0.034095
0.000000
0.000000
0.000000
0.034095
0.000000
0.000000
0.000000
0.011141
0.00000
0.00000
0.00000
Kondo, J.
Dock-Bregeon, A.C.
Willkomm, D.K.
Hartmann, R.K.
Westhof, E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
29.330
29.330
89.760
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
DK
Acta Crystallogr.,Sect.F
1744-3091
69
634
639
10.1107/S1744309113013018
23722840
Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet
2013
10.2210/pdb4jrt/pdb
pdb_00004jrt
100
1
CCD
2009-07-04
SINGLE WAVELENGTH
M
x-ray
1
1.0723
1.0
ID23-1
ESRF
1.0723
SYNCHROTRON
ESRF BEAMLINE ID23-1
3979.408
RNA (5'-R(P*GP*GP*GP*UP*GP*GP*UP*GP*CP*GP*GP*G)-3')
1
syn
polymer
3723.264
RNA (5'-R(P*CP*CP*UP*GP*CP*AP*CP*UP*GP*CP*CP*C)-3')
1
syn
polymer
18.015
water
23
nat
water
no
no
GGGUGGUGCGGG
GGGUGGUGCGGG
A
polyribonucleotide
no
no
CCUGCACUGCCC
CCUGCACUGCCC
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.51
50.92
VAPOR DIFFUSION
7.0
Sodium Cacodylate, Lithium acetate, PEG3350, pH 7.0, vapor diffusion, temperature 310K
310
-6.256
1
19
A
1
B
24
-4.942
A_G1:C24_B
1
-7.088
0.311
0.352
0.130
1.802
1
19
A
2
B
23
8.360
A_G2:C23_B
2
-0.871
0.124
0.342
0.258
-8.634
1
19
A
3
B
22
4.737
A_G3:C22_B
3
-6.756
-0.252
0.013
-0.105
-0.350
1
28
A
4
B
21
3.016
A_U4:G21_B
4
-1.225
2.211
0.259
-0.288
-11.055
1
28
A
5
B
20
5.705
A_G5:U20_B
5
-15.663
-2.354
-0.568
-0.629
-12.358
1
19
A
6
B
19
6.328
A_G6:C19_B
6
-9.003
-0.423
-0.273
-0.136
-0.278
1
20
A
7
B
18
2.464
A_U7:A18_B
7
-5.301
-0.258
0.149
0.081
3.812
1
19
A
8
B
17
6.436
A_G8:C17_B
8
-11.757
-0.237
0.108
0.048
6.588
1
19
A
9
B
16
-2.766
A_C9:G16_B
9
-11.386
0.480
-0.332
-0.342
-2.968
1
28
A
10
B
15
1.587
A_G10:U15_B
10
-16.347
-1.798
0.159
-0.575
-10.692
1
19
A
11
B
14
4.768
A_G11:C14_B
11
-14.068
-0.573
-0.134
0.061
-13.977
1
19
A
12
B
13
6.827
A_G12:C13_B
12
-13.044
-0.498
-0.739
-0.066
3.077
33.290
A
A
1
2
-0.398
B
B
24
23
3.101
-0.228
0.421
-1.847
AA_G1G2:C23C24_BB
1
-2.351
4.108
33.209
-3.187
-1.106
1.819
36.379
A
A
2
3
32.991
B
B
23
22
3.198
19.560
-0.047
-1.704
AA_G2G3:C22C23_BB
2
2.154
-3.633
30.750
-5.010
0.326
2.721
39.581
A
A
3
4
11.658
B
B
22
21
2.992
7.845
0.209
-1.154
AA_G3U4:G21C22_BB
3
0.738
-1.096
38.819
-2.515
-0.233
1.236
23.166
A
A
4
5
39.709
B
B
21
20
3.232
14.449
1.029
-2.284
AA_U4G5:U20G21_BB
4
7.174
-19.714
16.681
-9.689
-0.575
2.885
38.140
A
A
5
6
12.334
B
B
20
19
3.292
7.968
-0.492
-1.859
AA_G5G6:C19U20_BB
5
-6.438
9.967
36.788
-3.815
-0.030
2.620
32.508
A
A
6
7
11.982
B
B
19
18
2.883
6.652
-0.572
-1.236
AA_G6U7:A18C19_BB
6
-3.275
5.899
31.673
-3.201
0.534
2.361
33.626
A
A
7
8
24.826
B
B
18
17
3.178
13.933
0.165
-1.354
AA_U7G8:C17A18_BB
7
2.912
-5.189
30.544
-4.367
0.139
2.706
34.262
A
A
8
9
20.628
B
B
17
16
3.279
11.892
-0.114
-1.039
AA_G8C9:G16C17_BB
8
3.549
-6.156
31.998
-3.537
0.724
1.647
31.020
A
A
9
10
32.496
B
B
16
15
3.231
16.486
1.158
-1.855
AA_C9G10:U15G16_BB
9
-3.257
6.420
26.169
-6.048
-2.675
3.132
36.019
A
A
10
11
8.557
B
B
15
14
3.391
5.273
-0.173
-1.603
AA_G10G11:C14U15_BB
10
-0.648
1.052
35.638
-3.344
0.187
3.097
35.071
A
A
11
12
14.912
B
B
14
13
3.557
8.841
0.616
-1.642
AA_G11G12:C13C14_BB
11
6.683
-11.272
33.326
-4.110
0.025
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Database references
Data collection
Database references
Refinement description
1
0
2013-06-05
1
1
2013-07-03
1
2
2023-11-08
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
PDBJ
2013-03-21
REL
REL
HOH
water
in vitro transcription
sample
in vitro transcription
sample
HOH (A 111) AND HOH (A 112) ARE CLOSED TO SYMMETRY-RELATED RNA MOLECULE.
353D
PDB ENTRY 353D
PDB
experimental model
HOH
2
3
HOH
HOH
101
A
HOH
5
3
HOH
HOH
102
A
HOH
6
3
HOH
HOH
103
A
HOH
7
3
HOH
HOH
104
A
HOH
8
3
HOH
HOH
105
A
HOH
10
3
HOH
HOH
106
A
HOH
11
3
HOH
HOH
107
A
HOH
12
3
HOH
HOH
108
A
HOH
20
3
HOH
HOH
109
A
HOH
23
3
HOH
HOH
110
A
HOH
24
3
HOH
HOH
111
A
HOH
26
3
HOH
HOH
112
A
HOH
28
3
HOH
HOH
113
A
HOH
25
3
HOH
HOH
114
A
HOH
1
3
HOH
HOH
101
B
HOH
3
3
HOH
HOH
102
B
HOH
4
3
HOH
HOH
103
B
HOH
9
3
HOH
HOH
104
B
HOH
13
3
HOH
HOH
105
B
HOH
19
3
HOH
HOH
106
B
HOH
21
3
HOH
HOH
107
B
HOH
22
3
HOH
HOH
108
B
HOH
27
3
HOH
HOH
109
B
G
1
n
1
G
1
A
G
2
n
2
G
2
A
G
3
n
3
G
3
A
U
4
n
4
U
4
A
G
5
n
5
G
5
A
G
6
n
6
G
6
A
U
7
n
7
U
7
A
G
8
n
8
G
8
A
C
9
n
9
C
9
A
G
10
n
10
G
10
A
G
11
n
11
G
11
A
G
12
n
12
G
12
A
C
13
n
1
C
13
B
C
14
n
2
C
14
B
U
15
n
3
U
15
B
G
16
n
4
G
16
B
C
17
n
5
C
17
B
A
18
n
6
A
18
B
C
19
n
7
C
19
B
U
20
n
8
U
20
B
G
21
n
9
G
21
B
C
22
n
10
C
22
B
C
23
n
11
C
23
B
C
24
n
12
C
24
B
author_and_software_defined_assembly
PISA
2
dimeric
1250
-9
4610
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
A
P
OP3
G
G
1
1
-0.078
0.012
1.607
1.529
N
1
B
B
P
OP3
C
C
13
13
-0.078
0.012
1.607
1.529
N
CNS_TOPPAR:dna-rna_rep.param
CNS_TOPPAR:water_rep.param
CNS_TOPPAR:ion.param
ccc_xplor.param
113.100
76.1548
41.680
21.0200
0.0000
0.0000
21.0200
0.0000
-42.0400
0.2275
0.1848
2.6000
20.7
220
2330
9.4000
99.4000
1.000
1.000
1
0.000
MOLECULAR REPLACEMENT
PDB ENTRY 353D
41.7378
2.6000
20.7
23
540
0
517
0
0.006
1.195
0.000
1.500
1.526
2.000
0.000
2.000
2.268
2.500
0.4593
0.3756
2.6900
22
211
233
10
100.0000
0.3398
0.3873
2.8000
25
198
223
10
100.0000
0.4286
0.3556
2.9300
26
225
251
10
100.0000
0.3369
0.2959
3.0800
15
203
218
10
100.0000
0.2870
0.2167
3.2800
23
223
246
10
100.0000
0.2602
0.2351
3.5300
19
198
217
10
100.0000
0.1995
0.1689
3.8800
18
222
240
10
100.0000
0.1901
0.1314
4.4500
26
214
240
10
99.2000
0.1971
0.1256
5.6000
22
212
234
10
100.0000
0.1843
0.1612
100.0000
24
204
228
10
94.6000
2.6
20.7
4JRT
2330
1
phasing
Jorge Navaza
ccp4@ccp4.ac.uk
Fortran_77
http://www.ccp4.ac.uk/
AMoRE
program
refinement
Axel T. Brunger
axel.brunger@yale.edu
Fortran_77
http://cns-online.org/
CNS
package
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
data reduction
CrystalClear
data scaling
CrystalClear
Crystal structure of an A-form RNA duplex containing three GU base pairs
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
24
B
N3
C
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
24
B
O2
C
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
24
B
N4
C
12
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
23
B
N3
C
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
23
B
O2
C
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
23
B
N4
C
11
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
B
C
22
B
N3
C
10
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
B
C
22
B
O2
C
10
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
B
C
22
B
N4
C
10
1_555
hydrog
TYPE_28_PAIR
A
U
4
A
N3
U
4
1_555
B
G
21
B
O6
G
9
1_555
hydrog
TYPE_28_PAIR
A
U
4
A
O2
U
4
1_555
B
G
21
B
N1
G
9
1_555
hydrog
TYPE_28_PAIR
A
G
5
A
N1
G
5
1_555
B
U
20
B
O2
U
8
1_555
hydrog
TYPE_28_PAIR
A
G
5
A
O6
G
5
1_555
B
U
20
B
N3
U
8
1_555
hydrog
WATSON-CRICK
A
G
6
A
N1
G
6
1_555
B
C
19
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
6
A
N2
G
6
1_555
B
C
19
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
6
A
O6
G
6
1_555
B
C
19
B
N4
C
7
1_555
hydrog
WATSON-CRICK
A
U
7
A
N3
U
7
1_555
B
A
18
B
N1
A
6
1_555
hydrog
WATSON-CRICK
A
U
7
A
O4
U
7
1_555
B
A
18
B
N6
A
6
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
8
1_555
B
C
17
B
N3
C
5
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
8
1_555
B
C
17
B
O2
C
5
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
8
1_555
B
C
17
B
N4
C
5
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
B
G
16
B
N1
G
4
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
B
G
16
B
O6
G
4
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
B
G
16
B
N2
G
4
1_555
hydrog
TYPE_28_PAIR
A
G
10
A
N1
G
10
1_555
B
U
15
B
O2
U
3
1_555
hydrog
TYPE_28_PAIR
A
G
10
A
O6
G
10
1_555
B
U
15
B
N3
U
3
1_555
hydrog
WATSON-CRICK
A
G
11
A
N1
G
11
1_555
B
C
14
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
11
A
N2
G
11
1_555
B
C
14
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
11
A
O6
G
11
1_555
B
C
14
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
G
12
A
N1
G
12
1_555
B
C
13
B
N3
C
1
1_555
hydrog
WATSON-CRICK
A
G
12
A
N2
G
12
1_555
B
C
13
B
O2
C
1
1_555
hydrog
WATSON-CRICK
A
G
12
A
O6
G
12
1_555
B
C
13
B
N4
C
1
1_555
RNA
A-form RNA, ribose-zipper motif, GU base pair, RNA
4JRT
PDB
1
4JRT
4JRT
PDB
2
4JRT
1
12
4JRT
1
12
4JRT
A
1
1
12
13
24
4JRT
13
24
4JRT
B
2
1
12
78
P 43