0.024088
0.000000
0.000000
0.000000
0.021901
0.000000
0.000000
0.000000
0.010243
0.00000
0.00000
0.00000
Yao, M.
Morita, H.
Okada, A.
Tanaka, I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
41.5
45.7
97.6
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
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
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
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
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
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
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
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
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
N
134
N
H
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
O
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
S
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
N
N
170
S
C
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
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
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
N
N
200
N
O
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
S
N
223
N
C
N
224
N
O
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
N
N
237
S
C
N
238
N
C
N
239
N
O
N
240
N
O
N
241
N
C
N
242
N
C
N
243
N
SE
N
244
N
C
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
N
N
257
S
C
N
258
N
C
N
259
N
O
N
260
N
C
Y
261
N
C
Y
262
N
C
Y
263
N
C
Y
264
N
C
Y
265
N
C
Y
266
N
C
N
267
N
O
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
N
N
280
S
C
N
281
N
C
N
282
N
O
N
283
N
C
N
284
N
C
N
285
N
C
N
286
N
O
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
N
N
297
S
C
N
298
N
C
N
299
N
O
N
300
N
C
N
301
N
O
N
302
N
O
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
N
N
311
S
C
N
312
N
C
N
313
N
O
N
314
R
C
N
315
N
O
N
316
N
C
N
317
N
O
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
N
N
328
S
C
N
329
N
C
N
330
N
O
N
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
N
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
C
N
341
N
O
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
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
N
N
355
S
C
N
356
N
C
N
357
N
O
N
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
C
N
365
N
O
N
366
N
O
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
N
N
379
S
C
N
380
N
C
N
381
N
O
N
382
N
C
N
383
N
C
N
384
N
C
N
385
N
O
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
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
doub
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
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
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
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
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
doub
N
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
sing
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
doub
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
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
doub
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
sing
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
doub
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
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
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
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
doub
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
Y
254
N
doub
Y
255
N
sing
Y
256
N
sing
N
257
N
sing
Y
258
N
doub
N
259
N
sing
Y
260
N
doub
N
261
N
sing
Y
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
doub
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
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
doub
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
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
doub
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
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
doub
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
Y
323
N
doub
Y
324
N
sing
Y
325
N
sing
N
326
N
sing
Y
327
N
doub
Y
328
N
sing
Y
329
N
sing
N
330
N
sing
Y
331
N
sing
Y
332
N
doub
N
333
N
sing
Y
334
N
doub
N
335
N
sing
Y
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
doub
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
Y
351
N
doub
Y
352
N
sing
Y
353
N
sing
N
354
N
sing
Y
355
N
doub
N
356
N
sing
Y
357
N
doub
N
358
N
sing
Y
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
doub
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
DK
ACTA CRYSTALLOGR.,SECT.F
1744-3091
62
1196
1200
10.1107/S1744309106046616
17142895
The structure of Pyrococcus horikoshii 2'-5' RNA ligase at 1.94 A resolution reveals a possible open form with a wider active-site cleft
2006
10.2210/pdb1vgj/pdb
pdb_00001vgj
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
2004-03-23
ADSC
SINGLE WAVELENGTH
M
x-ray
1
0.97950
1.0
BL44B2
SPring-8
0.97950
SYNCHROTRON
SPRING-8 BEAMLINE BL44B2
21271.248
Hypothetical protein PH0099
1
man
polymer
18.015
water
41
nat
water
2'-5' RNA ligase
no
yes
(MSE)RAFIAIDVNESVRDSLVRAQDYIGSKEAKIKFVERENLHITLKFLGEITEEQAEEIKNILKKIAEKYKKHEVKVK
GIGVFPNPNYIRVIWAGIENDEIIRE(MSE)AREIEDELAKLGFKKEGNFVAHITLGRVKFVKDKLGLT(MSE)KLKELA
NEDFGSFVVDAIELKKSTLTPKGPIYETLARFELSE
MRAFIAIDVNESVRDSLVRAQDYIGSKEAKIKFVERENLHITLKFLGEITEEQAEEIKNILKKIAEKYKKHEVKVKGIGV
FPNPNYIRVIWAGIENDEIIREMAREIEDELAKLGFKKEGNFVAHITLGRVKFVKDKLGLTMKLKELANEDFGSFVVDAI
ELKKSTLTPKGPIYETLARFELSE
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
Pyrococcus
Escherichia
sample
PH0099
53953
Pyrococcus horikoshii
562
Escherichia coli
B834(DE3)
Plasmid
pET-26b
1
2.19
43.5
VAPOR DIFFUSION, HANGING DROP
4.6
Ammonium acetate, Sodium acetate, PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
Data collection
1
0
2005-06-07
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-10-25
1
4
2023-11-15
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
Y
PDBJ
Y
PDBJ
2004-04-27
REL
REL
HOH
water
1IUH
PDB entry 1iuh
PDB
experimental model
HOH
201
2
HOH
HOH
201
A
HOH
202
2
HOH
HOH
202
A
HOH
203
2
HOH
HOH
203
A
HOH
204
2
HOH
HOH
204
A
HOH
205
2
HOH
HOH
205
A
HOH
206
2
HOH
HOH
206
A
HOH
207
2
HOH
HOH
207
A
HOH
208
2
HOH
HOH
208
A
HOH
209
2
HOH
HOH
209
A
HOH
210
2
HOH
HOH
210
A
HOH
211
2
HOH
HOH
211
A
HOH
212
2
HOH
HOH
212
A
HOH
213
2
HOH
HOH
213
A
HOH
214
2
HOH
HOH
214
A
HOH
215
2
HOH
HOH
215
A
HOH
216
2
HOH
HOH
216
A
HOH
217
2
HOH
HOH
217
A
HOH
218
2
HOH
HOH
218
A
HOH
219
2
HOH
HOH
219
A
HOH
220
2
HOH
HOH
220
A
HOH
221
2
HOH
HOH
221
A
HOH
222
2
HOH
HOH
222
A
HOH
223
2
HOH
HOH
223
A
HOH
224
2
HOH
HOH
224
A
HOH
225
2
HOH
HOH
225
A
HOH
226
2
HOH
HOH
226
A
HOH
227
2
HOH
HOH
227
A
HOH
228
2
HOH
HOH
228
A
HOH
229
2
HOH
HOH
229
A
HOH
230
2
HOH
HOH
230
A
HOH
231
2
HOH
HOH
231
A
HOH
232
2
HOH
HOH
232
A
HOH
233
2
HOH
HOH
233
A
HOH
234
2
HOH
HOH
234
A
HOH
235
2
HOH
HOH
235
A
HOH
236
2
HOH
HOH
236
A
HOH
237
2
HOH
HOH
237
A
HOH
238
2
HOH
HOH
238
A
HOH
239
2
HOH
HOH
239
A
HOH
240
2
HOH
HOH
240
A
HOH
241
2
HOH
HOH
241
A
MSE
1
n
1
MSE
1
A
ARG
2
n
2
ARG
2
A
ALA
3
n
3
ALA
3
A
PHE
4
n
4
PHE
4
A
ILE
5
n
5
ILE
5
A
ALA
6
n
6
ALA
6
A
ILE
7
n
7
ILE
7
A
ASP
8
n
8
ASP
8
A
VAL
9
n
9
VAL
9
A
ASN
10
n
10
ASN
10
A
GLU
11
n
11
GLU
11
A
SER
12
n
12
SER
12
A
VAL
13
n
13
VAL
13
A
ARG
14
n
14
ARG
14
A
ASP
15
n
15
ASP
15
A
SER
16
n
16
SER
16
A
LEU
17
n
17
LEU
17
A
VAL
18
n
18
VAL
18
A
ARG
19
n
19
ARG
19
A
ALA
20
n
20
ALA
20
A
GLN
21
n
21
GLN
21
A
ASP
22
n
22
ASP
22
A
TYR
23
n
23
TYR
23
A
ILE
24
n
24
ILE
24
A
GLY
25
n
25
GLY
25
A
SER
26
n
26
SER
26
A
LYS
27
n
27
LYS
27
A
GLU
28
n
28
GLU
28
A
ALA
29
n
29
ALA
29
A
LYS
30
n
30
LYS
30
A
ILE
31
n
31
ILE
31
A
LYS
32
n
32
LYS
32
A
PHE
33
n
33
PHE
33
A
VAL
34
n
34
VAL
34
A
GLU
35
n
35
GLU
35
A
ARG
36
n
36
ARG
36
A
GLU
37
n
37
GLU
37
A
ASN
38
n
38
ASN
38
A
LEU
39
n
39
LEU
39
A
HIS
40
n
40
HIS
40
A
ILE
41
n
41
ILE
41
A
THR
42
n
42
THR
42
A
LEU
43
n
43
LEU
43
A
LYS
44
n
44
LYS
44
A
PHE
45
n
45
PHE
45
A
LEU
46
n
46
LEU
46
A
GLY
47
n
47
GLY
47
A
GLU
48
n
48
GLU
48
A
ILE
49
n
49
ILE
49
A
THR
50
n
50
THR
50
A
GLU
51
n
51
GLU
51
A
GLU
52
n
52
GLU
52
A
GLN
53
n
53
GLN
53
A
ALA
54
n
54
ALA
54
A
GLU
55
n
55
GLU
55
A
GLU
56
n
56
GLU
56
A
ILE
57
n
57
ILE
57
A
LYS
58
n
58
LYS
58
A
ASN
59
n
59
ASN
59
A
ILE
60
n
60
ILE
60
A
LEU
61
n
61
LEU
61
A
LYS
62
n
62
LYS
62
A
LYS
63
n
63
LYS
63
A
ILE
64
n
64
ILE
64
A
ALA
65
n
65
ALA
65
A
GLU
66
n
66
GLU
66
A
LYS
67
n
67
LYS
67
A
TYR
68
n
68
TYR
68
A
LYS
69
n
69
LYS
69
A
LYS
70
n
70
LYS
70
A
HIS
71
n
71
HIS
71
A
GLU
72
n
72
GLU
72
A
VAL
73
n
73
VAL
73
A
LYS
74
n
74
LYS
74
A
VAL
75
n
75
VAL
75
A
LYS
76
n
76
LYS
76
A
GLY
77
n
77
GLY
77
A
ILE
78
n
78
ILE
78
A
GLY
79
n
79
GLY
79
A
VAL
80
n
80
VAL
80
A
PHE
81
n
81
PHE
81
A
PRO
82
n
82
PRO
82
A
ASN
83
n
83
ASN
83
A
PRO
84
n
84
PRO
84
A
ASN
85
n
85
ASN
85
A
TYR
86
n
86
TYR
86
A
ILE
87
n
87
ILE
87
A
ARG
88
n
88
ARG
88
A
VAL
89
n
89
VAL
89
A
ILE
90
n
90
ILE
90
A
TRP
91
n
91
TRP
91
A
ALA
92
n
92
ALA
92
A
GLY
93
n
93
GLY
93
A
ILE
94
n
94
ILE
94
A
GLU
95
n
95
GLU
95
A
ASN
96
n
96
ASN
96
A
ASP
97
n
97
ASP
97
A
GLU
98
n
98
GLU
98
A
ILE
99
n
99
ILE
99
A
ILE
100
n
100
ILE
100
A
ARG
101
n
101
ARG
101
A
GLU
102
n
102
GLU
102
A
MSE
103
n
103
MSE
103
A
ALA
104
n
104
ALA
104
A
ARG
105
n
105
ARG
105
A
GLU
106
n
106
GLU
106
A
ILE
107
n
107
ILE
107
A
GLU
108
n
108
GLU
108
A
ASP
109
n
109
ASP
109
A
GLU
110
n
110
GLU
110
A
LEU
111
n
111
LEU
111
A
ALA
112
n
112
ALA
112
A
LYS
113
n
113
LYS
113
A
LEU
114
n
114
LEU
114
A
GLY
115
n
115
GLY
115
A
PHE
116
n
116
PHE
116
A
LYS
117
n
117
LYS
117
A
LYS
118
n
118
LYS
118
A
GLU
119
n
119
GLU
119
A
GLY
120
n
120
GLY
120
A
ASN
121
n
121
ASN
121
A
PHE
122
n
122
PHE
122
A
VAL
123
n
123
VAL
123
A
ALA
124
n
124
ALA
124
A
HIS
125
n
125
HIS
125
A
ILE
126
n
126
ILE
126
A
THR
127
n
127
THR
127
A
LEU
128
n
128
LEU
128
A
GLY
129
n
129
GLY
129
A
ARG
130
n
130
ARG
130
A
VAL
131
n
131
VAL
131
A
LYS
132
n
132
LYS
132
A
PHE
133
n
133
PHE
133
A
VAL
134
n
134
VAL
134
A
LYS
135
n
135
LYS
135
A
ASP
136
n
136
ASP
136
A
LYS
137
n
137
LYS
137
A
LEU
138
n
138
LEU
138
A
GLY
139
n
139
GLY
139
A
LEU
140
n
140
LEU
140
A
THR
141
n
141
THR
141
A
MSE
142
n
142
MSE
142
A
LYS
143
n
143
LYS
143
A
LEU
144
n
144
LEU
144
A
LYS
145
n
145
LYS
145
A
GLU
146
n
146
GLU
146
A
LEU
147
n
147
LEU
147
A
ALA
148
n
148
ALA
148
A
ASN
149
n
149
ASN
149
A
GLU
150
n
150
GLU
150
A
ASP
151
n
151
ASP
151
A
PHE
152
n
152
PHE
152
A
GLY
153
n
153
GLY
153
A
SER
154
n
154
SER
154
A
PHE
155
n
155
PHE
155
A
VAL
156
n
156
VAL
156
A
VAL
157
n
157
VAL
157
A
ASP
158
n
158
ASP
158
A
ALA
159
n
159
ALA
159
A
ILE
160
n
160
ILE
160
A
GLU
161
n
161
GLU
161
A
LEU
162
n
162
LEU
162
A
LYS
163
n
163
LYS
163
A
LYS
164
n
164
LYS
164
A
SER
165
n
165
SER
165
A
THR
166
n
166
THR
166
A
LEU
167
n
167
LEU
167
A
THR
168
n
168
THR
168
A
PRO
169
n
169
PRO
169
A
LYS
170
n
170
LYS
170
A
GLY
171
n
171
GLY
171
A
PRO
172
n
172
PRO
172
A
ILE
173
n
173
ILE
173
A
TYR
174
n
174
TYR
174
A
GLU
175
n
175
GLU
175
A
THR
176
n
176
THR
176
A
LEU
177
n
177
LEU
177
A
ALA
178
n
178
ALA
178
A
ARG
179
n
179
ARG
179
A
PHE
180
n
180
PHE
180
A
GLU
181
n
181
GLU
181
A
LEU
182
n
182
LEU
182
A
SER
183
n
183
SER
183
A
GLU
184
n
184
GLU
184
A
author_defined_assembly
1
monomeric
A
MSE
1
SELENOMETHIONINE
A
MSE
1
MET
A
MSE
103
SELENOMETHIONINE
A
MSE
103
MET
A
MSE
142
SELENOMETHIONINE
A
MSE
142
MET
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
LEU
43
A
O
LEU
43
A
N
ILE
5
A
N
ILE
5
A
N
PHE
4
A
N
PHE
4
A
O
LYS
163
A
O
LYS
163
A
N
ILE
160
A
N
ILE
160
A
O
PHE
180
A
O
PHE
180
A
N
LYS
32
A
N
LYS
32
A
O
ARG
130
A
O
ARG
130
A
O
LEU
128
A
O
LEU
128
A
N
ILE
90
A
N
ILE
90
A
O
GLU
95
A
O
GLU
95
A
N
LYS
74
A
N
LYS
74
A
N
HIS
71
A
N
HIS
71
A
O
VAL
157
A
O
VAL
157
1
-3.51
0.50
120.30
116.79
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
36
36
36
N
1
-13.72
2.20
98.90
85.18
A
A
A
CG
SE
CE
MSE
MSE
MSE
103
103
103
N
1
A
A
CA
CB
ALA
ALA
20
20
0.144
0.021
1.520
1.664
N
1
A
A
CB
CG2
VAL
VAL
75
75
0.130
0.021
1.524
1.654
N
1
A
TYR
86
53.61
87.78
33.802
1.29
0.00
0.00
-0.99
0.00
-0.30
0.942
0.915
CNS also was used for the refinement
0.26487
0.21047
0.21584
1.94
10.00
1414
14194
12780
10.0
100.00
4.068
0.120
RANDOM
1
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
0.203
0.184
0.80
0.80
1.40
PDB entry 1iuh
Engh & Huber
BABINET MODEL WITH MASK
1.94
10.00
41
1529
0
0
1488
0.027
0.022
1510
1.966
1.976
2022
5.898
5.000
183
0.156
0.200
228
0.010
0.020
1095
0.237
0.200
625
0.212
0.200
54
0.245
0.200
45
0.143
0.200
5
1.602
1.500
913
2.848
2.000
1475
4.291
3.000
597
7.231
4.500
547
0.289
0.219
1.988
112
891
1003
20
50.2
1.94
50
1VGJ
14330
14330
-3.0
0.047
0.047
1
16.5
7.0
99.9
0.384
1.94
2.01
1394
0.384
6.6
99.6
refinement
REFMAC
5.1.19
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii
1
N
N
2
N
N
Biological unit is a monomer in the asymmetric unit.
A
ASN
10
A
ASN
10
HELX_P
A
GLY
25
A
GLY
25
1
1
16
A
GLU
35
A
GLU
35
HELX_P
A
ASN
38
A
ASN
38
5
2
4
A
THR
50
A
THR
50
HELX_P
A
GLU
66
A
GLU
66
1
3
17
A
ASP
97
A
ASP
97
HELX_P
A
LYS
113
A
LYS
113
1
4
17
A
ASP
136
A
ASP
136
HELX_P
A
LEU
147
A
LEU
147
1
5
12
covale
1.341
both
A
MSE
1
A
C
MSE
1
1_555
A
ARG
2
A
N
ARG
2
1_555
covale
1.354
both
A
GLU
102
A
C
GLU
102
1_555
A
MSE
103
A
N
MSE
103
1_555
covale
1.330
both
A
MSE
103
A
C
MSE
103
1_555
A
ALA
104
A
N
ALA
104
1_555
covale
1.326
both
A
THR
141
A
C
THR
141
1_555
A
MSE
142
A
N
MSE
142
1_555
covale
1.327
both
A
MSE
142
A
C
MSE
142
1_555
A
LYS
143
A
N
LYS
143
1_555
LIGASE
Alpha+Beta, LigT-like, STRUCTURAL GENOMICS, LIGASE
A
PHE
81
A
PHE
81
1
A
PRO
82
A
PRO
82
-1.44
Y099_PYRHO
UNP
1
1
O57823
MRAFIAIDVNESVRDSLVRAQDYIGSKEAKIKFVERENLHITLKFLGEITEEQAEEIKNILKKIAEKYKKHEVKVKGIGV
FPNPNYIRVIWAGIENDEIIREMAREIEDELAKLGFKKEGNFVAHITLGRVKFVKDKLGLTMKLKELANEDFGSFVVDAI
ELKKSTLTPKGPIYETLARFELSE
1
184
1VGJ
1
184
O57823
A
1
1
184
1
MET
modified residue
MSE
1
1VGJ
A
O57823
UNP
1
1
1
MET
modified residue
MSE
103
1VGJ
A
O57823
UNP
103
103
1
MET
modified residue
MSE
142
1VGJ
A
O57823
UNP
142
142
4
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
HIS
40
A
HIS
40
A
GLY
47
A
GLY
47
A
ARG
2
A
ARG
2
A
ASP
8
A
ASP
8
A
ALA
159
A
ALA
159
A
THR
168
A
THR
168
A
GLY
171
A
GLY
171
A
GLU
181
A
GLU
181
A
ALA
29
A
ALA
29
A
PHE
33
A
PHE
33
A
HIS
125
A
HIS
125
A
VAL
134
A
VAL
134
A
ILE
87
A
ILE
87
A
GLU
95
A
GLU
95
A
HIS
71
A
HIS
71
A
PRO
82
A
PRO
82
A
ASP
151
A
ASP
151
A
VAL
157
A
VAL
157
19
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