0.014328
0.008272
0.000000
0.000000
0.016544
0.000000
0.000000
0.000000
0.017091
0.00000
0.00000
0.00000
Nishino, T.
Komori, K.
Ishino, Y.
Morikawa, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
69.795
69.795
58.509
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
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
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
C
Y
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
N
247
N
O
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
H
N
257
N
H
N
258
N
H
N
259
N
N
N
260
S
C
N
261
N
C
N
262
N
O
N
263
N
C
N
264
N
C
N
265
N
C
N
266
N
O
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
H
N
274
N
H
N
275
N
H
N
276
N
N
N
277
S
C
N
278
N
C
N
279
N
O
N
280
N
C
N
281
N
O
N
282
N
O
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
R
C
N
295
N
O
N
296
N
C
N
297
N
O
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
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
Y
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
Y
317
N
C
N
318
N
O
N
319
N
O
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
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
N
N
332
S
C
N
333
N
C
N
334
N
O
N
335
N
C
N
336
N
C
N
337
N
C
N
338
N
O
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
H
N
349
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
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
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
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
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
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
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
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
Y
304
N
doub
Y
305
N
sing
Y
306
N
sing
N
307
N
sing
Y
308
N
doub
N
309
N
sing
Y
310
N
doub
N
311
N
sing
Y
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
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
doub
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
UK
Structure
STRUE6
2005
0969-2126
11
445
457
10.1016/S0969-2126(03)00046-7
12679022
X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease. Similarity between Its Endonuclease Domain and Restriction Enzymes
2003
10.2210/pdb1j22/pdb
pdb_00001j22
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
graphite
CCD
2001-11-01
ADSC QUANTUM 4
diamond
MAD
M
x-ray
1
1.00
1.0
0.97
1.0
0.9791
1.0
0.9794
1.0
BL38B1
SPring-8
1.00, 0.97, 0.9791, 0.9794
SYNCHROTRON
SPRING-8 BEAMLINE BL38B1
16116.660
ATP-dependent RNA helicase, putative
nuclease domain fragment
F55L, R63G
1
man
polymer
18.015
water
105
nat
water
Hef nuclease
no
no
MQEGVKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLFDQVKRLKEAYSRPIM
IVEGSLYGIRNVHPNAIRGAIAAVTVDFGVPIIFSSTPEETAQYIFLIAKREQEEREKPVRIR
MQEGVKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLFDQVKRLKEAYSRPIM
IVEGSLYGIRNVHPNAIRGAIAAVTVDFGVPIIFSSTPEETAQYIFLIAKREQEEREKPVRIR
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
Pyrococcus
Pyrococcus furiosus
DSM 3638
Escherichia
sample
186497
Pyrococcus furiosus
562
Escherichia coli
BL21DE3 codon plus RIL
plasmid
pET
1
2.59
52.16
MICRODIALYSIS
8.0
Tricine-NaOH, NaCl, NaN3, subtilisin, pH 8.0, MICRODIALYSIS, temperature 298K
298
database_2
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Source and taxonomy
Version format compliance
Database references
Data collection
1
0
2003-04-22
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-11-10
1
4
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
XPF/Mus81 homolog
XPF/Mus81 homolog, Ca cocrystal
XPF/Mus81 homolog, Mn cocrystal
PDBJ
Y
PDBJ
2002-12-25
REL
REL
HOH
water
HOH
1
2
HOH
HOH
144
A
HOH
2
2
HOH
HOH
145
A
HOH
3
2
HOH
HOH
146
A
HOH
4
2
HOH
HOH
147
A
HOH
5
2
HOH
HOH
148
A
HOH
6
2
HOH
HOH
149
A
HOH
7
2
HOH
HOH
150
A
HOH
8
2
HOH
HOH
151
A
HOH
9
2
HOH
HOH
152
A
HOH
10
2
HOH
HOH
153
A
HOH
11
2
HOH
HOH
154
A
HOH
12
2
HOH
HOH
155
A
HOH
13
2
HOH
HOH
156
A
HOH
14
2
HOH
HOH
157
A
HOH
15
2
HOH
HOH
158
A
HOH
16
2
HOH
HOH
159
A
HOH
18
2
HOH
HOH
160
A
HOH
19
2
HOH
HOH
161
A
HOH
20
2
HOH
HOH
162
A
HOH
21
2
HOH
HOH
163
A
HOH
22
2
HOH
HOH
164
A
HOH
23
2
HOH
HOH
165
A
HOH
24
2
HOH
HOH
166
A
HOH
25
2
HOH
HOH
167
A
HOH
26
2
HOH
HOH
168
A
HOH
27
2
HOH
HOH
169
A
HOH
28
2
HOH
HOH
170
A
HOH
29
2
HOH
HOH
171
A
HOH
30
2
HOH
HOH
172
A
HOH
31
2
HOH
HOH
173
A
HOH
32
2
HOH
HOH
174
A
HOH
33
2
HOH
HOH
175
A
HOH
34
2
HOH
HOH
176
A
HOH
36
2
HOH
HOH
177
A
HOH
37
2
HOH
HOH
178
A
HOH
38
2
HOH
HOH
179
A
HOH
39
2
HOH
HOH
180
A
HOH
40
2
HOH
HOH
181
A
HOH
41
2
HOH
HOH
182
A
HOH
42
2
HOH
HOH
183
A
HOH
43
2
HOH
HOH
184
A
HOH
44
2
HOH
HOH
185
A
HOH
45
2
HOH
HOH
186
A
HOH
46
2
HOH
HOH
187
A
HOH
47
2
HOH
HOH
188
A
HOH
48
2
HOH
HOH
189
A
HOH
49
2
HOH
HOH
190
A
HOH
50
2
HOH
HOH
191
A
HOH
51
2
HOH
HOH
192
A
HOH
52
2
HOH
HOH
193
A
HOH
53
2
HOH
HOH
194
A
HOH
54
2
HOH
HOH
195
A
HOH
55
2
HOH
HOH
196
A
HOH
56
2
HOH
HOH
197
A
HOH
57
2
HOH
HOH
198
A
HOH
58
2
HOH
HOH
199
A
HOH
59
2
HOH
HOH
200
A
HOH
60
2
HOH
HOH
201
A
HOH
61
2
HOH
HOH
202
A
HOH
62
2
HOH
HOH
203
A
HOH
63
2
HOH
HOH
204
A
HOH
64
2
HOH
HOH
205
A
HOH
65
2
HOH
HOH
206
A
HOH
66
2
HOH
HOH
207
A
HOH
67
2
HOH
HOH
208
A
HOH
68
2
HOH
HOH
209
A
HOH
69
2
HOH
HOH
210
A
HOH
70
2
HOH
HOH
211
A
HOH
71
2
HOH
HOH
212
A
HOH
72
2
HOH
HOH
213
A
HOH
73
2
HOH
HOH
214
A
HOH
74
2
HOH
HOH
215
A
HOH
75
2
HOH
HOH
216
A
HOH
76
2
HOH
HOH
217
A
HOH
77
2
HOH
HOH
218
A
HOH
78
2
HOH
HOH
219
A
HOH
79
2
HOH
HOH
220
A
HOH
80
2
HOH
HOH
221
A
HOH
81
2
HOH
HOH
222
A
HOH
82
2
HOH
HOH
223
A
HOH
83
2
HOH
HOH
224
A
HOH
84
2
HOH
HOH
225
A
HOH
85
2
HOH
HOH
226
A
HOH
87
2
HOH
HOH
227
A
HOH
88
2
HOH
HOH
228
A
HOH
89
2
HOH
HOH
229
A
HOH
90
2
HOH
HOH
230
A
HOH
91
2
HOH
HOH
231
A
HOH
92
2
HOH
HOH
232
A
HOH
93
2
HOH
HOH
233
A
HOH
94
2
HOH
HOH
234
A
HOH
95
2
HOH
HOH
235
A
HOH
96
2
HOH
HOH
236
A
HOH
97
2
HOH
HOH
237
A
HOH
98
2
HOH
HOH
238
A
HOH
99
2
HOH
HOH
239
A
HOH
100
2
HOH
HOH
240
A
HOH
101
2
HOH
HOH
241
A
HOH
102
2
HOH
HOH
242
A
HOH
103
2
HOH
HOH
243
A
HOH
104
2
HOH
HOH
244
A
HOH
105
2
HOH
HOH
245
A
HOH
106
2
HOH
HOH
246
A
HOH
107
2
HOH
HOH
247
A
HOH
108
2
HOH
HOH
248
A
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
VAL
5
n
5
VAL
5
A
LYS
6
n
6
LYS
6
A
VAL
7
n
7
VAL
7
A
VAL
8
n
8
VAL
8
A
VAL
9
n
9
VAL
9
A
ASP
10
n
10
ASP
10
A
SER
11
n
11
SER
11
A
ARG
12
n
12
ARG
12
A
GLU
13
n
13
GLU
13
A
LEU
14
n
14
LEU
14
A
ARG
15
n
15
ARG
15
A
SER
16
n
16
SER
16
A
GLU
17
n
17
GLU
17
A
VAL
18
n
18
VAL
18
A
VAL
19
n
19
VAL
19
A
LYS
20
n
20
LYS
20
A
ARG
21
n
21
ARG
21
A
LEU
22
n
22
LEU
22
A
LYS
23
n
23
LYS
23
A
LEU
24
n
24
LEU
24
A
LEU
25
n
25
LEU
25
A
GLY
26
n
26
GLY
26
A
VAL
27
n
27
VAL
27
A
LYS
28
n
28
LYS
28
A
LEU
29
n
29
LEU
29
A
GLU
30
n
30
GLU
30
A
VAL
31
n
31
VAL
31
A
LYS
32
n
32
LYS
32
A
THR
33
n
33
THR
33
A
LEU
34
n
34
LEU
34
A
ASP
35
n
35
ASP
35
A
VAL
36
n
36
VAL
36
A
GLY
37
n
37
GLY
37
A
ASP
38
n
38
ASP
38
A
TYR
39
n
39
TYR
39
A
ILE
40
n
40
ILE
40
A
ILE
41
n
41
ILE
41
A
SER
42
n
42
SER
42
A
GLU
43
n
43
GLU
43
A
ASP
44
n
44
ASP
44
A
VAL
45
n
45
VAL
45
A
ALA
46
n
46
ALA
46
A
ILE
47
n
47
ILE
47
A
GLU
48
n
48
GLU
48
A
ARG
49
n
49
ARG
49
A
LYS
50
n
50
LYS
50
A
SER
51
n
51
SER
51
A
ALA
52
n
52
ALA
52
A
ASN
53
n
53
ASN
53
A
ASP
54
n
54
ASP
54
A
LEU
55
n
55
LEU
55
A
ILE
56
n
56
ILE
56
A
GLN
57
n
57
GLN
57
A
SER
58
n
58
SER
58
A
ILE
59
n
59
ILE
59
A
ILE
60
n
60
ILE
60
A
ASP
61
n
61
ASP
61
A
GLY
62
n
62
GLY
62
A
GLY
63
n
63
GLY
63
A
LEU
64
n
64
LEU
64
A
PHE
65
n
65
PHE
65
A
ASP
66
n
66
ASP
66
A
GLN
67
n
67
GLN
67
A
VAL
68
n
68
VAL
68
A
LYS
69
n
69
LYS
69
A
ARG
70
n
70
ARG
70
A
LEU
71
n
71
LEU
71
A
LYS
72
n
72
LYS
72
A
GLU
73
n
73
GLU
73
A
ALA
74
n
74
ALA
74
A
TYR
75
n
75
TYR
75
A
SER
76
n
76
SER
76
A
ARG
77
n
77
ARG
77
A
PRO
78
n
78
PRO
78
A
ILE
79
n
79
ILE
79
A
MET
80
n
80
MET
80
A
ILE
81
n
81
ILE
81
A
VAL
82
n
82
VAL
82
A
GLU
83
n
83
GLU
83
A
GLY
84
n
84
GLY
84
A
SER
85
n
85
SER
85
A
LEU
86
n
86
LEU
86
A
TYR
87
n
87
TYR
87
A
GLY
88
n
88
GLY
88
A
ILE
89
n
89
ILE
89
A
ARG
90
n
90
ARG
90
A
ASN
91
n
91
ASN
91
A
VAL
92
n
92
VAL
92
A
HIS
93
n
93
HIS
93
A
PRO
94
n
94
PRO
94
A
ASN
95
n
95
ASN
95
A
ALA
96
n
96
ALA
96
A
ILE
97
n
97
ILE
97
A
ARG
98
n
98
ARG
98
A
GLY
99
n
99
GLY
99
A
ALA
100
n
100
ALA
100
A
ILE
101
n
101
ILE
101
A
ALA
102
n
102
ALA
102
A
ALA
103
n
103
ALA
103
A
VAL
104
n
104
VAL
104
A
THR
105
n
105
THR
105
A
VAL
106
n
106
VAL
106
A
ASP
107
n
107
ASP
107
A
PHE
108
n
108
PHE
108
A
GLY
109
n
109
GLY
109
A
VAL
110
n
110
VAL
110
A
PRO
111
n
111
PRO
111
A
ILE
112
n
112
ILE
112
A
ILE
113
n
113
ILE
113
A
PHE
114
n
114
PHE
114
A
SER
115
n
115
SER
115
A
SER
116
n
116
SER
116
A
THR
117
n
117
THR
117
A
PRO
118
n
118
PRO
118
A
GLU
119
n
119
GLU
119
A
GLU
120
n
120
GLU
120
A
THR
121
n
121
THR
121
A
ALA
122
n
122
ALA
122
A
GLN
123
n
123
GLN
123
A
TYR
124
n
124
TYR
124
A
ILE
125
n
125
ILE
125
A
PHE
126
n
126
PHE
126
A
LEU
127
n
127
LEU
127
A
ILE
128
n
128
ILE
128
A
ALA
129
n
129
ALA
129
A
LYS
130
n
130
LYS
130
A
ARG
131
n
131
ARG
131
A
GLU
132
n
132
GLU
132
A
GLN
133
n
133
GLN
133
A
GLU
134
n
134
GLU
134
A
GLU
135
n
135
GLU
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
author_defined_assembly
2
dimeric
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
5_674
x-y+1,-y+2,-z-1/3
crystal symmetry operation
0.0000000000
120.8884861143
-19.5030000000
A
O
GLU
30
A
O
GLU
30
A
N
VAL
9
A
N
VAL
9
A
N
VAL
8
A
N
VAL
8
A
O
ILE
40
A
O
ILE
40
A
N
TYR
39
A
N
TYR
39
A
O
ILE
47
A
O
ILE
47
A
N
GLU
48
A
N
GLU
48
A
O
ILE
81
A
O
ILE
81
A
N
VAL
82
A
N
VAL
82
A
O
SER
115
A
O
SER
115
1
A
MET
1
A
MET
1
1
Y
1
A
GLN
2
A
GLN
2
1
Y
1
A
GLU
3
A
GLU
3
1
Y
1
A
GLY
4
A
GLY
4
1
Y
1
A
ARG
136
A
ARG
136
1
Y
1
A
GLU
137
A
GLU
137
1
Y
1
A
LYS
138
A
LYS
138
1
Y
1
A
PRO
139
A
PRO
139
1
Y
1
A
VAL
140
A
VAL
140
1
Y
1
A
ARG
141
A
ARG
141
1
Y
1
A
ILE
142
A
ILE
142
1
Y
1
A
ARG
143
A
ARG
143
1
Y
1
A
ARG
90
-61.33
-150.22
1
A
ASN
91
51.65
8.00
0.238
0.223
1.8
50
1585
15634
14049
random
1
0
MAD
Engh & Huber
0.26
0.23
5
0.13
0.11
1.8
50
105
1134
0
0
1029
0.0054
1.107
21.71
0.742
0.2602
0.2485
1.82
57
450
1.8
50
1J22
15854
15484
2
2
0.052
1
17.3
97.7
0.118
1.80
1.86
1
100
data reduction
MOSFLM
data reduction
TRUNCATE
refinement
CNS
data scaling
CCP4
(TRUNCATE)
phasing
CNS
Crystal structure of archaeal XPF/Mus81 homolog, Hef from Pyrococcus furiosus, nuclease domain, selenomet derivative
1
N
N
2
N
N
The second part of the biological assembly is generated by the two fold axis:x-y+1,2-y,-z-1/3
A
ARG
12
A
ARG
12
HELX_P
A
LEU
14
A
LEU
14
5
1
3
A
SER
16
A
SER
16
HELX_P
A
LEU
25
A
LEU
25
1
2
10
A
ALA
52
A
ALA
52
HELX_P
A
ASP
61
A
ASP
61
1
3
10
A
GLY
63
A
GLY
63
HELX_P
A
TYR
75
A
TYR
75
1
4
13
A
HIS
93
A
HIS
93
HELX_P
A
ASP
107
A
ASP
107
1
5
15
A
THR
117
A
THR
117
HELX_P
A
GLU
135
A
GLU
135
1
6
19
HYDROLASE
structure-specific endonuclease, HYDROLASE
Q8TZH8_PYRFU
UNP
1
547
Q8TZH8
AQEGVKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDFIQSIIDGRLFDQVKRLKEAYSRPIM
IVEGSLYGIRNVHPNAIRGAIAAVTVDFGVPIIFSSTPEETAQYIFLIAKREQEEREKPVRIR
548
689
1J22
2
143
Q8TZH8
A
1
2
143
1
initiating methionine
MET
1
1J22
A
Q8TZH8
UNP
1
1
PHE
engineered mutation
LEU
55
1J22
A
Q8TZH8
UNP
601
55
1
ARG
engineered mutation
GLY
63
1J22
A
Q8TZH8
UNP
609
63
6
parallel
anti-parallel
anti-parallel
parallel
parallel
A
LYS
28
A
LYS
28
A
LYS
32
A
LYS
32
A
LYS
6
A
LYS
6
A
ASP
10
A
ASP
10
A
TYR
39
A
TYR
39
A
ILE
40
A
ILE
40
A
VAL
45
A
VAL
45
A
SER
51
A
SER
51
A
ARG
77
A
ARG
77
A
GLU
83
A
GLU
83
A
ILE
112
A
ILE
112
A
SER
115
A
SER
115
152
P 31 2 1