data_11607
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish
;
_BMRB_accession_number 11607
_BMRB_flat_file_name bmr11607.str
_Entry_type original
_Submission_date 2016-02-03
_Accession_date 2016-03-17
_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 Otsu Maina . .
2 Norose Nao . .
3 Arai Nao . .
4 Terao Ryo . .
5 Kajikawa Masaki . .
6 Okada Norihiro . .
7 Kawai Gota . .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 97
"13C chemical shifts" 33
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2017-02-06 original BMRB .
stop_
_Original_release_date 2016-03-17
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title
;
Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish
;
_Citation_status 'in preparation'
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID ?
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Otsu Maina . .
2 Norose Nao . .
3 Arai Nao . .
4 Terao Ryo . .
5 Kajikawa Masaki . .
6 Okada Norihiro . .
7 Kawai Gota . .
stop_
_Journal_abbreviation 'Not known'
_Journal_volume .
_Journal_issue .
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first .
_Page_last .
_Year .
_Details .
save_
##################################
# Molecular system description #
##################################
save_assembly
_Saveframe_category molecular_system
_Mol_system_name 'Reverse transcriptase recognition site of transcript of a LINE from Denio Renio, LS-1'
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
'RNA (34-MER)' $RNA_(34-MER)
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_(34-MER)
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class RNA
_Name_common RNA_(34-MER)
_Molecular_mass 10859.578
_Mol_thiol_state 'not present'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 34
_Mol_residue_sequence
;
GGCGCUUUGACACAAUCUAC
AUUGUAAAAGCGCC
;
loop_
_Residue_seq_code
_Residue_author_seq_code
_Residue_label
1 1 G 2 2 G 3 3 C 4 4 G 5 5 C
6 6 U 7 7 U 8 8 U 9 9 G 10 10 A
11 11 C 12 12 A 13 13 C 14 14 A 15 15 A
16 16 U 17 17 C 18 18 U 19 19 A 20 20 C
21 21 A 22 22 U 23 23 U 24 24 G 25 25 U
26 26 A 27 27 A 28 28 A 29 29 A 30 30 G
31 31 C 32 32 G 33 33 C 34 34 C
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
_Details
$RNA_(34-MER) zebrafish 7955 Eukaryota Metazoa Denio Renio 'A part of transcript of a LINE, CR1-1_DR'
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_(34-MER) 'enzymatic semisynthesis' . . . . . 'In vitro transcription with the T7 RNA polymerase'
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_ZfL2-1-34_D2O
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$RNA_(34-MER) 0.3 mM 'natural abundance'
$RNA_(34-MER) 0.26 mM '[U-100% 13C; U-100% 15N]'
'sodium phosphate' 20 mM 'natural abundance'
'sodium chloride' 50 mM 'natural abundance'
D2O 100 % [U-2H]
stop_
save_
save_ZfL2-1-34_H2O
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$RNA_(34-MER) 0.18 mM '[U-13C; U-15N]-Ade'
$RNA_(34-MER) 0.19 mM '[U-13C; U-15N]-Gua'
'sodium phosphate' 20 mM 'natural abundance'
'sodium chloride' 50 mM 'natural abundance'
H2O 95 % 'natural abundance'
D2O 5 % [U-2H]
stop_
save_
############################
# Computer software used #
############################
save_TOPSPIN
_Saveframe_category software
_Name TOPSPIN
_Version 2.1
loop_
_Vendor
_Address
_Electronic_address
'Bruker Biospin' . .
stop_
loop_
_Task
collection
processing
stop_
_Details .
save_
save_CNSSOLVE
_Saveframe_category software
_Name CNSSOLVE
_Version 1.3
loop_
_Vendor
_Address
_Electronic_address
'Brunger, Adams, Clore, Gros, Nilges and Read' . .
stop_
loop_
_Task
refinement
'structure solution'
stop_
_Details .
save_
save_SPARKY
_Saveframe_category software
_Name SPARKY
_Version 3.114
loop_
_Vendor
_Address
_Electronic_address
Goddard . .
stop_
loop_
_Task
'peak picking'
stop_
_Details .
save_
save_X-PLOR_NIH
_Saveframe_category software
_Name X-PLOR_NIH
_Version 2.32
loop_
_Vendor
_Address
_Electronic_address
'Schwieters, Kuszewski, Tjandra and Clore' . .
stop_
loop_
_Task
'grid search'
stop_
_Details .
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model Avance
_Field_strength 600
_Details .
save_
save_spectrometer_2
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model DRX
_Field_strength 600
_Details .
save_
save_spectrometer_3
_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 $ZfL2-1-34_D2O
save_
save_2D_1H-1H_TOCSY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_Sample_label $ZfL2-1-34_D2O
save_
save_2D_1H-13C_HSQC_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-13C HSQC'
_Sample_label $ZfL2-1-34_D2O
save_
save_2D_1H-13C_HSQC_4
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-13C HSQC'
_Sample_label $ZfL2-1-34_D2O
save_
save_2D_1H-13C_HSQC_5
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-13C HSQC'
_Sample_label $ZfL2-1-34_H2O
save_
save_2D_1H-13C_TROSY_6
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-13C TROSY'
_Sample_label $ZfL2-1-34_D2O
save_
save_2D_1H-13C_TROSY_7
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-13C TROSY'
_Sample_label $ZfL2-1-34_D2O
save_
#######################
# Sample conditions #
#######################
save_sample_conditions_1
_Saveframe_category sample_conditions
_Details '20 mM Phosphate sodium buffer, 50 mM NaCl'
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
'ionic strength' 50 . mM
pH 6.5 . pH
pressure 1 . atm
temperature 288 . 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 C 13 'methyl protons' ppm 0 na indirect . . . 0.251449530
DSS H 1 'methyl protons' ppm 0 na direct . . . 1
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 NOESY'
'2D 1H-13C HSQC'
stop_
loop_
_Sample_label
$ZfL2-1-34_D2O
stop_
_Sample_conditions_label $sample_conditions_1
_Chem_shift_reference_set_label $chemical_shift_reference_1
_Mol_system_component_name 'RNA (34-MER)'
_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 5.85 0.01 1
2 1 1 G H2' H 4.98 0.01 1
3 1 1 G H8 H 8.19 0.01 1
4 1 1 G C8 C 136.42 0.16 1
5 2 2 G H1' H 5.96 0.01 1
6 2 2 G H8 H 7.68 0.01 1
7 2 2 G C8 C 133.95 0.16 1
8 3 3 C H1' H 5.59 0.01 1
9 3 3 C H5 H 5.28 0.01 1
10 3 3 C H6 H 7.70 0.01 1
11 4 4 G H1' H 5.76 0.01 1
12 4 4 G H8 H 7.58 0.01 1
13 4 4 G C8 C 133.17 0.16 1
14 5 5 C H1' H 5.52 0.01 1
15 5 5 C H5 H 5.25 0.01 1
16 5 5 C H6 H 7.72 0.01 1
17 6 6 U H1' H 5.54 0.01 1
18 6 6 U H5 H 5.44 0.01 1
19 6 6 U H6 H 7.90 0.01 1
20 6 6 U C5 C 100.51 0.16 1
21 7 7 U H1' H 5.64 0.01 1
22 7 7 U H5 H 5.59 0.01 1
23 7 7 U H6 H 8.02 0.01 1
24 8 8 U H1' H 5.62 0.01 1
25 8 8 U H5 H 5.54 0.01 1
26 8 8 U H6 H 7.83 0.01 1
27 9 9 G H1' H 5.43 0.01 1
28 9 9 G H8 H 7.68 0.01 1
29 9 9 G C8 C 135.12 0.16 1
30 10 10 A H2 H 7.49 0.01 1
31 10 10 A H8 H 7.77 0.01 1
32 10 10 A C2 C 151.61 0.16 1
33 10 10 A C8 C 137.44 0.16 1
34 11 11 C H1' H 6.05 0.01 1
35 11 11 C H5 H 5.81 0.01 1
36 11 11 C H6 H 7.82 0.01 1
37 12 12 A H1' H 5.90 0.01 1
38 12 12 A H2 H 7.33 0.01 1
39 12 12 A H8 H 8.39 0.01 1
40 12 12 A C2 C 150.45 0.16 1
41 12 12 A C8 C 138.05 0.16 1
42 13 13 C H1' H 5.41 0.01 1
43 13 13 C H5 H 5.23 0.01 1
44 13 13 C H6 H 7.58 0.01 1
45 14 14 A H1' H 5.87 0.01 1
46 14 14 A H2 H 6.75 0.01 1
47 14 14 A H8 H 7.95 0.01 1
48 14 14 A C2 C 149.33 0.16 1
49 14 14 A C8 C 136.71 0.16 1
50 15 15 A H1' H 5.91 0.01 1
51 15 15 A H2 H 7.79 0.01 1
52 15 15 A H8 H 7.76 0.01 1
53 15 15 A C2 C 151.16 0.16 1
54 15 15 A C8 C 136.25 0.16 1
55 16 16 U H1' H 5.56 0.01 1
56 16 16 U H5 H 5.03 0.01 1
57 16 16 U H6 H 7.34 0.01 1
58 17 17 C H1' H 5.69 0.01 1
59 17 17 C H2' H 4.24 0.01 1
60 17 17 C H3' H 4.48 0.01 1
61 17 17 C H5 H 5.91 0.01 1
62 17 17 C H6 H 7.76 0.01 1
63 17 17 C C6 C 140.09 0.16 1
64 18 18 U H1' H 5.65 0.01 1
65 18 18 U H5 H 5.77 0.01 1
66 18 18 U H6 H 7.66 0.01 1
67 18 18 U C5 C 102.59 0.16 1
68 18 18 U C6 C 140.58 0.16 1
69 19 19 A H1' H 5.63 0.01 1
70 19 19 A H2 H 7.95 0.01 1
71 19 19 A H8 H 8.00 0.01 1
72 19 19 A C2 C 152.19 0.16 1
73 19 19 A C8 C 138.52 0.16 1
74 20 20 C H1' H 5.94 0.01 1
75 20 20 C H5 H 5.88 0.01 1
76 20 20 C H6 H 7.81 0.01 1
77 21 21 A H1' H 5.79 0.01 1
78 21 21 A H2 H 7.87 0.01 1
79 21 21 A H8 H 8.30 0.01 1
80 21 21 A C2 C 151.11 0.16 1
81 21 21 A C8 C 138.08 0.16 1
82 22 22 U H1' H 5.59 0.01 1
83 22 22 U H5 H 5.13 0.01 1
84 22 22 U H6 H 7.68 0.01 1
85 23 23 U H1' H 5.69 0.01 1
86 23 23 U H5 H 5.57 0.01 1
87 23 23 U H6 H 7.96 0.01 1
88 24 24 G H1' H 5.76 0.01 1
89 24 24 G H8 H 7.72 0.01 1
90 24 24 G C8 C 133.54 0.16 1
91 25 25 U H1' H 5.57 0.01 1
92 25 25 U H5 H 5.07 0.01 1
93 25 25 U H6 H 7.56 0.01 1
94 26 26 A H1' H 5.81 0.01 1
95 26 26 A H2 H 7.32 0.01 1
96 26 26 A H2' H 4.56 0.01 1
97 26 26 A H3' H 4.72 0.01 1
98 26 26 A H8 H 8.08 0.01 1
99 26 26 A C2 C 151.59 0.16 1
100 26 26 A C8 C 138.07 0.16 1
101 27 27 A H1' H 5.61 0.01 1
102 27 27 A H2 H 6.95 0.01 1
103 27 27 A H8 H 8.21 0.01 1
104 27 27 A C2 C 149.82 0.16 1
105 28 28 A H1' H 5.83 0.01 1
106 28 28 A H2 H 7.11 0.01 1
107 28 28 A H8 H 7.83 0.01 1
108 28 28 A C2 C 149.89 0.16 1
109 28 28 A C8 C 136.99 0.16 1
110 29 29 A H1' H 5.85 0.01 1
111 29 29 A H2 H 7.40 0.01 1
112 29 29 A H8 H 7.71 0.01 1
113 29 29 A C2 C 150.32 0.16 1
114 29 29 A C8 C 136.04 0.16 1
115 30 30 G H1' H 5.56 0.01 1
116 30 30 G H8 H 7.15 0.01 1
117 30 30 G C8 C 132.63 0.16 1
118 31 31 C H1' H 5.50 0.01 1
119 31 31 C H5 H 5.17 0.01 1
120 31 31 C H6 H 7.54 0.01 1
121 31 31 C C5 C 94.68 0.16 1
122 31 31 C C6 C 137.35 0.16 1
123 32 32 G H8 H 7.60 0.01 1
124 32 32 G C8 C 133.65 0.16 1
125 33 33 C H1' H 5.55 0.01 1
126 33 33 C H5 H 5.24 0.01 1
127 33 33 C H6 H 7.73 0.01 1
128 34 34 C H5 H 5.55 0.01 1
129 34 34 C H6 H 7.70 0.01 1
130 34 34 C C5 C 95.33 0.16 1
stop_
save_