0.009603
0.005545
0.000000
0.000000
0.011089
0.000000
0.000000
0.000000
0.014038
0.00000
0.00000
0.00000
Yanagisawa, T.
Ishii, R.
Yokoyama, S.
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
104.129
104.129
71.234
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
378
634
652
10.1016/j.jmb.2008.02.045
18387634
Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase
2008
10.2210/pdb2e3c/pdb
pdb_00002e3c
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
1
CCD
2005-07-25
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
BL41XU
SPring-8
1.0000
SYNCHROTRON
SPRING-8 BEAMLINE BL41XU
33344.164
Pyrrolysyl-tRNA synthetase
6.1.1.26
C-terminal catalytic domain
1
man
polymer
18.015
water
41
nat
water
no
no
MGSSHHHHHHSSGLVPRGSHMASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYL
GKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIF
EIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVG
PIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL
MGSSHHHHHHSSGLVPRGSHMASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYL
GKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIF
EIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVG
PIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL
A
trt001000322.4
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
Methanosarcina
JCM9314
Escherichia
sample
pylS
2209
Methanosarcina mazei
562
Escherichia coli
BL21(DE3) codon plus
plasmid
pET28c
1
3.34
63.20
VAPOR DIFFUSION, HANGING DROP
7
Na/Cacodylate, MgCl2, PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
RIKEN Structural Genomics/Proteomics Initiative
RSGI
NPPSFA, National Project on Protein Structural and Functional Analyses
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
repository
Initial release
Version format compliance
Data collection
Database references
Refinement description
1
0
2007-12-11
1
1
2011-07-13
1
2
2023-10-25
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
The same protein complexed with pyrrolysine and AMPPNP
The same protein complexed with AMPPNP
The same protein complexed with Boc-Lys and AMPPNP
Y
PDBJ
Y
PDBJ
2006-11-22
REL
REL
HOH
water
THIS CONFLICT IS DUE TO THE STRAIN DIFFERENCE
(JCM9314 AND GOE1).
2DXH
PDB
experimental model
TIP
2
2
HOH
HOH
2
A
TIP
3
2
HOH
HOH
3
A
TIP
4
2
HOH
HOH
4
A
TIP
5
2
HOH
HOH
5
A
TIP
6
2
HOH
HOH
6
A
TIP
7
2
HOH
HOH
7
A
TIP
9
2
HOH
HOH
9
A
TIP
11
2
HOH
HOH
11
A
TIP
12
2
HOH
HOH
12
A
TIP
13
2
HOH
HOH
13
A
TIP
14
2
HOH
HOH
14
A
TIP
16
2
HOH
HOH
16
A
TIP
17
2
HOH
HOH
17
A
TIP
18
2
HOH
HOH
18
A
TIP
19
2
HOH
HOH
19
A
TIP
20
2
HOH
HOH
20
A
TIP
22
2
HOH
HOH
22
A
TIP
23
2
HOH
HOH
23
A
TIP
24
2
HOH
HOH
24
A
TIP
26
2
HOH
HOH
26
A
TIP
32
2
HOH
HOH
32
A
TIP
34
2
HOH
HOH
34
A
TIP
36
2
HOH
HOH
36
A
TIP
40
2
HOH
HOH
40
A
TIP
44
2
HOH
HOH
44
A
TIP
46
2
HOH
HOH
46
A
TIP
53
2
HOH
HOH
53
A
TIP
54
2
HOH
HOH
54
A
TIP
56
2
HOH
HOH
56
A
TIP
60
2
HOH
HOH
60
A
TIP
61
2
HOH
HOH
61
A
TIP
67
2
HOH
HOH
67
A
TIP
75
2
HOH
HOH
75
A
TIP
76
2
HOH
HOH
76
A
TIP
83
2
HOH
HOH
83
A
TIP
89
2
HOH
HOH
89
A
TIP
90
2
HOH
HOH
90
A
TIP
92
2
HOH
HOH
92
A
TIP
96
2
HOH
HOH
96
A
TIP
107
2
HOH
HOH
107
A
TIP
500
2
HOH
HOH
500
A
n
1
-21
A
n
2
-20
A
n
3
-19
A
n
4
-18
A
n
5
-17
A
n
6
-16
A
n
7
-15
A
n
8
-14
A
n
9
-13
A
n
10
-12
A
n
11
-11
A
n
12
-10
A
n
13
-9
A
n
14
-8
A
n
15
-7
A
n
16
-6
A
n
17
-5
A
n
18
-4
A
n
19
-3
A
n
20
-2
A
n
21
-1
A
n
22
185
A
n
23
186
A
ALA
187
n
24
ALA
187
A
PRO
188
n
25
PRO
188
A
ALA
189
n
26
ALA
189
A
LEU
190
n
27
LEU
190
A
THR
191
n
28
THR
191
A
LYS
192
n
29
LYS
192
A
SER
193
n
30
SER
193
A
GLN
194
n
31
GLN
194
A
THR
195
n
32
THR
195
A
ASP
196
n
33
ASP
196
A
ARG
197
n
34
ARG
197
A
LEU
198
n
35
LEU
198
A
GLU
199
n
36
GLU
199
A
VAL
200
n
37
VAL
200
A
LEU
201
n
38
LEU
201
A
LEU
202
n
39
LEU
202
A
ASN
203
n
40
ASN
203
A
PRO
204
n
41
PRO
204
A
LYS
205
n
42
LYS
205
A
ASP
206
n
43
ASP
206
A
GLU
207
n
44
GLU
207
A
n
45
208
A
n
46
209
A
n
47
210
A
n
48
211
A
SER
212
n
49
SER
212
A
GLY
213
n
50
GLY
213
A
LYS
214
n
51
LYS
214
A
PRO
215
n
52
PRO
215
A
PHE
216
n
53
PHE
216
A
ARG
217
n
54
ARG
217
A
GLU
218
n
55
GLU
218
A
LEU
219
n
56
LEU
219
A
GLU
220
n
57
GLU
220
A
SER
221
n
58
SER
221
A
GLU
222
n
59
GLU
222
A
LEU
223
n
60
LEU
223
A
LEU
224
n
61
LEU
224
A
SER
225
n
62
SER
225
A
ARG
226
n
63
ARG
226
A
ARG
227
n
64
ARG
227
A
LYS
228
n
65
LYS
228
A
LYS
229
n
66
LYS
229
A
ASP
230
n
67
ASP
230
A
LEU
231
n
68
LEU
231
A
GLN
232
n
69
GLN
232
A
GLN
233
n
70
GLN
233
A
ILE
234
n
71
ILE
234
A
TYR
235
n
72
TYR
235
A
ALA
236
n
73
ALA
236
A
GLU
237
n
74
GLU
237
A
GLU
238
n
75
GLU
238
A
ARG
239
n
76
ARG
239
A
GLU
240
n
77
GLU
240
A
ASN
241
n
78
ASN
241
A
TYR
242
n
79
TYR
242
A
LEU
243
n
80
LEU
243
A
GLY
244
n
81
GLY
244
A
LYS
245
n
82
LYS
245
A
LEU
246
n
83
LEU
246
A
GLU
247
n
84
GLU
247
A
ARG
248
n
85
ARG
248
A
GLU
249
n
86
GLU
249
A
ILE
250
n
87
ILE
250
A
THR
251
n
88
THR
251
A
ARG
252
n
89
ARG
252
A
PHE
253
n
90
PHE
253
A
PHE
254
n
91
PHE
254
A
VAL
255
n
92
VAL
255
A
ASP
256
n
93
ASP
256
A
ARG
257
n
94
ARG
257
A
GLY
258
n
95
GLY
258
A
PHE
259
n
96
PHE
259
A
LEU
260
n
97
LEU
260
A
GLU
261
n
98
GLU
261
A
ILE
262
n
99
ILE
262
A
LYS
263
n
100
LYS
263
A
SER
264
n
101
SER
264
A
PRO
265
n
102
PRO
265
A
ILE
266
n
103
ILE
266
A
LEU
267
n
104
LEU
267
A
ILE
268
n
105
ILE
268
A
PRO
269
n
106
PRO
269
A
LEU
270
n
107
LEU
270
A
GLU
271
n
108
GLU
271
A
TYR
272
n
109
TYR
272
A
ILE
273
n
110
ILE
273
A
GLU
274
n
111
GLU
274
A
ARG
275
n
112
ARG
275
A
MET
276
n
113
MET
276
A
GLY
277
n
114
GLY
277
A
ILE
278
n
115
ILE
278
A
ASP
279
n
116
ASP
279
A
ASN
280
n
117
ASN
280
A
ASP
281
n
118
ASP
281
A
THR
282
n
119
THR
282
A
GLU
283
n
120
GLU
283
A
LEU
284
n
121
LEU
284
A
SER
285
n
122
SER
285
A
LYS
286
n
123
LYS
286
A
GLN
287
n
124
GLN
287
A
ILE
288
n
125
ILE
288
A
PHE
289
n
126
PHE
289
A
ARG
290
n
127
ARG
290
A
VAL
291
n
128
VAL
291
A
ASP
292
n
129
ASP
292
A
LYS
293
n
130
LYS
293
A
ASN
294
n
131
ASN
294
A
PHE
295
n
132
PHE
295
A
CYS
296
n
133
CYS
296
A
LEU
297
n
134
LEU
297
A
ARG
298
n
135
ARG
298
A
PRO
299
n
136
PRO
299
A
MET
300
n
137
MET
300
A
LEU
301
n
138
LEU
301
A
ALA
302
n
139
ALA
302
A
PRO
303
n
140
PRO
303
A
ASN
304
n
141
ASN
304
A
LEU
305
n
142
LEU
305
A
TYR
306
n
143
TYR
306
A
ASN
307
n
144
ASN
307
A
TYR
308
n
145
TYR
308
A
LEU
309
n
146
LEU
309
A
ARG
310
n
147
ARG
310
A
LYS
311
n
148
LYS
311
A
LEU
312
n
149
LEU
312
A
ASP
313
n
150
ASP
313
A
ARG
314
n
151
ARG
314
A
ALA
315
n
152
ALA
315
A
LEU
316
n
153
LEU
316
A
PRO
317
n
154
PRO
317
A
ASP
318
n
155
ASP
318
A
PRO
319
n
156
PRO
319
A
ILE
320
n
157
ILE
320
A
LYS
321
n
158
LYS
321
A
ILE
322
n
159
ILE
322
A
PHE
323
n
160
PHE
323
A
GLU
324
n
161
GLU
324
A
ILE
325
n
162
ILE
325
A
GLY
326
n
163
GLY
326
A
PRO
327
n
164
PRO
327
A
CYS
328
n
165
CYS
328
A
TYR
329
n
166
TYR
329
A
ARG
330
n
167
ARG
330
A
LYS
331
n
168
LYS
331
A
GLU
332
n
169
GLU
332
A
SER
333
n
170
SER
333
A
ASP
334
n
171
ASP
334
A
GLY
335
n
172
GLY
335
A
LYS
336
n
173
LYS
336
A
GLU
337
n
174
GLU
337
A
HIS
338
n
175
HIS
338
A
LEU
339
n
176
LEU
339
A
GLU
340
n
177
GLU
340
A
GLU
341
n
178
GLU
341
A
PHE
342
n
179
PHE
342
A
THR
343
n
180
THR
343
A
MET
344
n
181
MET
344
A
LEU
345
n
182
LEU
345
A
ASN
346
n
183
ASN
346
A
PHE
347
n
184
PHE
347
A
CYS
348
n
185
CYS
348
A
GLN
349
n
186
GLN
349
A
MET
350
n
187
MET
350
A
GLY
351
n
188
GLY
351
A
SER
352
n
189
SER
352
A
GLY
353
n
190
GLY
353
A
CYS
354
n
191
CYS
354
A
THR
355
n
192
THR
355
A
ARG
356
n
193
ARG
356
A
GLU
357
n
194
GLU
357
A
ASN
358
n
195
ASN
358
A
LEU
359
n
196
LEU
359
A
GLU
360
n
197
GLU
360
A
SER
361
n
198
SER
361
A
ILE
362
n
199
ILE
362
A
ILE
363
n
200
ILE
363
A
THR
364
n
201
THR
364
A
ASP
365
n
202
ASP
365
A
PHE
366
n
203
PHE
366
A
LEU
367
n
204
LEU
367
A
ASN
368
n
205
ASN
368
A
HIS
369
n
206
HIS
369
A
LEU
370
n
207
LEU
370
A
GLY
371
n
208
GLY
371
A
ILE
372
n
209
ILE
372
A
ASP
373
n
210
ASP
373
A
PHE
374
n
211
PHE
374
A
LYS
375
n
212
LYS
375
A
ILE
376
n
213
ILE
376
A
VAL
377
n
214
VAL
377
A
GLY
378
n
215
GLY
378
A
n
216
379
A
n
217
380
A
n
218
381
A
n
219
382
A
VAL
383
n
220
VAL
383
A
TYR
384
n
221
TYR
384
A
GLY
385
n
222
GLY
385
A
ASP
386
n
223
ASP
386
A
THR
387
n
224
THR
387
A
LEU
388
n
225
LEU
388
A
ASP
389
n
226
ASP
389
A
VAL
390
n
227
VAL
390
A
MET
391
n
228
MET
391
A
HIS
392
n
229
HIS
392
A
GLY
393
n
230
GLY
393
A
ASP
394
n
231
ASP
394
A
LEU
395
n
232
LEU
395
A
GLU
396
n
233
GLU
396
A
LEU
397
n
234
LEU
397
A
SER
398
n
235
SER
398
A
SER
399
n
236
SER
399
A
ALA
400
n
237
ALA
400
A
VAL
401
n
238
VAL
401
A
VAL
402
n
239
VAL
402
A
GLY
403
n
240
GLY
403
A
PRO
404
n
241
PRO
404
A
ILE
405
n
242
ILE
405
A
PRO
406
n
243
PRO
406
A
LEU
407
n
244
LEU
407
A
ASP
408
n
245
ASP
408
A
ARG
409
n
246
ARG
409
A
GLU
410
n
247
GLU
410
A
TRP
411
n
248
TRP
411
A
GLY
412
n
249
GLY
412
A
ILE
413
n
250
ILE
413
A
ASP
414
n
251
ASP
414
A
LYS
415
n
252
LYS
415
A
PRO
416
n
253
PRO
416
A
TRP
417
n
254
TRP
417
A
ILE
418
n
255
ILE
418
A
GLY
419
n
256
GLY
419
A
ALA
420
n
257
ALA
420
A
GLY
421
n
258
GLY
421
A
PHE
422
n
259
PHE
422
A
GLY
423
n
260
GLY
423
A
LEU
424
n
261
LEU
424
A
GLU
425
n
262
GLU
425
A
ARG
426
n
263
ARG
426
A
LEU
427
n
264
LEU
427
A
LEU
428
n
265
LEU
428
A
LYS
429
n
266
LYS
429
A
VAL
430
n
267
VAL
430
A
LYS
431
n
268
LYS
431
A
HIS
432
n
269
HIS
432
A
ASP
433
n
270
ASP
433
A
PHE
434
n
271
PHE
434
A
LYS
435
n
272
LYS
435
A
ASN
436
n
273
ASN
436
A
ILE
437
n
274
ILE
437
A
LYS
438
n
275
LYS
438
A
ARG
439
n
276
ARG
439
A
ALA
440
n
277
ALA
440
A
ALA
441
n
278
ALA
441
A
ARG
442
n
279
ARG
442
A
SER
443
n
280
SER
443
A
GLY
444
n
281
GLY
444
A
SER
445
n
282
SER
445
A
TYR
446
n
283
TYR
446
A
TYR
447
n
284
TYR
447
A
ASN
448
n
285
ASN
448
A
GLY
449
n
286
GLY
449
A
ILE
450
n
287
ILE
450
A
SER
451
n
288
SER
451
A
THR
452
n
289
THR
452
A
ASN
453
n
290
ASN
453
A
LEU
454
n
291
LEU
454
A
author_and_software_defined_assembly
PISA
2
dimeric
4680
-19.0
24350
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
4_565
-x,-y+1,z
crystal symmetry operation
-52.0645000000
90.1783592707
0.0000000000
A
N
LEU
260
A
N
LEU
97
A
O
LYS
321
A
O
LYS
158
A
N
GLY
326
A
N
GLY
163
A
O
MET
344
A
O
MET
181
A
N
LEU
345
A
N
LEU
182
A
O
PHE
422
A
O
PHE
259
A
O
GLY
419
A
O
GLY
256
A
N
VAL
401
A
N
VAL
238
A
O
ALA
400
A
O
ALA
237
A
N
LEU
388
A
N
LEU
225
A
O
MET
391
A
O
MET
228
A
N
LYS
375
A
N
LYS
212
A
N
ILE
268
A
N
ILE
105
A
O
CYS
296
A
O
CYS
133
A
O
PHE
295
A
O
PHE
132
A
N
VAL
291
A
N
VAL
128
A
N
TYR
447
A
N
TYR
284
A
O
ILE
450
A
O
ILE
287
1
A
MET
-21
A
MET
1
1
Y
1
A
GLY
-20
A
GLY
2
1
Y
1
A
SER
-19
A
SER
3
1
Y
1
A
SER
-18
A
SER
4
1
Y
1
A
HIS
-17
A
HIS
5
1
Y
1
A
HIS
-16
A
HIS
6
1
Y
1
A
HIS
-15
A
HIS
7
1
Y
1
A
HIS
-14
A
HIS
8
1
Y
1
A
HIS
-13
A
HIS
9
1
Y
1
A
HIS
-12
A
HIS
10
1
Y
1
A
SER
-11
A
SER
11
1
Y
1
A
SER
-10
A
SER
12
1
Y
1
A
GLY
-9
A
GLY
13
1
Y
1
A
LEU
-8
A
LEU
14
1
Y
1
A
VAL
-7
A
VAL
15
1
Y
1
A
PRO
-6
A
PRO
16
1
Y
1
A
ARG
-5
A
ARG
17
1
Y
1
A
GLY
-4
A
GLY
18
1
Y
1
A
SER
-3
A
SER
19
1
Y
1
A
HIS
-2
A
HIS
20
1
Y
1
A
MET
-1
A
MET
21
1
Y
1
A
ALA
185
A
ALA
22
1
Y
1
A
SER
186
A
SER
23
1
Y
1
A
ILE
208
A
ILE
45
1
Y
1
A
SER
209
A
SER
46
1
Y
1
A
LEU
210
A
LEU
47
1
Y
1
A
ASN
211
A
ASN
48
1
Y
1
A
ASP
379
A
ASP
216
1
Y
1
A
SER
380
A
SER
217
1
Y
1
A
CYS
381
A
CYS
218
1
Y
1
A
MET
382
A
MET
219
1
Y
1
A
LYS
214
-39.82
140.99
1
A
GLU
237
-96.92
-80.64
1
A
ARG
275
-58.03
-3.24
1
A
ASN
280
-43.37
-15.49
1
A
THR
282
-41.92
161.17
1
A
ASP
292
66.57
179.65
1
A
ASN
294
-133.72
-54.34
1
A
ALA
315
-147.57
-20.62
1
A
ASP
334
65.88
-131.15
1
A
LYS
336
-48.26
62.75
1
A
ASP
386
-9.15
105.05
1
A
SER
398
177.66
147.50
1
A
ILE
413
-85.68
-73.46
1
A
ASN
453
-104.41
77.73
protein_rep.param
protein.top
water_rep.param
water.top
ion.param
ion.top
77.1
-14.61
7.15
0.00
-14.61
0.00
29.22
0.254
0.007
0.200
0.200
2.65
38.10
1295
12551
10.3
97.3
RANDOM
1388388.20
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
2DXH
FLAT MODEL
39.4333
0.29724
0.40
0.31
5.00
0.59
0.56
2.65
38.10
41
2152
0
0
2111
0.008
1.5
22.5
0.94
4.03
1.50
6.33
2.00
5.99
2.00
8.17
2.50
0.363
0.025
0.335
2.82
208
1668
6
11.1
87.3
45.6
2.64
50
2E3C
12559
1
91.9
2.64
2.67
67.6
refinement
CNS
1.1
data collection
HKL-2000
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
MOLREP
Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase
1
N
N
2
N
N
A
THR
191
A
THR
28
HELX_P
A
LEU
201
A
LEU
38
1
1
11
A
PRO
215
A
PRO
52
HELX_P
A
GLU
237
A
GLU
74
1
2
23
A
ASN
241
A
ASN
78
HELX_P
A
ARG
257
A
ARG
94
1
3
17
A
LEU
270
A
LEU
107
HELX_P
A
ARG
275
A
ARG
112
1
4
6
A
GLU
283
A
GLU
120
HELX_P
A
ILE
288
A
ILE
125
1
5
6
A
LEU
301
A
LEU
138
HELX_P
A
ARG
314
A
ARG
151
1
6
14
A
THR
355
A
THR
192
HELX_P
A
GLY
371
A
GLY
208
1
7
17
A
ILE
405
A
ILE
242
HELX_P
A
GLY
412
A
GLY
249
5
8
8
A
LEU
424
A
LEU
261
HELX_P
A
ASP
433
A
ASP
270
1
9
10
A
ASN
436
A
ASN
273
HELX_P
A
ALA
440
A
ALA
277
5
10
5
LIGASE
aminoacyl-tRNA synthetase, tRNA, pyrrolysine, translation, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, LIGASE
A
ALA
187
A
ALA
24
1
A
PRO
188
A
PRO
25
-0.06
A
ASP
318
A
ASP
155
1
A
PRO
319
A
PRO
156
-0.02
A
GLY
403
A
GLY
240
1
A
PRO
404
A
PRO
241
0.07
Q8PWY1_METMA
UNP
1
185
Q8PWY1
ASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKS
PILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTM
LNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGL
ERLLKVKHDFKNIKRAARSESYYNGISTNL
185
454
2E3C
185
454
Q8PWY1
A
1
22
291
1
expression tag
MET
-21
2E3C
A
Q8PWY1
UNP
1
1
expression tag
GLY
-20
2E3C
A
Q8PWY1
UNP
2
1
expression tag
SER
-19
2E3C
A
Q8PWY1
UNP
3
1
expression tag
SER
-18
2E3C
A
Q8PWY1
UNP
4
1
expression tag
HIS
-17
2E3C
A
Q8PWY1
UNP
5
1
expression tag
HIS
-16
2E3C
A
Q8PWY1
UNP
6
1
expression tag
HIS
-15
2E3C
A
Q8PWY1
UNP
7
1
expression tag
HIS
-14
2E3C
A
Q8PWY1
UNP
8
1
expression tag
HIS
-13
2E3C
A
Q8PWY1
UNP
9
1
expression tag
HIS
-12
2E3C
A
Q8PWY1
UNP
10
1
expression tag
SER
-11
2E3C
A
Q8PWY1
UNP
11
1
expression tag
SER
-10
2E3C
A
Q8PWY1
UNP
12
1
expression tag
GLY
-9
2E3C
A
Q8PWY1
UNP
13
1
expression tag
LEU
-8
2E3C
A
Q8PWY1
UNP
14
1
expression tag
VAL
-7
2E3C
A
Q8PWY1
UNP
15
1
expression tag
PRO
-6
2E3C
A
Q8PWY1
UNP
16
1
expression tag
ARG
-5
2E3C
A
Q8PWY1
UNP
17
1
expression tag
GLY
-4
2E3C
A
Q8PWY1
UNP
18
1
expression tag
SER
-3
2E3C
A
Q8PWY1
UNP
19
1
expression tag
HIS
-2
2E3C
A
Q8PWY1
UNP
20
1
expression tag
MET
-1
2E3C
A
Q8PWY1
UNP
21
1
GLU
SEE REMARK 999
GLY
444
2E3C
A
Q8PWY1
UNP
444
281
7
3
2
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
260
A
LEU
97
A
ILE
262
A
ILE
99
A
ILE
320
A
ILE
157
A
TYR
329
A
TYR
166
A
GLU
341
A
GLU
178
A
MET
350
A
MET
187
A
TRP
417
A
TRP
254
A
GLY
423
A
GLY
260
A
LEU
395
A
LEU
232
A
VAL
402
A
VAL
239
A
THR
387
A
THR
224
A
HIS
392
A
HIS
229
A
LYS
375
A
LYS
212
A
VAL
377
A
VAL
214
A
LEU
267
A
LEU
104
A
PRO
269
A
PRO
106
A
PHE
295
A
PHE
132
A
LEU
297
A
LEU
134
A
ARG
290
A
ARG
127
A
VAL
291
A
VAL
128
A
TYR
446
A
TYR
283
A
TYR
447
A
TYR
284
A
ILE
450
A
ILE
287
A
SER
451
A
SER
288
172
P 64