1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Cabello-Villegas, J.
Winkler, M.E.
Nikonowicz, E.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
R
C
N
122
N
O
N
123
R
C
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
O
N
130
N
C
N
131
N
C
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
doub
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
319
1015
1034
10.1016/S0022-2836(02)00382-0
12079344
Solution conformations of unmodified and A(37)N(6)-dimethylallyl modified anticodon stem-loops of Escherichia coli tRNA(Phe).
2002
10.2210/pdb1j4y/pdb
pdb_00001j4y
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
5466.324
anticodon stem-loop of tRNA(Phe)
1
syn
polymer
no
no
GGGGAUUGAAAAUCCCC
GGGGAUUGAAAAUCCCC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-13.752
1
19
A
1
A
17
-3.272
A_G1:C17_A
1
-4.119
-0.459
-1.274
-0.531
-2.803
1
19
A
2
A
16
-1.740
A_G2:C16_A
2
12.085
-0.017
-0.218
-0.196
-23.359
1
19
A
3
A
15
-4.287
A_G3:C15_A
3
-3.786
0.133
-0.534
0.044
-8.709
1
19
A
4
A
14
-0.609
A_G4:C14_A
4
-7.071
0.407
-0.775
-0.002
-17.666
1
20
A
5
A
13
2.716
A_A5:U13_A
5
-21.510
0.121
-1.016
-0.025
-23.210
1
20
A
6
A
12
1.557
A_U6:A12_A
6
-15.197
0.613
0.688
-0.102
-26.473
1
A
7
A
11
45.988
A_U7:A11_A
7
20.618
2.382
1.678
-0.149
2.419
24.703
A
A
1
2
21.535
A
A
17
16
3.004
8.951
-0.876
-1.378
AA_G1G2:C16C17_AA
1
-4.695
11.295
22.570
-5.588
0.805
1.150
53.610
A
A
2
3
55.101
A
A
16
15
4.178
43.413
0.684
-1.813
AA_G2G3:C15C16_AA
2
0.462
-0.586
32.243
-4.891
-0.728
1.990
33.500
A
A
3
4
38.615
A
A
15
14
3.423
20.645
1.339
-1.449
AA_G3G4:C14C15_AA
3
4.681
-8.755
26.114
-5.701
-1.601
3.139
31.059
A
A
4
5
23.831
A
A
14
13
3.887
12.378
1.685
-1.617
AA_G4A5:U13C14_AA
4
4.365
-8.405
28.211
-5.702
-2.202
3.477
29.057
A
A
5
6
-0.425
A
A
13
12
3.663
-0.212
0.439
-1.954
AA_A5U6:A12U13_AA
5
-6.839
13.755
28.257
-3.844
-2.538
3.940
52.301
A
A
6
7
-51.612
A
A
12
11
5.195
-39.272
1.011
-1.701
AA_U6U7:A11A12_AA
6
-18.502
24.316
29.902
2.864
-3.406
database_2
pdbx_nmr_exptl_sample_conditions
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Experimental preparation
Data collection
1
0
2002-07-17
1
1
2008-04-26
1
2
2011-07-13
1
3
2022-02-23
1
4
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_exptl_sample_conditions.pressure_units
_pdbx_nmr_software.name
1KKA contains the ensemble
RCSB
Y
RCSB
2001-12-12
REL
REL
T7 RNA polymerase in vitro transcription
sample
The structure was determined using 1H, 13C, 15N and 31P heteronuclear NMR spectroscopy.
1
3D_15N-separated_NOESY
3D_13C-separated_NOESY
DQF-COSY
HNN-COSY
10 mM KPi, 10mM NaCl
6.8
1
atm
298
K
10 mM KPi, 10mM NaCl
6.8
1
atm
288
K
294 NOE distance constraints, 36 base pair constraints, 70 torsion angle constraints. Global fold without torsion angle constraints. Refinement with torsion angle constraints.
simulated annealing
2mM ACSL-Phe, 15N, 13C
10 mM Potassium Phosphate, 10mM NaCl, 0.02mM EDTA.
90% H2O-10% D2O or 100% D2O.
Brunger, A.
refinement
X-PLOR
3.861
MSI-Biosym
data analysis
Felix
98
Brunger
structure solution
X-PLOR
3.1
500
Bruker
AMX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
G
3
n
3
G
3
A
G
4
n
4
G
4
A
A
5
n
5
A
5
A
U
6
n
6
U
6
A
U
7
n
7
U
7
A
G
8
n
8
G
8
A
A
9
n
9
A
9
A
A
10
n
10
A
10
A
A
11
n
11
A
11
A
A
12
n
12
A
12
A
U
13
n
13
U
13
A
C
14
n
14
C
14
A
C
15
n
15
C
15
A
C
16
n
16
C
16
A
C
17
n
17
C
17
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
4.47
0.50
113.10
117.57
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
1
-2.59
0.40
106.40
103.81
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
1
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
1
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
1
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
3
3
3
N
1
-2.70
0.40
106.40
103.70
A
A
A
C8
N9
C4
G
G
G
3
3
3
N
1
4.51
0.50
113.10
117.61
A
A
A
N7
C8
N9
G
G
G
4
4
4
N
1
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
4
4
4
N
1
3.72
0.50
113.80
117.52
A
A
A
N7
C8
N9
A
A
A
5
5
5
N
1
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
8
8
8
N
1
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
8
8
8
N
1
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
A
A
A
9
9
9
N
1
3.55
0.50
113.80
117.35
A
A
A
N7
C8
N9
A
A
A
10
10
10
N
1
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
11
11
11
N
1
3.78
0.50
113.80
117.58
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
Solution Structure of the Unmodified Anticodon Stem-loop from E. coli tRNA(Phe)
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
17
A
N3
C
17
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
17
A
O2
C
17
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
17
A
N4
C
17
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
16
A
N3
C
16
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
16
A
O2
C
16
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
16
A
N4
C
16
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
17
A
N3
C
17
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
17
A
O2
C
17
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
17
A
N4
C
17
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
A
C
15
A
N3
C
15
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
A
C
15
A
O2
C
15
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
A
C
15
A
N4
C
15
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
14
A
N3
C
14
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
14
A
O2
C
14
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
14
A
N4
C
14
1_555
hydrog
WATSON-CRICK
A
A
5
A
N1
A
5
1_555
A
U
13
A
N3
U
13
1_555
hydrog
WATSON-CRICK
A
A
5
A
N6
A
5
1_555
A
U
13
A
O4
U
13
1_555
hydrog
WATSON-CRICK
A
U
6
A
N3
U
6
1_555
A
A
12
A
N1
A
12
1_555
hydrog
WATSON-CRICK
A
U
6
A
O4
U
6
1_555
A
A
12
A
N6
A
12
1_555
hydrog
U-A PAIR
A
U
7
A
O2
U
7
1_555
A
A
10
A
N6
A
10
1_555
hydrog
U-A PAIR
A
U
7
A
N3
U
7
1_555
A
A
11
A
N1
A
11
1_555
RNA
RNA stem-loop, trinucleotide loop, hairpin, RNA
1J4Y
PDB
1
1J4Y
1
17
1J4Y
1
17
1J4Y
A
1
1
17