data_17788 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Minor conformer of the DNA-peptide conjugate bridged by trimethylene tether ; _BMRB_accession_number 17788 _BMRB_flat_file_name bmr17788.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 Kozekov Ivan D. . 3 Rizzo Carmelo J. . 4 McCullough Amanda . . 5 LLoyd R. S. . 6 Stone Michael P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 187 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-04-23 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17786 (5'S)-8,5'-cyclo-2'-deoxyguanosine 17787 (5'S)-8,5'-cyclo-2'-deoxyguanosine 17789 (5'S)-8,5'-cyclo-2'-deoxyadenosine 17790 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' 17791 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' stop_ _Original_release_date 2014-04-23 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title '-Hydroxy-1,N2-propano-2'-deoxyguanosine DNA adduct conjugates the N-terminal amine of the KWKK peptide via a carbinolamine linkage.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21561113 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huang Hai . . 2 Wang Hao . . 3 Voehler Markus W. . 4 Kozekova Albena . . 5 Rizzo Carmelo J. . 6 McCullough Amanda K. . 7 Lloyd 'R. Stephen' . . 8 Stone Michael P. . stop_ _Journal_abbreviation 'Chem. Res. Toxicol.' _Journal_name_full 'Chemical research in toxicology' _Journal_volume 24 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1123 _Page_last 1133 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'gamma-hydroxy-1,N2-propano-2'-deoxyguanosine adduct' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') $DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') $DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') entity_3 $entity_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*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3')_ _Molecular_mass 3045.029 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GCTAGCGAGTCC loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DT 4 DA 5 DG 6 DC 7 DG 8 DA 9 DG 10 DT 11 DC 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3')_ _Molecular_mass 3045.029 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence GGACTCGCTAGC loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DA 4 DC 5 DT 6 DC 7 DG 8 DC 9 DT 10 DA 11 DG 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_3 _Molecular_mass 591.773 _Mol_thiol_state 'not present' _Details . _Residue_count 5 _Mol_residue_sequence XKWKK loop_ _Residue_seq_code _Residue_label 1 TME 2 LYS 3 TRP 4 LYS 5 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_TME _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common PROPANE _BMRB_code . _PDB_code TME _Standard_residue_derivative . _Molecular_mass 44.096 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Aug 2 15:39:16 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H13 H13 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H31 H31 H . 0 . ? H32 H32 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 C1 C2 ? ? SING C1 H11 ? ? SING C1 H12 ? ? SING C1 H13 ? ? SING C2 C3 ? ? SING C2 H21 ? ? SING C2 H22 ? ? SING C3 H31 ? ? SING C3 H32 ? ? SING C3 H33 ? ? 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(P*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') . . . . . . $DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') . . . . . . $entity_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*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') 'chemical synthesis' . . . . . $DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') 'chemical synthesis' . . . . . $entity_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*CP*TP*AP*GP*CP*GP*AP*GP*TP*C)-3') 1 mM 'natural abundance' $DNA_(5'-D(P*GP*AP*CP*TP*CP*GP*CP*TP*AP*G)-3') 1 mM 'natural abundance' $entity_3 1 mM 'natural abundance' D2O 100 % '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 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 'ionic strength' 100 . mM pH 8.9 . pH pressure 1 . atm temperature 298 . 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 4.773 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_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*CP*TP*AP*GP*CP*GP*AP*GP*TP*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 1 1 DG H1' H 6.02 . . 2 1 1 DG H2' H 2.68 . . 3 1 1 DG H2'' H 2.80 . 2 4 1 1 DG H3' H 4.86 . . 5 1 1 DG H8 H 7.99 . 1 6 2 2 DC H1' H 6.08 . . 7 2 2 DC H2' H 2.14 . . 8 2 2 DC H2'' H 2.53 . 2 9 2 2 DC H3' H 4.84 . . 10 2 2 DC H5 H 5.40 . 1 11 2 2 DC H6 H 7.55 . 1 12 3 3 DT H1' H 5.58 . . 13 3 3 DT H2' H 2.16 . . 14 3 3 DT H2'' H 2.45 . 2 15 3 3 DT H3' H 4.89 . . 16 3 3 DT H6 H 7.42 . 1 17 3 3 DT H71 H 1.68 . 1 18 3 3 DT H72 H 1.68 . 1 19 3 3 DT H73 H 1.68 . 1 20 4 4 DA H1' H 6.07 . . 21 4 4 DA H2 H 7.43 . 1 22 4 4 DA H2' H 2.76 . . 23 4 4 DA H2'' H 2.92 . 2 24 4 4 DA H3' H 5.07 . . 25 4 4 DA H8 H 8.23 . 1 26 5 5 DG H1' H 5.67 . . 27 5 5 DG H2' H 2.49 . . 28 5 5 DG H2'' H 2.60 . 2 29 5 5 DG H3' H 4.97 . . 30 5 5 DG H8 H 7.67 . 1 31 6 6 DC H1' H 5.65 . . 32 6 6 DC H2' H 1.86 . . 33 6 6 DC H2'' H 2.33 . 2 34 6 6 DC H3' H 4.79 . . 35 6 6 DC H5 H 5.21 . 1 36 6 6 DC H6 H 7.20 . 1 37 7 7 DG H1' H 5.71 . . 38 7 7 DG H2' H 2.65 . . 39 7 7 DG H2'' H 2.76 . 2 40 7 7 DG H3' H 4.98 . . 41 7 7 DG H8 H 7.84 . 1 42 8 8 DA H1' H 6.17 . . 43 8 8 DA H2 H 7.83 . 1 44 8 8 DA H2' H 2.76 . . 45 8 8 DA H2'' H 2.87 . 2 46 8 8 DA H3' H 5.04 . . 47 8 8 DA H8 H 8.05 . 1 48 9 9 DG H1' H 5.63 . . 49 9 9 DG H2' H 2.21 . . 50 9 9 DG H2'' H 2.42 . 2 51 9 9 DG H3' H 4.58 . . 52 9 9 DG H8 H 7.40 . 1 53 10 10 DT H1' H 6.05 . . 54 10 10 DT H2' H 2.12 . . 55 10 10 DT H2'' H 2.52 . 2 56 10 10 DT H3' H 4.82 . . 57 10 10 DT H6 H 7.24 . 1 58 10 10 DT H71 H 1.19 . 1 59 10 10 DT H72 H 1.19 . 1 60 10 10 DT H73 H 1.19 . 1 61 11 11 DC H1' H 6.10 . . 62 11 11 DC H2' H 2.23 . . 63 11 11 DC H2'' H 2.50 . 2 64 11 11 DC H3' H 4.85 . . 65 11 11 DC H5 H 5.70 . 1 66 11 11 DC H6 H 7.60 . 1 67 12 12 DC H1' H 6.26 . . 68 12 12 DC H2' H 2.29 . . 69 12 12 DC H2'' H 2.29 . 2 70 12 12 DC H3' H 4.57 . . 71 12 12 DC H5 H 5.82 . 1 72 12 12 DC H6 H 7.69 . 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*GP*AP*CP*TP*CP*GP*CP*TP*AP*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 13 1 DG H1' H 5.64 . . 2 13 1 DG H2' H 2.48 . . 3 13 1 DG H2'' H 2.66 . 2 4 13 1 DG H3' H 4.82 . . 5 13 1 DG H8 H 7.83 . 1 6 14 2 DG H1' H 5.60 . . 7 14 2 DG H2' H 2.70 . . 8 14 2 DG H2'' H 2.80 . 2 9 14 2 DG H3' H 5.04 . . 10 14 2 DG H8 H 7.85 . 1 11 15 3 DA H1' H 6.29 . . 12 15 3 DA H2 H 7.93 . 1 13 15 3 DA H2' H 2.75 . . 14 15 3 DA H2'' H 2.94 . 2 15 15 3 DA H3' H 5.07 . . 16 15 3 DA H8 H 8.21 . 1 17 16 4 DC H1' H 5.80 . . 18 16 4 DC H2' H 1.95 . . 19 16 4 DC H2'' H 2.49 . 2 20 16 4 DC H3' H 4.68 . . 21 16 4 DC H5 H 5.23 . 1 22 16 4 DC H6 H 7.27 . 1 23 17 5 DT H1' H 6.10 . . 24 17 5 DT H2' H 2.19 . . 25 17 5 DT H2'' H 2.59 . 2 26 17 5 DT H3' H 4.90 . . 27 17 5 DT H6 H 7.40 . 1 28 17 5 DT H71 H 1.53 . 1 29 17 5 DT H72 H 1.53 . 1 30 17 5 DT H73 H 1.53 . 1 31 18 6 DC H1' H 5.76 . . 32 18 6 DC H2' H 2.03 . . 33 18 6 DC H2'' H 2.29 . 2 34 18 6 DC H3' H 4.82 . . 35 18 6 DC H5 H 5.62 . 1 36 18 6 DC H6 H 7.46 . 1 37 19 7 DG H1' H 5.91 . . 38 19 7 DG H2' H 2.64 . . 39 19 7 DG H2'' H 2.73 . 2 40 19 7 DG H3' H 4.93 . . 41 19 7 DG H8 H 7.85 . 1 42 20 8 DC H1' H 5.75 . . 43 20 8 DC H2' H 1.90 . . 44 20 8 DC H2'' H 2.32 . 2 45 20 8 DC H3' H 4.62 . . 46 20 8 DC H5 H 5.28 . 1 47 20 8 DC H6 H 7.30 . 1 48 21 9 DT H1' H 5.54 . . 49 21 9 DT H2' H 2.09 . . 50 21 9 DT H2'' H 2.38 . 2 51 21 9 DT H3' H 4.84 . . 52 21 9 DT H6 H 7.35 . 1 53 21 9 DT H71 H 1.63 . 1 54 21 9 DT H72 H 1.63 . 1 55 21 9 DT H73 H 1.63 . 1 56 22 10 DA H1' H 6.04 . . 57 22 10 DA H2 H 7.44 . 1 58 22 10 DA H2' H 2.74 . . 59 22 10 DA H2'' H 2.88 . 2 60 22 10 DA H3' H 5.04 . . 61 22 10 DA H8 H 8.21 . 1 62 23 11 DG H1' H 5.81 . . 63 23 11 DG H2' H 2.47 . . 64 23 11 DG H2'' H 2.64 . 2 65 23 11 DG H3' H 4.95 . . 66 23 11 DG H8 H 7.69 . 1 67 24 12 DC H1' H 6.14 . . 68 24 12 DC H2' H 2.12 . . 69 24 12 DC H2'' H 2.19 . 2 70 24 12 DC H3' H 4.46 . . 71 24 12 DC H5 H 5.40 . 1 72 24 12 DC H6 H 7.42 . 1 stop_ save_ save_assigned_chem_shift_list_1_3 _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 entity_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 25 1 TME H21 H 2.53 . . 2 25 1 TME H22 H 2.68 . . 3 25 1 TME H11 H 1.16 . . 4 25 1 TME H12 H 1.16 . . 5 25 1 TME H13 H 1.16 . . 6 25 1 TME H31 H 1.53 . . 7 25 1 TME H32 H 1.53 . . 8 25 1 TME H33 H 1.83 . . 9 26 2 LYS HA H 3.00 . 1 10 26 2 LYS HB2 H 1.56 . 2 11 26 2 LYS HB3 H 1.56 . 2 12 26 2 LYS HG2 H 1.23 . 2 13 26 2 LYS HG3 H 1.31 . 2 14 26 2 LYS HD2 H 1.68 . 2 15 26 2 LYS HD3 H 1.68 . 2 16 26 2 LYS HE2 H 2.96 . 2 17 26 2 LYS HE3 H 2.96 . 2 18 27 3 TRP HA H 4.89 . 1 19 27 3 TRP HB2 H 3.15 . 2 20 27 3 TRP HB3 H 3.41 . 2 21 27 3 TRP HD1 H 7.41 . 1 22 27 3 TRP HE3 H 7.74 . 1 23 27 3 TRP HZ2 H 7.52 . 1 24 27 3 TRP HZ3 H 7.19 . 1 25 27 3 TRP HH2 H 7.26 . 1 26 28 4 LYS HA H 4.43 . 1 27 28 4 LYS HB2 H 1.80 . 2 28 28 4 LYS HB3 H 1.90 . 2 29 28 4 LYS HG2 H 1.47 . 2 30 28 4 LYS HG3 H 1.50 . 2 31 28 4 LYS HD2 H 1.72 . 2 32 28 4 LYS HD3 H 1.72 . 2 33 28 4 LYS HE2 H 3.01 . 2 34 28 4 LYS HE3 H 3.01 . 2 35 29 5 LYS HA H 4.19 . 1 36 29 5 LYS HB2 H 1.73 . 2 37 29 5 LYS HB3 H 1.87 . 2 38 29 5 LYS HG2 H 1.44 . 2 39 29 5 LYS HG3 H 1.44 . 2 40 29 5 LYS HD2 H 1.69 . 2 41 29 5 LYS HD3 H 1.69 . 2 42 29 5 LYS HE2 H 2.98 . 2 43 29 5 LYS HE3 H 2.98 . 2 stop_ save_