0.013144
0.000000
0.000000
0.000000
0.013144
0.000000
0.000000
0.000000
0.017152
0.00000
0.00000
0.00000
Huang, R.H.
Xie, W.
Zhou, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
76.083
76.083
58.302
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
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
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
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
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
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
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
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
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
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
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
R
C
N
309
N
O
N
310
N
C
N
311
N
O
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
N
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
N
335
N
O
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
N
359
N
O
N
360
N
O
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
O
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
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
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
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
doub
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
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
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
doub
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
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
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
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
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
doub
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
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
367
872
881
10.1016/j.jmb.2007.01.048
17292915
Structure of tRNA Dimethylallyltransferase: RNA Modification
through a Channel
2007
10.2210/pdb3crm/pdb
pdb_00003crm
100
1
1
CCD
2006-02-15
SINGLE WAVELENGTH
M
x-ray
1
M
x-ray
1
0.98
1.0
22-BM
APS
0.98
SYNCHROTRON
APS BEAMLINE 22-BM
35844.117
tRNA delta(2)-isopentenylpyrophosphate transferase
2.5.1.8
1
man
polymer
18.015
water
109
nat
water
IPP transferase, Isopentenyl-diphosphate:tRNA isopentenyltransferase, IPTase, IPPT, tRNA DMATase
no
no
MSSLPPAIFLMGPTAAGKTDLAMALADALPCELISVDSALIYRGMDIGTAKPSRELLARYPHRLIDIRDPAESYSAAEFR
ADALAAMAKATARGRIPLLVGGTMLYYKALLEGLADMPGADPEVRAAIEAEAQAEGWEALHRQLAEVDPESAARIHPNDP
QRLMRALEVYRLGGVSMSDLRRRQSAEKADFDASGRNQLPYTVAQLAIAPEQRQVLHARIAQRFRQMLEQGFIAEVEALH
ARSDLHAGLPSIRAVGYRQVWDYLDGKLSYAEMTERGIIATRQLAKRQFTWLRSWSHLHWMDSLAGDNLPRALRYLKTVS
ILA
MSSLPPAIFLMGPTAAGKTDLAMALADALPCELISVDSALIYRGMDIGTAKPSRELLARYPHRLIDIRDPAESYSAAEFR
ADALAAMAKATARGRIPLLVGGTMLYYKALLEGLADMPGADPEVRAAIEAEAQAEGWEALHRQLAEVDPESAARIHPNDP
QRLMRALEVYRLGGVSMSDLRRRQSAEKADFDASGRNQLPYTVAQLAIAPEQRQVLHARIAQRFRQMLEQGFIAEVEALH
ARSDLHAGLPSIRAVGYRQVWDYLDGKLSYAEMTERGIIATRQLAKRQFTWLRSWSHLHWMDSLAGDNLPRALRYLKTVS
ILA
A
polypeptide(L)
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
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
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
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
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
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
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
n
n
n
n
n
n
n
n
Pseudomonas
Escherichia
Escherichia coli
sample
miaA
287
Pseudomonas aeruginosa
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
pLM-1
1
2.35
47.74
VAPOR DIFFUSION, HANGING DROP
8.5
PEG 6000, pH 8.5, vapor diffusion, hanging drop, temperature 278K
278
chem_comp_atom
chem_comp_bond
database_2
struct_ref_seq_dif
repository
Initial release
Version format compliance
Data collection
Database references
1
0
2008-04-29
1
1
2011-07-13
1
2
2024-02-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Structure of tRNA Dimethylallyltransferase: RNA Modification through a Channel
Structure of tRNA Dimethylallyltransferase: RNA Modification through a Channel
RCSB
Y
RCSB
2008-04-07
REL
REL
HOH
water
WAT
1
2
HOH
HOH
324
A
WAT
2
2
HOH
HOH
325
A
WAT
3
2
HOH
HOH
326
A
WAT
4
2
HOH
HOH
327
A
WAT
5
2
HOH
HOH
328
A
WAT
6
2
HOH
HOH
329
A
WAT
7
2
HOH
HOH
330
A
WAT
8
2
HOH
HOH
331
A
WAT
9
2
HOH
HOH
332
A
WAT
10
2
HOH
HOH
333
A
WAT
11
2
HOH
HOH
334
A
WAT
12
2
HOH
HOH
335
A
WAT
13
2
HOH
HOH
336
A
WAT
14
2
HOH
HOH
337
A
WAT
15
2
HOH
HOH
338
A
WAT
16
2
HOH
HOH
339
A
WAT
17
2
HOH
HOH
340
A
WAT
18
2
HOH
HOH
341
A
WAT
19
2
HOH
HOH
342
A
WAT
20
2
HOH
HOH
343
A
WAT
21
2
HOH
HOH
344
A
WAT
22
2
HOH
HOH
345
A
WAT
23
2
HOH
HOH
346
A
WAT
24
2
HOH
HOH
347
A
WAT
25
2
HOH
HOH
348
A
WAT
26
2
HOH
HOH
349
A
WAT
27
2
HOH
HOH
350
A
WAT
28
2
HOH
HOH
351
A
WAT
29
2
HOH
HOH
352
A
WAT
30
2
HOH
HOH
353
A
WAT
31
2
HOH
HOH
354
A
WAT
32
2
HOH
HOH
355
A
WAT
33
2
HOH
HOH
356
A
WAT
34
2
HOH
HOH
357
A
WAT
35
2
HOH
HOH
358
A
WAT
36
2
HOH
HOH
359
A
WAT
37
2
HOH
HOH
360
A
WAT
38
2
HOH
HOH
361
A
WAT
39
2
HOH
HOH
362
A
WAT
40
2
HOH
HOH
363
A
WAT
41
2
HOH
HOH
364
A
WAT
42
2
HOH
HOH
365
A
WAT
43
2
HOH
HOH
366
A
WAT
44
2
HOH
HOH
367
A
WAT
45
2
HOH
HOH
368
A
WAT
46
2
HOH
HOH
369
A
WAT
47
2
HOH
HOH
370
A
WAT
48
2
HOH
HOH
371
A
WAT
49
2
HOH
HOH
372
A
WAT
50
2
HOH
HOH
373
A
WAT
51
2
HOH
HOH
374
A
WAT
52
2
HOH
HOH
375
A
WAT
53
2
HOH
HOH
376
A
WAT
54
2
HOH
HOH
377
A
WAT
55
2
HOH
HOH
378
A
WAT
56
2
HOH
HOH
379
A
WAT
57
2
HOH
HOH
380
A
WAT
58
2
HOH
HOH
381
A
WAT
59
2
HOH
HOH
382
A
WAT
60
2
HOH
HOH
383
A
WAT
61
2
HOH
HOH
384
A
WAT
62
2
HOH
HOH
385
A
WAT
63
2
HOH
HOH
386
A
WAT
64
2
HOH
HOH
387
A
WAT
65
2
HOH
HOH
388
A
WAT
66
2
HOH
HOH
389
A
WAT
67
2
HOH
HOH
390
A
WAT
68
2
HOH
HOH
391
A
WAT
69
2
HOH
HOH
392
A
WAT
70
2
HOH
HOH
393
A
WAT
71
2
HOH
HOH
394
A
WAT
72
2
HOH
HOH
395
A
WAT
73
2
HOH
HOH
396
A
WAT
74
2
HOH
HOH
397
A
WAT
75
2
HOH
HOH
398
A
WAT
76
2
HOH
HOH
399
A
WAT
77
2
HOH
HOH
400
A
WAT
78
2
HOH
HOH
401
A
WAT
79
2
HOH
HOH
402
A
WAT
80
2
HOH
HOH
403
A
WAT
81
2
HOH
HOH
404
A
WAT
82
2
HOH
HOH
405
A
WAT
83
2
HOH
HOH
406
A
WAT
84
2
HOH
HOH
407
A
WAT
85
2
HOH
HOH
408
A
WAT
86
2
HOH
HOH
409
A
WAT
87
2
HOH
HOH
410
A
WAT
88
2
HOH
HOH
411
A
WAT
89
2
HOH
HOH
412
A
WAT
90
2
HOH
HOH
413
A
WAT
91
2
HOH
HOH
414
A
WAT
92
2
HOH
HOH
415
A
WAT
93
2
HOH
HOH
416
A
WAT
94
2
HOH
HOH
417
A
WAT
95
2
HOH
HOH
418
A
WAT
96
2
HOH
HOH
419
A
WAT
97
2
HOH
HOH
420
A
WAT
98
2
HOH
HOH
421
A
WAT
99
2
HOH
HOH
422
A
WAT
100
2
HOH
HOH
423
A
WAT
101
2
HOH
HOH
424
A
WAT
102
2
HOH
HOH
425
A
WAT
103
2
HOH
HOH
426
A
WAT
104
2
HOH
HOH
427
A
WAT
105
2
HOH
HOH
428
A
WAT
106
2
HOH
HOH
429
A
WAT
107
2
HOH
HOH
430
A
WAT
108
2
HOH
HOH
431
A
WAT
109
2
HOH
HOH
432
A
n
1
1
A
n
2
2
A
SER
3
n
3
SER
3
A
LEU
4
n
4
LEU
4
A
PRO
5
n
5
PRO
5
A
PRO
6
n
6
PRO
6
A
ALA
7
n
7
ALA
7
A
ILE
8
n
8
ILE
8
A
PHE
9
n
9
PHE
9
A
LEU
10
n
10
LEU
10
A
MET
11
n
11
MET
11
A
GLY
12
n
12
GLY
12
A
PRO
13
n
13
PRO
13
A
THR
14
n
14
THR
14
A
ALA
15
n
15
ALA
15
A
ALA
16
n
16
ALA
16
A
GLY
17
n
17
GLY
17
A
LYS
18
n
18
LYS
18
A
THR
19
n
19
THR
19
A
ASP
20
n
20
ASP
20
A
LEU
21
n
21
LEU
21
A
ALA
22
n
22
ALA
22
A
MET
23
n
23
MET
23
A
ALA
24
n
24
ALA
24
A
LEU
25
n
25
LEU
25
A
ALA
26
n
26
ALA
26
A
ASP
27
n
27
ASP
27
A
ALA
28
n
28
ALA
28
A
LEU
29
n
29
LEU
29
A
PRO
30
n
30
PRO
30
A
CYS
31
n
31
CYS
31
A
GLU
32
n
32
GLU
32
A
LEU
33
n
33
LEU
33
A
ILE
34
n
34
ILE
34
A
SER
35
n
35
SER
35
A
VAL
36
n
36
VAL
36
A
ASP
37
n
37
ASP
37
A
SER
38
n
38
SER
38
A
ALA
39
n
39
ALA
39
A
LEU
40
n
40
LEU
40
A
ILE
41
n
41
ILE
41
A
TYR
42
n
42
TYR
42
A
ARG
43
n
43
ARG
43
A
GLY
44
n
44
GLY
44
A
MET
45
n
45
MET
45
A
ASP
46
n
46
ASP
46
A
ILE
47
n
47
ILE
47
A
GLY
48
n
48
GLY
48
A
THR
49
n
49
THR
49
A
ALA
50
n
50
ALA
50
A
LYS
51
n
51
LYS
51
A
PRO
52
n
52
PRO
52
A
SER
53
n
53
SER
53
A
ARG
54
n
54
ARG
54
A
GLU
55
n
55
GLU
55
A
LEU
56
n
56
LEU
56
A
LEU
57
n
57
LEU
57
A
ALA
58
n
58
ALA
58
A
ARG
59
n
59
ARG
59
A
TYR
60
n
60
TYR
60
A
PRO
61
n
61
PRO
61
A
HIS
62
n
62
HIS
62
A
ARG
63
n
63
ARG
63
A
LEU
64
n
64
LEU
64
A
ILE
65
n
65
ILE
65
A
ASP
66
n
66
ASP
66
A
ILE
67
n
67
ILE
67
A
ARG
68
n
68
ARG
68
A
ASP
69
n
69
ASP
69
A
PRO
70
n
70
PRO
70
A
ALA
71
n
71
ALA
71
A
GLU
72
n
72
GLU
72
A
SER
73
n
73
SER
73
A
TYR
74
n
74
TYR
74
A
SER
75
n
75
SER
75
A
ALA
76
n
76
ALA
76
A
ALA
77
n
77
ALA
77
A
GLU
78
n
78
GLU
78
A
PHE
79
n
79
PHE
79
A
ARG
80
n
80
ARG
80
A
ALA
81
n
81
ALA
81
A
ASP
82
n
82
ASP
82
A
ALA
83
n
83
ALA
83
A
LEU
84
n
84
LEU
84
A
ALA
85
n
85
ALA
85
A
ALA
86
n
86
ALA
86
A
MET
87
n
87
MET
87
A
ALA
88
n
88
ALA
88
A
LYS
89
n
89
LYS
89
A
ALA
90
n
90
ALA
90
A
THR
91
n
91
THR
91
A
ALA
92
n
92
ALA
92
A
ARG
93
n
93
ARG
93
A
GLY
94
n
94
GLY
94
A
ARG
95
n
95
ARG
95
A
ILE
96
n
96
ILE
96
A
PRO
97
n
97
PRO
97
A
LEU
98
n
98
LEU
98
A
LEU
99
n
99
LEU
99
A
VAL
100
n
100
VAL
100
A
GLY
101
n
101
GLY
101
A
GLY
102
n
102
GLY
102
A
THR
103
n
103
THR
103
A
MET
104
n
104
MET
104
A
LEU
105
n
105
LEU
105
A
TYR
106
n
106
TYR
106
A
TYR
107
n
107
TYR
107
A
LYS
108
n
108
LYS
108
A
ALA
109
n
109
ALA
109
A
LEU
110
n
110
LEU
110
A
LEU
111
n
111
LEU
111
A
GLU
112
n
112
GLU
112
A
GLY
113
n
113
GLY
113
A
n
114
114
A
n
115
115
A
n
116
116
A
n
117
117
A
n
118
118
A
n
119
119
A
n
120
120
A
n
121
121
A
n
122
122
A
n
123
123
A
n
124
124
A
n
125
125
A
n
126
126
A
n
127
127
A
n
128
128
A
n
129
129
A
n
130
130
A
n
131
131
A
n
132
132
A
n
133
133
A
n
134
134
A
n
135
135
A
n
136
136
A
n
137
137
A
n
138
138
A
n
139
139
A
n
140
140
A
n
141
141
A
n
142
142
A
n
143
143
A
n
144
144
A
n
145
145
A
n
146
146
A
n
147
147
A
n
148
148
A
n
149
149
A
n
150
150
A
n
151
151
A
n
152
152
A
n
153
153
A
n
154
154
A
n
155
155
A
n
156
156
A
n
157
157
A
n
158
158
A
n
159
159
A
n
160
160
A
n
161
161
A
n
162
162
A
n
163
163
A
n
164
164
A
n
165
165
A
n
166
166
A
n
167
167
A
n
168
168
A
n
169
169
A
n
170
170
A
n
171
171
A
n
172
172
A
n
173
173
A
n
174
174
A
n
175
175
A
n
176
176
A
n
177
177
A
n
178
178
A
n
179
179
A
n
180
180
A
n
181
181
A
n
182
182
A
n
183
183
A
n
184
184
A
n
185
185
A
n
186
186
A
n
187
187
A
n
188
188
A
n
189
189
A
n
190
190
A
n
191
191
A
n
192
192
A
n
193
193
A
n
194
194
A
n
195
195
A
n
196
196
A
n
197
197
A
n
198
198
A
LEU
199
n
199
LEU
199
A
PRO
200
n
200
PRO
200
A
TYR
201
n
201
TYR
201
A
THR
202
n
202
THR
202
A
VAL
203
n
203
VAL
203
A
ALA
204
n
204
ALA
204
A
GLN
205
n
205
GLN
205
A
LEU
206
n
206
LEU
206
A
ALA
207
n
207
ALA
207
A
ILE
208
n
208
ILE
208
A
ALA
209
n
209
ALA
209
A
PRO
210
n
210
PRO
210
A
GLU
211
n
211
GLU
211
A
GLN
212
n
212
GLN
212
A
ARG
213
n
213
ARG
213
A
GLN
214
n
214
GLN
214
A
VAL
215
n
215
VAL
215
A
LEU
216
n
216
LEU
216
A
HIS
217
n
217
HIS
217
A
ALA
218
n
218
ALA
218
A
ARG
219
n
219
ARG
219
A
ILE
220
n
220
ILE
220
A
ALA
221
n
221
ALA
221
A
GLN
222
n
222
GLN
222
A
ARG
223
n
223
ARG
223
A
PHE
224
n
224
PHE
224
A
ARG
225
n
225
ARG
225
A
GLN
226
n
226
GLN
226
A
MET
227
n
227
MET
227
A
LEU
228
n
228
LEU
228
A
GLU
229
n
229
GLU
229
A
GLN
230
n
230
GLN
230
A
GLY
231
n
231
GLY
231
A
PHE
232
n
232
PHE
232
A
ILE
233
n
233
ILE
233
A
ALA
234
n
234
ALA
234
A
GLU
235
n
235
GLU
235
A
VAL
236
n
236
VAL
236
A
GLU
237
n
237
GLU
237
A
ALA
238
n
238
ALA
238
A
LEU
239
n
239
LEU
239
A
HIS
240
n
240
HIS
240
A
ALA
241
n
241
ALA
241
A
ARG
242
n
242
ARG
242
A
SER
243
n
243
SER
243
A
ASP
244
n
244
ASP
244
A
LEU
245
n
245
LEU
245
A
HIS
246
n
246
HIS
246
A
ALA
247
n
247
ALA
247
A
GLY
248
n
248
GLY
248
A
LEU
249
n
249
LEU
249
A
PRO
250
n
250
PRO
250
A
SER
251
n
251
SER
251
A
ILE
252
n
252
ILE
252
A
ARG
253
n
253
ARG
253
A
ALA
254
n
254
ALA
254
A
VAL
255
n
255
VAL
255
A
GLY
256
n
256
GLY
256
A
TYR
257
n
257
TYR
257
A
ARG
258
n
258
ARG
258
A
GLN
259
n
259
GLN
259
A
VAL
260
n
260
VAL
260
A
TRP
261
n
261
TRP
261
A
ASP
262
n
262
ASP
262
A
TYR
263
n
263
TYR
263
A
LEU
264
n
264
LEU
264
A
ASP
265
n
265
ASP
265
A
GLY
266
n
266
GLY
266
A
LYS
267
n
267
LYS
267
A
LEU
268
n
268
LEU
268
A
SER
269
n
269
SER
269
A
TYR
270
n
270
TYR
270
A
ALA
271
n
271
ALA
271
A
GLU
272
n
272
GLU
272
A
MET
273
n
273
MET
273
A
THR
274
n
274
THR
274
A
GLU
275
n
275
GLU
275
A
ARG
276
n
276
ARG
276
A
GLY
277
n
277
GLY
277
A
ILE
278
n
278
ILE
278
A
ILE
279
n
279
ILE
279
A
ALA
280
n
280
ALA
280
A
THR
281
n
281
THR
281
A
ARG
282
n
282
ARG
282
A
GLN
283
n
283
GLN
283
A
LEU
284
n
284
LEU
284
A
ALA
285
n
285
ALA
285
A
LYS
286
n
286
LYS
286
A
ARG
287
n
287
ARG
287
A
GLN
288
n
288
GLN
288
A
PHE
289
n
289
PHE
289
A
THR
290
n
290
THR
290
A
TRP
291
n
291
TRP
291
A
LEU
292
n
292
LEU
292
A
ARG
293
n
293
ARG
293
A
SER
294
n
294
SER
294
A
TRP
295
n
295
TRP
295
A
SER
296
n
296
SER
296
A
HIS
297
n
297
HIS
297
A
LEU
298
n
298
LEU
298
A
HIS
299
n
299
HIS
299
A
TRP
300
n
300
TRP
300
A
MET
301
n
301
MET
301
A
ASP
302
n
302
ASP
302
A
SER
303
n
303
SER
303
A
LEU
304
n
304
LEU
304
A
ALA
305
n
305
ALA
305
A
GLY
306
n
306
GLY
306
A
ASP
307
n
307
ASP
307
A
ASN
308
n
308
ASN
308
A
LEU
309
n
309
LEU
309
A
PRO
310
n
310
PRO
310
A
ARG
311
n
311
ARG
311
A
ALA
312
n
312
ALA
312
A
LEU
313
n
313
LEU
313
A
ARG
314
n
314
ARG
314
A
TYR
315
n
315
TYR
315
A
LEU
316
n
316
LEU
316
A
LYS
317
n
317
LYS
317
A
THR
318
n
318
THR
318
A
VAL
319
n
319
VAL
319
A
SER
320
n
320
SER
320
A
ILE
321
n
321
ILE
321
A
LEU
322
n
322
LEU
322
A
ALA
323
n
323
ALA
323
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
A
O
ARG
63
A
O
ARG
63
A
N
LEU
33
A
N
LEU
33
A
N
GLU
32
A
N
GLU
32
A
O
LEU
98
A
O
LEU
98
A
O
LEU
99
A
O
LEU
99
A
N
LEU
10
A
N
LEU
10
A
N
PHE
9
A
N
PHE
9
A
O
LEU
206
A
O
LEU
206
A
N
ALA
207
A
N
ALA
207
A
O
MET
301
A
O
MET
301
1
A
MET
1
A
MET
1
1
Y
1
A
SER
2
A
SER
2
1
Y
1
A
LEU
114
A
LEU
114
1
Y
1
A
ALA
115
A
ALA
115
1
Y
1
A
ASP
116
A
ASP
116
1
Y
1
A
MET
117
A
MET
117
1
Y
1
A
PRO
118
A
PRO
118
1
Y
1
A
GLY
119
A
GLY
119
1
Y
1
A
ALA
120
A
ALA
120
1
Y
1
A
ASP
121
A
ASP
121
1
Y
1
A
PRO
122
A
PRO
122
1
Y
1
A
GLU
123
A
GLU
123
1
Y
1
A
VAL
124
A
VAL
124
1
Y
1
A
ARG
125
A
ARG
125
1
Y
1
A
ALA
126
A
ALA
126
1
Y
1
A
ALA
127
A
ALA
127
1
Y
1
A
ILE
128
A
ILE
128
1
Y
1
A
GLU
129
A
GLU
129
1
Y
1
A
ALA
130
A
ALA
130
1
Y
1
A
GLU
131
A
GLU
131
1
Y
1
A
ALA
132
A
ALA
132
1
Y
1
A
GLN
133
A
GLN
133
1
Y
1
A
ALA
134
A
ALA
134
1
Y
1
A
GLU
135
A
GLU
135
1
Y
1
A
GLY
136
A
GLY
136
1
Y
1
A
TRP
137
A
TRP
137
1
Y
1
A
GLU
138
A
GLU
138
1
Y
1
A
ALA
139
A
ALA
139
1
Y
1
A
LEU
140
A
LEU
140
1
Y
1
A
HIS
141
A
HIS
141
1
Y
1
A
ARG
142
A
ARG
142
1
Y
1
A
GLN
143
A
GLN
143
1
Y
1
A
LEU
144
A
LEU
144
1
Y
1
A
ALA
145
A
ALA
145
1
Y
1
A
GLU
146
A
GLU
146
1
Y
1
A
VAL
147
A
VAL
147
1
Y
1
A
ASP
148
A
ASP
148
1
Y
1
A
PRO
149
A
PRO
149
1
Y
1
A
GLU
150
A
GLU
150
1
Y
1
A
SER
151
A
SER
151
1
Y
1
A
ALA
152
A
ALA
152
1
Y
1
A
ALA
153
A
ALA
153
1
Y
1
A
ARG
154
A
ARG
154
1
Y
1
A
ILE
155
A
ILE
155
1
Y
1
A
HIS
156
A
HIS
156
1
Y
1
A
PRO
157
A
PRO
157
1
Y
1
A
ASN
158
A
ASN
158
1
Y
1
A
ASP
159
A
ASP
159
1
Y
1
A
PRO
160
A
PRO
160
1
Y
1
A
GLN
161
A
GLN
161
1
Y
1
A
ARG
162
A
ARG
162
1
Y
1
A
LEU
163
A
LEU
163
1
Y
1
A
MET
164
A
MET
164
1
Y
1
A
ARG
165
A
ARG
165
1
Y
1
A
ALA
166
A
ALA
166
1
Y
1
A
LEU
167
A
LEU
167
1
Y
1
A
GLU
168
A
GLU
168
1
Y
1
A
VAL
169
A
VAL
169
1
Y
1
A
TYR
170
A
TYR
170
1
Y
1
A
ARG
171
A
ARG
171
1
Y
1
A
LEU
172
A
LEU
172
1
Y
1
A
GLY
173
A
GLY
173
1
Y
1
A
GLY
174
A
GLY
174
1
Y
1
A
VAL
175
A
VAL
175
1
Y
1
A
SER
176
A
SER
176
1
Y
1
A
MET
177
A
MET
177
1
Y
1
A
SER
178
A
SER
178
1
Y
1
A
ASP
179
A
ASP
179
1
Y
1
A
LEU
180
A
LEU
180
1
Y
1
A
ARG
181
A
ARG
181
1
Y
1
A
ARG
182
A
ARG
182
1
Y
1
A
ARG
183
A
ARG
183
1
Y
1
A
GLN
184
A
GLN
184
1
Y
1
A
SER
185
A
SER
185
1
Y
1
A
ALA
186
A
ALA
186
1
Y
1
A
GLU
187
A
GLU
187
1
Y
1
A
LYS
188
A
LYS
188
1
Y
1
A
ALA
189
A
ALA
189
1
Y
1
A
ASP
190
A
ASP
190
1
Y
1
A
PHE
191
A
PHE
191
1
Y
1
A
ASP
192
A
ASP
192
1
Y
1
A
ALA
193
A
ALA
193
1
Y
1
A
SER
194
A
SER
194
1
Y
1
A
GLY
195
A
GLY
195
1
Y
1
A
ARG
196
A
ARG
196
1
Y
1
A
ASN
197
A
ASN
197
1
Y
1
A
GLN
198
A
GLN
198
1
Y
1
A
VAL
36
-119.98
78.26
1
A
GLU
112
-112.76
-114.52
CNS_TOPPAR:protein_rep.param
CNS_TOPPAR:water_rep.param
CNS_TOPPAR:ion.param
34.767
3.852
0.000
0.000
3.852
0.000
-7.705
0.230
0.211
1.900
50.000
1856
23614
7.000
89.400
0.877
1
1.00
43.373
1.900
50.000
109
1954
0
0
1845
0.005
1.150
1.368
1.500
2.363
2.000
1.995
2.000
3.604
2.500
1.9
50.0
3CRM
26417
25202
1,2
refinement
Axel T. Brunger
axel.brunger@yale.edu
Fortran_77
http://cns.csb.yale.edu/v1.1/
CNS
package
data extraction
PDB
sw-help@rcsb.rutgers.edu
September 10, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.005
Structure of tRNA Dimethylallyltransferase: RNA Modification through a Channel
1
N
N
2
N
N
A
GLY
17
A
GLY
17
HELX_P
A
LEU
29
A
LEU
29
1
1
13
A
SER
53
A
SER
53
HELX_P
A
TYR
60
A
TYR
60
1
2
8
A
SER
75
A
SER
75
HELX_P
A
ARG
93
A
ARG
93
1
3
19
A
THR
103
A
THR
103
HELX_P
A
GLU
112
A
GLU
112
1
4
10
A
GLN
212
A
GLN
212
HELX_P
A
GLN
230
A
GLN
230
1
5
19
A
GLY
231
A
GLY
231
HELX_P
A
ALA
241
A
ALA
241
1
6
11
A
PRO
250
A
PRO
250
HELX_P
A
ALA
254
A
ALA
254
5
7
5
A
GLY
256
A
GLY
256
HELX_P
A
ASP
265
A
ASP
265
1
8
10
A
SER
269
A
SER
269
HELX_P
A
SER
294
A
SER
294
1
9
26
A
ASP
307
A
ASP
307
HELX_P
A
VAL
319
A
VAL
319
1
10
13
TRANSFERASE
Transferase, ATP-binding, Nucleotide-binding, Nucleotidyltransferase, tRNA processing
MIAA_PSEAE
UNP
1
1
Q9HUL9
MSSLPPAIFLMGPTAAGKTDLAMALADALPCELISVDSALIYRGMDIGTAKPSRELLARYPHRLIDIRDPAESYSAAEFR
ADALAAMAKATARGRIPLLVGGTMLYYKALLEGLADMPGADPEVRAAIEAEAQAEGWEALHRQLAEVDPESAARIHPNDP
QRLMRALEVYRLGGVSMSDLRRRQSAEKADFDASGRNQLPYTVAQLAIAPEQRQVLHARIAQRFRQMLEQGFIAEVEALH
ARSDLHAGLPSIRAVGYRQVWDYLDGKLSYAEMTERGIIATRQLAKRQFTWLRSWSHLHWMDSLAGDNLPRALKYLKTVS
ILA
1
323
3CRM
1
323
Q9HUL9
A
1
1
323
1
LYS
conflict
ARG
314
3CRM
A
Q9HUL9
UNP
314
314
6
parallel
parallel
parallel
parallel
parallel
A
HIS
62
A
HIS
62
A
ARG
63
A
ARG
63
A
CYS
31
A
CYS
31
A
VAL
36
A
VAL
36
A
ILE
96
A
ILE
96
A
GLY
101
A
GLY
101
A
PRO
6
A
PRO
6
A
MET
11
A
MET
11
A
THR
202
A
THR
202
A
ALA
209
A
ALA
209
A
HIS
299
A
HIS
299
A
ASP
302
A
ASP
302
76
P 41