DG H8 H 7.997 0.005 1 7 2 2 DT H1' H 6.001 0.005 . 8 2 2 DT H2' H 2.220 0.005 . 9 2 2 DT H2'' H 2.586 0.005 2 10 2 2 DT H3' H 4.958 0.005 . 11 2 2 DT H4' H 4.292 0.005 . 12 2 2 DT H6 H 7.402 0.005 1 13 2 2 DT H71 H 1.429 0.005 . 14 2 2 DT H72 H 1.429 0.005 . 15 2 2 DT H73 H 1.429 0.005 . 16 3 3 DG H1' H 5.876 0.005 . 17 3 3 DG H2' H 2.640 0.005 . 18 3 3 DG H2'' H 2.740 0.005 2 19 3 3 DG H3' H 5.014 0.005 . 20 3 3 DG H4' H 4.398 0.005 . 21 3 3 DG H8 H 7.908 0.005 1 22 4 4 DC H1' H 6.121 0.005 . 23 4 4 DC H2' H 2.224 0.005 . 24 4 4 DC H2'' H 3.440 0.005 2 25 4 4 DC H3' H 5.014 0.005 . 26 4 4 DC H4' H 4.395 0.005 . 27 4 4 DC H5 H 5.432 0.005 1 28 4 4 DC H6 H 7.551 0.005 1 29 5 5 2LF H1' H 6.140 0.005 . 30 5 5 2LF H2' H 2.550 0.005 . 31 5 5 2LF H'2' H 2.269 0.005 . 32 5 5 2LF H3' H 4.865 0.005 . 33 5 5 2LF H4' H 5.123 0.005 . 34 5 5 2LF H5' H 5.559 0.005 . 35 6 6 DT H1' H 6.078 0.005 . 36 6 6 DT H2' H 2.311 0.005 . 37 6 6 DT H2'' H 2.711 0.005 2 38 6 6 DT H3' H 4.912 0.005 . 39 6 6 DT H4' H 4.357 0.005 . 40 6 6 DT H6 H 7.544 0.005 1 41 6 6 DT H71 H 1.812 0.005 . 42 6 6 DT H72 H 1.812 0.005 . 43 6 6 DT H73 H 1.812 0.005 . 44 7 7 DG H1' H 6.004 0.005 . 45 7 7 DG H2' H 2.559 0.005 . 46 7 7 DG H2'' H 2.816 0.005 2 47 7 7 DG H3' H 4.942 0.005 . 48 7 7 DG H4' H 4.380 0.005 . 49 7 7 DG H8 H 7.781 0.005 1 50 8 8 DT H1' H 6.029 0.005 . 51 8 8 DT H2' H 2.154 0.005 . 52 8 8 DT H2'' H 2.607 0.005 2 53 8 8 DT H3' H 4.892 0.005 . 54 8 8 DT H4' H 4.275 0.005 . 55 8 8 DT H6 H 7.262 0.005 1 56 8 8 DT H71 H 1.340 0.005 . 57 8 8 DT H72 H 1.340 0.005 . 58 8 8 DT H73 H 1.340 0.005 . 59 9 9 DT H1' H 6.164 0.005 . 60 9 9 DT H2' H 2.187 0.005 . 61 9 9 DT H2'' H 2.629 0.005 2 62 9 9 DT H3' H 4.923 0.005 . 63 9 9 DT H6 H 7.469 0.005 1 64 9 9 DT H71 H 1.629 0.005 . 65 9 9 DT H72 H 1.629 0.005 . 66 9 9 DT H73 H 1.629 0.005 . 67 10 10 DT H1' H 5.884 0.005 . 68 10 10 DT H2' H 2.018 0.005 . 69 10 10 DT H2'' H 2.414 0.005 2 70 10 10 DT H3' H 4.933 0.005 . 71 10 10 DT H6 H 7.332 0.005 1 72 10 10 DT H71 H 1.740 0.005 1 73 10 10 DT H72 H 1.740 0.005 1 74 10 10 DT H73 H 1.740 0.005 1 75 11 11 DG H1' H 6.106 0.005 . 76 11 11 DG H2'' H 2.748 0.005 . 77 11 11 DG H3' H 5.038 0.005 . 78 11 11 DG H4' H 4.440 0.005 . 79 11 11 DG H8 H 8.008 0.005 1 80 12 12 DT H1' H 6.284 0.005 . 81 12 12 DT H2' H 2.291 0.005 . 82 12 12 DT H3' H 4.580 0.005 . 83 12 12 DT H4' H 4.127 0.005 . 84 12 12 DT H6 H 7.468 0.005 1 85 12 12 DT H71 H 1.672 0.005 . 86 12 12 DT H72 H 1.672 0.005 . 87 12 12 DT H73 H 1.672 0.005 . 88 13 13 DA H1' H 6.205 0.005 . 89 13 13 DA H2' H 2.616 0.005 . 90 13 13 DA H2'' H 2.777 0.005 2 91 13 13 DA H3' H 4.854 0.005 . 92 13 13 DA H4' H 4.264 0.005 . 93 13 13 DA H8 H 8.212 0.005 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(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-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 14 2 DC H1' H 5.168 0.005 . 2 14 2 DC H2' H 2.018 0.005 . 3 14 2 DC H2'' H 2.247 0.005 2 4 14 2 DC H3' H 4.808 0.005 . 5 14 2 DC H5 H 5.522 0.005 1 6 14 2 DC H6 H 7.430 0.005 1 7 15 3 DA H1' H 5.797 0.005 . 8 15 3 DA H2' H 2.768 0.005 . 9 15 3 DA H2'' H 2.871 0.005 2 10 15 3 DA H3' H 5.071 0.005 . 11 15 3 DA H4' H 4.396 0.005 . 12 15 3 DA H8 H 8.232 0.005 1 13 16 4 DA H1' H 5.922 0.005 . 14 16 4 DA H2' H 2.685 0.005 . 15 16 4 DA H2'' H 2.892 0.005 2 16 16 4 DA H3' H 5.093 0.005 . 17 16 4 DA H4' H 4.479 0.005 . 18 16 4 DA H8 H 8.145 0.005 1 19 17 5 DA H1' H 6.092 0.005 . 20 17 5 DA H2 H 7.576 0.005 1 21 17 5 DA H2' H 2.603 0.005 . 22 17 5 DA H2'' H 2.874 0.005 2 23 17 5 DA H3' H 5.017 0.005 . 24 17 5 DA H4' H 4.482 0.005 . 25 17 5 DA H8 H 8.074 0.005 1 26 18 6 DC H1' H 5.661 0.005 . 27 18 6 DC H2' H 1.994 0.005 . 28 18 6 DC H2'' H 2.408 0.005 2 29 18 6 DC H5 H 5.181 0.005 1 30 18 6 DC H6 H 7.174 0.005 1 31 19 7 DA H1' H 6.119 0.005 . 32 19 7 DA H2' H 2.456 0.005 . 33 19 7 DA H2'' H 2.809 0.005 2 34 19 7 DA H3' H 4.981 0.005 . 35 19 7 DA H4' H 4.319 0.005 . 36 19 7 DA H8 H 7.969 0.005 1 37 20 8 DC H1' H 5.399 0.005 . 38 20 8 DC H2' H 1.993 0.005 . 39 20 8 DC H2'' H 2.320 0.005 2 40 20 8 DC H3' H 4.809 0.005 . 41 20 8 DC H5 H 5.149 0.005 1 42 20 8 DC H6 H 7.178 0.005 1 43 21 9 DG H1' H 5.834 0.005 . 44 21 9 DG H2' H 2.520 0.005 . 45 21 9 DG H2'' H 2.704 0.005 2 46 21 9 DG H3' H 4.925 0.005 . 47 21 9 DG H4' H 4.296 0.005 . 48 21 9 DG H8 H 7.808 0.005 1 49 22 10 DC H1' H 5.614 0.005 . 50 22 10 DC H2' H 2.057 0.005 . 51 22 10 DC H2'' H 2.394 0.005 2 52 22 10 DC H3' H 4.848 0.005 . 53 22 10 DC H5 H 5.365 0.005 1 54 22 10 DC H6 H 7.335 0.005 1 55 23 11 DA H1' H 6.283 0.005 . 56 23 11 DA H2' H 2.692 0.005 . 57 23 11 DA H2'' H 2.895 0.005 2 58 23 11 DA H3' H 5.027 0.005 . 59 23 11 DA H4' H 4.413 0.005 . 60 23 11 DA H8 H 8.268 0.005 1 61 24 12 DC H1' H 6.136 0.005 . 62 24 12 DC H2' H 2.133 0.005 . 63 24 12 DC H2'' H 2.169 0.005 2 64 24 12 DC H3' H 4.505 0.005 . 65 24 12 DC H4' H 4.054 0.005 . 66 24 12 DC H5 H 5.445 0.005 1 67 24 12 DC H6 H 7.419 0.005 1 stop_ save_