0.030506
0.000000
0.000000
0.000000
0.030506
0.000000
0.000000
0.000000
0.009756
0.00000
0.00000
0.00000
Xiong, Y.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.0
90.0
90.0
32.78
32.78
102.5
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
H2 O
18.015
WATER
non-polymer
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
H
N
113
N
H
N
114
N
O
N
115
N
P
N
116
N
O
N
117
N
O
N
118
N
O
N
119
N
C
N
120
R
C
N
121
N
O
N
122
S
C
N
123
N
O
N
124
R
C
N
125
N
O
N
126
R
C
N
127
N
N
N
128
N
C
N
129
N
O
N
130
N
N
N
131
N
C
N
132
N
O
N
133
N
C
N
134
N
C
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
145
N
H
N
146
N
H
N
147
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
sing
N
119
N
sing
N
120
N
doub
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
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
UK
RNA
RNARFU
2122
1355-8382
6
1316
1324
10.1017/S135583820000090X
10999608
Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge.
2000
10.2210/pdb1dqh/pdb
pdb_00001dqh
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
263
1
IMAGE PLATE
RIGAKU RAXIS IIC
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU300
2806.735
RNA (5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)-3')
HELIX II OF 5S RRNA
1
syn
polymer
3231.988
RNA (5'-R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3')
1
syn
polymer
18.015
water
57
nat
water
no
no
GCCACCCUG
GCCACCCUG
A
polyribonucleotide
no
no
CAGGGUCGGC
CAGGGUCGGC
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.28
46.05
VAPOR DIFFUSION, HANGING DROP
6.0
MGCL2, CACL2, CACODYLATE, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
MGCL2
1
CACL2
1
CACODYLATE
1
MPD
1
MPD
2
-1.806
1
19
A
1
B
19
0.072
A_G1:C19_B
1
-9.823
-0.273
0.185
-0.127
0.018
1
19
A
2
B
18
-1.095
A_C2:G18_B
2
-14.895
0.304
0.239
-0.226
-1.435
1
19
A
3
B
17
-2.191
A_C3:G17_B
3
-11.965
0.067
0.300
-0.128
10.217
1
20
A
4
B
15
1.003
A_A4:U15_B
4
-5.123
-0.117
0.271
-0.114
13.201
1
19
A
5
B
14
-2.123
A_C5:G14_B
5
-10.938
0.423
-0.070
-0.116
7.330
1
19
A
6
B
13
-0.668
A_C6:G13_B
6
-16.022
0.185
0.005
-0.236
1.426
1
19
A
7
B
12
-0.584
A_C7:G12_B
7
-10.165
0.233
0.004
-0.185
0.191
1
20
A
8
B
11
6.545
A_U8:A11_B
8
-14.295
0.097
0.046
-0.159
-5.036
1
19
A
9
B
10
0.161
A_G9:C10_B
9
-10.958
-0.103
0.055
-0.142
3.052
38.738
A
A
1
2
8.322
B
B
19
18
3.227
5.499
-0.716
-1.323
AA_G1C2:G18C19_BB
1
-2.385
3.610
38.289
-2.645
0.798
3.015
35.465
A
A
2
3
10.524
B
B
18
17
3.229
6.378
0.346
-0.983
AA_C2C3:G17G18_BB
2
0.791
-1.305
34.897
-2.514
-0.456
2.971
33.862
A
A
3
4
2.149
B
B
17
15
3.047
1.251
0.528
-1.255
AA_C3A4:U15G17_BB
3
-1.698
2.917
33.798
-2.341
-1.158
3.113
33.190
A
A
4
5
8.305
B
B
15
14
3.351
4.728
-0.402
-1.467
AA_A4C5:G14U15_BB
4
0.205
-0.360
32.860
-3.355
0.737
2.997
34.300
A
A
5
6
12.084
B
B
14
13
3.397
7.078
0.621
-1.720
AA_C5C6:G13G14_BB
5
0.820
-1.400
33.574
-4.015
-0.925
2.783
30.669
A
A
6
7
15.728
B
B
13
12
3.432
8.219
-0.412
-2.075
AA_C6C7:G12G13_BB
6
-1.398
2.675
29.540
-5.492
0.512
2.740
32.844
A
A
7
8
16.247
B
B
12
11
3.219
9.066
0.731
-1.495
AA_C7U8:A11G12_BB
7
2.268
-4.064
31.521
-4.090
-0.932
2.543
33.996
A
A
8
9
21.264
B
B
11
10
3.293
12.172
-0.071
-1.555
AA_U8G9:C10A11_BB
8
0.417
-0.728
31.800
-4.456
0.183
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Version format compliance
Other
Data collection
Database references
1
0
2000-11-13
1
1
2008-04-27
1
2
2011-07-13
1
3
2012-07-25
1
4
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2000-01-04
REL
REL
HOH
water
WAT
103
3
HOH
HOH
103
A
WAT
107
3
HOH
HOH
107
A
WAT
108
3
HOH
HOH
108
A
WAT
124
3
HOH
HOH
124
A
WAT
126
3
HOH
HOH
126
A
WAT
127
3
HOH
HOH
127
A
WAT
131
3
HOH
HOH
131
A
WAT
132
3
HOH
HOH
132
A
WAT
133
3
HOH
HOH
133
A
WAT
135
3
HOH
HOH
135
A
WAT
140
3
HOH
HOH
140
A
WAT
141
3
HOH
HOH
141
A
WAT
142
3
HOH
HOH
142
A
WAT
145
3
HOH
HOH
145
A
WAT
151
3
HOH
HOH
151
A
WAT
153
3
HOH
HOH
153
A
WAT
155
3
HOH
HOH
155
A
WAT
156
3
HOH
HOH
156
A
WAT
100
3
HOH
HOH
100
B
WAT
101
3
HOH
HOH
101
B
WAT
102
3
HOH
HOH
102
B
WAT
104
3
HOH
HOH
104
B
WAT
105
3
HOH
HOH
105
B
WAT
106
3
HOH
HOH
106
B
WAT
109
3
HOH
HOH
109
B
WAT
110
3
HOH
HOH
110
B
WAT
111
3
HOH
HOH
111
B
WAT
112
3
HOH
HOH
112
B
WAT
113
3
HOH
HOH
113
B
WAT
114
3
HOH
HOH
114
B
WAT
115
3
HOH
HOH
115
B
WAT
116
3
HOH
HOH
116
B
WAT
117
3
HOH
HOH
117
B
WAT
118
3
HOH
HOH
118
B
WAT
119
3
HOH
HOH
119
B
WAT
120
3
HOH
HOH
120
B
WAT
121
3
HOH
HOH
121
B
WAT
122
3
HOH
HOH
122
B
WAT
123
3
HOH
HOH
123
B
WAT
125
3
HOH
HOH
125
B
WAT
128
3
HOH
HOH
128
B
WAT
129
3
HOH
HOH
129
B
WAT
130
3
HOH
HOH
130
B
WAT
134
3
HOH
HOH
134
B
WAT
136
3
HOH
HOH
136
B
WAT
137
3
HOH
HOH
137
B
WAT
138
3
HOH
HOH
138
B
WAT
139
3
HOH
HOH
139
B
WAT
143
3
HOH
HOH
143
B
WAT
144
3
HOH
HOH
144
B
WAT
146
3
HOH
HOH
146
B
WAT
147
3
HOH
HOH
147
B
WAT
148
3
HOH
HOH
148
B
WAT
149
3
HOH
HOH
149
B
WAT
150
3
HOH
HOH
150
B
WAT
152
3
HOH
HOH
152
B
WAT
154
3
HOH
HOH
154
B
G
1
n
1
G
1
A
C
2
n
2
C
2
A
C
3
n
3
C
3
A
A
4
n
4
A
4
A
C
5
n
5
C
5
A
C
6
n
6
C
6
A
C
7
n
7
C
7
A
U
8
n
8
U
8
A
G
9
n
9
G
9
A
C
10
n
1
C
10
B
A
11
n
2
A
11
B
G
12
n
3
G
12
B
G
13
n
4
G
13
B
G
14
n
5
G
14
B
U
15
n
6
U
15
B
C
16
n
7
C
16
B
G
17
n
8
G
17
B
G
18
n
9
G
18
B
C
19
n
10
C
19
B
author_defined_assembly
2
dimeric
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
0.2430000
0.2020000
0.2020000
1.7
10.0
653
6645
6022
10.8
90.6
RANDOM
1
THROUGHOUT
2.0
MOLECULAR REPLACEMENT
CNS
1.7
10.0
57
456
0
399
0
0.008
1.26
1.7
22.59
1DQH
6696
6070
2.0
1.0
0.0790000
1
20.2
4.9
90.7
phasing
AMoRE
refinement
CNS
0.9
data reduction
DENZO
data scaling
SCALEPACK
CRYSTAL STRUCTURE OF HELIX II OF THE X. LAEVIS SOMATIC 5S RRNA WITH A CYTOSINE BULGE IN TWO CONFORMATIONS
1
N
N
2
N
N
3
N
N
3
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
19
B
N3
C
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
19
B
O2
C
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
19
B
N4
C
10
1_555
hydrog
WATSON-CRICK
A
C
2
A
N3
C
2
1_555
B
G
18
B
N1
G
9
1_555
hydrog
WATSON-CRICK
A
C
2
A
N4
C
2
1_555
B
G
18
B
O6
G
9
1_555
hydrog
WATSON-CRICK
A
C
2
A
O2
C
2
1_555
B
G
18
B
N2
G
9
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
B
G
17
B
N1
G
8
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
B
G
17
B
O6
G
8
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
B
G
17
B
N2
G
8
1_555
hydrog
WATSON-CRICK
A
A
4
A
N1
A
4
1_555
B
U
15
B
N3
U
6
1_555
hydrog
WATSON-CRICK
A
A
4
A
N6
A
4
1_555
B
U
15
B
O4
U
6
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
B
G
14
B
N1
G
5
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
B
G
14
B
O6
G
5
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
B
G
14
B
N2
G
5
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
B
G
13
B
N1
G
4
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
B
G
13
B
O6
G
4
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
B
G
13
B
N2
G
4
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
B
G
12
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
B
G
12
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
B
G
12
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
U
8
A
N3
U
8
1_555
B
A
11
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
U
8
A
O4
U
8
1_555
B
A
11
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
9
1_555
B
C
10
B
N3
C
1
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
9
1_555
B
C
10
B
O2
C
1
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
9
1_555
B
C
10
B
N4
C
1
1_555
RNA
DOUBLE HELIX, CYTOSINE BULGE, RNA
1DQH
PDB
1
1DQH
1DQH
PDB
2
1DQH
1
9
1DQH
1
9
1DQH
A
1
1
9
10
19
1DQH
10
19
1DQH
B
2
1
10
96
tetragonal
P 43 21 2