0.014348
0.008284
0.000000
0.000000
0.016567
0.000000
0.000000
0.000000
0.011890
0.00000
0.00000
0.00000
Jovine, L.
Hainzl, T.
Oubridge, C.
Scott, W.G.
Li, J.
Sixma, T.K.
Wonacott, A.
Skarzynski, T.
Nagai, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
69.697
69.697
84.102
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
Lu 3
174.967
LUTETIUM (III) ION
LU
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
C10 H15 N5 O11 P2
443.201
n
GUANOSINE-3',5'-DIPHOSPHATE
RNA linking
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
LU
N
115
N
MG
N
116
N
P
N
117
N
O
N
118
N
O
N
119
N
O
N
120
N
P
N
121
N
O
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
Y
133
N
N
Y
134
N
C
Y
135
N
N
Y
136
N
C
N
137
N
C
N
138
N
O
N
139
N
N
N
140
N
C
N
141
N
N
N
142
N
N
Y
143
N
C
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
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
S
N
160
N
O
N
161
N
O
N
162
N
O
N
163
N
O
N
164
N
O
N
165
N
P
N
166
N
O
N
167
N
O
N
168
N
O
N
169
N
C
N
170
R
C
N
171
N
O
N
172
S
C
N
173
N
O
N
174
R
C
N
175
N
O
N
176
R
C
N
177
N
N
N
178
N
C
N
179
N
O
N
180
N
N
N
181
N
C
N
182
N
O
N
183
N
C
N
184
N
C
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
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
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
Y
147
N
sing
Y
148
N
sing
Y
149
N
doub
N
150
N
sing
Y
151
N
sing
N
152
N
sing
Y
153
N
doub
N
154
N
doub
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
doub
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
doub
N
164
N
doub
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
doub
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
doub
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
N
198
N
sing
N
199
N
doub
N
200
N
sing
N
201
N
sing
UK
Structure Fold.Des.
FODEFH
1263
0969-2126
8
527
540
10.1016/S0969-2126(00)00137-4
10801497
Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.
2000
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
56
1033
1037
10.1107/S0907444900006910
Crystallization and preliminary X-ray analysis of the conserved domain IV of E. coli 4.5S RNA
2000
10.2210/pdb1duh/pdb
pdb_00001duh
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
IMAGE PLATE
1999-08-01
MARRESEARCH
MAD
M
x-ray
1
1.0302
1.0
1.3366
1.0
1.3369
1.0
0.9968
1.0
1.3359
1.0
5.2R
ELETTRA
1.0302, 1.3366, 1.3369, 0.9968, 1.3359
SYNCHROTRON
ELETTRA BEAMLINE 5.2R
14663.736
4.5S RNA DOMAIN IV
DOMAIN IV
1
syn
polymer
174.967
LUTETIUM (III) ION
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
96.063
SULFATE ION
2
syn
non-polymer
18.015
water
6
nat
water
no
yes
CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGA(PGP)
CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAG
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
n
n
n
n
n
n
n
n
n
n
n
n
1
4.15
76.9
VAPOR DIFFUSION, SITTING DROP
6.0
CRYSTALLIZED FROM 1.60-1.90 M (NH4)2SO4, 0.09 M MAGNESIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.0, AT 303 K. CRYSTALS WERE STABILISED AT 292 K IN A SOLUTION OF 2.20 M (NH4)2SO4, 0.01 M MGCL2, 0.05 M BIS-TRIS-HCL PH 6.0. SOAK CONDITIONS: CRYSTALS WERE SOAKED IN STABILISATION SOLUTION CONTAINING 0.002 M LUTETIUM CHLORIDE HEXAHYDRATE. CRYOPROTECTION CONDITIONS: AFTER ADDITION OF 20% GLYCEROL (W/V) TO THE SOAK SOLUTION, CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN., VAPOR DIFFUSION, SITTING DROP, temperature 303.15K
303.15
MAGNESIUM ACETATE
1
SODIUM CACODYLATE
1
BIS-TRIS-HCL
1
(NH4)2SO4
1
MGCL2
1
LUCL3
1
(NH4)2SO4
2
BIS-TRIS-HCL
2
10.286
1
19
A
31
A
75
1.428
A_C31:PGP75_A
1
-13.615
0.569
-0.156
-0.528
1.281
1
20
A
32
A
74
4.093
A_U32:A74_A
2
-16.429
-0.039
0.276
-0.305
-0.876
1
19
A
33
A
73
0.198
A_C33:G73_A
3
-9.775
0.330
0.294
-0.321
5.243
1
20
A
34
A
72
10.563
A_U34:A72_A
4
-0.181
0.090
-0.205
-0.089
6.409
1
A
35
A
71
9.821
A_G35:C71_A
5
-7.541
0.339
1.035
0.088
0.363
1
28
A
36
A
70
3.557
A_U36:G70_A
6
-7.213
1.988
0.561
-0.384
-5.645
1
28
A
37
A
69
2.583
A_U37:G69_A
7
-8.165
2.087
0.134
-0.582
-6.795
1
20
A
38
A
68
4.613
A_U38:A68_A
8
-9.445
0.353
0.567
-0.045
-0.012
1
19
A
43
A
66
1.259
A_G43:C66_A
9
-2.060
-0.732
-0.125
-0.192
-6.507
1
19
A
44
A
65
-0.024
A_G44:C65_A
10
-10.547
0.125
-0.052
-0.109
-4.324
1
28
A
45
A
64
4.099
A_U45:G64_A
11
-4.440
1.965
0.096
-0.572
1.310
6
A
46
A
63
-21.379
A_C46:A63_A
12
-8.844
6.134
0.654
-4.675
1.160
4
25
A
47
A
62
-85.633
A_A47:C62_A
13
-1.218
-2.817
0.001
-0.616
4.374
A
48
A
61
-18.635
A_G48:G61_A
14
-9.848
-6.967
0.717
-2.593
8.697
8
A
49
A
60
-13.183
A_G49:A60_A
15
-8.319
-0.526
-0.106
1.433
15.035
1
20
A
50
A
59
-2.650
A_U50:A59_A
16
-8.684
-0.617
0.064
-0.217
9.258
1
19
A
51
A
58
2.004
A_C51:G58_A
17
-4.855
-0.651
-0.102
-0.156
2.227
1
19
A
52
A
57
1.910
A_C52:G57_A
18
-9.075
0.724
-0.069
-0.404
-5.500
9
11
A
53
A
56
-6.386
A_G53:A56_A
19
-8.266
6.399
-0.162
-3.747
17.406
9
11
A
54
A
55
13.660
A_G54:A55_A
20
6.587
6.232
0.677
-4.144
-17.406
9
11
A
55
A
54
13.660
A_A55:G54_A
21
6.587
-6.232
0.677
-4.144
5.500
9
11
A
56
A
53
-6.386
A_A56:G53_A
22
-8.266
-6.399
-0.162
-3.747
-2.227
1
19
A
57
A
52
1.910
A_G57:C52_A
23
-9.075
-0.724
-0.069
-0.404
-9.258
1
19
A
58
A
51
2.004
A_G58:C51_A
24
-4.855
0.651
-0.102
-0.156
-15.035
1
20
A
59
A
50
-2.650
A_A59:U50_A
25
-8.684
0.617
0.064
-0.217
-8.697
8
A
60
A
49
-13.183
A_A60:G49_A
26
-8.319
0.526
-0.106
1.433
-4.374
A
61
A
48
-18.635
A_G61:G48_A
27
-9.847
6.967
0.717
-2.593
-1.160
4
25
A
62
A
47
-85.633
A_C62:A47_A
28
-1.218
2.817
0.001
-0.616
-1.310
6
A
63
A
46
-21.379
A_A63:C46_A
29
-8.844
-6.134
0.654
-4.675
4.324
1
28
A
64
A
45
4.099
A_G64:U45_A
30
-4.440
-1.965
0.096
-0.572
6.507
1
19
A
65
A
44
-0.024
A_C65:G44_A
31
-10.547
-0.125
-0.052
-0.109
0.012
1
19
A
66
A
43
1.259
A_C66:G43_A
32
-2.060
0.732
-0.125
-0.192
6.795
1
20
A
68
A
38
4.613
A_A68:U38_A
33
-9.445
-0.353
0.567
-0.045
5.645
1
28
A
69
A
37
2.583
A_G69:U37_A
34
-8.165
-2.087
0.134
-0.582
-0.363
1
28
A
70
A
36
3.557
A_G70:U36_A
35
-7.213
-1.988
0.561
-0.384
-6.409
1
A
71
A
35
9.821
A_C71:G35_A
36
-7.541
-0.339
1.035
0.088
-5.243
1
20
A
72
A
34
10.563
A_A72:U34_A
37
-0.181
-0.090
-0.205
-0.089
0.876
1
19
A
73
A
33
0.198
A_G73:C33_A
38
-9.775
-0.330
0.294
-0.321
-1.281
1
20
A
74
A
32
4.093
A_A74:U32_A
39
-16.429
0.039
0.276
-0.305
-10.286
1
19
A
75
A
31
1.428
A_PGP75:C31_A
40
-13.615
-0.569
-0.156
-0.528
1.992
35.970
A
A
31
32
28.901
A
A
75
74
3.199
17.133
0.236
-1.722
AA_C31U32:A74PGP75_AA
1
-3.713
6.264
31.534
-4.864
-0.831
3.209
38.107
A
A
32
33
0.065
A
A
74
73
3.204
0.042
-0.222
-1.421
AA_U32C33:G73A74_AA
2
-1.535
2.351
38.077
-2.181
0.150
3.199
27.716
A
A
33
34
-0.271
A
A
73
72
3.195
-0.130
-0.149
-1.557
AA_C33U34:A72G73_AA
3
0.497
-1.038
27.711
-3.219
0.429
2.431
34.426
A
A
34
35
14.520
A
A
72
71
2.981
8.427
-0.180
-1.763
AA_U34G35:C71A72_AA
4
-8.355
14.396
32.374
-4.101
-0.809
3.234
38.466
A
A
35
36
1.260
A
A
71
70
3.296
0.828
-0.141
-1.421
AA_G35U36:G70C71_AA
5
4.114
-6.257
38.245
-2.259
0.725
2.614
37.013
A
A
36
37
10.759
A
A
70
69
3.048
6.736
0.283
-2.106
AA_U36U37:G69G70_AA
6
8.568
-13.686
35.426
-4.120
0.575
1.145
27.692
A
A
37
38
36.165
A
A
69
68
3.009
16.236
-0.871
-2.286
AA_U37U38:A68G69_AA
7
-0.448
0.999
22.504
-7.542
1.744
5.505
79.614
A
A
38
43
12.601
A
A
68
66
6.092
16.050
-1.271
-2.525
AA_U38G43:C66A68_AA
8
4.766
-3.742
78.121
-2.745
1.222
3.026
37.641
A
A
43
44
8.399
A
A
66
65
3.349
5.399
-0.131
-2.114
AA_G43G44:C65C66_AA
9
-1.910
2.971
37.218
-3.964
-0.040
3.222
35.792
A
A
44
45
-0.752
A
A
65
64
3.197
-0.462
0.246
-1.632
AA_G44U45:G64C65_AA
10
0.888
-1.445
35.778
-2.590
-0.275
2.934
55.061
A
A
45
46
9.564
A
A
64
63
3.233
8.799
-0.763
-1.280
AA_U45C46:A63G64_AA
11
4.962
-5.394
54.197
-1.880
1.105
3.973
7.291
A
A
46
47
26.079
A
A
63
62
2.855
3.130
-4.712
-0.110
AA_C46A47:C62A63_AA
12
-2.539
21.153
6.077
-13.423
26.867
2.724
29.327
A
A
47
48
13.822
A
A
62
61
2.797
6.928
4.977
-1.480
AA_A47G48:G61C62_AA
13
2.123
-4.236
28.436
-4.204
-9.438
3.166
53.621
A
A
48
49
4.817
A
A
61
60
3.275
4.341
0.229
-1.402
AA_G48G49:A60G61_AA
14
1.775
-1.970
53.430
-1.822
-0.144
2.630
26.297
A
A
49
50
5.604
A
A
60
59
2.940
2.530
0.232
-2.074
AA_G49U50:A59A60_AA
15
-5.164
11.439
25.672
-5.144
-1.706
2.883
33.893
A
A
50
51
12.577
A
A
59
58
3.407
7.266
0.472
-1.861
AA_U50C51:G58A59_AA
16
-3.371
5.835
32.960
-4.333
-1.338
3.282
39.621
A
A
51
52
5.326
A
A
58
57
3.473
3.605
0.263
-2.036
AA_C51C52:G57G58_AA
17
0.082
-0.122
39.464
-3.440
-0.379
3.488
54.847
A
A
52
53
4.948
A
A
57
56
3.588
4.550
-0.276
-0.882
AA_C52G53:A56G57_AA
18
3.494
-3.799
54.569
-1.252
0.526
2.770
33.565
A
A
53
54
14.498
A
A
56
55
2.861
8.213
1.280
-0.942
AA_G53G54:A55A56_AA
19
7.980
-14.086
31.604
-2.828
-1.053
-0.722
-10.157
A
A
54
55
68.697
A
A
55
54
4.165
-9.461
0.000
-2.406
AA_G54A55:G54A55_AA
20
0.000
0.000
-3.699
26.862
0.000
2.770
33.565
A
A
55
56
14.498
A
A
54
53
2.861
8.213
-1.280
-0.942
AA_A55A56:G53G54_AA
21
-7.980
14.085
31.604
-2.828
1.053
3.488
54.847
A
A
56
57
4.948
A
A
53
52
3.588
4.550
0.276
-0.882
AA_A56G57:C52G53_AA
22
-3.494
3.799
54.569
-1.252
-0.526
3.282
39.621
A
A
57
58
5.326
A
A
52
51
3.473
3.605
-0.263
-2.036
AA_G57G58:C51C52_AA
23
-0.082
0.122
39.464
-3.440
0.379
2.883
33.893
A
A
58
59
12.577
A
A
51
50
3.407
7.266
-0.472
-1.861
AA_G58A59:U50C51_AA
24
3.371
-5.835
32.960
-4.333
1.338
2.630
26.297
A
A
59
60
5.604
A
A
50
49
2.940
2.530
-0.232
-2.074
AA_A59A60:G49U50_AA
25
5.164
-11.439
25.672
-5.144
1.706
3.166
53.620
A
A
60
61
4.817
A
A
49
48
3.275
4.341
-0.229
-1.402
AA_A60G61:G48G49_AA
26
-1.775
1.970
53.430
-1.822
0.144
2.724
29.327
A
A
61
62
13.822
A
A
48
47
2.797
6.928
-4.977
-1.480
AA_G61C62:A47G48_AA
27
-2.123
4.236
28.436
-4.204
9.438
3.973
7.291
A
A
62
63
26.079
A
A
47
46
2.855
3.130
4.712
-0.110
AA_C62A63:C46A47_AA
28
2.539
-21.153
6.077
-13.424
-26.867
2.934
55.061
A
A
63
64
9.564
A
A
46
45
3.233
8.799
0.763
-1.280
AA_A63G64:U45C46_AA
29
-4.962
5.394
54.197
-1.880
-1.105
3.222
35.792
A
A
64
65
-0.752
A
A
45
44
3.197
-0.462
-0.246
-1.632
AA_G64C65:G44U45_AA
30
-0.888
1.445
35.778
-2.590
0.275
3.026
37.641
A
A
65
66
8.399
A
A
44
43
3.349
5.399
0.131
-2.114
AA_C65C66:G43G44_AA
31
1.910
-2.971
37.218
-3.964
0.040
5.505
79.614
A
A
66
68
12.601
A
A
43
38
6.092
16.050
1.271
-2.525
AA_C66A68:U38G43_AA
32
-4.766
3.742
78.121
-2.745
-1.222
1.145
27.692
A
A
68
69
36.165
A
A
38
37
3.009
16.236
0.871
-2.286
AA_A68G69:U37U38_AA
33
0.448
-0.999
22.504
-7.542
-1.744
2.614
37.013
A
A
69
70
10.759
A
A
37
36
3.048
6.736
-0.283
-2.106
AA_G69G70:U36U37_AA
34
-8.568
13.686
35.426
-4.120
-0.575
3.234
38.466
A
A
70
71
1.260
A
A
36
35
3.296
0.828
0.141
-1.421
AA_G70C71:G35U36_AA
35
-4.114
6.257
38.245
-2.259
-0.725
2.431
34.426
A
A
71
72
14.520
A
A
35
34
2.981
8.427
0.180
-1.763
AA_C71A72:U34G35_AA
36
8.355
-14.396
32.374
-4.101
0.809
3.199
27.716
A
A
72
73
-0.271
A
A
34
33
3.195
-0.130
0.149
-1.557
AA_A72G73:C33U34_AA
37
-0.497
1.038
27.711
-3.219
-0.429
3.209
38.107
A
A
73
74
0.065
A
A
33
32
3.204
0.042
0.222
-1.421
AA_G73A74:U32C33_AA
38
1.535
-2.351
38.077
-2.181
-0.150
1.992
35.970
A
A
74
75
28.901
A
A
32
31
3.199
17.133
-0.236
-1.722
AA_A74PGP75:C31U32_AA
39
3.713
-6.264
31.534
-4.864
0.831
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-05-08
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2000-01-17
REL
REL
LU
LUTETIUM (III) ION
MG
MAGNESIUM ION
SO4
SULFATE ION
HOH
water
RNA SEQUENCE TAKEN FROM ESCHERICHIA COLI 4.5S RNA. THE RNA WAS PRODUCED BY T7 RNA POLYMERASE IN VITRO TRANSCRIPTION USING RIBOZYME TECHNOLOGY
sample
LU
1
2
LU
LU
1
A
MG
2
3
MG
MG
2
A
SO4
3
4
SO4
SO4
3
A
SO4
4
4
SO4
SO4
4
A
HOH
1
5
HOH
HOH
101
A
HOH
2
5
HOH
HOH
102
A
HOH
3
5
HOH
HOH
103
A
HOH
4
5
HOH
HOH
104
A
HOH
5
5
HOH
HOH
105
A
HOH
6
5
HOH
HOH
106
A
C
31
n
1
C
31
A
U
32
n
2
U
32
A
C
33
n
3
C
33
A
U
34
n
4
U
34
A
G
35
n
5
G
35
A
U
36
n
6
U
36
A
U
37
n
7
U
37
A
U
38
n
8
U
38
A
A
39
n
9
A
39
A
C
40
n
10
C
40
A
C
41
n
11
C
41
A
A
42
n
12
A
42
A
G
43
n
13
G
43
A
G
44
n
14
G
44
A
U
45
n
15
U
45
A
C
46
n
16
C
46
A
A
47
n
17
A
47
A
G
48
n
18
G
48
A
G
49
n
19
G
49
A
U
50
n
20
U
50
A
C
51
n
21
C
51
A
C
52
n
22
C
52
A
G
53
n
23
G
53
A
G
54
n
24
G
54
A
A
55
n
25
A
55
A
A
56
n
26
A
56
A
G
57
n
27
G
57
A
G
58
n
28
G
58
A
A
59
n
29
A
59
A
A
60
n
30
A
60
A
G
61
n
31
G
61
A
C
62
n
32
C
62
A
A
63
n
33
A
63
A
G
64
n
34
G
64
A
C
65
n
35
C
65
A
C
66
n
36
C
66
A
A
67
n
37
A
67
A
A
68
n
38
A
68
A
G
69
n
39
G
69
A
G
70
n
40
G
70
A
C
71
n
41
C
71
A
A
72
n
42
A
72
A
G
73
n
43
G
73
A
A
74
n
44
A
74
A
PGP
75
n
45
PGP
75
A
author_defined_assembly
2
dimeric
A
A
59
A
O3'
A
29
1_555
A
MG
2
C
MG
MG
1_555
A
A
60
A
OP1
A
30
1_555
62.1
A
PGP
75
GUANOSINE-3',5'-DIPHOSPHATE
A
PGP
45
G
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
-0.5000000000
0.8660254038
0.0000000000
0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
DNA_RNA_REP+.PARAM
DNA_RNA+.TOP
ION_REP+.PARAM
ION+.TOP
WATER_REP.PARA
WATER.TOP
80.6
26.51
21.46
0.00
26.51
0.00
-53.03
A LOW RESOLUTION LIMIT OF 8.0 A WAS USED FOR INITIAL B FACTOR AND BULK SOLVENT CORRECTIONS. NUCLEOTIDE A39 WAS REFINED WITH OCCUPANCY OF 0.5 TO ACCOUNT FOR ITS ALTERNATIVELY ORDERED AND DISORDERED CONFORMATION IN ADJACENT MOLECULES WITHIN THE CRYSTAL. THE APPARENT DISCREPANCY BETWEEN DATA COMPLETENESS IN SCALING AND REFINEMENT IS DUE TO THE VERY HIGH ANISOTROPY OF THE CRYSTAL DIFFRACTION, SO THAT, ALTHOUGH DATA COVERAGE WAS COMPLETE UP TO 2.70 A RESOLUTION, A SIGNIFICANT PROPORTION OF REFLECTIONS AT HIGH RESOLUTION WERE EXTINCT. THIS RESULTS IN THE HIGH R SYM IN THE OUTER SHELL, AND THE LOWER EFFECTIVE DATA COMPLETENESS DURING REFINEMENT (EXTINCT REFLECTIONS WERE OMITTED BY CNS).
0.2450000
0.008
0.2300000
0.2710000
0.2440000
2.70
22.50
909
12560
10539
8.6
83.9
RANDOM
1101782.89
0.00
1
RESTRAINED
THROUGHOUT
0.0
0.0
MAD
PARKINSON ET AL.
FLAT MODEL
36.81
0.266
0.53
0.50
5.00
0.90
0.92
2.70
22.50
6
988
12
970
0
0.006
1.0
15.6
1.24
0.5310000
0.057
0.5310000
2.82
86
858
8
5.5
60.0
0.4370000
0.042
0.4370000
2.97
106
1022
8
6.8
72.3
0.3640000
0.033
0.3630000
3.16
119
1150
8
7.5
80.4
0.3120000
0.029
0.3120000
3.40
117
1292
8
7.5
89.7
0.2510000
0.024
0.2510000
3.74
108
1287
8
7.0
89.9
0.2290000
0.020
0.2290000
4.29
132
1295
8
8.4
91.1
0.1760000
0.016
0.1760000
5.40
114
1417
8
7.2
97.0
0.1540000
0.014
0.1550000
60.36
125
1300
8
8.0
90.6
100.3
2.70
22.50
1DUH
12371
12371
0
0
0.0760000
1
14.5
4.2
98.5
0.5930000
2.70
2.80
2.1
4.1
100.0
refinement
CNS
data reduction
DENZO
data scaling
SCALEPACK
phasing
CNS
CRYSTAL STRUCTURE OF THE CONSERVED DOMAIN IV OF E. COLI 4.5S RNA
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
covale
1.607
both
A
A
74
A
O3'
A
44
1_555
A
PGP
75
A
P
PGP
45
1_555
metalc
1.918
A
MG
2
C
MG
MG
1_555
A
A
59
A
O3'
A
29
1_555
metalc
2.738
A
MG
2
C
MG
MG
1_555
A
A
60
A
OP1
A
30
1_555
hydrog
WATSON-CRICK
A
C
31
A
N3
C
1
1_555
A
PGP
75
A
N1
PGP
45
4_555
hydrog
WATSON-CRICK
A
C
31
A
N4
C
1
1_555
A
PGP
75
A
O6
PGP
45
4_555
hydrog
WATSON-CRICK
A
C
31
A
O2
C
1
1_555
A
PGP
75
A
N2
PGP
45
4_555
hydrog
WATSON-CRICK
A
U
32
A
N3
U
2
1_555
A
A
74
A
N1
A
44
4_555
hydrog
WATSON-CRICK
A
U
32
A
O4
U
2
1_555
A
A
74
A
N6
A
44
4_555
hydrog
WATSON-CRICK
A
C
33
A
N3
C
3
1_555
A
G
73
A
N1
G
43
4_555
hydrog
WATSON-CRICK
A
C
33
A
N4
C
3
1_555
A
G
73
A
O6
G
43
4_555
hydrog
WATSON-CRICK
A
C
33
A
O2
C
3
1_555
A
G
73
A
N2
G
43
4_555
hydrog
WATSON-CRICK
A
U
34
A
N3
U
4
1_555
A
A
72
A
N1
A
42
4_555
hydrog
WATSON-CRICK
A
U
34
A
O4
U
4
1_555
A
A
72
A
N6
A
42
4_555
hydrog
G-C PAIR
A
G
35
A
N1
G
5
1_555
A
C
71
A
N3
C
41
4_555
hydrog
TYPE_28_PAIR
A
U
36
A
N3
U
6
1_555
A
G
70
A
O6
G
40
4_555
hydrog
TYPE_28_PAIR
A
U
36
A
O2
U
6
1_555
A
G
70
A
N1
G
40
4_555
hydrog
TYPE_28_PAIR
A
U
37
A
N3
U
7
1_555
A
G
69
A
O6
G
39
4_555
hydrog
TYPE_28_PAIR
A
U
37
A
O2
U
7
1_555
A
G
69
A
N1
G
39
4_555
hydrog
WATSON-CRICK
A
U
38
A
N3
U
8
1_555
A
A
68
A
N1
A
38
4_555
hydrog
WATSON-CRICK
A
U
38
A
O4
U
8
1_555
A
A
68
A
N6
A
38
4_555
hydrog
WATSON-CRICK
A
G
43
A
N1
G
13
1_555
A
C
66
A
N3
C
36
4_555
hydrog
WATSON-CRICK
A
G
43
A
N2
G
13
1_555
A
C
66
A
O2
C
36
4_555
hydrog
WATSON-CRICK
A
G
43
A
O6
G
13
1_555
A
C
66
A
N4
C
36
4_555
hydrog
WATSON-CRICK
A
G
44
A
N1
G
14
1_555
A
C
65
A
N3
C
35
4_555
hydrog
WATSON-CRICK
A
G
44
A
N2
G
14
1_555
A
C
65
A
O2
C
35
4_555
hydrog
WATSON-CRICK
A
G
44
A
O6
G
14
1_555
A
C
65
A
N4
C
35
4_555
hydrog
TYPE_28_PAIR
A
U
45
A
N3
U
15
1_555
A
G
64
A
O6
G
34
4_555
hydrog
TYPE_28_PAIR
A
U
45
A
O2
U
15
1_555
A
G
64
A
N1
G
34
4_555
hydrog
C-A MISPAIR
A
C
46
A
O2
C
16
1_555
A
A
63
A
N6
A
33
4_555
hydrog
TYPE_25_PAIR
A
A
47
A
N6
A
17
1_555
A
C
62
A
N3
C
32
4_555
hydrog
TYPE_25_PAIR
A
A
47
A
N7
A
17
1_555
A
C
62
A
N4
C
32
4_555
hydrog
G-G MISPAIR
A
G
48
A
O6
G
18
1_555
A
G
61
A
N2
G
31
4_555
hydrog
TYPE_8_PAIR
A
G
49
A
N1
G
19
1_555
A
A
60
A
N1
A
30
4_555
hydrog
TYPE_8_PAIR
A
G
49
A
O6
G
19
1_555
A
A
60
A
N6
A
30
4_555
hydrog
WATSON-CRICK
A
U
50
A
N3
U
20
1_555
A
A
59
A
N1
A
29
4_555
hydrog
WATSON-CRICK
A
U
50
A
O4
U
20
1_555
A
A
59
A
N6
A
29
4_555
hydrog
WATSON-CRICK
A
C
51
A
N3
C
21
1_555
A
G
58
A
N1
G
28
4_555
hydrog
WATSON-CRICK
A
C
51
A
N4
C
21
1_555
A
G
58
A
O6
G
28
4_555
hydrog
WATSON-CRICK
A
C
51
A
O2
C
21
1_555
A
G
58
A
N2
G
28
4_555
hydrog
WATSON-CRICK
A
C
52
A
N3
C
22
1_555
A
G
57
A
N1
G
27
4_555
hydrog
WATSON-CRICK
A
C
52
A
N4
C
22
1_555
A
G
57
A
O6
G
27
4_555
hydrog
WATSON-CRICK
A
C
52
A
O2
C
22
1_555
A
G
57
A
N2
G
27
4_555
hydrog
TYPE_11_PAIR
A
G
53
A
N2
G
23
1_555
A
A
56
A
N7
A
26
4_555
hydrog
TYPE_11_PAIR
A
G
53
A
N3
G
23
1_555
A
A
56
A
N6
A
26
4_555
hydrog
TYPE_11_PAIR
A
G
54
A
N2
G
24
1_555
A
A
55
A
N7
A
25
4_555
hydrog
TYPE_11_PAIR
A
G
54
A
N3
G
24
1_555
A
A
55
A
N6
A
25
4_555
hydrog
TYPE_11_PAIR
A
A
55
A
N6
A
25
1_555
A
G
54
A
N3
G
24
4_555
hydrog
TYPE_11_PAIR
A
A
55
A
N7
A
25
1_555
A
G
54
A
N2
G
24
4_555
hydrog
TYPE_11_PAIR
A
A
56
A
N6
A
26
1_555
A
G
53
A
N3
G
23
4_555
hydrog
TYPE_11_PAIR
A
A
56
A
N7
A
26
1_555
A
G
53
A
N2
G
23
4_555
hydrog
WATSON-CRICK
A
G
57
A
N1
G
27
1_555
A
C
52
A
N3
C
22
4_555
hydrog
WATSON-CRICK
A
G
57
A
N2
G
27
1_555
A
C
52
A
O2
C
22
4_555
hydrog
WATSON-CRICK
A
G
57
A
O6
G
27
1_555
A
C
52
A
N4
C
22
4_555
hydrog
WATSON-CRICK
A
G
58
A
N1
G
28
1_555
A
C
51
A
N3
C
21
4_555
hydrog
WATSON-CRICK
A
G
58
A
N2
G
28
1_555
A
C
51
A
O2
C
21
4_555
hydrog
WATSON-CRICK
A
G
58
A
O6
G
28
1_555
A
C
51
A
N4
C
21
4_555
hydrog
WATSON-CRICK
A
A
59
A
N1
A
29
1_555
A
U
50
A
N3
U
20
4_555
hydrog
WATSON-CRICK
A
A
59
A
N6
A
29
1_555
A
U
50
A
O4
U
20
4_555
hydrog
TYPE_8_PAIR
A
A
60
A
N1
A
30
1_555
A
G
49
A
N1
G
19
4_555
hydrog
TYPE_8_PAIR
A
A
60
A
N6
A
30
1_555
A
G
49
A
O6
G
19
4_555
hydrog
G-G MISPAIR
A
G
61
A
N2
G
31
1_555
A
G
48
A
O6
G
18
4_555
hydrog
TYPE_25_PAIR
A
C
62
A
N3
C
32
1_555
A
A
47
A
N6
A
17
4_555
hydrog
TYPE_25_PAIR
A
C
62
A
N4
C
32
1_555
A
A
47
A
N7
A
17
4_555
hydrog
A-C MISPAIR
A
A
63
A
N6
A
33
1_555
A
C
46
A
O2
C
16
4_555
hydrog
TYPE_28_PAIR
A
G
64
A
N1
G
34
1_555
A
U
45
A
O2
U
15
4_555
hydrog
TYPE_28_PAIR
A
G
64
A
O6
G
34
1_555
A
U
45
A
N3
U
15
4_555
hydrog
WATSON-CRICK
A
C
65
A
N3
C
35
1_555
A
G
44
A
N1
G
14
4_555
hydrog
WATSON-CRICK
A
C
65
A
N4
C
35
1_555
A
G
44
A
O6
G
14
4_555
hydrog
WATSON-CRICK
A
C
65
A
O2
C
35
1_555
A
G
44
A
N2
G
14
4_555
hydrog
WATSON-CRICK
A
C
66
A
N3
C
36
1_555
A
G
43
A
N1
G
13
4_555
hydrog
WATSON-CRICK
A
C
66
A
N4
C
36
1_555
A
G
43
A
O6
G
13
4_555
hydrog
WATSON-CRICK
A
C
66
A
O2
C
36
1_555
A
G
43
A
N2
G
13
4_555
hydrog
WATSON-CRICK
A
A
68
A
N1
A
38
1_555
A
U
38
A
N3
U
8
4_555
hydrog
WATSON-CRICK
A
A
68
A
N6
A
38
1_555
A
U
38
A
O4
U
8
4_555
hydrog
TYPE_28_PAIR
A
G
69
A
N1
G
39
1_555
A
U
37
A
O2
U
7
4_555
hydrog
TYPE_28_PAIR
A
G
69
A
O6
G
39
1_555
A
U
37
A
N3
U
7
4_555
hydrog
TYPE_28_PAIR
A
G
70
A
N1
G
40
1_555
A
U
36
A
O2
U
6
4_555
hydrog
TYPE_28_PAIR
A
G
70
A
O6
G
40
1_555
A
U
36
A
N3
U
6
4_555
hydrog
C-G PAIR
A
C
71
A
O2
C
41
1_555
A
G
35
A
N2
G
5
4_555
hydrog
WATSON-CRICK
A
A
72
A
N1
A
42
1_555
A
U
34
A
N3
U
4
4_555
hydrog
WATSON-CRICK
A
A
72
A
N6
A
42
1_555
A
U
34
A
O4
U
4
4_555
hydrog
WATSON-CRICK
A
G
73
A
N1
G
43
1_555
A
C
33
A
N3
C
3
4_555
hydrog
WATSON-CRICK
A
G
73
A
N2
G
43
1_555
A
C
33
A
O2
C
3
4_555
hydrog
WATSON-CRICK
A
G
73
A
O6
G
43
1_555
A
C
33
A
N4
C
3
4_555
hydrog
WATSON-CRICK
A
A
74
A
N1
A
44
1_555
A
U
32
A
N3
U
2
4_555
hydrog
WATSON-CRICK
A
A
74
A
N6
A
44
1_555
A
U
32
A
O4
U
2
4_555
hydrog
WATSON-CRICK
A
PGP
75
A
N1
PGP
45
1_555
A
C
31
A
N3
C
1
4_555
hydrog
WATSON-CRICK
A
PGP
75
A
N2
PGP
45
1_555
A
C
31
A
O2
C
1
4_555
hydrog
WATSON-CRICK
A
PGP
75
A
O6
PGP
45
1_555
A
C
31
A
N4
C
1
4_555
RNA
4.5S RNA, DOMAIN IV, HELIX 8, SIGNAL RECOGNITION PARTICLE, SRP, FFH, SRP54, ELONGATION FACTOR G, EF-G, 23S RNA, NON-CANONICAL BASE PAIRS, MISMATCH, RNA
ECRNA45
EMBL
1
X01074
192
235
1DUH
31
74
X01074
A
1
1
44
BINDING SITE FOR RESIDUE LU A 1
A
LU
1
Software
1
BINDING SITE FOR RESIDUE MG A 2
A
MG
2
Software
2
BINDING SITE FOR RESIDUE SO4 A 3
A
SO4
3
Software
1
BINDING SITE FOR RESIDUE SO4 A 4
A
SO4
4
Software
3
A
PGP
75
A
PGP
45
1
1_555
A
A
59
A
A
29
2
1_555
A
A
60
A
A
30
2
1_555
A
C
31
A
C
1
1
1_555
A
G
48
A
G
18
3
1_555
A
G
49
A
G
19
3
1_555
A
C
62
A
C
32
3
4_555
154
trigonal
P 32 2 1