data_19017
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
Solution structure of an intramolecular propeller-type G-quadruplex containing a single bulge
;
_BMRB_accession_number 19017
_BMRB_flat_file_name bmr19017.str
_Entry_type original
_Submission_date 2013-02-08
_Accession_date 2013-02-08
_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 'Thachappilly Mukundan' Vineeth . .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 183
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2014-02-07 update BMRB 'update entry citation'
2013-05-30 original author 'original release'
stop_
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title 'Bulges in g-quadruplexes: broadening the definition of g-quadruplex-forming sequences.'
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 23521617
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Mukundan 'Vineeth Thachappilly' . .
2 Phan 'Anh Tuan' . .
stop_
_Journal_abbreviation 'J. Am. Chem. Soc.'
_Journal_name_full 'Journal of the American Chemical Society'
_Journal_volume 135
_Journal_issue 13
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 5017
_Page_last 5028
_Year 2013
_Details .
save_
##################################
# Molecular system description #
##################################
save_assembly
_Saveframe_category molecular_system
_Mol_system_name 'Bulges in G-quadruplexes'
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
DNA_1 $DNA_1
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_1
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class DNA
_Name_common DNA_1
_Molecular_mass 6034.914
_Mol_thiol_state 'not present'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 19
_Mol_residue_sequence TTGTGGTGGGTGGGTGGGT
loop_
_Residue_seq_code
_Residue_author_seq_code
_Residue_label
1 1 DT 2 2 DT 3 3 DG 4 4 DT 5 5 DG
6 6 DG 7 7 DT 8 8 DG 9 9 DG 10 10 DG
11 11 DT 12 12 DG 13 13 DG 14 14 DG 15 15 DT
16 16 DG 17 17 DG 18 18 DG 19 19 DT
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_1 . . . . . .
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_1 '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
_Concentration_min_value
_Concentration_max_value
_Isotopic_labeling
$DNA_1 . mM 0.1 2.0 'natural abundance'
H2O 90 % . . 'natural abundance'
D2O 10 % . . 'natural abundance'
'Potassium Ion' 60 mM . . 'natural abundance'
stop_
save_
############################
# Computer software used #
############################
save_X-PLOR_NIH
_Saveframe_category software
_Name 'X-PLOR NIH'
_Version .
loop_
_Vendor
_Address
_Electronic_address
'Schwieters, Kuszewski, Tjandra and Clore' . .
stop_
loop_
_Task
'geometry optimization'
refinement
stop_
_Details .
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model Avance
_Field_strength 600
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_2D_1H-1H_TOCSY_1
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_Sample_label $sample_1
save_
save_2D_1H-13C_HSQC_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-13C HSQC'
_Sample_label $sample_1
save_
save_2D_1H-1H_NOESY_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_Sample_label $sample_1
save_
save_2D_1H-13C_JR-HMBC_4
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-13C JR-HMBC'
_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' 0.05 . M
pH 7.0 . 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
DSS H 1 'methyl protons' ppm 0.0 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
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Experiment_label
'2D 1H-1H TOCSY'
'2D 1H-13C HSQC'
'2D 1H-1H NOESY'
'2D 1H-13C JR-HMBC'
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_1
_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 DT H1' H 5.724 0.01 1
2 1 1 DT H2' H 1.935 0.01 1
3 1 1 DT H2'' H 2.278 0.01 1
4 1 1 DT H3' H 4.514 0.01 1
5 1 1 DT H4' H 4.162 0.01 1
6 1 1 DT H5' H 3.436 0.01 2
7 1 1 DT H5'' H 3.454 0.01 2
8 1 1 DT H6 H 7.216 0.01 1
9 1 1 DT H71 H 1.612 0.01 1
10 1 1 DT H72 H 1.612 0.01 1
11 1 1 DT H73 H 1.612 0.01 1
12 2 2 DT H1' H 5.750 0.01 1
13 2 2 DT H2' H 1.738 0.01 1
14 2 2 DT H2'' H 2.265 0.01 1
15 2 2 DT H3' H 4.558 0.01 1
16 2 2 DT H4' H 3.452 0.01 1
17 2 2 DT H5' H 3.240 0.01 2
18 2 2 DT H5'' H 3.587 0.01 2
19 2 2 DT H6 H 7.252 0.01 1
20 2 2 DT H71 H 1.570 0.01 1
21 2 2 DT H72 H 1.570 0.01 1
22 2 2 DT H73 H 1.570 0.01 1
23 3 3 DG H1 H 11.984 0.01 1
24 3 3 DG H1' H 6.263 0.01 1
25 3 3 DG H2' H 3.139 0.01 1
26 3 3 DG H2'' H 3.685 0.01 1
27 3 3 DG H3' H 5.114 0.01 1
28 3 3 DG H4' H 4.397 0.01 1
29 3 3 DG H5' H 3.930 0.01 2
30 3 3 DG H5'' H 4.032 0.01 2
31 3 3 DG H8 H 8.096 0.01 1
32 4 4 DT H1' H 6.443 0.01 1
33 4 4 DT H2' H 2.577 0.01 1
34 4 4 DT H2'' H 2.689 0.01 1
35 4 4 DT H3' H 4.976 0.01 1
36 4 4 DT H4' H 4.434 0.01 1
37 4 4 DT H5' H 4.223 0.01 2
38 4 4 DT H5'' H 4.275 0.01 2
39 4 4 DT H6 H 7.728 0.01 1
40 4 4 DT H71 H 1.965 0.01 1
41 4 4 DT H72 H 1.965 0.01 1
42 4 4 DT H73 H 1.965 0.01 1
43 5 5 DG H1 H 11.525 0.01 1
44 5 5 DG H1' H 6.268 0.01 1
45 5 5 DG H2' H 2.869 0.01 1
46 5 5 DG H2'' H 2.955 0.01 1
47 5 5 DG H3' H 4.902 0.01 1
48 5 5 DG H4' H 4.566 0.01 1
49 5 5 DG H5' H 4.313 0.01 2
50 5 5 DG H5'' H 4.386 0.01 2
51 5 5 DG H8 H 7.566 0.01 1
52 6 6 DG H1 H 11.382 0.01 1
53 6 6 DG H1' H 6.487 0.01 1
54 6 6 DG H2' H 2.670 0.01 1
55 6 6 DG H2'' H 2.601 0.01 1
56 6 6 DG H3' H 5.109 0.01 1
57 6 6 DG H4' H 4.690 0.01 1
58 6 6 DG H5' H 4.296 0.01 2
59 6 6 DG H5'' H 4.392 0.01 2
60 6 6 DG H8 H 7.891 0.01 1
61 7 7 DT H1' H 6.551 0.01 1
62 7 7 DT H2' H 2.686 0.01 1
63 7 7 DT H2'' H 2.485 0.01 1
64 7 7 DT H3' H 5.149 0.01 1
65 7 7 DT H4' H 4.676 0.01 1
66 7 7 DT H5' H 4.318 0.01 2
67 7 7 DT H5'' H 4.374 0.01 2
68 7 7 DT H6 H 7.878 0.01 1
69 7 7 DT H71 H 1.993 0.01 1
70 7 7 DT H72 H 1.993 0.01 1
71 7 7 DT H73 H 1.993 0.01 1
72 8 8 DG H1 H 11.883 0.01 1
73 8 8 DG H1' H 6.132 0.01 1
74 8 8 DG H2' H 2.455 0.01 1
75 8 8 DG H2'' H 2.966 0.01 1
76 8 8 DG H3' H 5.156 0.01 1
77 8 8 DG H4' H 4.458 0.01 1
78 8 8 DG H5' H 4.280 0.01 2
79 8 8 DG H5'' H 4.358 0.01 2
80 8 8 DG H8 H 8.023 0.01 1
81 9 9 DG H1 H 11.507 0.01 1
82 9 9 DG H1' H 6.221 0.01 1
83 9 9 DG H2' H 2.963 0.01 1
84 9 9 DG H2'' H 2.693 0.01 1
85 9 9 DG H3' H 5.106 0.01 1
86 9 9 DG H4' H 4.595 0.01 1
87 9 9 DG H5' H 4.278 0.01 2
88 9 9 DG H8 H 7.998 0.01 1
89 10 10 DG H1 H 11.382 0.01 1
90 10 10 DG H1' H 6.494 0.01 1
91 10 10 DG H2' H 2.712 0.01 1
92 10 10 DG H2'' H 2.604 0.01 1
93 10 10 DG H3' H 5.134 0.01 1
94 10 10 DG H4' H 4.673 0.01 1
95 10 10 DG H5' H 4.329 0.01 2
96 10 10 DG H5'' H 4.444 0.01 2
97 10 10 DG H8 H 7.862 0.01 1
98 11 11 DT H1' H 6.541 0.01 1
99 11 11 DT H2' H 2.680 0.01 1
100 11 11 DT H2'' H 2.489 0.01 1
101 11 11 DT H3' H 5.153 0.01 1
102 11 11 DT H4' H 4.637 0.01 1
103 11 11 DT H5' H 4.315 0.01 2
104 11 11 DT H5'' H 4.374 0.01 2
105 11 11 DT H6 H 7.877 0.01 1
106 11 11 DT H71 H 1.993 0.01 1
107 11 11 DT H72 H 1.993 0.01 1
108 11 11 DT H73 H 1.993 0.01 1
109 12 12 DG H1 H 11.821 0.01 1
110 12 12 DG H1' H 6.186 0.01 1
111 12 12 DG H2' H 2.534 0.01 1
112 12 12 DG H2'' H 2.991 0.01 1
113 12 12 DG H3' H 5.164 0.01 1
114 12 12 DG H4' H 4.464 0.01 1
115 12 12 DG H5' H 4.283 0.01 2
116 12 12 DG H5'' H 4.356 0.01 2
117 12 12 DG H8 H 8.016 0.01 1
118 13 13 DG H1 H 11.454 0.01 1
119 13 13 DG H1' H 6.225 0.01 1
120 13 13 DG H2' H 2.689 0.01 1
121 13 13 DG H2'' H 2.924 0.01 1
122 13 13 DG H3' H 5.104 0.01 1
123 13 13 DG H4' H 4.586 0.01 1
124 13 13 DG H5' H 4.282 0.01 2
125 13 13 DG H5'' H 4.347 0.01 2
126 13 13 DG H8 H 7.974 0.01 1
127 14 14 DG H1 H 11.182 0.01 1
128 14 14 DG H1' H 6.494 0.01 1
129 14 14 DG H2' H 2.700 0.01 1
130 14 14 DG H2'' H 2.612 0.01 1
131 14 14 DG H3' H 5.133 0.01 1
132 14 14 DG H4' H 4.669 0.01 1
133 14 14 DG H5' H 4.332 0.01 2
134 14 14 DG H5'' H 4.433 0.01 2
135 14 14 DG H8 H 7.828 0.01 1
136 15 15 DT H1' H 6.549 0.01 1
137 15 15 DT H2' H 2.682 0.01 1
138 15 15 DT H2'' H 2.489 0.01 1
139 15 15 DT H3' H 5.148 0.01 1
140 15 15 DT H4' H 4.643 0.01 1
141 15 15 DT H5' H 4.300 0.01 2
142 15 15 DT H5'' H 4.387 0.01 2
143 15 15 DT H6 H 7.876 0.01 1
144 15 15 DT H71 H 1.993 0.01 1
145 15 15 DT H72 H 1.993 0.01 1
146 15 15 DT H73 H 1.993 0.01 1
147 16 16 DG H1 H 11.639 0.01 1
148 16 16 DG H1' H 6.133 0.01 1
149 16 16 DG H2' H 2.411 0.01 1
150 16 16 DG H2'' H 2.878 0.01 1
151 16 16 DG H3' H 5.158 0.01 1
152 16 16 DG H4' H 4.469 0.01 1
153 16 16 DG H5' H 4.283 0.01 2
154 16 16 DG H5'' H 4.347 0.01 2
155 16 16 DG H8 H 7.963 0.01 1
156 17 17 DG H1 H 11.709 0.01 1
157 17 17 DG H1' H 6.096 0.01 1
158 17 17 DG H2' H 2.759 0.01 1
159 17 17 DG H2'' H 2.749 0.01 1
160 17 17 DG H3' H 5.099 0.01 1
161 17 17 DG H4' H 4.548 0.01 1
162 17 17 DG H5' H 4.285 0.01 2
163 17 17 DG H5'' H 4.227 0.01 2
164 17 17 DG H8 H 8.045 0.01 1
165 18 18 DG H1 H 11.321 0.01 1
166 18 18 DG H1' H 6.302 0.01 1
167 18 18 DG H2' H 2.614 0.01 1
168 18 18 DG H2'' H 2.776 0.01 1
169 18 18 DG H3' H 4.874 0.01 1
170 18 18 DG H4' H 4.510 0.01 1
171 18 18 DG H5' H 4.308 0.01 2
172 18 18 DG H8 H 7.695 0.01 1
173 19 19 DT H1' H 5.980 0.01 1
174 19 19 DT H2' H 2.101 0.01 1
175 19 19 DT H2'' H 2.148 0.01 1
176 19 19 DT H3' H 4.454 0.01 1
177 19 19 DT H4' H 4.014 0.01 1
178 19 19 DT H5' H 4.084 0.01 2
179 19 19 DT H5'' H 4.230 0.01 2
180 19 19 DT H6 H 7.281 0.01 1
181 19 19 DT H71 H 1.592 0.01 1
182 19 19 DT H72 H 1.592 0.01 1
183 19 19 DT H73 H 1.592 0.01 1
stop_
save_