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_