0.009371
0.000000
0.000000
0.000000
0.008376
0.000000
0.000000
0.000000
0.015706
0.00000
0.00000
0.00000
Rajan, R.
Taneja, B.
Mondragon, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
106.717
119.390
63.670
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
Structure
STRUE6
2005
0969-2126
18
829
838
10.1016/j.str.2010.03.006
20637419
Structures of minimal catalytic fragments of topoisomerase v reveals conformational changes relevant for DNA binding.
2010
10.2210/pdb3m7g/pdb
pdb_00003m7g
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
78
1
CCD
2006-03-05
RAYONIX MX-225
SINGLE WAVELENGTH
M
x-ray
1
0.97872
1.0
5ID-B
APS
0.97872
SYNCHROTRON
APS BEAMLINE 5ID-B
31468.398
Topoisomerase V
N-terminal 31kDa fragment (Topo-31)
1
man
polymer
18.015
water
29
nat
water
no
no
MALVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNV
IVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVD
EVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDE
RTAKRHVKRRDRLLEELYEHLEELSERYL
MALVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNV
IVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVD
EVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDE
RTAKRHVKRRDRLLEELYEHLEELSERYL
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
AV19
sample
MK1436, top5, Topoisomerase V
190192
Methanopyrus kandleri
562
Escherichia coli
BL21 Rosetta (DE3)
pET15b
plasmid
1
3.23
61.87
VAPOR DIFFUSION, SITTING DROP
5.5
0.1M Sodium citrate pH 5.5, 23% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
295
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Data collection
Refinement description
Data collection
Database references
Refinement description
1
0
2010-08-04
1
1
2011-07-13
1
2
2019-07-17
1
3
2023-09-06
_software.classification
_software.name
_software.version
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Structure of the N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride
Structure of the N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride
Structure of the N-terminal 44 kDa fragment of topoisomerase V in the presence of dioxane.
RCSB
Y
RCSB
2010-03-16
REL
REL
HOH
water
2CSB
Topoisomerase domain of topo-61 strcture (2CSB)
PDB
experimental model
HOH
1
2
HOH
HOH
270
A
HOH
2
2
HOH
HOH
271
A
HOH
3
2
HOH
HOH
272
A
HOH
4
2
HOH
HOH
273
A
HOH
5
2
HOH
HOH
274
A
HOH
6
2
HOH
HOH
275
A
HOH
7
2
HOH
HOH
276
A
HOH
8
2
HOH
HOH
277
A
HOH
9
2
HOH
HOH
278
A
HOH
10
2
HOH
HOH
279
A
HOH
11
2
HOH
HOH
280
A
HOH
12
2
HOH
HOH
281
A
HOH
13
2
HOH
HOH
282
A
HOH
14
2
HOH
HOH
283
A
HOH
15
2
HOH
HOH
284
A
HOH
16
2
HOH
HOH
285
A
HOH
17
2
HOH
HOH
286
A
HOH
18
2
HOH
HOH
287
A
HOH
19
2
HOH
HOH
288
A
HOH
20
2
HOH
HOH
289
A
HOH
21
2
HOH
HOH
290
A
HOH
22
2
HOH
HOH
291
A
HOH
23
2
HOH
HOH
292
A
HOH
24
2
HOH
HOH
293
A
HOH
25
2
HOH
HOH
294
A
HOH
26
2
HOH
HOH
295
A
HOH
27
2
HOH
HOH
296
A
HOH
28
2
HOH
HOH
297
A
HOH
29
2
HOH
HOH
298
A
n
1
1
A
n
2
2
A
LEU
3
n
3
LEU
3
A
VAL
4
n
4
VAL
4
A
TYR
5
n
5
TYR
5
A
ASP
6
n
6
ASP
6
A
ALA
7
n
7
ALA
7
A
GLU
8
n
8
GLU
8
A
PHE
9
n
9
PHE
9
A
VAL
10
n
10
VAL
10
A
GLY
11
n
11
GLY
11
A
SER
12
n
12
SER
12
A
GLU
13
n
13
GLU
13
A
ARG
14
n
14
ARG
14
A
GLU
15
n
15
GLU
15
A
PHE
16
n
16
PHE
16
A
GLU
17
n
17
GLU
17
A
GLU
18
n
18
GLU
18
A
GLU
19
n
19
GLU
19
A
ARG
20
n
20
ARG
20
A
GLU
21
n
21
GLU
21
A
THR
22
n
22
THR
22
A
PHE
23
n
23
PHE
23
A
LEU
24
n
24
LEU
24
A
LYS
25
n
25
LYS
25
A
GLY
26
n
26
GLY
26
A
VAL
27
n
27
VAL
27
A
LYS
28
n
28
LYS
28
A
ALA
29
n
29
ALA
29
A
TYR
30
n
30
TYR
30
A
ASP
31
n
31
ASP
31
A
GLY
32
n
32
GLY
32
A
VAL
33
n
33
VAL
33
A
LEU
34
n
34
LEU
34
A
ALA
35
n
35
ALA
35
A
THR
36
n
36
THR
36
A
ARG
37
n
37
ARG
37
A
TYR
38
n
38
TYR
38
A
LEU
39
n
39
LEU
39
A
MET
40
n
40
MET
40
A
GLU
41
n
41
GLU
41
A
ARG
42
n
42
ARG
42
A
SER
43
n
43
SER
43
A
SER
44
n
44
SER
44
A
SER
45
n
45
SER
45
A
ALA
46
n
46
ALA
46
A
LYS
47
n
47
LYS
47
A
ASN
48
n
48
ASN
48
A
ASP
49
n
49
ASP
49
A
GLU
50
n
50
GLU
50
A
GLU
51
n
51
GLU
51
A
LEU
52
n
52
LEU
52
A
LEU
53
n
53
LEU
53
A
GLU
54
n
54
GLU
54
A
LEU
55
n
55
LEU
55
A
HIS
56
n
56
HIS
56
A
GLN
57
n
57
GLN
57
A
ASN
58
n
58
ASN
58
A
PHE
59
n
59
PHE
59
A
ILE
60
n
60
ILE
60
A
LEU
61
n
61
LEU
61
A
LEU
62
n
62
LEU
62
A
THR
63
n
63
THR
63
A
GLY
64
n
64
GLY
64
A
SER
65
n
65
SER
65
A
TYR
66
n
66
TYR
66
A
ALA
67
n
67
ALA
67
A
CYS
68
n
68
CYS
68
A
SER
69
n
69
SER
69
A
ILE
70
n
70
ILE
70
A
ASP
71
n
71
ASP
71
A
PRO
72
n
72
PRO
72
A
THR
73
n
73
THR
73
A
GLU
74
n
74
GLU
74
A
ASP
75
n
75
ASP
75
A
ARG
76
n
76
ARG
76
A
TYR
77
n
77
TYR
77
A
GLN
78
n
78
GLN
78
A
ASN
79
n
79
ASN
79
A
VAL
80
n
80
VAL
80
A
ILE
81
n
81
ILE
81
A
VAL
82
n
82
VAL
82
A
ARG
83
n
83
ARG
83
A
GLY
84
n
84
GLY
84
A
VAL
85
n
85
VAL
85
A
ASN
86
n
86
ASN
86
A
PHE
87
n
87
PHE
87
A
ASP
88
n
88
ASP
88
A
GLU
89
n
89
GLU
89
A
ARG
90
n
90
ARG
90
A
VAL
91
n
91
VAL
91
A
GLN
92
n
92
GLN
92
A
ARG
93
n
93
ARG
93
A
LEU
94
n
94
LEU
94
A
SER
95
n
95
SER
95
A
THR
96
n
96
THR
96
A
GLY
97
n
97
GLY
97
A
GLY
98
n
98
GLY
98
A
SER
99
n
99
SER
99
A
PRO
100
n
100
PRO
100
A
ALA
101
n
101
ALA
101
A
ARG
102
n
102
ARG
102
A
TYR
103
n
103
TYR
103
A
ALA
104
n
104
ALA
104
A
ILE
105
n
105
ILE
105
A
VAL
106
n
106
VAL
106
A
TYR
107
n
107
TYR
107
A
ARG
108
n
108
ARG
108
A
ARG
109
n
109
ARG
109
A
GLY
110
n
110
GLY
110
A
TRP
111
n
111
TRP
111
A
ARG
112
n
112
ARG
112
A
ALA
113
n
113
ALA
113
A
ILE
114
n
114
ILE
114
A
ALA
115
n
115
ALA
115
A
LYS
116
n
116
LYS
116
A
ALA
117
n
117
ALA
117
A
LEU
118
n
118
LEU
118
A
ASP
119
n
119
ASP
119
A
ILE
120
n
120
ILE
120
A
ASP
121
n
121
ASP
121
A
GLU
122
n
122
GLU
122
A
GLU
123
n
123
GLU
123
A
ASP
124
n
124
ASP
124
A
VAL
125
n
125
VAL
125
A
PRO
126
n
126
PRO
126
A
ALA
127
n
127
ALA
127
A
ILE
128
n
128
ILE
128
A
GLU
129
n
129
GLU
129
A
VAL
130
n
130
VAL
130
A
ARG
131
n
131
ARG
131
A
ALA
132
n
132
ALA
132
A
VAL
133
n
133
VAL
133
A
LYS
134
n
134
LYS
134
A
ARG
135
n
135
ARG
135
A
ASN
136
n
136
ASN
136
A
PRO
137
n
137
PRO
137
A
LEU
138
n
138
LEU
138
A
GLN
139
n
139
GLN
139
A
PRO
140
n
140
PRO
140
A
ALA
141
n
141
ALA
141
A
LEU
142
n
142
LEU
142
A
TYR
143
n
143
TYR
143
A
ARG
144
n
144
ARG
144
A
ILE
145
n
145
ILE
145
A
LEU
146
n
146
LEU
146
A
VAL
147
n
147
VAL
147
A
ARG
148
n
148
ARG
148
A
TYR
149
n
149
TYR
149
A
GLY
150
n
150
GLY
150
A
ARG
151
n
151
ARG
151
A
VAL
152
n
152
VAL
152
A
ASP
153
n
153
ASP
153
A
LEU
154
n
154
LEU
154
A
MET
155
n
155
MET
155
A
PRO
156
n
156
PRO
156
A
VAL
157
n
157
VAL
157
A
THR
158
n
158
THR
158
A
VAL
159
n
159
VAL
159
A
ASP
160
n
160
ASP
160
A
GLU
161
n
161
GLU
161
A
VAL
162
n
162
VAL
162
A
PRO
163
n
163
PRO
163
A
PRO
164
n
164
PRO
164
A
GLU
165
n
165
GLU
165
A
MET
166
n
166
MET
166
A
ALA
167
n
167
ALA
167
A
GLY
168
n
168
GLY
168
A
GLU
169
n
169
GLU
169
A
PHE
170
n
170
PHE
170
A
GLU
171
n
171
GLU
171
A
ARG
172
n
172
ARG
172
A
LEU
173
n
173
LEU
173
A
ILE
174
n
174
ILE
174
A
GLU
175
n
175
GLU
175
A
ARG
176
n
176
ARG
176
A
TYR
177
n
177
TYR
177
A
ASP
178
n
178
ASP
178
A
VAL
179
n
179
VAL
179
A
PRO
180
n
180
PRO
180
A
ILE
181
n
181
ILE
181
A
ASP
182
n
182
ASP
182
A
GLU
183
n
183
GLU
183
A
LYS
184
n
184
LYS
184
A
GLU
185
n
185
GLU
185
A
GLU
186
n
186
GLU
186
A
ARG
187
n
187
ARG
187
A
ILE
188
n
188
ILE
188
A
LEU
189
n
189
LEU
189
A
GLU
190
n
190
GLU
190
A
ILE
191
n
191
ILE
191
A
LEU
192
n
192
LEU
192
A
ARG
193
n
193
ARG
193
A
GLU
194
n
194
GLU
194
A
ASN
195
n
195
ASN
195
A
PRO
196
n
196
PRO
196
A
TRP
197
n
197
TRP
197
A
THR
198
n
198
THR
198
A
PRO
199
n
199
PRO
199
A
HIS
200
n
200
HIS
200
A
ASP
201
n
201
ASP
201
A
GLU
202
n
202
GLU
202
A
ILE
203
n
203
ILE
203
A
ALA
204
n
204
ALA
204
A
ARG
205
n
205
ARG
205
A
ARG
206
n
206
ARG
206
A
LEU
207
n
207
LEU
207
A
GLY
208
n
208
GLY
208
A
LEU
209
n
209
LEU
209
A
SER
210
n
210
SER
210
A
VAL
211
n
211
VAL
211
A
SER
212
n
212
SER
212
A
GLU
213
n
213
GLU
213
A
VAL
214
n
214
VAL
214
A
GLU
215
n
215
GLU
215
A
GLY
216
n
216
GLY
216
A
GLU
217
n
217
GLU
217
A
LYS
218
n
218
LYS
218
A
ASP
219
n
219
ASP
219
A
PRO
220
n
220
PRO
220
A
GLU
221
n
221
GLU
221
A
SER
222
n
222
SER
222
A
SER
223
n
223
SER
223
A
GLY
224
n
224
GLY
224
A
ILE
225
n
225
ILE
225
A
TYR
226
n
226
TYR
226
A
SER
227
n
227
SER
227
A
LEU
228
n
228
LEU
228
A
TRP
229
n
229
TRP
229
A
SER
230
n
230
SER
230
A
ARG
231
n
231
ARG
231
A
VAL
232
n
232
VAL
232
A
VAL
233
n
233
VAL
233
A
VAL
234
n
234
VAL
234
A
ASN
235
n
235
ASN
235
A
ILE
236
n
236
ILE
236
A
GLU
237
n
237
GLU
237
A
TYR
238
n
238
TYR
238
A
ASP
239
n
239
ASP
239
A
GLU
240
n
240
GLU
240
A
ARG
241
n
241
ARG
241
A
THR
242
n
242
THR
242
A
ALA
243
n
243
ALA
243
A
LYS
244
n
244
LYS
244
A
ARG
245
n
245
ARG
245
A
HIS
246
n
246
HIS
246
A
VAL
247
n
247
VAL
247
A
LYS
248
n
248
LYS
248
A
ARG
249
n
249
ARG
249
A
ARG
250
n
250
ARG
250
A
ASP
251
n
251
ASP
251
A
ARG
252
n
252
ARG
252
A
LEU
253
n
253
LEU
253
A
LEU
254
n
254
LEU
254
A
GLU
255
n
255
GLU
255
A
GLU
256
n
256
GLU
256
A
LEU
257
n
257
LEU
257
A
TYR
258
n
258
TYR
258
A
GLU
259
n
259
GLU
259
A
HIS
260
n
260
HIS
260
A
LEU
261
n
261
LEU
261
A
GLU
262
n
262
GLU
262
A
GLU
263
n
263
GLU
263
A
LEU
264
n
264
LEU
264
A
SER
265
n
265
SER
265
A
GLU
266
n
266
GLU
266
A
ARG
267
n
267
ARG
267
A
TYR
268
n
268
TYR
268
A
LEU
269
n
269
LEU
269
A
0.0044
0.0241
0.0040
0.2756
0.1567
0.1301
0.0439
0.0070
0.0258
0.0000
-0.0271
-0.0188
0.0164
-0.0009
-0.0169
0.0966
0.0030
-0.0034
-0.0086
0.0026
-0.0394
refined
37.0640
17.2540
1.3770
X-RAY DIFFRACTION
-1
-1
X-RAY DIFFRACTION
1
author_defined_assembly
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
N
GLU
8
A
N
GLU
8
A
O
GLN
78
A
O
GLN
78
A
N
VAL
82
A
N
VAL
82
A
O
VAL
85
A
O
VAL
85
1
A
MET
1
A
MET
1
1
Y
1
A
ALA
2
A
ALA
2
1
Y
1
A
ASP
75
-160.95
24.57
1
A
VAL
125
27.69
74.20
1
A
VAL
130
-142.38
45.35
1
A
ALA
132
-39.90
133.27
1
A
VAL
133
-111.89
-72.08
1
A
ALA
167
-142.38
-114.62
1
A
ARG
176
-36.05
-28.67
1
A
ASP
178
49.81
13.06
1
A
GLU
221
-101.52
53.96
68.261
3.74
0.00
0.00
-2.25
0.00
-1.49
0.957
0.933
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.24772
0.20004
0.20250
2.40
79.56
821
15419
5.1
99.61
16.113
0.178
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.230
0.80
0.80
1.20
Topoisomerase domain of topo-61 strcture (2CSB)
MAXIMUM LIKELIHOOD
MASK
2.40
79.56
29
2232
0
0
2203
0.015
0.022
2244
1.419
1.980
3036
5.466
5.000
266
37.259
22.984
124
17.634
15.000
404
19.025
15.000
30
0.093
0.200
328
0.005
0.020
1742
0.217
0.200
1089
0.311
0.200
1531
0.166
0.200
85
0.191
0.200
28
0.240
0.200
5
1.815
1.500
1381
3.044
2.000
2163
3.597
3.000
987
5.461
4.500
873
0.311
0.243
2.462
55
1136
20
99.83
2.4
79.79
3M7G
16304
16259
0.117
0.108
1
8.2
6.9
94.2
0.689
2.4
2.53
2.2
0.637
6.9
95.7
refinement
REFMAC
5.2.0019
refinement
PHENIX
(phenix.refine: 1.5_2)
data reduction
XDS
data scaling
SCALA
phasing
AMoRE
N
Structure of topoisomerase domain of topoisomerase V protein
1
N
N
2
N
N
A
SER
12
A
SER
12
HELX_P
A
ARG
42
A
ARG
42
1
1
31
A
SER
45
A
SER
45
HELX_P
A
SER
69
A
SER
69
1
2
25
A
PHE
87
A
PHE
87
HELX_P
A
ARG
93
A
ARG
93
1
3
7
A
SER
99
A
SER
99
HELX_P
A
VAL
106
A
VAL
106
1
4
8
A
ARG
109
A
ARG
109
HELX_P
A
LEU
118
A
LEU
118
1
5
10
A
ASP
121
A
ASP
121
HELX_P
A
VAL
125
A
VAL
125
5
6
5
A
GLN
139
A
GLN
139
HELX_P
A
TYR
149
A
TYR
149
1
7
11
A
THR
158
A
THR
158
HELX_P
A
VAL
162
A
VAL
162
5
8
5
A
PRO
163
A
PRO
163
HELX_P
A
ALA
167
A
ALA
167
5
9
5
A
PHE
170
A
PHE
170
HELX_P
A
ARG
176
A
ARG
176
1
10
7
A
ASP
182
A
ASP
182
HELX_P
A
ASN
195
A
ASN
195
1
11
14
A
PRO
199
A
PRO
199
HELX_P
A
GLY
208
A
GLY
208
1
12
10
A
SER
210
A
SER
210
HELX_P
A
GLY
216
A
GLY
216
1
13
7
A
GLY
224
A
GLY
224
HELX_P
A
VAL
234
A
VAL
234
1
14
11
A
ASP
239
A
ASP
239
HELX_P
A
LEU
269
A
LEU
269
1
15
31
ISOMERASE
topoisomerase V, type IC topoisomerase, isomerase, minimal catalytic fragment of topoisomerase V
Q977W1_METKA
UNP
1
1
Q977W1
MALVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEELLELHQNFILLTGSYACSIDPTEDRYQNV
IVRGVNFDERVQRLSTGGSPARYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRVDLMPVTVD
EVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDEIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDE
RTAKRHVKRRDRLLEELYEHLEELSERYL
1
269
3M7G
1
269
Q977W1
A
1
1
269
3
anti-parallel
anti-parallel
A
TYR
5
A
TYR
5
A
PHE
9
A
PHE
9
A
TYR
77
A
TYR
77
A
VAL
82
A
VAL
82
A
VAL
85
A
VAL
85
A
ASN
86
A
ASN
86
20
C 2 2 21