data_16951
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
The Structure of RNA Internal Loops with Tandem AG Pairs: 5'GAGC/3'CGAG
;
_BMRB_accession_number 16951
_BMRB_flat_file_name bmr16951.str
_Entry_type new
_Submission_date 2010-05-25
_Accession_date 2010-05-25
_Entry_origination author
_NMR_STAR_version 2.1.1
_Experimental_method NMR
_Details 'Tandem AG pairs with GC closing pairs: r(GACGAGCGUCA)2'
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Hammond Nicholas B. .
2 Kennedy Scott D. .
3 Turner Douglas H. .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 107
"13C chemical shifts" 50
"31P chemical shifts" 10
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2010-07-09 update BMRB 'complete entry citation'
2010-07-02 original author 'original release'
stop_
loop_
_Related_BMRB_accession_number
_Relationship
16950 GACAAGUGUCA
16952 GACUAGAGUCA
16953 GGUAGGCCA
stop_
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title 'RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.'
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 20481618
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Hammond Nicholas B. .
2 Tolbert Blanton S. .
3 Kierzek Ryszard . .
4 Turner Douglas H. .
5 Kennedy Scott D. .
stop_
_Journal_abbreviation Biochemistry
_Journal_name_full Biochemistry
_Journal_volume 49
_Journal_issue 27
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 5817
_Page_last 5827
_Year 2010
_Details .
save_
##################################
# Molecular system description #
##################################
save_assembly
_Saveframe_category molecular_system
_Mol_system_name 5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3'
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
'RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_1' $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')
'RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_2' $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-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_RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class RNA
_Name_common RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')
_Molecular_mass 3530.203
_Mol_thiol_state 'not present'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 11
_Mol_residue_sequence GACGAGCGUCA
loop_
_Residue_seq_code
_Residue_label
1 G 2 A 3 C 4 G 5 A
6 G 7 C 8 G 9 U 10 C
11 A
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
$RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-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
_Details
$RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 'obtained from a vendor' . . . . . Dharmacon
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
$RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 1 mM 'natural abundance'
'sodium chloride' 80 mM 'natural abundance'
'sodium phosphate' 10 mM 'natural abundance'
EDTA 0.5 mM 'natural abundance'
H2O 90 % 'natural abundance'
D2O 10 % 'natural abundance'
stop_
save_
save_sample_2
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 1 mM 'natural abundance'
'sodium chloride' 80 mM 'natural abundance'
'sodium phosphate' 10 mM 'natural abundance'
EDTA 0.5 mM 'natural abundance'
D2O 100 % 'natural abundance'
stop_
save_
############################
# Computer software used #
############################
save_SPARKY
_Saveframe_category software
_Name SPARKY
_Version 3.12
loop_
_Vendor
_Address
_Electronic_address
Goddard . .
stop_
loop_
_Task
'chemical shift assignment'
'data analysis'
stop_
_Details .
save_
save_VNMR
_Saveframe_category software
_Name VNMR
_Version 6.1C
loop_
_Vendor
_Address
_Electronic_address
Varian . .
stop_
loop_
_Task
collection
stop_
_Details .
save_
save_CNS
_Saveframe_category software
_Name CNS
_Version 1.2
loop_
_Vendor
_Address
_Electronic_address
'Brunger, Adams, Clore, Gros, Nilges and Read' . .
stop_
loop_
_Task
'structure solution'
stop_
_Details .
save_
save_AMBER
_Saveframe_category software
_Name AMBER
_Version 9
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 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-13C_HSQC_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-13C HSQC'
_Sample_label $sample_1
save_
save_2D_1H-1H_TOCSY_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_Sample_label $sample_2
save_
save_2D_DQF-COSY_4
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D DQF-COSY'
_Sample_label $sample_2
save_
save_2D_1H-31P_HETCOR_5
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-31P HETCOR'
_Sample_label $sample_2
save_
save_2D_1H-1H_NOESY_6
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_Sample_label $sample_2
save_
#######################
# Sample conditions #
#######################
save_sample_conditions_1
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
temperature 273 . K
pH 6.1 . pH
pressure 1 . atm
'ionic strength' 0.1 . M
stop_
save_
save_sample_conditions_2
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
temperature 288 . K
pH 6.1 . pH
pressure 1 . atm
'ionic strength' 0.1 . M
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
DSS P 31 'methyl protons' ppm 0.00 na indirect . . . 0.404808636
DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530
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_
_Software_label
$SPARKY
stop_
loop_
_Experiment_label
'2D 1H-1H NOESY'
'2D 1H-13C HSQC'
'2D 1H-1H TOCSY'
'2D DQF-COSY'
'2D 1H-31P HETCOR'
stop_
loop_
_Sample_label
$sample_1
$sample_2
stop_
_Sample_conditions_label $sample_conditions_2
_Chem_shift_reference_set_label $chemical_shift_reference_1
_Mol_system_component_name 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_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 G H1 H 12.006 0.002 1
2 1 1 G H1' H 5.845 0.001 .
3 1 1 G H2' H 4.818 0.000 .
4 1 1 G H3' H 4.647 0.001 .
5 1 1 G H4' H 4.445 0.001 .
6 1 1 G H5' H 4.112 0.002 .
7 1 1 G H5'' H 3.974 0.001 2
8 1 1 G H8 H 8.115 0.001 1
9 1 1 G H21 H 7.745 0.000 2
10 1 1 G H22 H 6.160 0.002 2
11 1 1 G C1' C 93.112 0.000 .
12 1 1 G C2' C 75.152 0.000 .
13 1 1 G C3' C 74.017 0.000 .
14 1 1 G C4' C 84.751 0.000 .
15 1 1 G C8 C 138.786 0.000 1
16 2 2 A H1' H 6.004 0.001 .
17 2 2 A H2 H 7.699 0.001 1
18 2 2 A H2' H 4.628 0.001 .
19 2 2 A H3' H 4.725 0.001 .
20 2 2 A H4' H 4.538 0.002 .
21 2 2 A H5' H 4.651 0.001 .
22 2 2 A H5'' H 4.212 0.001 2
23 2 2 A H8 H 8.066 0.000 1
24 2 2 A H61 H 7.898 0.000 2
25 2 2 A H62 H 6.494 0.000 2
26 2 2 A HO2' H 6.918 0.000 .
27 2 2 A C1' C 92.814 0.000 .
28 2 2 A C2 C 154.042 0.000 1
29 2 2 A C2' C 75.554 0.000 .
30 2 2 A C3' C 72.527 0.000 .
31 2 2 A C4' C 82.244 0.000 .
32 2 2 A C8 C 139.685 0.000 1
33 2 2 A P P -4.012 0.000 1
34 3 3 C H1' H 5.306 0.001 .
35 3 3 C H2' H 4.215 0.000 .
36 3 3 C H3' H 4.395 0.004 .
37 3 3 C H4' H 4.371 0.002 .
38 3 3 C H5 H 5.243 0.001 1
39 3 3 C H5' H 4.492 0.002 .
40 3 3 C H5'' H 4.075 0.004 2
41 3 3 C H6 H 7.388 0.001 1
42 3 3 C H41 H 8.150 0.000 2
43 3 3 C H42 H 6.892 0.001 2
44 3 3 C C2' C 75.511 0.000 .
45 3 3 C C3' C 72.292 0.000 .
46 3 3 C C4' C 81.821 0.000 .
47 3 3 C C5 C 97.700 0.000 1
48 3 3 C C6 C 139.843 0.000 1
49 3 3 C P P -3.925 0.000 1
50 4 4 G H1 H 12.444 0.003 1
51 4 4 G H1' H 5.584 0.001 .
52 4 4 G H2' H 3.973 0.001 .
53 4 4 G H3' H 4.808 0.002 .
54 4 4 G H4' H 4.354 0.000 .
55 4 4 G H5' H 4.573 0.000 .
56 4 4 G H5'' H 4.099 0.000 2
57 4 4 G H8 H 7.570 0.001 1
58 4 4 G H21 H 7.301 0.004 2
59 4 4 G H22 H 5.444 0.001 2
60 4 4 G C1' C 92.658 0.000 .
61 4 4 G C2' C 75.726 0.000 .
62 4 4 G C3' C 72.617 0.000 .
63 4 4 G C4' C 81.893 0.000 .
64 4 4 G C8 C 136.651 0.000 1
65 4 4 G P P -4.021 0.000 1
66 5 5 A H1' H 6.119 0.001 .
67 5 5 A H2 H 7.763 0.001 1
68 5 5 A H2' H 4.812 0.000 .
69 5 5 A H3' H 4.813 0.001 .
70 5 5 A H4' H 4.489 0.002 .
71 5 5 A H5' H 4.572 0.000 .
72 5 5 A H5'' H 4.172 0.000 2
73 5 5 A H8 H 8.226 0.001 1
74 5 5 A H61 H 7.668 0.000 2
75 5 5 A H62 H 7.668 0.000 2
76 5 5 A C1' C 91.071 0.000 .
77 5 5 A C2 C 153.981 0.000 1
78 5 5 A C2' C 76.229 0.000 .
79 5 5 A C8 C 140.094 0.000 1
80 5 5 A P P -4.301 0.000 1
81 6 6 G H1 H 12.831 0.002 1
82 6 6 G H1' H 5.559 0.001 .
83 6 6 G H2' H 4.573 0.000 .
84 6 6 G H3' H 4.102 0.006 .
85 6 6 G H4' H 4.529 0.000 .
86 6 6 G H5' H 4.276 0.001 .
87 6 6 G H5'' H 4.116 0.000 2
88 6 6 G H8 H 7.104 0.001 1
89 6 6 G H21 H 5.753 0.003 2
90 6 6 G H22 H 5.753 0.003 2
91 6 6 G C2' C 75.367 0.000 .
92 6 6 G P P -3.530 0.001 1
93 7 7 C H1' H 5.563 0.001 .
94 7 7 C H2' H 4.463 0.000 .
95 7 7 C H3' H 4.507 0.002 .
96 7 7 C H4' H 4.425 0.000 .
97 7 7 C H5 H 5.170 0.001 1
98 7 7 C H6 H 7.451 0.001 1
99 7 7 C H41 H 8.397 0.000 2
100 7 7 C H42 H 6.828 0.002 2
101 7 7 C C2' C 75.090 0.000 .
102 7 7 C C3' C 71.892 0.000 .
103 7 7 C C4' C 81.903 0.000 .
104 7 7 C C5 C 98.039 0.000 1
105 7 7 C C6 C 140.142 0.000 1
106 7 7 C P P -4.403 0.000 1
107 8 8 G H1 H 13.173 0.001 1
108 8 8 G H1' H 5.604 0.001 .
109 8 8 G H2' H 4.363 0.001 .
110 8 8 G H3' H 4.589 0.001 .
111 8 8 G H4' H 4.421 0.003 .
112 8 8 G H5' H 4.516 0.002 .
113 8 8 G H5'' H 4.067 0.004 2
114 8 8 G H8 H 7.549 0.000 1
115 8 8 G H21 H 8.147 0.006 2
116 8 8 G H22 H 5.854 0.001 2
117 8 8 G C2' C 75.464 0.000 .
118 8 8 G C3' C 72.364 0.000 .
119 8 8 G C4' C 82.163 0.000 .
120 8 8 G C8 C 135.933 0.000 1
121 8 8 G P P -3.965 0.000 1
122 9 9 U H1' H 5.452 0.001 .
123 9 9 U H2' H 4.395 0.000 .
124 9 9 U H3 H 14.348 0.002 1
125 9 9 U H3' H 4.440 0.002 .
126 9 9 U H4' H 4.380 0.000 .
127 9 9 U H5 H 5.046 0.001 1
128 9 9 U H5' H 4.536 0.001 .
129 9 9 U H5'' H 4.049 0.000 2
130 9 9 U H6 H 7.726 0.001 1
131 9 9 U C1' C 93.542 0.000 .
132 9 9 U C2' C 75.383 0.000 .
133 9 9 U C3' C 72.227 0.000 .
134 9 9 U C4' C 81.602 0.000 .
135 9 9 U C5 C 102.613 0.000 1
136 9 9 U C6 C 141.404 0.000 1
137 9 9 U P P -4.510 0.000 1
138 10 10 C H1' H 5.543 0.001 .
139 10 10 C H2' H 4.381 0.000 .
140 10 10 C H3' H 4.442 0.002 .
141 10 10 C H4' H 4.381 0.000 .
142 10 10 C H5 H 5.521 0.001 1
143 10 10 C H5' H 4.498 0.000 .
144 10 10 C H5'' H 4.075 0.000 2
145 10 10 C H6 H 7.737 0.002 1
146 10 10 C H41 H 8.201 0.001 2
147 10 10 C H42 H 7.000 0.002 2
148 10 10 C C2' C 75.240 0.000 .
149 10 10 C C5 C 97.729 0.000 1
150 10 10 C C6 C 140.942 0.000 1
151 10 10 C P P -4.074 0.000 1
152 11 11 A H1' H 5.924 0.001 .
153 11 11 A H2 H 7.324 0.001 1
154 11 11 A H2' H 4.022 0.001 .
155 11 11 A H3' H 4.284 0.002 .
156 11 11 A H4' H 4.223 0.002 .
157 11 11 A H5' H 4.445 0.000 .
158 11 11 A H5'' H 4.046 0.001 2
159 11 11 A H8 H 8.037 0.000 1
160 11 11 A H61 H 6.526 0.003 2
161 11 11 A C1' C 91.720 0.000 .
162 11 11 A C2 C 154.336 0.000 1
163 11 11 A C2' C 77.965 0.000 .
164 11 11 A C3' C 70.301 0.000 .
165 11 11 A C4' C 83.921 0.000 .
166 11 11 A C8 C 140.130 0.000 1
167 11 11 A P P -3.801 0.000 1
stop_
save_