1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Huber, P.W.
Rife, J.P.
Moore, P.B.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
312
823
832
10.1006/jmbi.2001.4966
11575935
The structure of helix III in Xenopus oocyte 5 S rRNA: an RNA stem containing a two-nucleotide bulge.
2001
10.2210/pdb1jur/pdb
pdb_00001jur
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
Helix III domain of Xenopus Oocyte 5 S rRNA
7135.346
5'-R(*GP*GP*CP*CP*UP*GP*AP*GP*GP*AP*GP*AP*CP*UP*CP*AP*GP*AP*AP*GP*CP*C)-3'
1
syn
polymer
no
no
GGCCUGAGGAGACUCAGAAGCC
GGCCUGAGGAGACUCAGAAGCC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
8.114
1
19
A
1
A
22
-3.470
A_G1:C22_A
1
-9.493
0.329
-0.342
-0.055
-4.325
1
19
A
2
A
21
-3.046
A_G2:C21_A
2
-14.804
-0.695
-0.242
-0.273
-23.600
1
19
A
3
A
20
-2.833
A_C3:G20_A
3
0.310
0.285
0.469
-0.029
11.307
1
19
A
4
A
17
-7.731
A_C4:G17_A
4
-25.487
-0.669
0.117
-0.118
0.125
1
20
A
5
A
16
-1.550
A_U5:A16_A
5
-12.452
0.102
0.476
-0.118
6.567
1
19
A
6
A
15
-2.873
A_G6:C15_A
6
-11.669
-0.089
0.124
-0.095
-11.360
1
20
A
7
A
14
-9.361
A_A7:U14_A
7
-0.845
-0.461
-0.163
-0.059
32.027
1
19
A
8
A
13
-5.391
A_G8:C13_A
8
32.131
0.602
1.001
-0.026
41.164
A
9
A
12
26.482
A_G9:A12_A
9
44.043
6.009
0.769
-3.461
0.838
28.069
A
A
1
2
43.940
A
A
22
21
3.541
19.150
-0.287
-2.525
AA_G1G2:C21C22_AA
1
-6.590
15.121
19.537
-8.796
-0.644
3.043
39.766
A
A
2
3
20.403
A
A
21
20
3.848
13.606
-0.030
-1.762
AA_G2C3:G20C21_AA
2
-2.960
4.439
37.341
-4.312
-0.330
1.894
76.129
A
A
3
4
20.906
A
A
20
17
4.332
24.596
3.352
-1.377
AA_C3C4:G17G20_AA
3
-36.277
30.834
63.873
-1.900
-3.874
3.629
34.511
A
A
4
5
-1.041
A
A
17
16
3.601
-0.614
-0.322
-1.766
AA_C4U5:A16G17_AA
4
-6.573
11.144
33.893
-2.870
-0.594
3.342
30.394
A
A
5
6
-4.534
A
A
16
15
3.177
-2.373
-0.271
-2.146
AA_U5G6:C15A16_AA
5
-1.877
3.586
30.247
-3.618
0.142
2.954
30.171
A
A
6
7
11.648
A
A
15
14
3.466
6.024
-0.791
-2.285
AA_G6A7:U14C15_AA
6
-0.012
0.024
29.578
-5.605
1.518
2.565
34.311
A
A
7
8
-20.777
A
A
14
13
2.171
-11.774
0.139
-2.076
AA_A7G8:C13U14_AA
7
-11.636
20.534
30.159
-2.089
-1.648
1.256
41.723
A
A
8
9
29.512
A
A
13
12
2.481
20.170
0.871
-1.793
AA_G8G9:A12C13_AA
8
-4.302
6.295
36.469
-3.821
-1.501
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-01-16
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
RCSB
Y
RCSB
2001-08-26
REL
REL
The stem of this hairpin occurs naturally in Xenopus Oocytes.
sample
This structure was determined using standard 2D homonuclear techniques.
structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the lowest energy
30
9
2D NOESY
2D NOESY
DQF-COSY
2D_13C_separated_HMQC
2D_31P_separated_COSY
100 mM KCl
6.5
ambient
10
K
100 mM KCl
6.5
ambient
30
K
In addition to the experimentally derived distance constraints and dihedral angle constraints, the structures were computed using 22 non-experimental constraints to ensure Watson-Crick Base pairing and tetraloop formation.
torsion angle dynamics
1
closest to the average
2mM Helix III hairpin;
5mM Cacodylate buffer (pH 6.5);
100 mM KCl
90% H2O/10% D2O
2mM Helix III hairpin;
5mM Cacodylate buffer (pH 6.5);
100 mM KCl
100% D2O
Varian
collection
VNMR
Biosym
processing
Felix
95
Brunger
structure solution
X-PLOR
3.851
Brunger
refinement
X-PLOR
3.851
500
Varian
UNITY
600
Varian
UNITYPLUS
800
Varian
INOVA
500
GE
OMEGA
G
1
n
1
G
1
A
G
2
n
2
G
2
A
C
3
n
3
C
3
A
C
4
n
4
C
4
A
U
5
n
5
U
5
A
G
6
n
6
G
6
A
A
7
n
7
A
7
A
G
8
n
8
G
8
A
G
9
n
9
G
9
A
A
10
n
10
A
10
A
G
11
n
11
G
11
A
A
12
n
12
A
12
A
C
13
n
13
C
13
A
U
14
n
14
U
14
A
C
15
n
15
C
15
A
A
16
n
16
A
16
A
G
17
n
17
G
17
A
A
18
n
18
A
18
A
A
19
n
19
A
19
A
G
20
n
20
G
20
A
C
21
n
21
C
21
A
C
22
n
22
C
22
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
A
G
1
0.077
SIDE CHAIN
1
A
C
3
0.071
SIDE CHAIN
1
A
G
8
0.064
SIDE CHAIN
1
A
G
9
0.101
SIDE CHAIN
1
A
A
10
0.085
SIDE CHAIN
1
A
G
11
0.068
SIDE CHAIN
1
A
A
12
0.125
SIDE CHAIN
1
A
C
13
0.120
SIDE CHAIN
1
A
G
17
0.092
SIDE CHAIN
1
A
A
18
0.091
SIDE CHAIN
1
A
G
20
0.095
SIDE CHAIN
1
A
C
22
0.060
SIDE CHAIN
2
A
G
1
0.080
SIDE CHAIN
2
A
G
9
0.069
SIDE CHAIN
2
A
A
10
0.082
SIDE CHAIN
2
A
G
11
0.065
SIDE CHAIN
2
A
A
12
0.097
SIDE CHAIN
2
A
C
13
0.148
SIDE CHAIN
2
A
G
17
0.083
SIDE CHAIN
2
A
A
19
0.087
SIDE CHAIN
2
A
G
20
0.100
SIDE CHAIN
3
A
C
3
0.084
SIDE CHAIN
3
A
A
7
0.076
SIDE CHAIN
3
A
G
8
0.091
SIDE CHAIN
3
A
G
9
0.082
SIDE CHAIN
3
A
A
10
0.067
SIDE CHAIN
3
A
A
12
0.120
SIDE CHAIN
3
A
C
13
0.191
SIDE CHAIN
3
A
G
17
0.090
SIDE CHAIN
3
A
A
18
0.110
SIDE CHAIN
3
A
G
20
0.119
SIDE CHAIN
3
A
C
22
0.073
SIDE CHAIN
4
A
G
1
0.074
SIDE CHAIN
4
A
G
9
0.092
SIDE CHAIN
4
A
A
10
0.093
SIDE CHAIN
4
A
G
11
0.088
SIDE CHAIN
4
A
A
12
0.085
SIDE CHAIN
4
A
C
13
0.131
SIDE CHAIN
4
A
A
16
0.070
SIDE CHAIN
4
A
A
18
0.132
SIDE CHAIN
4
A
G
20
0.147
SIDE CHAIN
5
A
G
1
0.077
SIDE CHAIN
5
A
G
6
0.080
SIDE CHAIN
5
A
A
7
0.079
SIDE CHAIN
5
A
A
10
0.072
SIDE CHAIN
5
A
A
12
0.071
SIDE CHAIN
5
A
C
13
0.143
SIDE CHAIN
5
A
U
14
0.098
SIDE CHAIN
5
A
A
18
0.135
SIDE CHAIN
5
A
A
19
0.112
SIDE CHAIN
5
A
G
20
0.127
SIDE CHAIN
5
A
C
22
0.064
SIDE CHAIN
6
A
U
5
0.061
SIDE CHAIN
6
A
A
7
0.062
SIDE CHAIN
6
A
G
9
0.084
SIDE CHAIN
6
A
A
10
0.073
SIDE CHAIN
6
A
A
12
0.091
SIDE CHAIN
6
A
C
13
0.148
SIDE CHAIN
6
A
G
17
0.095
SIDE CHAIN
6
A
G
20
0.143
SIDE CHAIN
6
A
C
21
0.074
SIDE CHAIN
7
A
G
9
0.123
SIDE CHAIN
7
A
A
10
0.055
SIDE CHAIN
7
A
G
11
0.066
SIDE CHAIN
7
A
A
12
0.094
SIDE CHAIN
7
A
C
13
0.145
SIDE CHAIN
7
A
U
14
0.066
SIDE CHAIN
7
A
G
17
0.083
SIDE CHAIN
7
A
G
20
0.105
SIDE CHAIN
7
A
C
21
0.077
SIDE CHAIN
7
A
C
22
0.077
SIDE CHAIN
8
A
G
1
0.077
SIDE CHAIN
8
A
G
2
0.058
SIDE CHAIN
8
A
C
3
0.099
SIDE CHAIN
8
A
C
4
0.076
SIDE CHAIN
8
A
G
9
0.055
SIDE CHAIN
8
A
A
10
0.079
SIDE CHAIN
8
A
G
11
0.055
SIDE CHAIN
8
A
C
13
0.156
SIDE CHAIN
8
A
G
17
0.071
SIDE CHAIN
8
A
A
18
0.067
SIDE CHAIN
8
A
A
19
0.060
SIDE CHAIN
8
A
C
22
0.072
SIDE CHAIN
9
A
G
8
0.136
SIDE CHAIN
9
A
G
9
0.097
SIDE CHAIN
9
A
A
10
0.092
SIDE CHAIN
9
A
A
12
0.115
SIDE CHAIN
9
A
C
13
0.092
SIDE CHAIN
9
A
A
18
0.061
SIDE CHAIN
9
A
G
20
0.149
SIDE CHAIN
9
A
C
21
0.066
SIDE CHAIN
1
-9.49
0.70
101.30
91.81
A
A
A
C3'
C2'
C1'
A
A
A
12
12
12
N
1
7.85
1.30
114.00
121.85
A
A
A
N9
C1'
C2'
A
A
A
12
12
12
N
1
7.20
0.70
108.50
115.70
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
1
9.16
1.20
119.70
128.86
A
A
A
C3'
O3'
P
A
A
A
18
18
19
Y
1
4.68
0.70
108.50
113.18
A
A
A
O4'
C1'
N9
A
A
A
19
19
19
N
2
-9.30
0.70
101.30
92.00
A
A
A
C3'
C2'
C1'
A
A
A
12
12
12
N
2
-3.41
0.40
120.30
116.89
A
A
A
C6
N1
C2
C
C
C
13
13
13
N
2
8.43
0.70
108.50
116.93
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
2
6.45
0.90
109.80
116.25
A
A
A
C5'
C4'
O4'
G
G
G
17
17
17
N
3
10.90
1.60
113.70
124.60
A
A
A
C2'
C3'
O3'
C
C
C
3
3
3
N
3
10.86
1.60
113.70
124.56
A
A
A
C2'
C3'
O3'
A
A
A
12
12
12
N
3
-8.97
0.70
101.30
92.33
A
A
A
C3'
C2'
C1'
A
A
A
12
12
12
N
3
8.71
1.30
114.00
122.71
A
A
A
N9
C1'
C2'
A
A
A
12
12
12
N
3
-3.06
0.40
120.30
117.24
A
A
A
C6
N1
C2
C
C
C
13
13
13
N
3
7.99
0.70
108.50
116.49
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
3
4.27
0.70
108.50
112.77
A
A
A
O4'
C1'
N9
G
G
G
17
17
17
N
4
9.79
1.60
113.70
123.49
A
A
A
C2'
C3'
O3'
A
A
A
10
10
10
N
4
-9.37
0.70
101.30
91.93
A
A
A
C3'
C2'
C1'
A
A
A
12
12
12
N
4
8.15
0.70
108.50
116.65
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
5
-9.00
0.70
101.30
92.30
A
A
A
C3'
C2'
C1'
A
A
A
12
12
12
N
5
7.86
1.30
114.00
121.86
A
A
A
N9
C1'
C2'
A
A
A
12
12
12
N
5
-2.53
0.40
120.30
117.77
A
A
A
C6
N1
C2
C
C
C
13
13
13
N
5
6.92
0.70
108.50
115.42
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
5
3.02
0.50
113.80
116.82
A
A
A
N7
C8
N9
A
A
A
16
16
16
N
5
5.43
0.70
108.50
113.93
A
A
A
O4'
C1'
N9
A
A
A
18
18
18
N
5
4.81
0.70
108.50
113.31
A
A
A
O4'
C1'
N9
A
A
A
19
19
19
N
6
4.56
0.70
108.50
113.06
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
6
-9.47
0.70
101.30
91.83
A
A
A
C3'
C2'
C1'
A
A
A
12
12
12
N
6
4.47
0.70
108.50
112.97
A
A
A
O4'
C1'
N9
A
A
A
12
12
12
N
6
-3.11
0.40
120.30
117.19
A
A
A
C6
N1
C2
C
C
C
13
13
13
N
6
7.15
0.70
108.50
115.65
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
6
3.10
0.50
113.80
116.90
A
A
A
N7
C8
N9
A
A
A
16
16
16
N
7
9.73
1.60
113.70
123.43
A
A
A
C2'
C3'
O3'
A
A
A
12
12
12
N
7
-8.94
0.70
101.30
92.36
A
A
A
C3'
C2'
C1'
A
A
A
12
12
12
N
7
-3.13
0.40
120.30
117.17
A
A
A
C6
N1
C2
C
C
C
13
13
13
N
7
7.84
0.70
108.50
116.34
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
8
-4.63
0.70
109.70
105.07
A
A
A
C1'
O4'
C4'
G
G
G
1
1
1
N
8
5.49
0.70
108.50
113.99
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
8
-8.20
0.70
101.30
93.10
A
A
A
C3'
C2'
C1'
A
A
A
12
12
12
N
8
8.00
1.30
114.00
122.00
A
A
A
N9
C1'
C2'
A
A
A
12
12
12
N
8
-3.65
0.40
120.30
116.65
A
A
A
C6
N1
C2
C
C
C
13
13
13
N
8
8.42
0.70
108.50
116.92
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
8
5.44
0.70
108.50
113.94
A
A
A
O4'
C1'
N9
G
G
G
17
17
17
N
9
5.21
0.70
108.50
113.71
A
A
A
O4'
C1'
N9
G
G
G
1
1
1
N
9
-2.54
0.40
120.30
117.76
A
A
A
C6
N1
C2
C
C
C
4
4
4
N
9
9.73
1.60
113.70
123.43
A
A
A
C2'
C3'
O3'
A
A
A
12
12
12
N
9
-8.38
0.70
101.30
92.92
A
A
A
C3'
C2'
C1'
A
A
A
12
12
12
N
9
-2.77
0.40
105.80
103.03
A
A
A
C8
N9
C4
A
A
A
12
12
12
N
9
4.40
0.70
108.50
112.90
A
A
A
O4'
C1'
N1
U
U
U
14
14
14
N
9
7.30
0.70
108.50
115.80
A
A
A
O4'
C1'
N9
A
A
A
16
16
16
N
1
A
A
C8
N9
A
A
16
16
-0.056
0.008
1.373
1.317
N
2
A
A
C8
N9
A
A
16
16
-0.055
0.008
1.373
1.318
N
3
A
A
C8
N9
A
A
16
16
-0.056
0.008
1.373
1.317
N
4
A
A
C8
N9
A
A
16
16
-0.055
0.008
1.373
1.318
N
5
A
A
C8
N9
A
A
16
16
-0.057
0.008
1.373
1.316
N
6
A
A
C8
N9
A
A
16
16
-0.056
0.008
1.373
1.317
N
7
A
A
C8
N9
A
A
16
16
-0.054
0.008
1.373
1.319
N
8
A
A
C8
N9
A
A
16
16
-0.055
0.008
1.373
1.318
N
9
A
A
C8
N9
A
A
16
16
-0.051
0.008
1.373
1.322
N
Solution Structure of Helix III in Xenopus Oocyte 5S rRNA.
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
22
A
N3
C
22
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
22
A
O2
C
22
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
22
A
N4
C
22
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
21
A
N3
C
21
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
21
A
O2
C
21
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
21
A
N4
C
21
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
20
A
N1
G
20
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
20
A
O6
G
20
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
20
A
N2
G
20
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
G
17
A
N1
G
17
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
G
17
A
O6
G
17
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
G
17
A
N2
G
17
1_555
hydrog
C-A MISPAIR
A
C
4
A
O2
C
4
1_555
A
A
19
A
N6
A
19
1_555
hydrog
WATSON-CRICK
A
U
5
A
N3
U
5
1_555
A
A
16
A
N1
A
16
1_555
hydrog
WATSON-CRICK
A
U
5
A
O4
U
5
1_555
A
A
16
A
N6
A
16
1_555
hydrog
WATSON-CRICK
A
G
6
A
N1
G
6
1_555
A
C
15
A
N3
C
15
1_555
hydrog
WATSON-CRICK
A
G
6
A
N2
G
6
1_555
A
C
15
A
O2
C
15
1_555
hydrog
WATSON-CRICK
A
G
6
A
O6
G
6
1_555
A
C
15
A
N4
C
15
1_555
hydrog
WATSON-CRICK
A
A
7
A
N1
A
7
1_555
A
U
14
A
N3
U
14
1_555
hydrog
WATSON-CRICK
A
A
7
A
N6
A
7
1_555
A
U
14
A
O4
U
14
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
8
1_555
A
C
13
A
N3
C
13
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
8
1_555
A
C
13
A
O2
C
13
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
8
1_555
A
C
13
A
N4
C
13
1_555
hydrog
G-A MISPAIR
A
G
9
A
N3
G
9
1_555
A
A
12
A
N6
A
12
1_555
RNA
RNA, 5 S rRNA, bulge
1JUR
PDB
1
1JUR
1
22
1JUR
1
22
1JUR
A
1
1
22