0.008579
0.004953
0.000000
0.000000
0.009907
0.000000
0.000000
0.000000
0.017263
0.000000
0.000000
0.000000
Wedekind, J.E.
Jenkins, J.L.
Krucinska, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.000
90.000
120.000
116.558
116.558
57.926
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
O4 S -2
96.063
SULFATE ION
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
MG
N
115
N
S
N
116
N
O
N
117
N
O
N
118
N
O
N
119
N
O
N
120
N
O
N
121
N
P
N
122
N
O
N
123
N
O
N
124
N
O
N
125
N
C
N
126
R
C
N
127
N
O
N
128
S
C
N
129
N
O
N
130
R
C
N
131
N
O
N
132
R
C
N
133
N
N
N
134
N
C
N
135
N
O
N
136
N
N
N
137
N
C
N
138
N
O
N
139
N
C
N
140
N
C
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
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
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
doub
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
doub
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
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
N
153
N
sing
N
154
N
doub
N
155
N
sing
N
156
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
286
24626
24637
10.1074/jbc.M111.230375
21592962
Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation.
2011
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
284
11012
11016
19261617
The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain.
2010
10.2210/pdb3q51/pdb
pdb_00003q51
100
1
Rh coated flat mirror, toroidal focusing mirror
CCD
2010-04-16
MARMOSAIC 325 mm CCD
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.98
1.0
BL9-2
SSRL
0.98
SYNCHROTRON
SSRL BEAMLINE BL9-2
10599.417
PREQ1 RIBOSWITCH
1
syn
polymer
96.063
SULFATE ION
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
4
nat
water
no
no
CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG
CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG
A
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
n
n
n
n
n
n
n
n
n
1
5.358
77.044
VAPOR DIFFUSION, HANGING DROP
6.0
1.5 M Li2SO4, 0.2 M MES pH 6.0, 0.02 M Magnesium sulfate, and 0.002 M spermine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K
295
4.695
1
19
A
1
A
20
-5.939
A_C1:G20_A
1
-8.608
0.077
-0.141
-0.093
1.934
1
20
A
2
A
19
-1.308
A_U2:A19_A
2
-14.773
-0.224
0.185
-0.253
-10.408
1
19
A
3
A
18
-1.279
A_G3:C18_A
3
-9.593
0.159
-0.151
-0.107
-5.524
1
19
A
4
A
17
-3.067
A_G4:C17_A
4
-10.804
-0.161
0.215
-0.296
-11.988
1
19
A
5
A
16
-5.436
A_G5:C16_A
5
-14.052
0.258
-0.302
-0.131
-29.189
3
23
A
6
A
28
-72.010
A_U6:A28_A
6
-11.392
-0.380
0.761
3.134
-15.354
A
14
A
29
-12.132
A_A14:A29_A
7
-21.281
2.721
0.733
1.767
-4.611
1
19
A
11
A
30
-5.057
A_G11:C30_A
8
-20.129
-0.362
0.365
-0.527
18.766
6
10
A
8
A
31
-66.607
A_G8:A31_A
9
10.836
3.512
-0.561
-4.088
3.139
10
A
10
A
32
-23.985
A_A10:A32_A
10
-10.715
6.458
0.059
-4.602
1.935
1
19
A
33
A
9
-3.727
A_G33:C9_A
11
-4.286
0.234
0.246
-0.400
2.934
35.007
A
A
1
2
9.822
A
A
20
19
3.261
5.882
0.738
-1.732
AA_C1U2:A19G20_AA
1
-0.049
0.083
34.524
-3.723
-1.234
2.451
36.644
A
A
2
3
23.219
A
A
19
18
3.365
14.219
-0.359
-1.643
AA_U2G3:C18A19_AA
2
3.362
-5.491
33.698
-4.426
0.999
2.913
26.086
A
A
3
4
8.075
A
A
18
17
3.169
3.633
0.362
-1.548
AA_G3G4:C17C18_AA
3
-0.911
2.026
25.820
-4.356
-1.034
3.188
40.786
A
A
4
5
10.098
A
A
17
16
3.509
6.993
0.184
-1.665
AA_G4G5:C16C17_AA
4
4.300
-6.209
39.986
-3.187
0.227
-1.767
24.501
A
A
5
6
-9.937
A
A
16
28
1.634
-3.999
-6.395
-0.647
AA_G5U6:A28C16_AA
5
12.600
-31.312
20.675
-1.551
14.984
-1.615
176.600
A
A
6
14
-51.465
A
A
28
29
-2.805
-102.421
-0.244
-2.699
AA_U6A14:A29A28_AA
6
-139.238
69.965
123.176
-1.681
0.572
-3.221
-45.227
A
A
14
11
7.358
A
A
29
30
-3.316
-5.645
0.246
0.647
AA_A14G11:C30A29_AA
7
1.185
1.545
-44.876
-1.347
0.214
1.307
-174.828
A
A
11
8
4.626
A
A
30
31
3.165
-9.168
-2.608
3.093
AA_G11G8:A31C30_AA
8
-170.348
-85.946
-113.227
-1.512
-1.973
4.841
-160.792
A
A
8
10
-21.788
A
A
31
32
-1.892
39.513
-6.056
2.785
AA_G8A10:A32A31_AA
9
155.637
85.821
-17.086
-1.728
-1.826
1.407
-179.845
A
A
10
33
-46.832
A
A
32
9
1.738
93.644
1.482
3.079
AA_A10G33:C9A32_AA
10
-153.314
-76.673
-127.279
-1.732
0.427
audit_author
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_site
repository
Initial release
Version format compliance
Database references
Structure summary
Data collection
Database references
Derived calculations
Refinement description
1
0
2011-05-18
1
1
2011-07-13
1
2
2013-06-12
1
3
2018-01-24
1
4
2023-09-13
_audit_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal structure of PreQ1 riboswitch with PreQ0 metabolite bound
RCSB
Y
RCSB
2010-12-26
REL
REL
SO4
SULFATE ION
MG
MAGNESIUM ION
HOH
water
The RNA strand was chemically synthesized based on the sequence of a class I, Type 1 PreQ1 riboswitch aptamer from T. tengcongensis
sample
3GCA
PDB
experimental model
SO4
103
2
SO4
SO4
103
A
MG
105
3
MG
MG
105
A
HOH
200
4
HOH
HOH
200
A
HOH
201
4
HOH
HOH
201
A
HOH
202
4
HOH
HOH
202
A
HOH
203
4
HOH
HOH
203
A
C
1
n
1
C
1
A
U
2
n
2
U
2
A
G
3
n
3
G
3
A
G
4
n
4
G
4
A
G
5
n
5
G
5
A
U
6
n
6
U
6
A
C
7
n
7
C
7
A
G
8
n
8
G
8
A
C
9
n
9
C
9
A
A
10
n
10
A
10
A
G
11
n
11
G
11
A
U
12
n
12
U
12
A
n
13
13
A
A
14
n
14
A
14
A
C
15
n
15
C
15
A
C
16
n
16
C
16
A
C
17
n
17
C
17
A
C
18
n
18
C
18
A
A
19
n
19
A
19
A
G
20
n
20
G
20
A
U
21
n
21
U
21
A
U
22
n
22
U
22
A
A
23
n
23
A
23
A
A
24
n
24
A
24
A
C
25
n
25
C
25
A
A
26
n
26
A
26
A
A
27
n
27
A
27
A
A
28
n
28
A
28
A
A
29
n
29
A
29
A
C
30
n
30
C
30
A
A
31
n
31
A
31
A
A
32
n
32
A
32
A
G
33
n
33
G
33
A
author_and_software_defined_assembly
PISA
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
A
13
A
A
13
1
Y
104.740
56.6848
34.720
10.6047
0.0000
-0.0000
10.6047
0.0000
-21.2094
0.2722
0.2260
0.2306
2.8500
27.8400
561
5639
9.9500
97.5800
1.000
0.500
0.4000
copied R-free set from 3GCA
1
THROUGHOUT
0.000
FOURIER SYNTHESIS
0.7200
1.0000
3GCA
FLAT BULK SOLVENT MODEL
50.2930
0.2630
0.40
2.8500
27.8400
4
690
6
680
0
0.006
764
0.844
1186
0.056
159
0.008
32
19.382
377
0.3643
0.3714
3.1366
129
1210
1339
4
95.0000
0.3131
0.2379
3.5897
136
1243
1379
4
98.0000
0.2707
0.2294
4.5195
143
1279
1422
4
99.0000
0.2403
0.1907
27.8410
153
1346
1499
4
98.0000
70.4
2.85
50.000
3Q51
5771
0
-3
0.075
1.292
1
14.800
7.200
99.200
0.357
2.850
2.950
558
0.875
1
8.400
100.00
0.249
2.950
3.070
564
0.960
1
8.400
99.800
0.178
3.070
3.210
562
1.237
1
8.300
100.00
0.118
3.210
3.380
563
1.845
1
7.700
100.00
0.099
3.380
3.590
570
1.455
1
7.500
99.800
0.085
3.590
3.870
577
1.529
1
7.000
99.800
0.074
3.870
4.260
567
1.422
1
6.800
99.600
0.058
4.260
4.870
595
1.258
1
6.300
99.800
0.048
4.870
6.140
592
1.234
1
5.600
99.500
0.056
6.140
50.000
623
1.034
1
5.600
94.400
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
program
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
1.6.4_486
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
data collection
HKL-2000
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHENIX
1.6.4_486
Structural analysis of a class I PreQ1 riboswitch aptamer in the metabolite-free state.
1
N
N
2
N
N
3
N
N
4
N
N
hydrog
WATSON-CRICK
A
C
1
A
N3
C
1
1_555
A
G
20
A
N1
G
20
1_555
hydrog
WATSON-CRICK
A
C
1
A
N4
C
1
1_555
A
G
20
A
O6
G
20
1_555
hydrog
WATSON-CRICK
A
C
1
A
O2
C
1
1_555
A
G
20
A
N2
G
20
1_555
hydrog
WATSON-CRICK
A
U
2
A
N3
U
2
1_555
A
A
19
A
N1
A
19
1_555
hydrog
WATSON-CRICK
A
U
2
A
O4
U
2
1_555
A
A
19
A
N6
A
19
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
A
C
18
A
N3
C
18
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
A
C
18
A
O2
C
18
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
A
C
18
A
N4
C
18
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
17
A
N3
C
17
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
17
A
O2
C
17
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
17
A
N4
C
17
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
16
A
N3
C
16
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
16
A
O2
C
16
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
16
A
N4
C
16
1_555
hydrog
TYPE_10_PAIR
A
G
5
A
N2
G
5
1_555
A
A
27
A
N1
A
27
1_555
hydrog
TYPE_10_PAIR
A
G
5
A
N3
G
5
1_555
A
A
27
A
N6
A
27
1_555
hydrog
U-A PAIR
A
U
6
A
O4
U
6
1_555
A
A
14
A
N6
A
14
1_555
hydrog
HOOGSTEEN
A
U
6
A
N3
U
6
1_555
A
A
28
A
N7
A
28
1_555
hydrog
HOOGSTEEN
A
U
6
A
O4
U
6
1_555
A
A
28
A
N6
A
28
1_555
hydrog
C-G PAIR
A
C
7
A
N4
C
7
1_555
A
G
11
A
N7
G
11
1_555
hydrog
C-C MISPAIR
A
C
7
A
O2
C
7
1_555
A
C
30
A
N4
C
30
1_555
hydrog
TYPE_10_PAIR
A
G
8
A
N2
G
8
1_555
A
A
31
A
N1
A
31
1_555
hydrog
TYPE_10_PAIR
A
G
8
A
N3
G
8
1_555
A
A
31
A
N6
A
31
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
A
G
33
A
N1
G
33
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
A
G
33
A
O6
G
33
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
A
G
33
A
N2
G
33
1_555
hydrog
A-A MISPAIR
A
A
10
A
N3
A
10
1_555
A
A
32
A
N6
A
32
1_555
hydrog
WATSON-CRICK
A
G
11
A
N1
G
11
1_555
A
C
30
A
N3
C
30
1_555
hydrog
WATSON-CRICK
A
G
11
A
N2
G
11
1_555
A
C
30
A
O2
C
30
1_555
hydrog
WATSON-CRICK
A
G
11
A
O6
G
11
1_555
A
C
30
A
N4
C
30
1_555
hydrog
A-A MISPAIR
A
A
14
A
N1
A
14
1_555
A
A
29
A
N6
A
29
1_555
hydrog
C-A MISPAIR
A
C
16
A
O2
C
16
1_555
A
A
28
A
N6
A
28
1_555
hydrog
C-A MISPAIR
A
C
17
A
O2
C
17
1_555
A
A
26
A
N6
A
26
1_555
hydrog
G-U MISPAIR
A
G
20
A
N2
G
20
1_555
A
U
21
A
O4
U
21
1_555
RNA
PREQ1, PREQ0, RNA, RIBOSOMAL BINDING SITE, APTAMER, METABOLITE, Pseudoknot, H-type, RIBOSWITCH
3Q51
PDB
1
3Q51
CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG
1
33
3Q51
1
33
3Q51
A
1
1
33
BINDING SITE FOR RESIDUE SO4 A 103
A
SO4
103
Software
1
BINDING SITE FOR RESIDUE MG A 105
A
MG
105
Software
1
A
C
18
A
C
18
1
1_555
A
G
5
A
G
5
1
1_555
182
P 63 2 2