data_17423 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir ; _BMRB_accession_number 17423 _BMRB_flat_file_name bmr17423.str _Entry_type original _Submission_date 2011-01-22 _Accession_date 2011-01-22 _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 Julien Olivier . . 2 Beadle James R. . 3 Magee Wendy C. . 4 Chatterjee Subhrangsu . . 5 Hostetler Karl Y. . 6 Evans David H. . 7 Sykes Brian D. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 157 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-02-23 update BMRB 'update entry citation' 2011-02-09 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 17422 'CDV DNA duplex' stop_ save_ ############################# # Citation for this entry # ############################# save_Citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of a DNA duplex containing the potent anti-poxvirus agent cidofovir.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21280608 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Julien Olivier . . 2 Beadle James R. . 3 Magee Wendy C. . 4 Chatterjee Subhrangsu . . 5 Hostetler Karl Y. . 6 Evans David H. . 7 Sykes Brian D. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 133 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2264 _Page_last 2274 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Control DNA duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Control DNA duplex, chain A' $Control_DNA_duplex_chain_A 'Control DNA duplex, chain B' $Control_DNA_duplex_chain_B 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_Control_DNA_duplex_chain_A _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common Control_DNA_duplex_chain_A _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence CGCATGCTACGC loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DA 5 DT 6 DG 7 DC 8 DT 9 DA 10 DC 11 DG 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_Control_DNA_duplex_chain_B _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common Control_DNA_duplex_chain_B _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence GCGTAGCATGCG loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DT 5 DA 6 DG 7 DC 8 DA 9 DT 10 DG 11 DC 12 DG 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 $Control_DNA_duplex_chain_A . . . . . . $Control_DNA_duplex_chain_B . . . . . . 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 $Control_DNA_duplex_chain_A 'chemical synthesis' . . . . . $Control_DNA_duplex_chain_B '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 $Control_DNA_duplex_chain_A 2 mM 'natural abundance' $Control_DNA_duplex_chain_B 2 mM 'natural abundance' NaCl 50 mM 'natural abundance' Na2HPO4 20 mM 'natural abundance' EDTA 1 mM 'natural abundance' DSS-d6 0.25 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version 2.1B loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 4.9 loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version 8.0.b30 loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address 'T.L. James' . . stop_ loop_ _Task 'NOE calibration' stop_ _Details . save_ 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 'structure solution' refinement stop_ _Details . save_ save_CORMA _Saveframe_category software _Name CORMA _Version . loop_ _Vendor _Address _Electronic_address 'T.L. James' . . stop_ loop_ _Task 'structure validation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details ; The NMR samples were prepared in 95% H2O/5% D2O or 99.99% D2O, pH between 7.0-7.2, 50 mM NaCl, 20 mM Na2HPO4, 1 mM EDTA and 0.25 mM DSS-d6. ; loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.1 0.1 pH pressure 1 . atm 'ionic strength' 70 . 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 DSS H 1 'methyl protons' ppm 0.00 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 TOCSY' '2D DQF-COSY' '2D 1H-13C HSQC' 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 'Control DNA duplex, chain A' _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 5.7577 0.003 1 2 1 1 DC H2' H 2.4111 0.003 2 3 1 1 DC H2'' H 1.9679 0.003 2 4 1 1 DC H5 H 5.8885 0.003 1 5 1 1 DC H6 H 7.6223 0.003 1 6 1 1 DC H41 H 8.1555 0.003 2 7 1 1 DC H42 H 6.2986 0.003 2 8 2 2 DG H1 H 13.0201 0.003 1 9 2 2 DG H1' H 5.9118 0.003 1 10 2 2 DG H2' H 2.6682 0.003 2 11 2 2 DG H2'' H 2.7570 0.003 2 12 2 2 DG H3' H 4.9788 0.003 1 13 2 2 DG H8 H 7.9570 0.003 1 14 3 3 DC H1' H 5.6478 0.003 1 15 3 3 DC H2' H 2.0958 0.003 2 16 3 3 DC H2'' H 2.4421 0.003 2 17 3 3 DC H5 H 5.4326 0.003 1 18 3 3 DC H6 H 7.3818 0.003 1 19 3 3 DC H41 H 8.3176 0.003 2 20 3 3 DC H42 H 6.4402 0.003 2 21 4 4 DA H1' H 6.2482 0.003 1 22 4 4 DA H2 H 7.6259 0.003 1 23 4 4 DA H2' H 2.6767 0.003 2 24 4 4 DA H2'' H 2.9412 0.003 2 25 4 4 DA H3' H 5.0119 0.003 1 26 4 4 DA H8 H 8.3075 0.003 1 27 5 5 DT H1' H 5.7264 0.003 1 28 5 5 DT H2' H 1.9907 0.003 2 29 5 5 DT H2'' H 2.4089 0.003 2 30 5 5 DT H3 H 13.4086 0.003 1 31 5 5 DT H3' H 5.0135 0.003 1 32 5 5 DT H6 H 7.0776 0.003 1 33 5 5 DT H71 H 1.4339 0.003 1 34 5 5 DT H72 H 1.4339 0.003 1 35 5 5 DT H73 H 1.4339 0.003 1 36 6 6 DG H1 H 12.4951 0.003 1 37 6 6 DG H1' H 5.8216 0.003 1 38 6 6 DG H2' H 2.5893 0.003 2 39 6 6 DG H2'' H 2.6412 0.003 2 40 6 6 DG H3' H 4.9471 0.003 1 41 6 6 DG H8 H 7.7976 0.003 1 42 7 7 DC H1' H 5.8546 0.003 1 43 7 7 DC H2' H 2.0029 0.003 2 44 7 7 DC H2'' H 2.4393 0.003 2 45 7 7 DC H5 H 5.2230 0.003 1 46 7 7 DC H6 H 7.3548 0.003 1 47 7 7 DC H41 H 8.0911 0.003 2 48 7 7 DC H42 H 6.4365 0.003 2 49 8 8 DT H1' H 5.6113 0.003 1 50 8 8 DT H2' H 2.1217 0.003 2 51 8 8 DT H2'' H 2.4446 0.003 2 52 8 8 DT H3 H 13.6224 0.003 1 53 8 8 DT H6 H 7.3752 0.003 1 54 8 8 DT H71 H 1.6137 0.003 1 55 8 8 DT H72 H 1.6137 0.003 1 56 8 8 DT H73 H 1.6137 0.003 1 57 9 9 DA H1' H 6.1564 0.003 1 58 9 9 DA H2 H 7.4362 0.003 1 59 9 9 DA H2' H 2.7076 0.003 2 60 9 9 DA H2'' H 2.8396 0.003 2 61 9 9 DA H3' H 5.0156 0.003 1 62 9 9 DA H8 H 8.2835 0.003 1 63 10 10 DC H1' H 5.5664 0.003 1 64 10 10 DC H2' H 1.9045 0.003 2 65 10 10 DC H2'' H 2.2891 0.003 2 66 10 10 DC H5 H 5.2908 0.003 1 67 10 10 DC H6 H 7.2508 0.003 1 68 10 10 DC H41 H 8.1648 0.003 2 69 10 10 DC H42 H 6.5335 0.003 2 70 11 11 DG H1 H 13.0356 0.003 1 71 11 11 DG H1' H 5.9248 0.003 1 72 11 11 DG H2' H 2.5900 0.003 2 73 11 11 DG H2'' H 2.7070 0.003 2 74 11 11 DG H3' H 4.9504 0.003 1 75 11 11 DG H8 H 7.8480 0.003 1 76 12 12 DC H1' H 6.1582 0.003 1 77 12 12 DC H2' H 2.1701 0.003 2 78 12 12 DC H2'' H 1.8805 0.003 2 79 12 12 DC H5 H 5.4004 0.003 1 80 12 12 DC H6 H 7.4094 0.003 1 81 12 12 DC H41 H 8.1286 0.003 2 82 12 12 DC H42 H 6.4557 0.003 2 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 TOCSY' '2D DQF-COSY' '2D 1H-13C HSQC' 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 'Control DNA duplex, chain B' _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 12.7460 0.003 1 2 13 1 DG H1' H 5.9818 0.003 1 3 13 1 DG H2'' H 2.7844 0.003 2 4 13 1 DG H8 H 7.9312 0.003 1 5 14 2 DC H1' H 5.7559 0.003 1 6 14 2 DC H2' H 2.1363 0.003 2 7 14 2 DC H2'' H 2.4569 0.003 2 8 14 2 DC H5 H 5.3668 0.003 1 9 14 2 DC H6 H 7.4059 0.003 1 10 14 2 DC H41 H 8.4119 0.003 2 11 14 2 DC H42 H 6.5139 0.003 2 12 15 3 DG H1 H 12.8069 0.003 1 13 15 3 DG H1' H 5.9715 0.003 1 14 15 3 DG H2' H 2.6236 0.003 2 15 15 3 DG H2'' H 2.7763 0.003 2 16 15 3 DG H3' H 4.9782 0.003 1 17 15 3 DG H8 H 7.9088 0.003 1 18 16 4 DT H1' H 5.5801 0.003 1 19 16 4 DT H2' H 2.0165 0.003 2 20 16 4 DT H2'' H 2.3555 0.003 2 21 16 4 DT H3 H 13.4985 0.003 1 22 16 4 DT H3' H 4.9765 0.003 1 23 16 4 DT H6 H 7.1900 0.003 1 24 16 4 DT H71 H 1.4954 0.003 1 25 16 4 DT H72 H 1.4954 0.003 1 26 16 4 DT H73 H 1.4954 0.003 1 27 17 5 DA H1' H 6.0197 0.003 1 28 17 5 DA H2 H 7.3324 0.003 1 29 17 5 DA H2' H 2.7025 0.003 2 30 17 5 DA H2'' H 2.8789 0.003 2 31 17 5 DA H3' H 5.0306 0.003 1 32 17 5 DA H8 H 8.1613 0.003 1 33 18 6 DG H1 H 12.7152 0.003 1 34 18 6 DG H1' H 5.6869 0.003 1 35 18 6 DG H2' H 2.4705 0.003 2 36 18 6 DG H2'' H 2.6100 0.003 2 37 18 6 DG H8 H 7.6331 0.003 1 38 19 7 DC H1' H 5.6068 0.003 1 39 19 7 DC H2' H 2.0143 0.003 2 40 19 7 DC H2'' H 2.3946 0.003 2 41 19 7 DC H5 H 5.2360 0.003 1 42 19 7 DC H6 H 7.2693 0.003 1 43 19 7 DC H41 H 8.1386 0.003 2 44 19 7 DC H42 H 6.3016 0.003 2 45 20 8 DA H1' H 6.2093 0.003 1 46 20 8 DA H2 H 7.5726 0.003 1 47 20 8 DA H2' H 2.6348 0.003 2 48 20 8 DA H2'' H 2.9137 0.003 2 49 20 8 DA H3' H 4.9793 0.003 1 50 20 8 DA H8 H 8.2452 0.003 1 51 21 9 DT H1' H 5.7181 0.003 1 52 21 9 DT H2' H 1.9768 0.003 2 53 21 9 DT H2'' H 2.3638 0.003 2 54 21 9 DT H3 H 13.4863 0.003 1 55 21 9 DT H3' H 4.9779 0.003 1 56 21 9 DT H6 H 7.0935 0.003 1 57 21 9 DT H71 H 1.3968 0.003 1 58 21 9 DT H72 H 1.3968 0.003 1 59 21 9 DT H73 H 1.3968 0.003 1 60 22 10 DG H1 H 12.6218 0.003 1 61 22 10 DG H1' H 5.8183 0.003 1 62 22 10 DG H2' H 2.5913 0.003 2 63 22 10 DG H2'' H 2.6551 0.003 2 64 22 10 DG H8 H 7.8370 0.003 1 65 23 11 DC H1' H 5.7682 0.003 1 66 23 11 DC H2' H 1.8937 0.003 2 67 23 11 DC H2'' H 2.3256 0.003 2 68 23 11 DC H5 H 5.3900 0.003 1 69 23 11 DC H6 H 7.3256 0.003 1 70 23 11 DC H41 H 8.3946 0.003 2 71 23 11 DC H42 H 6.5338 0.003 2 72 24 12 DG H1 H 12.5107 0.003 1 73 24 12 DG H1' H 6.1414 0.003 1 74 24 12 DG H2' H 2.6049 0.003 2 75 24 12 DG H8 H 7.9329 0.003 1 stop_ save_